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Mystery at the heart of life

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By Biologic Institute’s Ann Gauger, at Christianity Today’s Behemoth, the secret life of cells:

Our bodies are made up of some 100 trillion cells. We tend to think of cells as static, because that’s how they were presented to us in textbooks. In fact, the cell is like the most antic, madcap, crowded (yet fantastically efficient) city you can picture. And at its heart lies a mystery—or I should say, several mysteries—involving three special kinds of molecules: DNA, RNA, and proteins.

These molecules are assembled into long chains called polymers, and are uniquely suited for the roles they play. More importantly, life absolutely depends upon them. We have to have DNA, RNA, and protein all present and active at the same time for a living organism to live.

How they work together so optimally and efficiently is not merely amazing, but also a great enigma, a mystery that lies at the heart of life itself. More. Paywall soon after. May be worth it.

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3,500 Replies to “Mystery at the heart of life

  1. 1
    bornagain77 says:

    The unfathomed complexity inherent in a ‘simple’ cell cannot be overstated. The folding of a single protein, out of the billion proteins present in a cell*, clearly gets this point across.
    It is known that proteins do not find their final folded form by random processes:

    The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications – Paul Nelson – October 23, 2012
    Excerpt: Anyone who has studied the protein folding problem will have met the famous Levinthal paradox, formulated in 1969 by the molecular biologist Cyrus Levinthal. Put simply, the Levinthal paradox states that when one calculates the number of possible topological (rotational) configurations for the amino acids in even a small (say, 100 residue) unfolded protein, random search could never find the final folded conformation of that same protein during the lifetime of the physical universe. Therefore, concluded Levinthal, given that proteins obviously do fold, they are doing so, not by random search, but by following favored pathways. The challenge of the protein folding problem is to learn what those pathways are.

    Confronting Science’s Logical Limits – John L. Casti – 1996
    Excerpt: It has been estimated that a supercomputer applying plausible rules for protein folding would need 10^127 years to find the final folded form for even a very short sequence consisting of just 100 amino acids. (The universe is 13.7 x 10^9 years old). In fact, in 1993 Aviezri S. Fraenkel of the University of Pennsylvania showed that the mathematical formulation of the protein-folding problem is computationally “hard” in the same way that the traveling-salesman problem is hard.

    That no one really has a firm clue how proteins are finding their final folded form is made clear by the immense time (a few weeks) it takes for a few hundred thousand computers, which are linked together, to find the final folded form of a single protein:

    A Few Hundred Thousand Computers vs. (The Folding Of) A Single Protein Molecule – video

    The reason why finding the final form of a folded protein is so hard for super-computers is that it is like the ‘traveling salesman’ puzzle, which are ‘Just about the meanest problems you can set a computer (on) ‘.

    DNA computer helps traveling salesman – Philip Ball – 2000
    Excerpt: Just about the meanest problems you can set a computer (on) belong to the class called ‘NP-complete’. The number of possible answers to these conundrums, and so the time required to find the correct solution, increases exponentially as the problem is scaled up in size. A famous example is the ‘traveling salesman’ puzzle, which involves finding the shortest route connecting all of a certain number of cities.,,,
    Solving the travelling-salesman problem is a little like finding the most stable folded shape of a protein’s chain-like molecular structure — in which the number of ‘cities’ can run to hundreds or even thousands.

    of note: protein folding is found to be ‘NP-complete’

    Combinatorial Algorithms for Protein Folding in Lattice
    Models: A Survey of Mathematical Results – 2009
    Excerpt: Protein Folding: Computational Complexity
    NP-completeness: from 10^300 to 2 Amino Acid Types
    NP-completeness: Protein Folding in Ad-Hoc Models
    NP-completeness: Protein Folding in the HP-Model

    Yet it is exactly this type of ‘traveling salesman problem’ that quantum computers excel at:

    Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins – May 8, 2013
    Excerpt: quantum computing is, “in some cases, really, really fast.”
    McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous “travelling salesperson” problem that’s been a foundation of theoretical computing for decades.,,,
    “This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast,” McGeoch says. “There are degrees of what it can do. If you want it to solve the exact problem it’s built to solve, at the problem sizes I tested, it’s thousands of times faster than anything I’m aware of. If you want it to solve more general problems of that size, I would say it competes — it does as well as some of the best things I’ve looked at. At this point it’s merely above average but shows a promising scaling trajectory.”

    Thus we have evidence that proteins are very likely finding their final folded form by some method of quantum computation. ,,,, If so, this far exceeds anything man has yet accomplished in regards to quantum computation although billions have been spent trying!
    Here is the paper that proved that protein folding belongs to the physics of the quantum world and that protein folding does not belong to the physics of the classical world:

    Physicists Discover Quantum Law of Protein Folding – February 22, 2011
    Quantum mechanics finally explains why protein folding depends on temperature in such a strange way.
    Excerpt: Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins.
    That’s a significant breakthrough. Luo and Lo’s equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics.

    And here is a paper outlining that quantum computation is indeed possible in proteins:

    Quantum states in proteins and protein assemblies:
    The essence of life? – STUART HAMEROFF, JACK TUSZYNSKI
    Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign.

    * A given cell may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time.

  2. 2
    Axel says:

    ‘ The cell is like the most antic, madcap, crowded (yet fantastically efficient) city you can picture.’

    Sounds like my Catholic Church, though Francis seems to have some work on his hands making it ‘fantastically’ efficient. At least, as regards the Curia and the Vatican bank.

  3. 3
    Seversky says:

    Our bodies are made up of some 100 trillion cells. We tend to think of cells as static, because that’s how they were presented to us in textbooks. In fact, the cell is like the most antic, madcap, crowded (yet fantastically efficient) city you can picture. And at its heart lies a mystery—or I should say, several mysteries—involving three special kinds of molecules: DNA, RNA, and proteins.

    Yes, you can say they are like a city or like a factory or whatever the current analogy is but it’s still an analogy. They are also very different from human cities and factories in so many ways. Do the similarities outweigh the differences or vice versa and by what measure?

    This is still the “I can’t believe it’s not butter” style of argument, it’s so complex I can’t believe it wasn’t designed. But our instinctive reaction to perceived complexity proves nothing, one way or the other.

    No argument, there are still mysteries at the heart of the cell but we still aren’t any closer to deciding if there was some intelligence involved.

  4. 4
    bornagain77 says:

    as to: “but we still aren’t any closer to deciding if there was some intelligence involved.”

    But WE are very decided that unguided processes were not involved! 🙂

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
    Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].

    38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
    39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
    40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
    41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
    42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
    43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589.

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
    Conclusions: Our analysis confirms mathematically what would seem intuitively obvious – multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?

    Biological Information – Overlapping Codes 10-25-2014 by Paul Giem – video

    Overlapping Genetic Codes 12-6-2014 by Paul Giem – video

  5. 5
    bornagain77 says:

    1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. – Book available in sections at http://www.worldscientific.com.....8818#t=toc
    2. Kapranov P., et al. 2005. Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997. Available at
    3. Birney E., et al. (Encode Project Consortium) 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816. Available at http://www.nature.com/nature/j.....05874.html
    4. Itzkovitz S., Hodis E., Sega E. 2010. Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589. Available at http://www.ncbi.nlm.nih.gov/pubmed/20841429
    5. He H., et al. 2007. Mapping the C. elegant noncoding transcriptome with a whole genome tiling microarray. Genome Res 17:1471-1477. Available at http://www.ncbi.nlm.nih.gov/pubmed/17785534
    6. http://www.mcld.co.uk/hiv/?q=HIV%20genome
    7. http://nsmn1.uh.edu/dgraur/niv.....thesis.pdf

  6. 6
    mahuna says:

    The thing about folding proteins is that 2 cells consistently fold them the SAME way. That is, it can’t be computationally hard to randomly fold a protein at Point A into Position B. The fact that this random fold is NOT useful requires that there be “assembly instructions”. You can start with a bag containing all of the pieces of a tent, but if you do NOT: 1) assemble them is something real close to the right order, and 2) emplace the pieces in SPECIFIC places, what you get is NOT a “tent”. Especially if you throw the fabric on the ground and pound the stakes through the middle of it. The fact that 2 isolated cells (isolated in time is probably more instructive than isolated in space) perform the assembly EXACTLY the same way argues strongly against any random process.

  7. 7
    Dionisio says:

    #3 Seversky

    No argument, there are still mysteries at the heart of the cell but we still aren’t any closer to deciding if there was some intelligence involved.

    Well, there are some folks out there who have decided for everybody else to tell our kids in public school textbooks that it’s a known fact that it all happened by the power of the magic formula RV+NS+T=E!
    As you well said, there are still mysteries at the heart of the biological systems.

  8. 8
    Dionisio says:

    #6 Mauna

    Yes, and sometimes even using the same chaperones!

    Now, where is the instructions manual for those procedures?

    Let’s ask gpuccio! 🙂

  9. 9
    Dionisio says:

    Close Encounter of the Third Kind: The ER Meets Endosomes at Fission Suites

    DOI: http://dx.doi.org/10.1016/j.devcel.2014.12.008

    The endoplasmic reticulum (ER) forms functional contacts with several cellular organelles and regulates processes such as mitochondrial fission.

    In a recent issue of Cell, Rowland et al. (2014) extend these findings to endosomes, showing that the ER contacts endosomes at sites containing the WASH subunit FAM21, where it forecasts fission events.


  10. 10
    Dionisio says:

    The biological functions of miRNAs

    DOI: http://dx.doi.org/10.1016/j.tcb.2014.11.004

    Despite their clear importance as a class of regulatory molecules, pinpointing the relevance of individual miRNAs has been challenging.

    Studies querying miRNA functions by overexpressing or silencing specific miRNAs have yielded data that are often at odds with those collected from loss-of-functions models.

    In addition, knockout studies suggest that many conserved miRNAs are dispensable for animal development or viability.

    In this review, we discuss these observations in the context of our current knowledge of miRNA biology and review the evidence implicating miRNA-mediated gene regulation in the mechanisms that ensure biological robustness.


  11. 11
    Dionisio says:

    Networking galore: intermediate filaments and cell migration.

    doi: 10.1016/j.ceb.2013.06.008.

    Intermediate filaments (IFs) are assembled from a diverse group of evolutionarily conserved proteins and are specified in a tissue-dependent, cell type-dependent, and context-dependent fashion in the body.

    IFs are involved in multiple cellular processes that are crucial for the maintenance of cell and tissue integrity and the response and adaptation to various stresses, as conveyed by the broad array of crippling clinical disorders caused by inherited mutations in IF coding sequences.

    Accordingly, the expression, assembly, and organization of IFs are tightly regulated.

    Migration is a fitting example of a cell-based phenomenon in which IFs participate as both effectors and regulators.

    With a particular focus on vimentin and keratin, we here review how the contributions of IFs to the cell’s mechanical properties, to cytoarchitecture and adhesion, and to regulatory pathways collectively exert a significant impact on cell migration.


  12. 12
    PeterJ says:

    Has anyone checked this out yet?


  13. 13
    Dionisio says:

    #12 PeterJ

    Interesting. Thanks.

    Didn’t know weed smoking was legal in K-tan 🙂

  14. 14
    Dionisio says:

    DnaK Functions as a Central Hub in the E. coli Chaperone Network

    DOI: http://dx.doi.org/10.1016/j.celrep.2011.12.007

    Cellular chaperone networks prevent potentially toxic protein aggregation and ensure proteome integrity.

    Here, we used Escherichia coli as a model to understand the organization of these networks, focusing on the cooperation of the DnaK system with the upstream chaperone Trigger factor (TF) and the downstream GroEL.

    Quantitative proteomics revealed that DnaK interacts with at least ?700 mostly cytosolic proteins, including ?180 relatively aggregation-prone proteins that utilize DnaK extensively during and after initial folding.

    Upon deletion of TF, DnaK interacts increasingly with ribosomal and other small, basic proteins, while its association with large multidomain proteins is reduced.

    DnaK also functions prominently in stabilizing proteins for subsequent folding by GroEL.

    These proteins accumulate on DnaK upon GroEL depletion and are then degraded, thus defining DnaK as a central organizer of the chaperone network.

    Combined loss of DnaK and TF causes proteostasis collapse with disruption of GroEL function, defective ribosomal biogenesis, and extensive aggregation of large proteins.


  15. 15
    Dionisio says:

    Polyphosphate Is a Primordial Chaperone

    DOI: http://dx.doi.org/10.1016/j.molcel.2014.01.012

    Composed of up to 1,000 phospho-anhydride bond-linked phosphate monomers, inorganic polyphosphate (polyP) is one of the most ancient, conserved, and enigmatic molecules in biology.

    Here we demonstrate that polyP functions as a hitherto unrecognized chaperone.

    We show that polyP stabilizes proteins in vivo, diminishes the need for other chaperone systems to survive proteotoxic stress conditions, and protects a wide variety of proteins against stress-induced unfolding and aggregation.

    In vitro studies reveal that polyP has protein-like chaperone qualities, binds to unfolding proteins with high affinity in an ATP-independent manner, and supports their productive refolding once nonstress conditions are restored.

    Our results uncover a universally important function for polyP and suggest that these long chains of inorganic phosphate may have served as one of nature’s first chaperones, a role that continues to the present day. [?]


  16. 16
    Dionisio says:

    Unraveling the Mechanism of Chaperone-Mediated Protein Folding

    Chaperones are special proteins that aid the folding, unfolding, assembly and disassembly of other proteins. Chaperones rely on a large and diverse set of co-chaperones that regulate their specificity and function.

    How these co-chaperones regulate protein folding and whether they have chaperone-independent biological functions is largely unknown.


  17. 17
    Dionisio says:

    Molecular Chaperones in Cellular Protein Folding: The Birth of a Field

    DOI: http://dx.doi.org/10.1016/j.cell.2014.03.029

  18. 18
    Dionisio says:

    Protein Folding and the Role of Chaperone Proteins in Neurodegenerative Disease


    Many neurodegenerative disorders are characterized by conformational changes in proteins that result in misfolding, aggregation, and intra- or extraneuronal accumulation of amyloid fibrils.

    Molecular chaperones provide a first line of defense against misfolded, aggregation-prone proteins, and are among the most potent suppressors of neurodegeneration known for animal models of human disease.

    We propose that molecular chaperones are neuroprotective because of their ability to modulate the earliest aberrant protein interactions that trigger pathogenic cascades.

    A detailed understanding of the molecular basis of protection by chaperones against neurodegeneration might lead to the development of therapies for neurodegenerative disorders that are associated with protein misfolding and aggregation.


  19. 19
    Dionisio says:

    Molecular chaperones in protein folding and proteostasis


    Most proteins must fold into defined three-dimensional structures to gain functional activity.

    But in the cellular environment, newly synthesized proteins are at great risk of aberrant folding and aggregation, potentially forming toxic species.

    To avoid these dangers, cells invest in a complex network of molecular chaperones, which use ingenious mechanisms to prevent aggregation and promote efficient folding.

    Because protein molecules are highly dynamic, constant chaperone surveillance is required to ensure protein homeostasis (proteostasis).

    Recent advances suggest that an age-related decline in proteostasis capacity allows the manifestation of various protein-aggregation diseases, including Alzheimer’s disease and Parkinson’s disease.

    Interventions in these and numerous other pathological states may spring from a detailed understanding of the pathways underlying proteome maintenance.


  20. 20
    Dionisio says:

    Structural characterization of the substrate transfer mechanism in Hsp70/?Hsp90 folding machinery mediated by ?Hop


    In eukarya, chaperones Hsp70 and ?Hsp90 act coordinately in the folding and maturation of a range of key proteins with the help of several co-chaperones, especially ?Hop.

    Although biochemical data define the ?Hop-mediated Hsp70–?Hsp90 substrate transfer mechanism, the intrinsic flexibility of these proteins and the dynamic nature of their complexes have limited the structural studies of this mechanism.


  21. 21
    Dionisio says:

    GroEL/ES Chaperonin Modulates the Mechanism and Accelerates the Rate of TIM-Barrel Domain Folding

    DOI: http://dx.doi.org/10.1016/j.cell.2014.03.038

    The GroEL/ES chaperonin system functions as a protein folding cage.

    Many obligate substrates of GroEL share the (??)8 TIM-barrel fold, but how the chaperonin promotes folding of these proteins is not known.


  22. 22
    Dionisio says:

    Orchestration of secretory protein folding by ER chaperones.

    doi: 10.1016/j.bbamcr.2013.03.007

    The endoplasmic reticulum is a major compartment of protein biogenesis in the cell, dedicated to production of secretory, membrane and organelle proteins.

    The secretome has distinct structural and post-translational characteristics, since folding in the ER occurs in an environment that is distinct in terms of its ionic composition, dynamics and requirements for quality control.

    The folding machinery in the ER therefore includes chaperones and folding enzymes that introduce, monitor and react to disulfide bonds, glycans, and fluctuations of luminal calcium.

    We describe the major chaperone networks in the lumen and discuss how they have distinct modes of operation that enable cells to accomplish highly efficient production of the secretome.

    This article is part of a Special Issue entitled: Functional and structural diversity of endoplasmic reticulum.


  23. 23
    Dionisio says:

    Endoplasmic reticulum chaperones and oxidoreductases

    doi: 10.3389/fonc.2014.00291.

    Endoplasmic reticulum (ER) chaperones and oxidoreductases are abundant enzymes that mediate the production of fully folded secretory and transmembrane proteins.


  24. 24
    Dionisio says:

    A dynamic study of protein secretion and aggregation in the secretory pathway

    doi: 10.1371/journal.pone.0108496

    Precise coordination of protein biogenesis, traffic and homeostasis within the early secretory compartment (ESC) is key for cell physiology.


  25. 25
    Dionisio says:

    YidC protein, a molecular chaperone for LacY protein folding via the SecYEG protein machinery.

    doi: 10.1074/jbc.M113.491613.


  26. 26
    Dionisio says:

    Chaperone machines for protein folding, unfolding and disaggregation



  27. 27
    Dionisio says:

    Getting Folded: Chaperone Proteins in Muscle Development, Maintenance and Disease

    DOI: 10.1002/ar.22980


  28. 28
    Seversky says:

    bornagain77 @ 4

    But WE are very decided that unguided processes were not involved! 🙂

    YOU may be. The rest of us aren’t so sure.

    Dionisio @ 7

    Well, there are some folks out there who have decided for everybody else to tell our kids in public school textbooks that it’s a known fact that it all happened by the power of the magic formula RV+NS+T=E!

    Then you’ll be happy to know that there are a few so-called science teachers who are failing in their duty to their students by teaching them in the science classroom that the theory of evolution is wrong and Christian creationism is right, the world was created by God out of nothing in six days flat. Which is the more magical? And what happened to the Christian duty not to bear false witness?

  29. 29
    Dionisio says:

    #28 Seversky

    Then you’ll be happy to know that there are a few so-called science teachers who are failing in their duty to their students by teaching them in the science classroom that the theory of evolution is wrong and Christian creationism is right, the world was created by God out of nothing in six days flat.

    Can you provide the source of that information?

    BTW, how do you know I’ll be happy to know that?

  30. 30
    Dionisio says:

    #28 Seversky

    The rest of us aren’t so sure.

    Who is “the rest of us”?

  31. 31
    Dionisio says:

    The many functions of the endoplasmic reticulum chaperones and folding enzymes

    DOI: 10.1002/iub.1272

    Endoplasmic reticulum (ER) is an essential sub-cellular compartment of the eukaryotic cell performing many diverse functions essential for the cell and the whole organism.

    ER molecular chaperones and folding enzymes are multidomain proteins that are designed to support nascent proteins entering ER lumen to achieve their native conformation, mediate post-translational modification, prevent misfolded protein aggregation, and facilitate exit from the ER.

    Typically the role of ER chaperones expands beyond protein folding. Here, we illustrate the multifunctional nature of many ER associated molecular chaperones and folding enzymes and unique functional overlap of these proteins all designed to support the many functions of the ER membrane. © 2014 IUBMB Life, 66(5):318–326, 2014



    Was this paper peer-reviewed?

    How could they miss that politically incorrect term twice?

  32. 32
    bornagain77 says:

    Seversky, besides people being paid by government funds to try to find the slightest hint that life might come from non-life, and dogmatic atheists/Neo-Darwinists, such as yourself who will deny even their very own mind before they will ever admit to any evidence for God, who exactly is this ‘we’ you are talking about?

    Suzan Mazur: Origin of life shifting to “nonmaterial events”? – December 15, 2013
    Excerpt: The first paradox is the tendency of organic matter to devolve and to give tar. If you can avoid that, you can start to try to assemble things that are not tarry, but then you encounter the water problem, which is related to the fact that every interesting bond that you want to make is unstable, thermodynamically, with respect to water. If you can solve that problem, you have the problem of entropy, that any of the building blocks are going to be present in a low concentration; therefore, to assemble a large number of those building blocks, you get a gene-like RNA — 100 nucleotides long — that fights entropy. And the fourth problem is that even if you can solve the entropy problem, you have a paradox that RNA enzymes, which are maybe catalytically active, are more likely to be active in the sense that destroys RNA rather than creates RNA.

    Chemistry by Chance: A Formula for Non-Life by Charles McCombs, Ph.D.
    Excerpt: The following eight obstacles in chemistry ensure that life by chance is untenable.
    1. The Problem of Unreactivity
    2. The Problem of Ionization
    3. The Problem of Mass Action
    4. The Problem of Reactivity
    5. The Problem of Selectivity
    6. The Problem of Solubility
    7. The Problem of Sugar
    8. The Problem of Chirality
    The chemical control needed for the formation of a specific sequence in a polymer chain is just not possible through random chance. The synthesis of proteins and DNA/RNA in the laboratory requires the chemist to control the reaction conditions, to thoroughly understand the reactivity and selectivity of each component, and to carefully control the order of addition of the components as the chain is building in size.

  33. 33
    Dionisio says:

    Tissue-Resident Memory T Cells

    DOI: http://dx.doi.org/10.1016/j.immuni.2014.12.007

    Tissue-resident memory T (Trm) cells constitute a recently identified lymphocyte lineage that occupies tissues without recirculating.

    They provide a first response against infections reencountered at body surfaces, where they accelerate pathogen clearance.

    Because Trm cells are not present within peripheral blood, they have not yet been well characterized, but are transcriptionally, phenotypically, and functionally distinct from recirculating central and effector memory T cells.


  34. 34
    Seversky says:

    Dionisio @ 30

    Who is “the rest of us”?

    Those of us who aren’t “WE”

  35. 35
    Seversky says:

    bornagain77 @ 32

    Seversky, besides people being paid by government funds to try to find the slightest hint that life might come from non-life, and dogmatic atheists/Neo-Darwinists, such as yourself who will deny even their very own mind before they will ever admit to any evidence for God, who exactly is this ‘we’ you are talking about?

    See previous comment re “WE”

    As for government funding of origins of life research, who else is going to put money into it? Not private enterprise because they will only put money into research that offers the prospect of a good return on their investment. This means that the pharmaceutical industry will only conduct research into diseases that afflict enough people to provide a lucrative market for any theraprutic agent they might develop. People who suffer from rarer ailments generally have to go without – unless the government stumps up some research funding.

    Suzan Mazur: Origin of life shifting to “nonmaterial events”? – December 15, 2013

    What’s a “nonmaterial event”?

  36. 36
    bornagain77 says:

    Any atheist who believes that life can come from non-life does so on pure blind faith in spite of a mountain of evidence against it EVER happening.
    Modern research has only further highlighted how impossible it is.
    The law of biogenesis, i.e. life comes only from life, remains as solid as ever!

    The Theist holds the Intellectual High-Ground – March 2011
    Excerpt: To get a range on the enormous challenges involved in bridging the gaping chasm between non-life and life, consider the following: “The difference between a mixture of simple chemicals and a bacterium, is much more profound than the gulf between a bacterium and an elephant.”
    (Dr. Robert Shapiro, Professor Emeritus of Chemistry, NYU)

    Scientists Prove Again that Life is the Result of Intelligent Design – Rabbi Moshe Averick – August 2011
    Excerpt: “To go from bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.” – Dr. Lynn Margulis

    The current status of origin-of-life chemistry. – Charles Garner – Dec. 2014 – video

    as to:

    “What’s a “nonmaterial event”?”

    That would be anything that cannot be reduced to a material basis, such as mind and information!

    “From the beginning of this book we have emphasized the enormous information content of even the simplest living systems. The information cannot in our view be generated by what are often called ‘natural’ processes, as for instance through meteorological and chemical processes occurring at the surface of a lifeless planet. As well as a suitable physical and chemical environment, a large initial store of information was also needed. We have argued that the requisite information came from an ‘intelligence’, –
    Sir Fred Hoyle, Chandra Wickramasinghe – A Theory of Cosmic Creationism – pg. 150

    Verse and Music:

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind.

    Joy Williams – 2000 Decembers ago

  37. 37
  38. 38
  39. 39
    Dionisio says:

    Chaperones for protein folding – unfolding and disassembling


  40. 40
  41. 41
    Dionisio says:

    Microtubules and chromosome segregation


  42. 42
  43. 43
    Dionisio says:

    New insights in the clockwork mechanism regulating lineage specification

    DOI: 10.1002/dvdy.24228

    Powerful transcription factors called fate determinants induce robust differentiation programs in multipotent cells and trigger lineage specification.

    These factors guarantee the differentiation of specific tissues/organs/cells at the right place and the right moment to form a fully functional organism.

    Fate determinants are activated by temporal, positional, epigenetic, and post-transcriptional cues, hence integrating complex and dynamic developmental networks.

    In turn, they activate specific transcriptional/epigenetic programs that secure novel molecular landscapes.

    In this review, we use the Drosophila Gcm glial determinant as a model to discuss the mechanisms that allow lineage specification in the nervous system.

    The dynamic regulation of Gcm via interlocked loops has recently emerged as a key event in the establishment of stable identity.

    Gcm induces gliogenesis while triggering its own extinction, thus preventing the appearance of metastable states and neoplastic processes.

    Using simple animal models that allow in vivo manipulations provides a key tool to disentangle the complex regulation of cell fate determinants.

    Developmental Dynamics, 2014. © 2014 Wiley Periodicals, Inc.


  44. 44
    Dionisio says:

    Keeping an eye on SOXC proteins

    DOI: 10.1002/dvdy.24235

    The formation of a mature, functional eye requires a complex series of cell proliferation, migration, induction among different germinal layers, and cell differentiation.

    These processes are regulated by extracellular cues such as the Wnt/BMP/Hh/Fgf signaling pathways, as well as cell intrinsic transcription factors that specify cell fate.

    In this review article, we provide an overview of stages of embryonic eye morphogenesis, extrinsic and intrinsic factors that are required for each stage, and pediatric ocular diseases that are associated with defective eye development.

    In addition, we focus on recent findings about the roles of the SOXC proteins in regulating vertebrate ocular development and implicating SOXC mutations in human ocular malformations.

    Developmental Dynamics, 2014. © 2014 Wiley Periodicals, Inc.


  45. 45
    Dionisio says:

    The present study, originally designed to investigate cellular and signaling mechanisms underlying the regulatory role of GPER in vascular SMC proliferation using G-1, unexpectedly revealed off-target effects of G-1.

    DOI: 10.1002/jcp.24817


    unexpectedly revealed ?

    What did they expect to find?

  46. 46
    Dionisio says:

    Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

    DOI: http://dx.doi.org/10.1016/j.cell.2013.06.052

    Intron retention (IR) is widely recognized as a consequence of mis-splicing that leads to failed excision of intronic sequences from pre-messenger RNAs.

    Our bioinformatic analyses of transcriptomic and proteomic data of normal white blood cell differentiation reveal IR as a physiological mechanism of gene expression control.

    IR regulates the expression of 86 functionally related genes, including those that determine the nuclear shape that is unique to granulocytes.

    Retention of introns in specific genes is associated with downregulation of splicing factors and higher GC content.

    IR, conserved between human and mouse, led to reduced mRNA and protein levels by triggering the nonsense-mediated decay (NMD) pathway.

    In contrast to the prevalent view that NMD is limited to mRNAs encoding aberrant proteins, our data establish that IR coupled with NMD is a conserved mechanism in normal granulopoiesis.

    Physiological IR may provide an energetically favorable level of dynamic gene expression control prior to sustained gene translation.


  47. 47
    Dionisio says:

    Seversky @ 34

    Why did you answer my question posted @ 30 but did NOT answer my two questions posted @ 29 ?

  48. 48
    Dionisio says:

    #34 Seversky


    Why did you answer my question posted @ 30 but did NOT answer my two questions posted @ 29 ?

    You don’t have to answer any questions, but it is kind of suspicious interesting that you answered the post 30 but did not answer post 29 which was also addressed to you.

  49. 49
  50. 50
    Dionisio says:

    New insights in the clockwork mechanism regulating lineage specification

    DOI: 10.1002/dvdy.24228

    Powerful transcription factors called fate determinants induce robust differentiation programs in multipotent cells and trigger lineage specification.

    These factors guarantee the differentiation of specific tissues/organs/cells at the right place and the right moment to form a fully functional organism.

    Fate determinants are activated by temporal, positional, epigenetic, and post-transcriptional cues, hence integrating complex and dynamic developmental networks.

    In turn, they activate specific transcriptional/epigenetic programs that secure novel molecular landscapes.

    In this review, we use the Drosophila Gcm glial determinant as a model to discuss the mechanisms that allow lineage specification in the nervous system.

    The dynamic regulation of Gcm via interlocked loops has recently emerged as a key event in the establishment of stable identity.

    Gcm induces gliogenesis while triggering its own extinction, thus preventing the appearance of metastable states and neoplastic processes.

    Using simple animal models that allow in vivo manipulations provides a key tool to disentangle the complex regulation of cell fate determinants.

    Developmental Dynamics, 2014. © 2014 Wiley Periodicals, Inc.


  51. 51
    Dionisio says:

    In Vivo Single-Cell Detection of Metabolic Oscillations in Stem Cells

    DOI: http://dx.doi.org/10.1016/j.celrep.2014.12.007

    Through the use of bulk measurements in metabolic organs, the circadian clock was shown to play roles in organismal energy homeostasis.

    However, the relationship between metabolic and circadian oscillations has not been studied in vivo at a single-cell level.

    Also, it is unknown whether the circadian clock controls metabolism in stem cells.

    We used a sensitive, noninvasive method to detect metabolic oscillations and circadian phase within epidermal stem cells in live mice at the single-cell level.

    We observe a higher NADH/NAD+ ratio, reflecting an increased glycolysis/oxidative phosphorylation ratio during the night compared to the day.

    Furthermore, we demonstrate that single-cell metabolic heterogeneity within the basal cell layer correlates with the circadian clock and that diurnal fluctuations in NADH/NAD+ ratio are Bmal1 dependent.

    Our data show that, in proliferating stem cells, the circadian clock coordinates activities of oxidative phosphorylation and glycolysis with DNA synthesis, perhaps as a protective mechanism against genotoxicity.


  52. 52
    Dionisio says:

    Erk Signaling Suppresses Embryonic Stem Cell Self-Renewal to Specify Endoderm

    DOI: http://dx.doi.org/10.1016/j.celrep.2014.11.032

    Fgf signaling via Erk activation has been associated with both neural induction and the generation of a primed state for the differentiation of embryonic stem cells (ESCs) to all somatic lineages.

    To dissect the role of Erk in both ESC self-renewal and lineage specification, we explored the requirements for this pathway in various in vitro differentiation settings.

    A combination of pharmacological inhibition of Erk signaling and genetic loss of function reveal a role for Erk signaling in endodermal, but not neural differentiation.

    Neural differentiation occurs normally despite a complete block to Erk phosphorylation.

    In support of this, Erk activation in ESCs derepresses primitive endoderm (PrE) gene expression as a consequence of inhibiting the pluripotent/epiblast network.

    The early response to Erk activation correlates with functional PrE priming, whereas sustained Erk activity results in PrE differentiation.

    Taken together, our results suggest that Erk signaling suppresses pluripotent gene expression to enable endodermal differentiation.


  53. 53
    Dionisio says:

    Spatial regulation of the spindle assembly checkpoint and anaphase-promoting complex

    DOI: 10.1111/mmi.12871

    The spindle assembly checkpoint (SAC) plays a critical role in preventing mitotic errors by inhibiting anaphase until all kinetochores are correctly attached to spindle microtubules.

    In spite of the economic and medical importance of filamentous fungi, relatively little is known about the behavior of SAC proteins in these organisms.

    In our efforts to understand the role of ?-tubulin in cell cycle regulation, we have created functional fluorescent protein fusions of four SAC proteins in Aspergillus nidulans, the homologs of Mad2, Mps1, Bub1/BubR1 and Bub3.

    Time-lapse imaging reveals that SAC proteins are in distinct compartments of the cell until early mitosis when they co-localize at the spindle pole body.

    SAC activity is, thus, spatially regulated in A.?nidulans.

    Likewise, Cdc20, an activator of the anaphase-promoting complex/cyclosome, is excluded from interphase nuclei, but enters nuclei at mitotic onset and accumulates to a higher level in mitotic nuclei than in the surrounding nucleoplasm before leaving in anaphase/telophase.

    The activity of this critical cell cycle regulatory complex is likely regulated by the location of Cdc20.

    Finally, the ?-tubulin mutation mipAD159 causes a nuclear-specific failure of nuclear localization of Mps1 and Bub1/R1 but not of Cdc20, Bub3 or Mad2.


  54. 54
    Dionisio says:

    Translational Regulation of the Post-Translational Circadian Mechanism

    •DOI: 10.1371/journal.pgen.1004628


  55. 55
    Dionisio says:

    Inhibition of FOXO1/3 Promotes Vascular Calcification

    doi: 10.1161/ATVBAHA.114.304786

    the present studies uncovered a novel molecular mechanism underlying PTEN/AKT/FOXO (forkhead box O)-mediated Runx2 upregulation and VSMC calcification.


  56. 56
    Dionisio says:

    O-GlcNAc Modification of the runt-Related Transcription Factor 2 (Runx2) Links Osteogenesis and Nutrient Metabolism in Bone Marrow Mesenchymal Stem Cells*

    doi: 10.1074/mcp.M114.040691

    Runx2 is the master switch controlling osteoblast differentiation and formation of the mineralized skeleton.

    The post-translational modification of Runx2 by phosphorylation, ubiquitinylation, and acetylation modulates its activity, stability, and interactions with transcriptional co-regulators and chromatin remodeling proteins downstream of osteogenic signals.

    Altogether, these findings link O-GlcNAc cycling to the Runx2-dependent regulation of the early ALP marker under osteoblast differentiation conditions.


  57. 57
    Dionisio says:

    Genomic Determinants of Gene Regulation by 1,25-Dihydroxyvitamin D3 during Osteoblast-lineage Cell Differentiation*?

    doi: 10.1074/jbc.M114.578104

    The biological effects of 1?,25-dihydroxyvitamin D3 (1,25 (OH)2D3) on osteoblast differentiation and function differ significantly depending upon the cellular state of maturation.

    Continued novel regulation by 1,25(OH)2D3, however, suggested that factors in addition to the VDR might also be involved.

    We conclude that each of these mechanisms may contribute to the diverse actions of 1,25(OH)2D3 on differentiating osteoblasts.


  58. 58
    Quest says:

    These molecules are assembled into long chains called polymers, and are uniquely suited for the roles they play. More importantly, life absolutely depends upon them. We have to have DNA, RNA, and protein all present and active at the same time for a living organism to live.

    What about the cell membrane…? Will DNA, RNA and proteins work together without it even if they are present and “active’ at the same time…? Or… will the cell continue to live and function if one of the components is removed from the living and active cell…?

    The answer is obvious to all logically thinking people… except the blind followers of Darwin… They believe that the obvious can somehow be omitted… ignored… so that their blind beliefs can be kept alive… but only in their blinded minds due to their hardened hearts…

  59. 59
    Dionisio says:

    #58 Quest

    Interesting observation. Thanks.

  60. 60
    Dionisio says:

    Kinetochore motors drive congression of peripheral polar chromosomes by overcoming random arm-ejection forces


    Accurate chromosome segregation during cell division in metazoans relies on proper chromosome congression at the equator.

    Chromosome congression is achieved after bi-orientation to both spindle poles shortly after nuclear envelope breakdown, or by the coordinated action of motor proteins that slide misaligned chromosomes along pre-existing spindle microtubules1.

    These proteins include the minus-end-directed kinetochore motor dynein2, 3, 4, 5, and the plus-end-directed motors ?CENP-E at kinetochores6, 7 and chromokinesins on chromosome arms8, 9, 10, 11.

    However, how these opposite and spatially distinct activities are coordinated to drive chromosome congression remains unknown.

    Here we used RNAi, chemical inhibition, kinetochore tracking and laser microsurgery to uncover the functional hierarchy between kinetochore and arm-associated motors, exclusively required for congression of peripheral polar chromosomes in human cells.

    We show that dynein poleward force counteracts chromokinesins to prevent stabilization of immature/incorrect end-on kinetochore–microtubule attachments and random ejection of polar chromosomes.

    At the poles, ?CENP-E becomes dominant over dynein and chromokinesins to bias chromosome ejection towards the equator.

    Thus, dynein and ?CENP-E at kinetochores drive congression of peripheral polar chromosomes by preventing arm-ejection forces mediated by chromokinesins from working in the wrong direction.


  61. 61
    Dionisio says:

    DNA methylation changes during cell differentiation

    overall perspective on the connections between DNA methylation and other epigenetic marks and the interplay with transcription factors


  62. 62
    Dionisio says:

    A two-step mechanism for epigenetic specification of centromere identity and function


    The basic determinant of chromosome inheritance, the centromere, is specified in many eukaryotes by an epigenetic mark.

    Using gene targeting in human cells and fission yeast, chromatin containing the centromere-specific histone H3 variant CENP-A is demonstrated to be the epigenetic mark that acts through a two-step mechanism to identify, maintain and propagate centromere function indefinitely.

    Initially, centromere position is replicated and maintained by chromatin assembled with the centromere-targeting domain (CATD) of CENP-A substituted into H3.

    Subsequently, nucleation of kinetochore assembly onto CATD-containing chromatin is shown to require either the amino- or carboxy-terminal tail of CENP-A for recruitment of inner kinetochore proteins, including stabilizing CENP-B binding to human centromeres or direct recruitment of CENP-C, respectively.


  63. 63
    Dionisio says:

    Membranes Organize Cellular Complexity


  64. 64
    Dionisio says:

    Fed up with so many boring references to research papers posted here lately?
    Wanna try something lighter, more entertaining?
    Considering that apparently the fiction genre has been more popular in literature history, here’s an amusing story, which I think was referred to in another post in this site in the last quarter of last year. (if this doesn’t make you laugh, perhaps nothing else will):

    An inside-out origin for the eukaryotic cell


    Although the origin of the eukaryotic cell has long been recognized as the single most profound change in cellular organization during the evolution of life on earth, this transition remains poorly understood.

    Models have always assumed that the nucleus and endomembrane system evolved within the cytoplasm of a prokaryotic cell.

    You may read more on this here: http://www.biomedcentral.com/1741-7007/12/76

    Enjoy it! 🙂

  65. 65
    Dionisio says:

    #64 follow-up / important reminder:


  66. 66
    Dionisio says:

    Targeting the Cell’s ‘Biological Clock’ in Promising New Cancer Therapy

    Cell biologists at UT Southwestern Medical Center have targeted telomeres with a small molecule called 6-thiodG that takes advantage of the cell’s “biological clock” to kill cancer cells and shrink tumor growth.


  67. 67
    Dionisio says:

    Sensors at Centrosomes Reveal Determinants of Local Separase Activity


  68. 68
    Dionisio says:

    CENP-W Plays a Role in Maintaining Bipolar Spindle Structure


    Kinetochore-microtubule stability governs the metaphase requirement for Eg5

    Although it is known that Kif15, a second mitotic kinesin, enforces spindle bipolarity in the absence of Eg5, how Kif15 functions in this capacity and/or whether other biochemical or physical properties of the spindle promote its bipolarity have been poorly studied.


    The spindle and kinetochore-associated (Ska) complex enhances binding of the anaphase-promoting complex/cyclosome (APC/C) to chromosomes and promotes mitotic exit.


    Molecular Characterization of an Intact p53 Pathway Subtype


  69. 69
    Dionisio says:

    Postnatal subventricular zone progenitors switch their fate to generate neurons with distinct synaptic input patterns

    doi: 10.1242/dev.110767

    It is unknown to what extent the distinct synaptic input patterns are already determined in SVZ progenitors and/or by the brain circuit into which neurons integrate.


  70. 70
    Dionisio says:

    Establishing neural crest identity: a gene regulatory recipe

    doi: 10.1242/dev.105445

    Neural crest development is thought to be controlled by a suite of transcriptional and epigenetic inputs arranged hierarchically in a gene regulatory network.


  71. 71
    Dionisio says:

    When DNA gets sent to time-out

    For a skin cell to do its job, it must turn on a completely different set of genes than a liver cell—and keep genes it doesn’t need switched off.

    One way of turning off large groups of genes at once is to send them to “time-out” at the edge of the nucleus, where they are kept quiet.

    New research from Johns Hopkins sheds light on how DNA gets sent to the nucleus’ far edge, a process critical to controlling genes and determining cell fate.

    “Now we have a lot of interesting questions to answer about how different types of cells use this mechanism to regulate different sets of genes.”


    “Now we have a lot of interesting questions to answer about how different types of cells use this mechanism to regulate different sets of genes.”?

    A new discovery, which may or may not have answered outstanding questions, has raised “a lot of interesting questions”! Doesn’t this seem like a never-ending story?


  72. 72
    Dionisio says:

    #71 addendum

    Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamina

    doi: 10.1083/jcb.201405110

    Nuclear organization has been implicated in regulating gene activity. Recently, large developmentally regulated regions of the genome dynamically associated with the nuclear lamina have been identified.

    However, little is known about how these lamina-associated domains (LADs) are directed to the nuclear lamina.


  73. 73
    Dionisio says:

    Rac1 functions as a reversible tension modulator to stabilize VE-cadherin trans-interaction

    doi: 10.1083/jcb.201409108

    The role of the RhoGTPase Rac1 in stabilizing mature endothelial adherens junctions (AJs) is not well understood.


  74. 74
    Dionisio says:

    Transient assembly of F-actin on the outer mitochondrial membrane contributes to mitochondrial fission

    doi: 10.1083/jcb.201404050

    In addition to established membrane remodeling roles in various cellular locations, actin has recently emerged as a participant in mitochondrial fission.

    However, the underlying mechanisms of its participation remain largely unknown.


    Can’t wait to see the revelation of the unknown part. 🙂

  75. 75
    Dionisio says:

    Actin is good at long division

    doi: 10.1083/jcb.2081iti2

    F-actin helps mitochondria divide by polymerizing on the organelles, Li et al. show.

    The GTPase Drp1 forms spirals around mitochondria to cut the organelles in two.

    Studies suggest that actin also has a role in mitochondrial division and recruitment of Drp1.

    The mechanisms, however, remain unclear.

    Mitochondria are abnormally long in both types of cells, suggesting that Drp1 accumulation and F-actin polymerization are necessary for mitochondrial fission.

    But how actin polymerization helps Drp1 cleave mitochondria remains unknown.


    Can’t wait to see the revelation of the unknown part. 🙂

  76. 76
    Dionisio says:

    Opposing ISWI- and CHD-class chromatin remodeling activities orchestrate heterochromatic DNA repair

    doi: 10.1083/jcb.201405077

    however, how heterochromatin compaction is actually adjusted after CHD3.1 dispersal is unknown.


  77. 77
    gpuccio says:


    “Doesn’t this seem like a never-ending story?”

    It does, indeed!

    The problem is: we learn layer after layer of complexity in the regulation cascade, but we never get to the decisions. How are the decisions made? What determines the different decisions?

    After all, different cells make different decisions, which activate different, unending layers of “differentiation” (yes, the word indeed comes from “different”, although we often forget it).

    Where do those different decisions come into existence? What codes for them? And for the strict connection between the decisions and the following multiple, endless layers of regulation?

    And why are there so many layers of regulation, parallel or sequential, and interconnected? The reasonable answer to that seems to be: to allow for more decisions, in the course of action: checkpoints, alternatives, meta-regulations, and so on.

    How does the neo darwinist paradigm help in understanding all that?

    Again, at least this answer is easy: it does not help at all.

  78. 78
    gpuccio says:


    Just a quick read of the abstract of the last paper you linked will be enough to give a taste of what we are discussing here:

    Heterochromatin is a barrier to DNA repair that correlates strongly with elevated somatic mutation in cancer. CHD class II nucleosome remodeling activity (specifically CHD3.1) retained by KAP-1 increases heterochromatin compaction and impedes DNA double-strand break (DSB) repair requiring Artemis. This obstruction is alleviated by chromatin relaxation via ATM-dependent KAP-1S824 phosphorylation (pKAP-1) and CHD3.1 dispersal from heterochromatic DSBs; however, how heterochromatin compaction is actually adjusted after CHD3.1 dispersal is unknown. In this paper, we demonstrate that Artemis-dependent DSB repair in heterochromatin requires ISWI (imitation switch)-class ACF1–SNF2H nucleosome remodeling. Compacted chromatin generated by CHD3.1 after DNA replication necessitates ACF1–SNF2H–mediated relaxation for DSB repair. ACF1–SNF2H requires RNF20 to bind heterochromatic DSBs, underlies RNF20-mediated chromatin relaxation, and functions downstream of pKAP-1–mediated CHD3.1 dispersal to enable DSB repair. CHD3.1 and ACF1–SNF2H display counteractive activities but similar histone affinities (via the plant homeodomains of CHD3.1 and ACF1), which we suggest necessitates a two-step dispersal and recruitment system regulating these opposing chromatin remodeling activities during DSB repair.

    And this is only part of a repair mechanism!

  79. 79
    Axel says:

    Easy-peasy! Random chance and Co.

  80. 80
    Dionisio says:

    gpuccio @ 77

    “Doesn’t this seem like a never-ending story?”

    It does, indeed!

    The problem is: we learn layer after layer of complexity in the regulation cascade, but we never get to the decisions. How are the decisions made? What determines the different decisions?

    After all, different cells make different decisions, which activate different, unending layers of “differentiation” (yes, the word indeed comes from “different”, although we often forget it).

    Where do those different decisions come into existence? What codes for them? And for the strict connection between the decisions and the following multiple, endless layers of regulation?

    And why are there so many layers of regulation, parallel or sequential, and interconnected? The reasonable answer to that seems to be: to allow for more decisions, in the course of action: checkpoints, alternatives, meta-regulations, and so on.

    How does the neo darwinist paradigm help in understanding all that?

    Again, at least this answer is easy: it does not help at all.

    Would anyone else like to comment on this?

    You may want to let all your interlocutors know that their comments are most welcome this time.


  81. 81
    Dionisio says:

    #78 gpuccio

    Just a quick read of the abstract of the last paper you linked will be enough to give a taste of what we are discussing here

    Well, what else can I say? It tastes divinely! 🙂

    And this is only part of a repair mechanism!


  82. 82
    Dionisio says:

    #79 Axel

    Easy-peasy! Random chance and Co.

    Of course! That’s obvious! Glad to see you finally understood that!

    Now see if you can convince our beloved friend gpuccio too.


  83. 83
    Dionisio says:

    Myosin VIII associates with microtubule ends and together with actin plays a role in guiding plant cell division

    DOI: http://dx.doi.org/10.7554/eLife.03498

    Plant cells divide using the phragmoplast, a microtubule-based structure that directs vesicles secretion to the nascent cell plate.

    The phragmoplast forms at the cell center and expands to reach a specified site at the cell periphery, tens or hundreds of microns distant.

    The mechanism responsible for guiding the phragmoplast remains largely unknown.


    Can’t wait to read newer reports about those ‘largely unknown’ mechanisms in the days ahead. 🙂

  84. 84
    Dionisio says:

    Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators



    Pseudoscientific fiction or fictional pseudoscience ?

    None of that. Just real science with bogus terminology scattered through the reports, to make it sound cool.

  85. 85
    Dionisio says:

    This took place last year, but still it’s interesting to read about it:

    The identification and isolation of stem cells is dependent on tools and strategies to distinguish stem cells from a heterogeneous cellular population.

    Stem cells can be characterized by cellular, molecular, and functional assays.

    Although much progress has been made, technical challenges persist in characterizing stem cell identity, lineage, and purity.


  86. 86
    AVS says:

    So let me get this straight Dio, you ask for explanations about how things evolved and then when presented with it, you just read the abstract and call it “pseudoscientific fiction or fictional pseudoscience?

    Yeah sounds about right.
    Thank you for making you and your friends look even more foolish than you already do.

  87. 87
    Dionisio says:

    #71 addendum

    How DNA Wallflowers Miss the Epigenetic Dance

    It seems likely that YY1 is involved in summoning the proteins that attach the molecular tags to the histones.

    But whether YY1 has additional roles, like acting as a magnet to bring the DNA to the lamina, is unclear.


  88. 88
    Dionisio says:

    #84 follow-up

    I knew those ‘tricky’ comments will prompt certain folks to comment on that post.

    The bait worked!

    They react so abruptly to the ‘tricky’ question, that can’t even notice it was just a question. Then to make things even worse, they stop reading the rest of the post, hence they miss the last two sentences.

    That makes me feel a little better about my proven poor reading comprehension… at least now I know I’m not alone. Although there’s a huge difference between not being good at reading and not wanting to read well intentionally. 🙂

  89. 89
    AVS says:

    Dio, you can say whatever you want but the fact that you try to belittle months of people’s work on something that you don’t even understand is all anybody needs to know to see how childish you are.

  90. 90
    Dionisio says:


    Dorogoi, ty umnitsa, prosto molodets! 🙂

  91. 91
    AVS says:

    If only you spoke Biologese 1/1000 as well as any other language, Dio.
    If only.

  92. 92
    Dionisio says:


    Trying damage control? Well, too late now.

    You swallowed the ‘tricky’ bait along with the hook!

    You didn’t even noticed it was just a question. Then, to make things worse, didn’t read the rest of the post, which clarify the whole meaning of the comments. Instead, you abruptly overreacted and started your usual personal attacks. Too bad, buddy. Next time be more cautious. 🙂

    Your comrades and fellow travelers may not like what you just did. 🙂

    This was an easy experiment on human communications and reactions to different textual messages. I appreciate you volunteered to participate in the experiment. Sorry for any inconvenience this may have caused to you. But perhaps someday you’ll look back at this embarrassing moment you just experienced and will see that it was not that bad after all.


    Why don’t you try and comment on gpuccio’s posts #77 better?

    Don’t know what to say about it?


  93. 93
    AVS says:

    Don’t worry Dio, I’m already sorting through Pucci’s hogwash on another post.

    And I’m glad to be of service. Whenever I see you talking out of your rear end, I’ll bring you back to planet Earth.

  94. 94
    Joe says:

    Whenever I see you talking out of your rear end, I’ll bring you back to planet Earth.

    LoL! As if…

  95. 95
    Dionisio says:

    Transport by Populations of Fast and Slow Kinesins Uncovers Novel Family-Dependent Motor Characteristics Important for In Vivo Function

    DOI: http://dx.doi.org/10.1016/j.bpj.2014.09.009

    Intracellular cargo transport frequently involves multiple motor types, either having opposite directionality or having the same directionality but different speeds.

    Although significant progress has been made in characterizing kinesin motors at the single-molecule level, predicting their ensemble behavior is challenging and requires tight coupling between experiments and modeling to uncover the underlying motor behavior.


  96. 96
    Dionisio says:

    Genomic Perspectives of Transcriptional Regulation in Forebrain Development

    DOI: http://dx.doi.org/10.1016/j.neuron.2014.11.021

    The activity of neurons in the primate lateral prefrontal cortex (LPFC) is strongly modulated by visual attention.

    Such a modulation has mostly been documented by averaging the activity of independently recorded neurons over repeated experimental trials.

    However, in realistic settings, ensembles of simultaneously active LPFC neurons must generate attentional signals on a single-trial basis, despite the individual and correlated variability of neuronal responses.

    Whether, under these circumstances, the LPFC can reliably generate attentional signals is unclear.


  97. 97
    Dionisio says:

    Visual Areas Exert Feedforward and Feedback Influences through Distinct Frequency Channels

    DOI: http://dx.doi.org/10.1016/j.neuron.2014.12.018

    Visual cortical areas subserve cognitive functions by interacting in both feedforward and feedback directions.

    While feedforward influences convey sensory signals, feedback influences modulate feedforward signaling according to the current behavioral context.


  98. 98
    Dionisio says:

    The drosophila Chmp1 protein determines wing cell fate through regulation of epidermal growth factor receptor signaling

    DOI: 10.1002/dvdy.24140

    Receptor down-regulation by the multivesicular body (MVB) pathway is critical for many cellular signaling events.

    MVB generation is mediated by the highly conserved ESCRT (0, I, II, and III) protein complexes.

    Chmp1 is an ESCRT-III component and a putative tumor suppressor in humans.

    However, published data on Chmp1 activity are conflicting and its role during tissue development is not well defined.


  99. 99
    Dionisio says:

    The condensin component ?NCAPG2 regulates microtubule–kinetochore attachment through recruitment of ?Polo-like kinase 1 to kinetochores



  100. 100
    Dionisio says:

    The outer kinetochore protein KNL-1 contains a defined oligomerization domain in nematodes

    Citable URI: http://hdl.handle.net/1721.1/92587

    The kinetochore is a large, macromolecular assembly that is essential for connecting chromosomes to microtubules during mitosis.

    Despite the recent identification of multiple kinetochore components, the nature and organization of the higher order kinetochore structure remain unknown.


  101. 101
    gpuccio says:


    Please, behave yourself! Our kind interlocutor AVS is already busy sorting through my hogwash on another post. Don’t distract him. He needs his full concentration… 🙂

  102. 102
    Dionisio says:

    A Protective Chaperone for the Kinetochore Adaptor Bub3

    DOI: http://dx.doi.org/10.1016/j.devcel.2014.01.024

    BuGZ Is Required for Bub3 Stability, Bub1 Kinetochore Function, and Chromosome Alignment

    DOI: http://dx.doi.org/10.1016/j.devcel.2013.12.014

    During mitosis, the spindle assembly checkpoint (SAC) monitors the attachment of kinetochores (KTs) to the plus ends of spindle microtubules (MTs) and prevents anaphase onset until chromosomes are aligned and KTs are under proper tension.


    A Microtubule-Associated Zinc Finger Protein, BuGZ, Regulates Mitotic Chromosome Alignment by Ensuring Bub3 Stability and Kinetochore Targeting

    DOI: http://dx.doi.org/10.1016/j.devcel.2013.12.013

    Equal chromosome segregation requires proper assembly of many proteins, including Bub3, onto kinetochores to promote kinetochore-microtubule interactions.

    BuGZ not only serves as a molecular chaperone for Bub3 but also enhances its loading onto kinetochores during prometaphase in a microtubule-dependent manner to promote chromosome alignment.


  103. 103
    Dionisio says:

    #101 gpuccio

    Sorry, but I did not realize our kind interlocutors needed so much time to understand what you wrote so clearly.

    Ok, I’ll try not to distract their attention away from that task that seems so difficult for them to do.


  104. 104
    Dionisio says:

    Epigenetics of kinetochore assembly


    Vertebrate centromeres are specified by the deposition of the histone H3 variant centromeric protein A (CENPA), but whether other epigenetic marks are important for centromeric chromatin function was unclear.

    Hori et al. now show that centromeric monomethylation of histone H4 at Lys20 (H4K20me1) is required for kinetochore assembly.


    Here’s a case where an outstanding question has been answered. 🙂

  105. 105
    Dionisio says:

    Extracellular matrix assembly: a multiscale deconstruction


    The biochemical and biophysical properties of the extracellular matrix (ECM) dictate tissue-specific cell behaviour.

    The molecules that are associated with the ECM of each tissue, including collagens, proteoglycans, laminins and fibronectin, and the manner in which they are assembled determine the structure and the organization of the resultant ECM.

    The product is a specific ECM signature that is comprised of unique compositional and topographical features that both reflect and facilitate the functional requirements of the tissue.


  106. 106
    Dionisio says:

    Remodelling the extracellular matrix in development and disease


    The extracellular matrix (ECM) is a highly dynamic structure that is present in all tissues and continuously undergoes controlled remodelling.

    This process involves quantitative and qualitative changes in the ECM, mediated by specific enzymes that are responsible for ECM degradation, such as metalloproteinases.

    The ECM interacts with cells to regulate diverse functions, including proliferation, migration and differentiation.

    ECM remodelling is crucial for regulating the morphogenesis of the intestine and lungs, as well as of the mammary and submandibular glands.

    Dysregulation of ECM composition, structure, stiffness and abundance contributes to several pathological conditions, such as fibrosis and invasive cancer.

    A better understanding of how the ECM regulates organ structure and function and of how ECM remodelling affects disease progression will contribute to the development of new therapeutics.


  107. 107
    Dionisio says:

    Mechanotransduction and extracellular matrix homeostasis


    Soft connective tissues at steady state are dynamic; resident cells continually read environmental cues and respond to them to promote homeostasis, including maintenance of the mechanical properties of the extracellular matrix (ECM) that are fundamental to cellular and tissue health.

    The mechanosensing process involves assessment of the mechanics of the ECM by the cells through integrins and the actomyosin cytoskeleton, and is followed by a mechanoregulation process, which includes the deposition, rearrangement or removal of the ECM to maintain overall form and function.

    Progress towards understanding the molecular, cellular and tissue-level effects that promote mechanical homeostasis has helped to identify key questions for future research.


  108. 108
    Dionisio says:

    Role of the extracellular matrix in regulating stem cell fate


    The field of stem cells and regenerative medicine offers considerable promise as a means of delivering new treatments for a wide range of diseases.

    In order to maximize the effectiveness of cell-based therapies — whether stimulating expansion of endogenous cells or transplanting cells into patients — it is essential to understand the environmental (niche) signals that regulate stem cell behaviour.

    One of those signals is from the extracellular matrix (ECM).

    New technologies have offered insights into how stem cells sense signals from the ECM and how they respond to these signals at the molecular level, which ultimately regulate their fate.


  109. 109
    Dionisio says:

    More examples of deleterious mutations?

    Mutation of the kinetochore protein, CENPF, linked to major health issues.


    Mutations in microtubule-regulating genes are associated with disorders of neuronal migration and microcephaly.



  110. 110
    Dionisio says:

    Another encouraging case of an answered question.

    Meikin is a conserved regulator of meiosis-I-specific kinetochore function


    The kinetochore is the crucial apparatus regulating chromosome segregation in mitosis and meiosis.

    Particularly in meiosis I, unlike in mitosis, sister kinetochores are captured by microtubules emanating from the same spindle pole (mono-orientation) and centromeric cohesion mediated by cohesin is protected in the following anaphase.

    Although meiotic kinetochore factors have been identified only in budding and fission yeasts, these molecules and their functions are thought to have diverged earlier.

    Therefore, a conserved mechanism for meiotic kinetochore regulation remains elusive.

    MEIKIN plays a crucial role in both mono-orientation and centromeric cohesion protection, partly by stabilizing the localization of the cohesin protector shugoshin.

    These functions are mediated mainly by the activity of Polo-like kinase PLK1, which is enriched to kinetochores in a MEIKIN-dependent manner.

    […] the long-awaited key regulator of meiotic kinetochore function is Meikin, which is conserved from yeasts to humans.


  111. 111
    Dionisio says:

    Geometry and force behind kinetochore orientation: lessons from meiosis


    During mitosis, replicated chromosomes (sister chromatids) become attached at the kinetochore by spindle microtubules emanating from opposite poles and segregate equationally.

    In the first division of meiosis, however, sister chromatids become attached from the same pole and co-segregate, whereas homologous chromosomes connected by chiasmata segregate to opposite poles. [why?]

    Disorder in this specialized chromosome attachment in meiosis is the leading cause of miscarriage in humans.

    Recent studies have elucidated the molecular mechanisms determining chromosome orientation, and consequently segregation, in meiosis.

    Comparative studies of meiosis and mitosis have led to the general principle that kinetochore geometry and tension exerted by microtubules synergistically generate chromosome orientation. [how?]


  112. 112
    Dionisio says:

    The centrosome orientation checkpoint is germline stem cell specific and operates prior to the spindle assembly checkpoint…

    Asymmetric cell division is utilized by a broad range of cell types to generate two daughter cells with distinct cell fates.

    In stem cell populations asymmetric cell division is believed to be crucial for maintaining tissue homeostasis, failure of which can lead to tissue degeneration or hyperplasia/tumorigenesis.

    Asymmetric cell divisions also underlie cell fate diversification during development.

    Accordingly, the mechanisms by which asymmetric cell division is achieved have been extensively studied, although the check points that are in place to protect against potential perturbation of the process are poorly understood.


  113. 113
    Dionisio says:

    Redundant Mechanisms to Form Silent Chromatin at Pericentromeric Regions Rely on BEND3 and DNA Methylation

    DOI: http://dx.doi.org/10.1016/j.molcel.2014.12.033

    DOI: http://dx.doi.org/10.1016/j.molcel.2014.10.001

    Constitutive heterochromatin is typically defined by high levels of DNA methylation and H3 lysine 9 trimethylation (H3K9Me3), whereas facultative heterochromatin displays DNA hypomethylation and high H3 lysine 27 trimethylation (H3K27Me3).

    The two chromatin types generally do not coexist at the same loci, suggesting mutual exclusivity.

    During development or in cancer, pericentromeric regions can adopt either epigenetic state, but the switching mechanism is unknown.

    DNA methylation controls heterochromatin architecture and inhibits Polycomb recruitment.

    BEND3, a protein enriched on pericentromeric chromatin in the absence of DNA methylation or H3K9Me3, allows Polycomb recruitment and H3K27Me3, resulting in a redundant pathway to generate repressive chromatin.

    This suggests that BEND3 is a key factor in mediating a switch from constitutive to facultative heterochromatin.


    Getting there. Work in progress. 🙂

  114. 114
    Dionisio says:

    SLX4: Not SIMply a Nuclease Scaffold?

    DOI: http://dx.doi.org/10.1016/j.molcel.2014.12.032

    SUMO-interacting motifs (SIMs) in the SLX4 DNA repair nuclease scaffold protein that promote its functions in genome stability maintenance pathways independently of its ubiquitin-binding properties

    Noncovalent Interactions with SUMO and Ubiquitin Orchestrate Distinct Functions of the SLX4 Complex in Genome Maintenance

    DOI: http://dx.doi.org/10.1016/j.molcel.2014.11.015

    SLX4, a coordinator of multiple DNA structure-specific endonucleases, is important for several DNA repair pathways.

    Noncovalent interactions of SLX4 with ubiquitin are required for localizing SLX4 to DNA interstrand crosslinks (ICLs), yet how SLX4 is targeted to other functional contexts remains unclear.

    The SIMs of SLX4 are dispensable for ICL repair but important for processing CPT-induced replication intermediates, suppressing fragile site instability, and localizing SLX4 to ALT telomeres.

    The localization of SLX4 to laser-induced DNA damage also requires the SIMs, as well as DNA end resection, UBC9, and MDC1.

    Furthermore, the SUMO binding of SLX4 enhances its interaction with specific DNA-damage sensors or telomere-binding proteins, including RPA, MRE11-RAD50-NBS1, and TRF2.

    Thus, the interactions of SLX4 with SUMO and ubiquitin increase its affinity for factors recognizing different DNA lesions or telomeres, helping to direct the SLX4 complex in distinct functional contexts.


    The SLX4 Complex Is a SUMO E3 Ligase that Impacts on Replication Stress Outcome and Genome Stability

    DOI: http://dx.doi.org/10.1016/j.molcel.2014.11.014

    The SLX4 Fanconi anemia protein is a tumor suppressor that may act as a key regulator that engages the cell into specific genome maintenance pathways.

    […] the SLX4 complex is a SUMO E3 ligase that SUMOylates SLX4 itself and the XPF subunit of the DNA repair/recombination XPF-ERCC1 endonuclease.

    This SLX4-dependent activity is mediated by a remarkably specific interaction between SLX4 and the SUMO-charged E2 conjugating enzyme UBC9 and relies not only on newly identified SUMO-interacting motifs (SIMs) in SLX4 but also on its BTB domain.

    In contrast to its ubiquitin-binding UBZ4 motifs, SLX4 SIMs are dispensable for its DNA interstrand crosslink repair functions.

    Instead, while detrimental in response to global replication stress, the SUMO E3 ligase activity of the SLX4 complex is critical to prevent mitotic catastrophe following common fragile site expression.


    Work in progress…

  115. 115
    Dionisio says:

    PLEKHM1: A Multiprotein Adaptor for the Endolysosomal System

    DOI: http://dx.doi.org/10.1016/j.molcel.2014.12.022

    Two papers by McEwan et al. ( McEwan et al., 2015a, 2015b ) identify interactions of PLEKHM1 with autophagosome-associated Atg8 proteins and Salmonella typhimurium effector, SifA, linking autophagy and the Salmonella-containing vacuole (SCV) to the endolysosomal Rab7/HOPS-regulated tethering machinery.

    PLEKHM1 Regulates Autophagosome-Lysosome Fusion through HOPS Complex and LC3/GABARAP Proteins

    DOI: http://dx.doi.org/10.1016/j.molcel.2014.11.006

    The lysosome is the final destination for degradation of endocytic cargo, plasma membrane constituents, and intracellular components sequestered by macroautophagy.

    Fusion of endosomes and autophagosomes with the lysosome depends on the GTPase Rab7 and the homotypic fusion and protein sorting (HOPS) complex, but adaptor proteins that link endocytic and autophagy pathways with lysosomes are poorly characterized.

    Depletion of PLEKHM1 blocks lysosomal degradation of endocytic (EGFR) cargo and enhances presentation of MHC class I molecules.

    Moreover, genetic loss of PLEKHM1 impedes autophagy flux upon mTOR inhibition and PLEKHM1 regulates clearance of protein aggregates in an autophagy- and LIR-dependent manner.

    PLEKHM1 is thus a multivalent endocytic adaptor involved in the lysosome fusion events controlling selective and nonselective autophagy pathways.


  116. 116
    Dionisio says:

    Functional Splicing Network Reveals Extensive Regulatory Potential of the Core Spliceosomal Machinery

    DOI: http://dx.doi.org/10.1016/j.molcel.2014.10.030

    Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome.

    The steps at which splicing can be regulated remain largely unknown.

    We systematically analyzed the effect of knocking down the components of the splicing machinery on alternative splicing events relevant for cell proliferation and apoptosis and used this information to reconstruct a network of functional interactions.

    The network accurately captures known physical and functional associations and identifies new ones, revealing remarkable regulatory potential of core spliceosomal components, related to the order and duration of their recruitment during spliceosome assembly.

    In contrast with standard models of regulation at early steps of splice site recognition, factors involved in catalytic activation of the spliceosome display regulatory properties.

    The network also sheds light on the antagonism between hnRNP C and U2AF, and on targets of antitumor drugs, and can be widely used to identify mechanisms of splicing regulation.


  117. 117
    Dionisio says:

    ATM-mediated Mad1 Serine 214 phosphorylation regulates Mad1 dimerization and the spindle assembly checkpoint.

    doi: 10.1093/carcin/bgu087.

    The spindle assembly checkpoint (SAC), which blocks anaphase onset until all chromosomes have bi-oriented, is one of the key self-monitoring systems of the eukaryotic cell cycle for genome stability.

    The mitotic arrest-deficient protein 1 (Mad1), a critical component of the SAC, is hyperphosphorylated in mitosis.

    However, the kinases responsible for Mad1 phosphorylation and its functional significance are not fully understood.


  118. 118
  119. 119
    Dionisio says:

    Regulation of autophagy by protein post-translational modification


    Autophagy is a lysosome-mediated intracellular protein degradation process that involves about 38 autophagy-related genes as well as key signaling pathways that sense cellular metabolic and redox status, and has an important role in quality control of macromolecules and organelles.

    As with other major cellular pathways, autophagy proteins are subjected to regulatory post-translational modification.

    Phosphorylation is so far the most intensively studied post-translational modification in the autophagy process, followed by ubiquitination and acetylation.

    An interesting and new area is also now emerging, which appears to complement these more traditional mechanisms, and includes O-GlcNAcylation and redox regulation at thiol residues.

    Identification of the full spectrum of post-translational modifications of autophagy proteins, and determination of their impact on autophagy will be crucial for a better understanding of autophagy regulation, its deficits in diseases, and how to exploit this process for disease therapies.


  120. 120
    Dionisio says:

    Post-translational Regulation of the Type III Inositol 1,4,5-Trisphosphate Receptor by miRNA-506.

    doi: 10.1074/jbc.M114.587030.

    The type III isoform of the inositol 1,4,5-trisphosphate receptor (InsP3R3) is apically localized and triggers Ca(2+) waves and secretion in a number of polarized epithelia.

    However, nothing is known about epigenetic regulation of this InsP3R isoform.


  121. 121
    Dionisio says:

    Toward a Genome-Wide Landscape of Translational Control

    doi: 10.1101/cshperspect.a012302

    Genome-wide analysis of translational control has taken strides in recent years owing to the advent of high-throughput technologies, including DNA microarrays and deep sequencing.

    Global studies have unraveled a principal role, among posttranscriptional mechanisms, for mRNA translation in determining protein levels in the cell.

    The impact of translational control in dynamic regulation of the proteome under different conditions is increasingly appreciated.

    Here we review genome-wide studies that use high-throughput techniques and bioinformatics to assess the role of mRNA translation in the regulation of protein levels;

    we also discuss how genome-wide data on mRNA translation can be obtained, analyzed, and used to identify mechanisms of translational control.


  122. 122
    Dionisio says:

    Principles of Translational Control: An Overview
    doi: 10.1101/cshperspect.a011528

    Regulation of mRNA Translation by Signaling Pathways
    doi: 10.1101/cshperspect.a012252

    The Mechanism of Eukaryotic Translation Initiation: New Insights and Challenges
    doi: 10.1101/cshperspect.a011544

  123. 123
    Dionisio says:

    RNA-mediated epigenetic regulation of gene expression.


    Diverse classes of RNA, ranging from small to long non-coding RNAs, have emerged as key regulators of gene expression, genome stability and defence against foreign genetic elements.

    Small RNAs modify chromatin structure and silence transcription by guiding Argonaute-containing complexes to complementary nascent RNA scaffolds and then mediating the recruitment of histone and DNA methyltransferases.

    In addition, recent advances suggest that chromatin-associated long non-coding RNA scaffolds also recruit chromatin-modifying complexes independently of small RNAs.

    These co-transcriptional silencing mechanisms form powerful RNA surveillance systems that detect and silence inappropriate transcription events, and provide a memory of these events via self-reinforcing epigenetic loops.


  124. 124
  125. 125
    Dionisio says:

    Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification.

    doi: 10.1038/nbt.2943.

    Little is known about the functional domain architecture of long noncoding RNAs (lncRNAs) because of a relative paucity of suitable methods to analyze RNA function at a domain level.
    These results suggest dChIRP can reveal lncRNA architecture and function with high precision and sensitivity.


    In Situ Dissection of RNA Functional Subunits by Domain-Specific Chromatin Isolation by RNA Purification (dChIRP).

    doi: 10.1007/978-1-4939-2253-6_12.

    Here we describe domain-specific chromatin isolation by RNA purification (dChIRP), a technique for dissecting the functional domains of a target RNA in situ.

    For an RNA of interest, dChIRP can identify domain-level intramolecular and intermolecular RNA-RNA, RNA-protein, and RNA-DNA interactions and maps the RNA’s genomic binding sites with higher precision than domain-agnostic methods.

    We illustrate how this technique has been applied to the roX1 lncRNA to resolve its domain-level architecture, discover its protein- and chromatin-interacting domains, and map its occupancy on the X chromosome.


  126. 126
    Dionisio says:

    Roles of long noncoding RNAs in brain development, functional diversification and neurodegenerative diseases

    doi: 10.1016/j.brainresbull.2013.06.001

    Long noncoding RNAs (lncRNAs) have been attracting immense research interest, while only a handful of lncRNAs have been characterized thoroughly.

    Their involvement in the fundamental cellular processes including regulate gene expression at epigenetics, transcription, and post-transcription highlighted a central role in cell homeostasis.

    However, lncRNAs studies are still at a relatively early stage, their definition, conservation, functions, and action mechanisms remain fairly complicated.

    Here, we give a systematic and comprehensive summary of the existing knowledge of lncRNAs in order to provide a better understanding of this new studying field. [why new? how long ago they started to look at this? ]

    lncRNAs play important roles in brain development, neuron function and maintenance, and neurodegenerative diseases are becoming increasingly evident.

    In this review, we also highlighted recent studies related lncRNAs in central nervous system (CNS) development and neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD) and amyotrophic lateral sclerosis (ALS), and elucidated some specific lncRNAs which may be important for understanding the pathophysiology of neurodegenerative diseases, also have the potential as therapeutic targets.


  127. 127
    Dionisio says:

    Developmental Programming of Long Non-Coding RNAs during Postnatal Liver Maturation…

    doi: 10.1371/journal.pone.0114917

    The liver is a vital organ with critical functions in metabolism, protein synthesis, and immune defense.

    Most of the liver functions are not mature at birth and many changes happen during postnatal liver development.

    However, it is unclear what changes occur in liver after birth, at what developmental stages they occur, and how the developmental processes are regulated.

    Long non-coding RNAs (lncRNAs) are involved in organ development and cell differentiation.

    We found around 15,000 genes expressed, including about 2,000 lncRNAs.

    Most lncRNAs were expressed at a lower level than coding RNAs.

    Both coding RNAs and lncRNAs displayed three major ontogenic patterns: enriched at neonatal, adolescent, or adult stages.

    Neighboring coding and non-coding RNAs showed the trend to exhibit highly correlated ontogenic expression patterns.

    Gene ontology (GO) analysis revealed that some lncRNAs enriched at neonatal ages have their neighbor protein coding genes also enriched at neonatal ages and associated with cell proliferation, immune activation related processes, tissue organization pathways, and hematopoiesis; other lncRNAs enriched at adolescent ages have their neighbor protein coding genes associated with different metabolic processes.

    These data reveal significant functional transition during postnatal liver development and imply the potential importance of lncRNAs in liver maturation.


  128. 128
    Dionisio says:

    Long Non-Coding RNAs Involved in Immune Responses.

    doi: 10.3389/fimmu.2014.00573

    A large number of human RNA transcripts, which do not encode proteins are defined as non-coding RNAs (ncRNAs).

    These ncRNAs are divided into two classes of different lengths; short and long ncRNAs.

    MicroRNAs are a major class of short ncRNAs, ~22 nucleotides in length that regulate gene expression at the post-transcriptional level.

    Long non-coding RNAs (lncRNAs) are more than 200 nucleotides in length and play roles in various biological pathways.

    In this review, we summarize the functions of lncRNAs which regulate immune responses.


  129. 129
    Dionisio says:

    Solving the centriole disengagement puzzle


    The microcephaly protein, Cep215, contributes to the engagement of duplicated centrioles in interphase.

    Now two distinct pools of Cep215 at centrosomes are identified, one bound to Cep68 and the other to pericentrin.

    Plk1-mediated degradation of Cep68 and separase-mediated cleavage of pericentrin release both pools of Cep215, thereby promoting centriole disengagement.


  130. 130
    Dionisio says:

    Degradation of ?Cep68 and ?PCNT cleavage mediate ?Cep215 removal from the PCM to allow centriole separation, disengagement and licensing


    An intercentrosomal linker keeps a cell’s two centrosomes joined together until it is dissolved at the onset of mitosis.

    A second connection keeps daughter centrioles engaged to their mothers until they lose their orthogonal arrangement at the end of mitosis.

    Centriole disengagement is required to license centrioles for duplication.

    We show that the intercentrosomal linker protein ?Cep68 is degraded in prometaphase through the SCF?TrCP (?Skp1–?Cul1–F-box protein) ubiquitin ligase complex. ?

    Cep68 degradation is initiated by ?PLK1 phosphorylation of ?Cep68 on Ser 332, allowing recognition by ?TrCP.

    We also found that ?Cep68 forms a complex with ?Cep215 (also known as ?Cdk5Rap2) and ?PCNT (also known as ?pericentrin), two PCM (pericentriolar material) proteins involved in centriole engagement. ?

    Cep68 and ?PCNT bind to different pools of ?Cep215.

    We propose that ?Cep68 degradation allows ?Cep215 removal from the peripheral PCM preventing centriole separation following disengagement, whereas ?PCNT cleavage mediates ?Cep215 removal from the core of the PCM to inhibit centriole disengagement and duplication.


  131. 131
    Dionisio says:

    Prostaglandin E2 regulates liver versus pancreas cell-fate decisions and endodermal outgrowth

    doi: 10.1016/j.devcel.2014.01.006.

    The liver and pancreas arise from common endodermal progenitors.

    How these distinct cell fates are specified is poorly understood.

    Here we describe prostaglandin E2 (PGE2) as a regulator of endodermal fate specification during development.

    Modulating PGE2 activity has opposing effects on liver versus pancreas specification […]

    The PGE2 synthetic enzyme cox2a and receptor ep2a are patterned such that cells closest to PGE2 synthesis acquire a liver fate, whereas more distant cells acquire a pancreas fate.

    PGE2 interacts with the bmp2b pathway to regulate fate specification.

    At later stages of development, PGE2 acting via the ep4a receptor promotes outgrowth of both the liver and pancreas.

    PGE2 remains important for adult organ growth, as it modulates liver regeneration.

    This work provides in vivo evidence that PGE2 may act as a morphogen to regulate cell-fate decisions and outgrowth of the embryonic endodermal anlagen.



  132. 132
    Dionisio says:

    Pioneer factors, genetic competence, and inductive signaling: programming liver and pancreas progenitors from the endoderm.

    The endoderm is a multipotent progenitor cell population in the embryo that gives rise to the liver, pancreas, and other cell types and provides paradigms for understanding cell-type specification.

    Studies of isolated embryo tissue cells and genetic approaches in vivo have defined fibroblast growth factor/mitogen-activated protein kinase (FGF/MAPK) and bone morphogenetic protein (BMP) signaling pathways that induce liver and pancreatic fates in the endoderm.

    In undifferentiated endoderm cells, the FoxA and GATA transcription factors [TF] are among the first to engage silent genes, helping to endow competence for cell-type specification.

    FoxA proteins can bind their target sites in highly compacted chromatin and open up the local region for other factors to bind; hence, they have been termed “pioneer factors.”

    We recently found that FoxA proteins remain bound to chromatin in mitosis, as an epigenetic mark.

    In embryonic stem cells, which lack FoxA, FoxA target sites can be occupied by FoxD3, which in turn helps to maintain a local demethylation of chromatin.

    By these means, a cascade of Fox factors helps to endow progenitor cells with the competence to activate genes in response to tissue-inductive signals.

    Understanding such epigenetic mechanisms for transcriptional competence coupled with knowledge of the relevant signals for cell-type specification should greatly facilitate efforts to predictably differentiate stem cells to liver and pancreatic fates.


  133. 133
    Dionisio says:

    Chromatin “pre-pattern” and epigenetic modulation in the cell fate choice of liver over pancreas in the endoderm

    doi: 10.4161/nucl.19321

    Understanding the basis for multipotency, whereby stem cells and other progenitors can differentiate into certain tissues and not others, provides insights into the mechanism of cell programming in development, homeostasis, and disease.

    We recently reported a screen of diverse chromatin marks to obtain clues about chromatin states in the multipotent embryonic endoderm.

    Genetic and pharmacologic tests of certain marks’ function demonstrated that the relevant chromatin modifying factors modulate the fate choice for liver or pancreas induction in the endoderm.

    The information about chromatin states from embryonic studies can be used to predict lineage-specific developmental potential and chromatin modifiers to enhance particular cell fate transitions from stem cells.


  134. 134
    Dionisio says:

    Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells.

    doi: 10.1016/j.stem.2012.11.023.

    Embryonic development is characterized by dynamic changes in gene expression, yet the role of chromatin remodeling in these cellular transitions remains elusive.

    These studies reveal dynamic chromatin remodeling during developmental lineage progression and identify possible strategies for improving cell differentiation in culture.


  135. 135
    Dionisio says:

    #134 addendum

    What about the ‘role’ that remains ‘elusive’? Did they mean that the role ‘remained’ elusive before their experiment finally cleared it?

    Is that ‘role’ described in the paper?

    The title of this paper refers to an ‘orchestration’ but is that ‘orchestration’ described in details within this paper, or through references to other sources?

    That’s something to look at later. But it’s not clear in the abstract.

    Just revealing that someone was at a location where certain event took place does not say what role that someone had in the given event.

    If we say that the role of that person in that event remains elusive, then we reveal that that person was at the location where the event occurred, still the person’s role in the event remains unclear.

    If we add that on the cases where the same person wasn’t present at the given location the referred event did not occur, then we can say that it looks as though that person’s presence makes a difference, but the ‘role’ of that person in that event still remains unclear.

    The abstract seems to indicate that their experiments confirmed that the presence or absence of the Chromatin remodeling made a difference, but it’s not clear how it made the difference.

    Perhaps the paper provides more details, but the abstract does not indicate explicitly that the ‘role’ is described, or the ‘orchestration’ is described.

    Later, if we look into the actual paper text, we might find the detailed description of the ‘role’ and the ‘orchestration’. In that case the abstract could have been written saying that the ‘role’ remained elusive until this paper, but no longer. But maybe that’s what they meant? we’ll have to look into the paper to see if that’s the case. That will have to wait until the next phase of the project. It’s not important now. This was just for illustration.

    Some interlocutors in this site have complained about my use of ‘bold’ characters to highlight part of the text. FYI – the highlighted text is a personal reminder to look for additional information (within the referred paper or somewhere else) in order to explain or describe with more details the highlighted text.

  136. 136
    Dionisio says:

    Hsp90-Tau Complex Reveals Molecular Basis for Specificity in Chaperone Action

    DOI: http://dx.doi.org/10.1016/j.cell.2014.01.037

    Protein folding in the cell relies on the orchestrated action of conserved families of molecular chaperones, the Hsp70 and Hsp90 systems.

    Hsp70 acts early and Hsp90 late in the folding path, yet the molecular basis of this timing is enigmatic, mainly because the substrate specificity of Hsp90 is poorly understood.

    Here, we obtained a structural model of Hsp90 in complex with its natural disease-associated substrate, the intrinsically disordered Tau protein.

    Hsp90 binds to a broad region in Tau that includes the aggregation-prone repeats.

    Complementarily, a 106-Å-long substrate-binding interface in Hsp90 enables many low-affinity contacts.

    This allows recognition of scattered hydrophobic residues in late folding intermediates that remain after early burial of the Hsp70 sites.

    Our model resolves the paradox of how Hsp90 specifically selects for late folding intermediates but also for some intrinsically disordered proteins—through the eyes of Hsp90 they look the same.


    How do Hsp70 and Hsp90 appear on the post-translational scene? how are they regulated to be available when needed for their combined chaperoning tasks? are they constantly produced, hence always available when needed? or produced on demand upon request by some signaling pathways and regulatory mechanisms?

  137. 137
    Dionisio says:

    Protein Folding in the Cell, from Atom to Organism

    doi: 10.1096/fj.14-1202ufm

    Proper cell function requires proper protein folding.

    Misfolding of specific proteins, caused either by mutation or environmental stress, underlies many human diseases, including cancer and diabetes and Parkinson’s, Huntington’s, and Alzheimer’s disease.


  138. 138
    Dionisio says:

    Revealing the inner workings of a molecular motor

    In research published in the Journal of Cell Biology, scientists from the RIKEN Brain Science Institute in Japan have made important steps toward understanding how dynein—a “molecular motor”—walks along tube-like structures in the cell to move cellular cargo from the outer structures toward the cell body of neurons.

    The action of this molecule is important for a number of cell functions including axonal transport and chromosome segregation, and its dysfunction is known to lead to a congenital developmental brain disorder known as lissencephaly.

    Read more at: http://phys.org/news/2015-01-r.....r.html#jCp


  139. 139
    Dionisio says:

    The epigenetic switchboard

    Epigenetic signals help determine which genes are activated at which time in a given cell.

    A novel analytical method enables systematic characterization of the relevant epigenetic tags, and reveals that the system adapts to the loss of single epigenetic writer and eraser enzymes.

    Read more at: http://phys.org/news/2015-01-e.....d.html#jCp

    How do those signals work? where do they come from? when? what triggers them? what determines their timing?
    Perhaps this is explained in the same paper or in other papers or textbooks?


  140. 140
    Dionisio says:

    noncoding RNA can be vital for successful pregnancy

    The proteins that underlie nearly all biological mechanisms are produced from RNA molecules transcribed from genetic sequences in DNA.

    However, a large proportion of transcribed RNA is not transcoded into proteins and appears to have no significant function.

    Shinichi Nakagawa from the RIKEN RNA Biology Laboratory and colleagues have now found that one particular long noncoding RNA (lncRNA) is essential for fertility in some circumstances.

    Read more at: http://phys.org/news/2015-01-m.....l.html#jCp

    Appearances can be deceiving.


  141. 141
    Dionisio says:

    Tumour-blocking role found for cell regulation molecule

    Manchester scientists have explored the role of a protein in regulating tumour development and found that it suppresses liver cancer growth in the lab.

    Read more at: http://phys.org/news/2015-01-t.....e.html#jCp

    JNK Suppresses Tumor Formation via a Gene-Expression Program Mediated by ATF2

    DOI: http://dx.doi.org/10.1016/j.celrep.2014.10.043


  142. 142
    Dionisio says:

    mysterious molecular mechanism powering cells

    A team led by structural biologists at The Scripps Research Institute (TSRI) has taken a big step toward understanding the intricate molecular mechanism of a metabolic enzyme produced in most forms of life on Earth.

    Read more at: http://phys.org/news/2015-01-s.....m.html#jCp

  143. 143
    Dionisio says:

    New insight on skull development

    For more than a century, scientists have attempted to understand how the bones of the skull develop in vertebrate embryos.

    Most have concluded that a single developmental pattern—first described in chickens—applies to all vertebrates.

    A new study conducted by Harvard researchers suggests that this may not be entirely true.

    Read more at: http://phys.org/news/2015-01-i.....s.html#jCp

    Old consensus broken? 🙂

    How come? what went wrong in their previous thinking?

  144. 144
    Dionisio says:

    Evidence that disproves a long-standing assumption?

    A Singapore-based research team has used fluorescent labeling of embryonic cell populations to pinpoint the origin of scales and fins in modern-day fish.

    These tissues […] were widely assumed to originate from an embryonic cell population known as the ‘trunk neural crest’.

    Now, research led by Tom Carney of the A*STAR Institute of Molecular and Cell Biology has shown that scales and fins actually develop from a cell population called the mesoderm.

    Read more at: http://phys.org/news/2013-08-e.....t.html#jCp

    What went wrong with their previous wide assumptions?

  145. 145
    Dionisio says:

    Morphology-based taxonomies do not accurately reflect genealogical relationships of rock sponges


    Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges

    •DOI: 10.1371/journal.pone.0116038


  146. 146
    Dionisio says:

    Researchers have looked at a species of fish to help unravel one of the biggest mysteries in evolutionary biology.

    “The importance of this work lies in the fundamental question: how and why do variants of the same animal exist in nature,” he said.

    “Colour variants of the same species are a striking example of biological variation, yet the adaptive significance and what evolutionary processes maintain them, remains unknown.”

    “Given the complexities of colour variants in species, more work is needed to understand how differences in colouration might influence the susceptibility of dark and gold individuals to different predators and under different environmental conditions,”

    Read more at: http://phys.org/news/2015-01-devil.html#jCp

    How do the associated mechanisms function? what effect do they have?

    Check the given paper or other papers for more details

    Where is the beef?

  147. 147
    Dionisio says:

    Ok, that’s cool, thanks.

    But how did it all start? 🙂


    Where is the beef?

  148. 148
    Dionisio says:

    Bleb-driven chemotaxis of Dictyostelium cells
    doi: 10.1083/jcb.201306147

    Dictyostelium uses ether?linked inositol phospholipids for intracellular signaling
    DOI 10.15252/embj.201488677

    How blebs and pseudopods cooperate during chemotaxis
    doi: 10.1073/pnas.1322291111

  149. 149
    Dionisio says:

    A unified vision of the building blocks of life?
    From the discovery of DNA to the sequencing of the human genome, the template-dependent formation of biological molecules from gene to RNA and protein has been the central tenet of biology.
    Yet the origins of many diseases, including allergy, Alzheimer’s disease, asthma, autism, diabetes, inflammatory bowel disease, Lou Gehrig’s disease, multiple sclerosis, Parkinson’s disease and rheumatoid arthritis, continue to evade our understanding.

  150. 150
    Dionisio says:

    Dom34 Rescues Ribosomes in 3? Untranslated Regions

    “As far as we know, this ‘scanning’ activity has never been seen before — it was a big surprise.” -Nick Guydosh, Ph.D.

    DOI: http://dx.doi.org/10.1016/j.cell.2014.02.006

    Ribosomes that stall before completing peptide synthesis must be recycled and returned to the cytoplasmic pool.

    The protein Dom34 and cofactors Hbs1 and Rli1 can dissociate stalled ribosomes in vitro, but the identity of targets in the cell is unknown.

    Here, we extend ribosome profiling methodology to reveal a high-resolution molecular characterization of Dom34 function in vivo.

    Dom34 removes stalled ribosomes from truncated mRNAs, but, in contrast, does not generally dissociate ribosomes on coding sequences known to trigger stalling, such as polyproline.

    We also show that Dom34 targets arrested ribosomes near the ends of 3? UTRs.

    These ribosomes appear to gain access to the 3? UTR via a mechanism that does not require decoding of the mRNA.

    These results suggest that ribosomes frequently enter downstream noncoding regions and that Dom34 carries out the important task of rescuing them.


  151. 151
    Dionisio says:

    The mitotic checkpoint protein kinase BUB1 is an engine in the TGF-? signaling apparatus

    DOI: 10.1126/scisignal.aaa4636

    The mitotic checkpoint guarantees faithful chromosomal segregation during cell division.

    …the mitotic checkpoint kinase BUB1 promotes the activity of TGF-? receptors, which adds new molecular links between these fundamental biological processes.


  152. 152
    Dionisio says:

    Know Your Limits: The Role of Boundaries in the Development of Spatial Representation

    DOI: http://dx.doi.org/10.1016/j.neuron.2014.03.017


  153. 153

    Dionisio, this slightly more recent paper for the development of spatial representation is also excellent:

    Coherence among Head Direction Cells before Eye Opening in Rat Pups.
    Bjerknes TL, Langston RF, Kruge IU, Moser EI, Moser MB.

    Mammalian navigation is thought to depend on an internal map of space consisting of functionally specialized cells in the hippocampus and the surrounding parahippocampal cortices [1-7]. Basic properties of this map are present when rat pups explore the world outside of their nest for the first time, around postnatal day 16-18 (P16-P18) [8-10]. One of the first functions to be expressed in navigating animals is the directional tuning of the head direction cells [8, 9]. To determine whether head direction tuning is expressed at even earlier ages, before the start of exploration, and to establish whether vision is necessary for the development of directional tuning, we recorded neural activity in pre- and parasubiculum, or medial entorhinal cortex, from P11 onward, 3-4 days before the eyelids unseal. Head direction cells were present from the first day of recording. Firing rates were lower than in adults, and preferred firing directions were less stable, drifting within trials and changing completely between trials. Yet the cells drifted coherently, i.e., relative firing directions were maintained from one trial to the next. Directional tuning stabilized shortly after eye opening. The data point to a hardwired attractor network for representation of head direction in which directional tuning develops before vision and visual input serves primarily to anchor firing direction to the external world.

    doi: 10.1016/j.cub.2014.11.009. Epub 2014 Nov 26.

    The bolded information at the end of its abstract is vital to the further development of the Grid Cell Attractor Network and earlier model that Edvard Moser knows about. The new paper seems to have been worded so that someone like myself would immediately recognize its significance, and know how to make it work in a computer model.

  154. 154
    Dionisio says:

    Mechanism of suppression of chromosomal instability by DNA polymerase POLQ.

    doi: 10.1371/journal.pgen.1004654

    Although a defect in the DNA polymerase POLQ leads to ionizing radiation sensitivity in mammalian cells, the relevant enzymatic pathway has not been identified.

    Here we define the specific mechanism by which POLQ restricts harmful DNA instability.

    This work clearly defines a role and mechanism for mammalian POLQ in an alternative end joining pathway that suppresses the formation of chromosomal translocations.

    Our findings depart from the prevailing view that alternative end joining processes are generically translocation-prone.


  155. 155
    Dionisio says:

    #153 Gary S. Gatlin

    Thank you for sharing the reference to that interesting paper.

  156. 156
    Dionisio says:

    Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean

    doi: 10.1534/genetics.114.170340


    Explain the details describing that resilience.

    Does the paper contain ALL the details?

    ALL? This means that no potential questions have been left unanswered?

  157. 157

    Dionisio I appreciate the paper that you provided, which linked to the open access Moser intelligence laboratory paper that was published just in time for Christmas. With my day job and all else I didn’t have time to keep up with their progress. Now I just need to figure out the details, which is sure not easy for a paper like this one. And I honestly doubt for something like this I’ll find much help from UD, Biologic or Discovery Institute.

  158. 158
    Dionisio says:

    Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamina

    doi: 10.1083/jcb.201405110

    Nuclear organization has been implicated in regulating gene activity.

    Recently, large developmentally regulated regions of the genome dynamically associated with the nuclear lamina have been identified.

    […]how these lamina-associated domains (LADs) are directed to the nuclear lamina. [?]


  159. 159
    Dionisio says:

    Regulation of RNA granule dynamics…

    DOI: http://dx.doi.org/10.7554/eLife.04591

    RNA granules have been likened to liquid droplets whose dynamics depend on the controlled dissolution and condensation of internal components.

    The molecules and reactions that drive these dynamics in vivo are not well understood.


  160. 160
    Dionisio says:

    Lentivirus?mediated silencing of spindle and kinetochore?associated protein 1

    doi: 10.3892/mmr.2015.3175

    Spindle and kinetochore?associated protein 1 (SKA1) is an important component of the human kinetochore, which plays a key role in mitosis.


  161. 161
    Dionisio says:

    The spindle checkpoint and chromosome segregation in meiosis

    DOI: 10.1111/febs.13166

    The spindle checkpoint is a key regulator of chromosome segregation in mitosis and meiosis.

    Its function is to prevent precocious anaphase onset before chromosomes have achieved bipolar attachment to the spindle.

    The spindle checkpoint comprises a complex set of signaling pathways that integrate microtubule dynamics, biomechanical forces at the kinetochores, and intricate regulation of protein interactions and post-translational modifications.

    Historically, many key observations that gave rise to the initial concepts of the spindle checkpoint were made in meiotic systems.

    In contrast with mitosis, the two distinct chromosome segregation events of meiosis present a special challenge for the regulation of checkpoint signaling.

    Preservation of fidelity in chromosome segregation in meiosis, controlled by the spindle checkpoint, also has a significant impact in human health.

    This review highlights the contributions from meiotic systems in understanding the spindle checkpoint as well as the role of checkpoint signaling in controlling the complex divisions of meiosis.


  162. 162
    Dionisio says:

    From Single-Cell Noise to Transcriptional Music

    Although an orchestra warming up before a performance may produce a meaningless mixture of sounds, the individual musicians are probably playing bits and pieces from the same score.

    If only listeners could isolate the fragmentary themes and motifs, and move them backwards and forwards in the imagination, order would emerge from chaos, the sense of musical arrangements would become clear.

    Something like this organizational power has been needed in single-cell genomics.

    Although individual cells all play from the same score—the genome—they don’t necessarily act as though they are following a conductor’s baton.

    Even cells of the same type may appear to be transcriptionally distinct simply because they are at different stages of the cell cycle, or are different ages.

    Confounding factors such as these can obscure deep commonalities or—to return to the orchestra analogy—unheard harmonies.


  163. 163
    Dionisio says:

    Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

    doi: 10.1073/pnas.1408993111


  164. 164
    Dionisio says:

    The centrosome orientation checkpoint is germline stem cell specific and operates prior to the spindle assembly checkpoint


    Asymmetric cell division is utilized by a broad range of cell types to generate two daughter cells with distinct cell fates.

    In stem cell populations asymmetric cell division is believed to be crucial for maintaining tissue homeostasis, failure of which can lead to tissue degeneration or hyperplasia/tumorigenesis.

    Asymmetric cell divisions also underlie cell fate diversification during development.

    Accordingly, the mechanisms by which asymmetric cell division is achieved have been extensively studied, although the check points that are in place to protect against potential perturbation of the process are poorly understood.

    This study may provide a framework for identifying and understanding similar mechanisms that might be in place in other asymmetrically dividing cell types.

  165. 165
    Dionisio says:

    Computational analysis of signaling patterns in single cells


    Signaling proteins are flexible in both form and function.

    They can bind to multiple molecular partners and integrate diverse types of cellular information.

    When imaged by time-lapse microscopy, many signaling proteins show complex patterns of activity or localization that vary from cell to cell.

    This heterogeneity is so prevalent that it has spurred the development of new computational strategies to analyze single-cell signaling patterns.

    A collective observation from these analyses is that cells appear less heterogeneous when their responses are normalized to, or synchronized with, other single-cell measurements.

    In many cases, these transformed signaling patterns show distinct dynamical trends that correspond with predictable phenotypic outcomes.

    When signaling mechanisms are unclear, computational models can suggest putative molecular interactions that are experimentally testable.

    Thus, computational analysis of single-cell signaling has not only provided new ways to quantify the responses of individual cells, but has helped resolve longstanding questions surrounding many well-studied human signaling proteins including NF-?B, p53, ERK1/2, and CDK2.

    A number of specific challenges lie ahead for single-cell analysis such as quantifying the contribution of non-cell autonomous signaling as well as the characterization of protein signaling dynamics in vivo.


  166. 166
    Dionisio says:

    TRAIP is a regulator of the spindle assembly checkpoint

    doi: 10.1242/?jcs.152579

    Accurate chromosome segregation during mitosis is temporally and spatially coordinated by fidelity-monitoring checkpoint systems.

    Deficiencies in these checkpoint systems can lead to chromosome segregation errors and aneuploidy,…

    the TRAF-interacting protein (TRAIP), a ubiquitously expressed nucleolar E3 ubiquitin ligase important for cellular proliferation, is localized close to mitotic chromosomes. [why is it there?]

    TRAIP regulates the spindle assembly checkpoint, MAD2 abundance at kinetochores and the accurate cellular distribution of chromosomes. [how does it do all that?]

    The TRAIP ubiquitin ligase activity is functionally required for the spindle assembly checkpoint control.


    What mechanisms determine that a protein is ubiquitously expressed? Branch out on this expression subtopic.

    What determines the localization of TRAIP? Branch out on this protein localization subtopic.

    Search the answers within the payer first, then in other papers.

  167. 167
    Dionisio says:

    Evolution leading to a potential revolution?



  168. 168
    Dionisio says:

    Tethering Sister Centromeres to Each Other Suggests the Spindle Checkpoint Detects Stretch within the Kinetochore

    •DOI: 10.1371/journal.pgen.1004492

    The spindle checkpoint ensures that newly born cells receive one copy of each chromosome by preventing chromosomes from segregating until they are all correctly attached to the spindle.

    The checkpoint monitors tension to distinguish between correctly aligned chromosomes and those with both sisters attached to the same spindle pole.

    Tension arises when sister kinetochores attach to and are pulled toward opposite poles, stretching the chromatin around centromeres and elongating kinetochores.

    We distinguished between two hypotheses for where the checkpoint monitors tension:
    -between the kinetochores, by detecting alterations in the distance between them, or
    -by responding to changes in the structure of the kinetochore itself.

    To distinguish these models, we inhibited chromatin stretch by tethering sister chromatids together by binding a tetrameric form of the Lac repressor to arrays of the Lac operator located on either side of a centromere.

    Inhibiting chromatin stretch did not activate the spindle checkpoint; [why?] these cells entered anaphase at the same time as control cells that express a dimeric version of the Lac repressor, which cannot cross link chromatids, and cells whose checkpoint has been inactivated.

    There is no dominant checkpoint inhibition when sister kinetochores are held together: cells expressing the tetrameric Lac repressor still arrest in response to microtubule-depolymerizing drugs.

    Tethering chromatids together does not disrupt kinetochore function; [why?] chromosomes are successfully segregated to opposite poles of the spindle.

    Our results indicate that the spindle checkpoint does not monitor inter-kinetochore separation, thus supporting the hypothesis that tension is measured within the kinetochore. [how?]


  169. 169
    Dionisio says:

    Molecular Determinants of ?-Synuclein Mutants’ Oligomerization and Membrane Interactions

    ACS Chem. Neurosci., Article ASAP
    DOI: 10.1021/cn500332w
    Publication Date (Web): January 5, 2015
    Copyright © 2015 American Chemical Society


    Parkinson’s disease (PD) is associated with the formation of toxic ?-synuclein oligomers that can penetrate the cell membrane. Familial forms of PD are caused by the point mutations A53T, A30P, E46K, and H50Q. Artificial point mutations E35K and E57K also increase oligomerization and pore formation. We generated structural conformations of ?-synuclein and the above-mentioned mutants using molecular dynamics. We elucidated four main regions in these conformers contacting the membrane and found that the region including residues 39–45 (Zone2) may have maximum membrane penetration. E57K mutant had the highest rate of interaction with the membrane, followed by A53T, E46K, and E35K mutants and wild type (wt) ?-synuclein. The mutant A30P had the smallest percentage of conformers that contact the membrane by Zone 2 than all other mutants and wt ?-synuclein. These results were confirmed experimentally in vitro. We identified the key amino acids that can interact with the membrane (Y38, E62, and N65 (first hydrophilic layer); E104, E105, and D115 (second hydrophilic layer), and V15 and V26 (central hydrophobic layer)) and the residues that are involved in the interprotein contacts (L38, V48, V49, Q62, and T64).

    Understanding the molecular interactions of ?-synuclein mutants is important for the design of compounds blocking the formation of toxic oligomers.

    How many details have to work right in the biological systems in order for the systems to function properly ?

  170. 170
    Dionisio says:

    CNS myelination requires cytoplasmic dynein function

    DOI: 10.1002/dvdy.24238

    Cytoplasmic dynein provides the main motor force for minus-end-directed transport of cargo on microtubules.

    Within the vertebrate central nervous system (CNS), proliferation, neuronal migration, and retrograde axon transport are among the cellular functions known to require dynein.

    Oligodendrocytes, the myelinating glial cell type of the CNS, migrate from their origins to their target axons and subsequently extend multiple long processes that ensheath axons with specialized insulating membrane.

    These processes are filled with microtubules, which facilitate molecular transport of myelin components.

    However, whether oligodendrocytes require cytoplasmic dynein to ensheath axons with myelin is not known.

    We identified a mutation of zebrafish dync1h1 in a forward genetic screen that caused a deficit of oligodendrocytes.

    Using in vivo imaging and gene expression analyses, we additionally found evidence that dync1h1 promotes axon ensheathment and myelin gene expression.

    In addition to its well known roles in axon transport and neuronal migration, cytoplasmic dynein contributes to neural development by promoting myelination.

    Developmental Dynamics, 2015. © 2014 Wiley Periodicals, Inc.


    For the above highlighted text, explain ‘how’ in details, by indicating the paper(s) where they answer such questions.

  171. 171
    Dionisio says:

    The complexity of cellular biology.

    (a) A subset of the chemical reactions that drive eukaryotic cell crawling.

    In brief, cells sense the environment through membrane bound proteins.

    Activation of these receptors leads to activation of a number of other proteins that promote the polymerization of actin.

    The biochemical reactions that govern the dynamics of actin are included.

    These chemical reactions produce cell motility.

    (b)–(d) Time series of a cancer cell (HT1080 fibrosarcoma cell) moving through a collagen I matrix.

    There are two hour intervals between each frame.

    (Images courtesy of D. Wirtz, Johns Hopkins University.)


    We have amassed a lot of data, and the more we put together, the more complex and harder to interpret the data becomes.

    Even if we consider a single cellular function (for instance, the ability of a eukaryotic cell to move along a substrate) the chemical reaction network that describes this behavior appears incomprehensible


    Drive, sense, leads, govern, produce, … how?

  172. 172
    Dionisio says:

    The telomere length can either be shortened or elongated by an enzyme called telomerase after each cell division.

    Interestingly, the shortest telomere is involved in controlling the ability of a cell to divide. [how does that controlling work?]

    Yet, its dynamics remains elusive.

    We present here a stochastic approach where we model this dynamics using a Markov jump process.

    We solve the forward Fokker-Planck equation to obtain the steady state distribution and the statistical moments of telomere lengths.

    We focus specifically on the shortest one and we estimate its length difference with the second shortest telomere.

    After extracting key parameters such as elongation and shortening dynamics from experimental data, we compute the length of telomeres in yeast and obtain as a possible prediction the minimum concentration of telomerase required to ensure a proper cell division.

    DOI: http://dx.doi.org/10.1103/PhysRevLett.111.228104


    How exactly is that dynamics? Timers, actors or executors, scenarios, signaling pathways. regulatory networks, etc.?

  173. 173
    Dionisio says:

    Molecular Signaling Network Motifs Provide a Mechanistic Basis for Cellular Threshold Responses

    Cellular response behaviors depend on the molecular pathway and circuitry in the cell and the manner in which chemicals perturb these circuits.

    Understanding circuit structures that are inherently capable of resisting small perturbations and producing threshold responses is an important step…

    These network motifs are basic building blocks of molecular circuits underpinning a variety of cellular functions, including adaptation, homeostasis, proliferation, differentiation, and apoptosis.

    For each motif, we present biological examples and models to illustrate how thresholds arise from specific network structures.

    Integral feedback, feedforward, and transcritical bifurcation motifs can generate thresholds.

    Other motifs (e.g., proportional feedback and ultra sensitivity)…

    Feedforward control may lead to nonmonotonic or hormetic responses.

    We conclude that network motifs provide a basis for understanding thresholds for cellular responses.

    Computational pathway modeling of these motifs and their combinations occurring in molecular signaling networks will be a key element…


  174. 174
    Dionisio says:

    The immune system is regulated by distinct signaling pathways that control the development and function of the immune cells.

    Accumulating evidence suggest that ligation of aryl hydrocarbon receptor (Ahr), an environmentally responsive transcription factor, results in multiple cross talks that are capable of modulating these pathways and their downstream responsive genes.

    Ahr is critically involved in the differentiation of Th17 and Tregs.

    Since these cells are reciprocally related, it may be suggested that Ahr is necessary to maintain the balance between these cells under normal conditions…

    Ahr is not simply a transcription factor responding to toxins, but it is also critical in the physiological functions of immune cell compartments,…

    …studying Ahr signaling and alternative pathways is still a valuable approach for…


    BioMed Research International
    Volume 2014 (2014), Article ID 520763, 14 pages

    Fascinating issues that raise questions about interesting interconnected structures/circuits and their interrelated functioning.

  175. 175
    Dionisio says:

    The Cdc20-binding Phe Box of the Spindle Checkpoint Protein BubR1 Maintains[?] the Mitotic Checkpoint Complex During Meiosis

    doi: 10.1074/jbc.M114.616490

    The spindle checkpoint ensures accurate chromosome segregation by monitoring [?] kinetochore-microtubule attachment.

    Unattached or tensionless kinetochores activate [?] the checkpoint and enhance [?] the production of the mitotic checkpoint complex (MCC) consisting of BubR1, Bub3, Mad2, and Cdc20.

    MCC is a critical checkpoint inhibitor [?] of the anaphase-promoting complex/cyclosome, a ubiquitin ligase required [?] for anaphase onset.

    The N-terminal region of BubR1 binds to both Cdc20 and Mad2, thus nucleating [?] MCC formation.

    The middle region of human BubR1 (BubR1M) also interacts [?] with Cdc20, but the nature and function of this interaction are not understood. [?]

    Here we identify two critical motifs within BubR1M that contribute [?] to Cdc20 binding and anaphase-promoting complex/cyclosome inhibition: a destruction box (D box) and a phenylalanine-containing motif termed the Phe box.

    A BubR1 mutant lacking these motifs is defective in MCC maintenance in mitotic human cells but is capable of supporting spindle-checkpoint function.

    Thus, the BubR1M-Cdc20 interaction indirectly contributes [?] to MCC homeostasis.

    Its apparent dispensability in the spindle checkpoint might be due to functional duality or redundant, competing mechanisms.


    [?] – any valid combination of these questions: why? how? when? where? what for?

  176. 176
    Dionisio says:

    Multiple assembly mechanisms anchor [?] the KMN spindle checkpoint platform at human mitotic kinetochore

    doi: 10.1083/jcb.201407074

    During mitosis, the spindle checkpoint senses [?] kinetochores not properly attached to spindle microtubules and prevents [?] precocious sister-chromatid separation and aneuploidy.

    The constitutive centromere-associated network (CCAN) at inner kinetochores anchors [?] the KMN network consisting of Knl1, the Mis12 complex (Mis12C), and the Ndc80 complex (Ndc80C) at outer kinetochores.

    KMN is a critical kinetochore receptor [?] for both microtubules and checkpoint proteins.

    Here, we show that nearly complete inactivation of KMN in human cells through multiple strategies produced [?] strong checkpoint defects even when all kinetochores lacked microtubule attachment.

    These KMN-inactivating strategies reveal multiple KMN assembly mechanisms at human mitotic kinetochores.

    In one mechanism, the centromeric kinase Aurora B phosphorylates Mis12C and strengthens [?] its binding to the CCAN subunit CENP-C.

    In another, CENP-T contributes [?] to KMN attachment in a CENP-H-I-K–dependent manner.

    Our study provides insights into the mechanisms of mitosis-specific assembly of the checkpoint platform KMN at human kinetochores.


    [?] – any valid combination of these questions: why? how? when? where? what for? Also, explain the availability (always or on demand?; everywhere or specifically localized?) of the factors involved in the mechanisms.

  177. 177
    Dionisio says:

    The importance of understanding, as precisely as possible, the interrelated functioning of interconnected biological subsystems, may be noticeable in this biomedical research example, dealing with single nucleotide polymorphisms (SNPs) of genes involved in spindle assembly checkpoint (SAC).


  178. 178
    Dionisio says:

    Spindle assembly checkpoint: the third decade.

    The spindle assembly checkpoint controls cell cycle progression during mitosis, synchronizing it with the attachment of chromosomes to spindle microtubules.

    After the discovery of the mitotic arrest deficient (MAD) and budding uninhibited by benzymidazole (BUB) genes as crucial checkpoint components in 1991, the second decade of checkpoint studies (2001-2010) witnessed crucial advances in the elucidation of the mechanism through which the checkpoint effector, the mitotic checkpoint complex, targets the anaphase-promoting complex (APC/C) to prevent progression into anaphase.

    Concomitantly, the discovery that the Ndc80 complex and other components of the microtubule-binding interface of kinetochores are essential for the checkpoint response finally asserted that kinetochores are crucial for the checkpoint response.

    Nevertheless, the relationship between kinetochores and checkpoint control remains poorly understood.

    Crucial advances in this area in the third decade of checkpoint studies (2011-2020) are likely to be brought about by the characterization of the mechanism of kinetochore recruitment, activation and inactivation of checkpoint proteins, which remains elusive for the majority of checkpoint components.

    Here, we take a molecular view on the main challenges hampering this task.


  179. 179
  180. 180
    Dionisio says:

    #178 addendum

    Nevertheless, the relationship between kinetochores and checkpoint control remains poorly understood. [well, that was over 3 years ago, but maybe by now they know what they didn’t know back then? Many papers on this subject have been published the last few years, shedding more light on the presented issues].

    Crucial advances in this area in the third decade of checkpoint studies (2011–2020) are likely to be brought about by the characterization of the mechanism of kinetochore recruitment, activation and inactivation of checkpoint proteins, which remains elusive for the majority of checkpoint components.


  181. 181
    Dionisio says:

    Structure-biological function relationship extended to mitotic arrest-deficient 2-like protein Mad2 native and mutants-new opportunity for genetic disorder control.



  182. 182
    Dionisio says:

    The dynamics of signal amplification by macromolecular assemblies for the control of chromosome segregation

    doi: 10.3389/fphys.2014.00368


  183. 183
    Dionisio says:

    The dynamics of signal amplification by macromolecular assemblies for the control of chromosome segregation

    doi: 10.3389/fphys.2014.00368

    The control of chromosome segregation relies on the spindle assembly checkpoint (SAC), a complex regulatory system that ensures the high fidelity of chromosome segregation in higher organisms by delaying the onset of anaphase until each chromosome is properly bi-oriented on the mitotic spindle.

    Central to this process is the establishment of multiple yet specific protein-protein interactions in a narrow time-space window.

    highly dynamic nature of multi-protein complexes that control chromosome segregation in which an intricate network of weak but cooperative interactions modulate signal amplification to ensure a proper SAC response.

    communication between the SAC and the kinetochore…

    …the challenges and opportunities for the definition and the manipulation of the flow of information in SAC signaling.


  184. 184
    Dionisio says:

    Active Transport Can Greatly Enhance Cdc20:Mad2 Formation


    To guarantee genomic integrity and viability, the cell must ensure proper distribution of the replicated chromosomes among the two daughter cells in mitosis.

    The mitotic spindle assembly checkpoint (SAC) is a central regulatory mechanism to achieve this goal.

    A dysfunction of this checkpoint may lead to aneuploidy and likely contributes to the development of cancer.

    Kinetochores of unattached or misaligned chromosomes are thought to generate a diffusible “wait-anaphase” signal, which is the basis for downstream events to inhibit the anaphase promoting complex/cyclosome (APC/C).

    The rate of Cdc20:C-Mad2 complex formation at the kinetochore is a key regulatory factor in the context of APC/C inhibition.

    Computer simulations of a quantitative SAC model show that the formation of Cdc20:C-Mad2 is too slow for checkpoint maintenance when cytosolic O-Mad2 has to encounter kinetochores by diffusion alone.

    Here, we show that an active transport of O-Mad2 towards the spindle mid-zone increases the efficiency of Mad2-activation.

    Our in-silico data indicate that this mechanism can greatly enhance the formation of Cdc20:Mad2 and furthermore gives an explanation on how the “wait-anaphase” signal can dissolve abruptly within a short time.

    Our results help to understand parts of the SAC mechanism that remain unclear.


  185. 185
    Dionisio says:

    Molecular Dynamics Simulation on the Conformational Transition of the Mad2 Protein from the Open to the Closed State


    The Mad2 protein, with two distinct conformations of open- and closed-states, is a key player in the spindle checkpoint.

    The closed Mad2 state is more active than the open one. [?]

    The interconversion between these two states might facilitate [?] the functional activity of the Mad2 protein.

    Motion correlation analysis revealed the allosteric network between the ?1 strand and ?7/8 sheet via communication of the ?5-?C loop and the ?6/4/5 sheet in this transition process.


  186. 186
    Dionisio says:

    Formation of multiprotein assemblies in the nucleus: the spindle assembly checkpoint

    doi: 10.1016/B978-0-12-800046-5.00006-0.

    Specific interactions within the cell must occur in a crowded environment and often in a narrow time-space framework to ensure cell survival.

    In the light that up to 10% of individual protein molecules present at one time in mammalian cells mediate signal transduction, the establishment of productive, specific interactions is a remarkable achievement.

    The spindle assembly checkpoint (SAC) is an […] essential self-monitoring system of the eukaryotic cell cycle that ensures the high fidelity of chromosome segregation by delaying the onset of anaphase until all chromosomes are properly bi-oriented on the mitotic spindle.

    The function of the SAC involves communication with the kinetochore, an essential multiprotein complex crucial for chromosome segregation that assembles on mitotic or meiotic centromeres to link centromeric DNA with microtubules.

    Interactions in the SAC and kinetochore-microtubule network often involve the reversible assembly of large multiprotein complexes in which regions of the polypeptide chain that exhibit low structure complexity undergo a disorder-to-order transition.

    The confinement and high density of protein molecules in the cell has a profound effect on the stability, folding rate, and biological functions of individual proteins and protein.

    Here, I discuss the role of large and highly flexible surfaces that mediate productive intermolecular interactions in SAC signaling and postulate that macromolecular crowding contributes to the exquisite regulation that is required for the timely and accurate segregation of chromosomes in higher organisms.

    © 2014 Elsevier Inc. All rights reserved.

  187. 187
    Dionisio says:

    Microtubule attachment and spindle assembly checkpoint signalling at the kinetochore.

    doi: 10.1038/nrm3494.

    In eukaryotes, chromosome segregation during cell division is facilitated by the kinetochore, a multiprotein structure that is assembled on centromeric DNA.

    The kinetochore attaches chromosomes to spindle microtubules, modulates the stability of these attachments and relays the microtubule-binding status to the spindle assembly checkpoint (SAC), a cell cycle surveillance pathway that delays chromosome segregation in response to unattached kinetochores.

    Recent studies are shaping current thinking on how each of these kinetochore-centred processes is achieved, and how their integration ensures faithful chromosome segregation, focusing on the essential roles of kinase-phosphatase signaling and the microtubule-binding KMN protein network.



  188. 188
    Dionisio says:

    Mitotic catenation is monitored and resolved by a PKC?-regulated pathway

    doi: 10.1038/ncomms6685

    Exit from mitosis is controlled by silencing of the spindle assembly checkpoint (SAC).

    It is important that preceding exit, all sister chromatid pairs are correctly bioriented, and that residual catenation is resolved, permitting complete sister chromatid separation in the ensuing anaphase.


  189. 189
    Dionisio says:

    Interesting presentation topics:

    Keystone Symposia on Molecular and Cellular Biology

    Endoderm Lineages in Development and Disease

    Endoderm Formation

    Kat Hadjantonakis, Sloan-Kettering Institute, USA
    Cell Dynamics and the Emergence &of Endoderm in the Early Mouse Embryo

    Kyra A. Campbell, Institute of Research in Biomedicine, Spain
    Short Talk: The Precise Cellular Behaviors Orchestrated by GATA Factor Activity during Endoderm Formation in Drosophila

    Ken W.Y. Cho, University of California, Irvine, USA
    Genome-Wide View of the Early Xenopus Endoderm Regulatory Program

    Ludovic Vallier, Wellcome Trust Sanger Institute, UK
    Cell Cycle Controls Endoderm Specification of Human Pluripotent Stem Cells

    Endoderm Patterning

    Aaron M. Zorn, Cincinnati /Children’s Hospital Medical Center, USA
    Endoderm Patterning and Early Organogenesis

    Francesca M. Spagnoli, Max Delbrück Center for Molecular Medicine, Germany
    Short Talk: Control of Cellular Plasticity between Liver and Pancreas

    Lori Sussel, Columbia University, USA
    Induction and Maintenance of Pancreatic Endoderm

    Heiko Lickert, Institute of Diabetes and Regeneration, Germany
    Novel Players in Pancreas Formation and Function

    Allen Wang, University of California, San Diego, USA
    Short Talk: A Poised Enhancer Landscape Is Indicative of Developmental Competence during Endodermal Lineage Diversification of Human Embryonic Stem Cells

    Organ Induction

    Susan E. Mango, Harvard University, USA
    Higher-Order Organization of the Nucleus as Embryos Transition from Developmental Plasticity to Differentiation

    Clare C. Blackburn, University of Edinburgh, UK
    Inducing a Thymus in vivo, and in vitro

    John M. Shannon, Cincinnati Children’s Hospital Medical Center, USA
    Short Talk: Specification of Respiratory Endoderm Occurs Early in Embryogenesis

    Elke A. Ober, University of Copenhagen, Denmark
    Cell-Cell Interactions Controlling Liver Bud Morphogenesis

    Li Chen, University of Houston, USA
    Short Talk: A Molecular Switch Regulating Pancreatic and Heart Development

    Wellington V. Cardoso, Columbia University Medical Center, USA
    Hippo-Yap Control of Lung Epithelial Morphogenesis and Differentiation

  190. 190
    Dionisio says:

    Biology, Driven by Data

    Cells are incredibly complicated machines with thousands of interacting parts — and disruptions to any of those interactions can cause disease.

    “The central challenge of this field is how you take all those different kinds of data to get a coherent picture of what’s going on in a cell, what is wrong in a diseased cell, and how you might fix it,” says Dr. Fraenkel, an associate professor of biological engineering.

    “One way to think about it is a map of a city where these proteins or genes are lighting up different things, and you have to figure out what the wiring is underneath that’s got them talking to each other,” says Dr. Fraenkel.


  191. 191
    Dionisio says:

    #189 addendum

    Keystone Symposia on Molecular and Cellular Biology

    Endoderm Lineages in Development and Disease


  192. 192
    Dionisio says:

    Oncoprotein YAP Regulates the Spindle Checkpoint Activation in a Mitotic Phosphorylation-dependent Manner through Upregulation of BubR1

    doi: 10.1074/jbc.M114.624411

    The transcriptional co-activator Yes-associated protein, YAP, functions as an oncogene; however, it is largely unclear how YAP exerts its oncogenic role.

    In this study, we further explored the functional significance of YAP and its mitotic phosphorylation in the spindle checkpoint.

    We found that the dynamic mitotic phosphorylation of YAP was CDC14-dependent.

    We also showed that YAP was required for the spindle checkpoint activation induced by spindle poisons.

    Mitotic phosphorylation of YAP was required for activation of the spindle checkpoint.

    Furthermore, enhanced expression of active YAP hyper-activated the spindle checkpoint and induced mitotic defects in a mitotic phosphorylation-dependent manner.

    Mechanistically, we documented that mitotic phosphorylation of YAP controlled transcription of genes associated with the spindle checkpoint.

    YAP constitutively associated with BUB1-related protein kinase (BubR1) and knockdown of BubR1 relieved YAP-driven hyper-activation of the spindle checkpoint.

    Finally, we demonstrated that YAP promoted epithelial cell invasion via both mitotic phosphorylation and BubR1-dependent mechanisms.

    Together, our results reveal a novel link between YAP and the spindle checkpoint, and indicate a potential mechanism underlying the oncogenic function of YAP through dysregulation of the spindle checkpoint.


  193. 193
    Dionisio says:

    Proteins of the mitotic checkpoint and spindle…



    With so many things that can go wrong and mess everything up, how does the whole system still work?

    Does the word robustness come to mind?

  194. 194
    Dionisio says:

    Spatio-temporal Model for Silencing of Mitotic Spindle Assembly Checkpoints

    The spindle assembly checkpoint arrests mitotic progression until each kinetochore secures a stable attachment to the spindle.

    Despite fluctuating noise, this checkpoint remains robust and remarkably sensitive to even a single unattached kinetochore among many attached kinetochores; moreover, the checkpoint is silenced only after the final kinetochore-spindle attachment.

    Experimental observations have shown that checkpoint components stream from attached kinetochores along microtubules towards spindle poles.

    Here we incorporate this streaming behavior into a theoretical model that accounts for the robustness of checkpoint silencing.

    Poleward streams are integrated at spindle poles, but are diverted by any unattached kinetochore; consequently, accumulation of checkpoint components at spindle poles increases markedly only when every kinetochore is properly attached.

    This step change robustly triggers checkpoint silencing after, and only after, the final kinetochore-spindle attachment.

    Our model offers a conceptual framework that highlights the role of spatio-temporal regulation in mitotic spindle checkpoint signaling and fidelity of chromosome segregation.


  195. 195
    Dionisio says:

    Signalling dynamics in the spindle checkpoint response


    The spindle checkpoint ensures proper chromosome segregation during cell division.

    Unravelling checkpoint signalling has been a long-standing challenge owing to the complexity of the structures and forces that regulate chromosome segregation.

    New reports have now substantially advanced our understanding of checkpoint signalling mechanisms at the kinetochore, the structure that connects microtubules and chromatin.

    In contrast to the traditional view of a binary checkpoint response — either completely on or off — new findings indicate that the checkpoint response strength is variable.

    This revised perspective provides insight into how checkpoint bypass can lead to aneuploidy and informs strategies to exploit these errors for cancer treatments.


  196. 196
    Dionisio says:

    A maternal effect rough deal mutation suggesting multiple pathways regulating Drosophila RZZ kinetochore recruitment

    doi: 10.1242/?jcs.165712

    Proper kinetochore recruitment and regulation of Dynein and the Mad1-Mad2 complex requires the Rod-Zw10-Zwilch (RZZ) complex.

    We describe rodZ3, a maternal-effect Drosophila mutation changing a single residue in the Rough Deal (Rod) subunit of RZZ.

    Although RZ3ZZ complex is present in early syncytial stage embryos laid by homozygous rodZ3 mothers, it is not recruited to kinetochores.

    Consequently, the embryos have no spindle assembly checkpoint (SAC), and syncytial mitoses are profoundly perturbed.

    The polar body (residual meiotic products) cannot remain in its SAC-dependent metaphase-like state, and decondenses into chromatin.

    In neuroblasts of homozygous rodZ3 larvae, RZ3ZZ recruitment is only partially reduced, the SAC is functional and mitosis is relatively normal.

    RZ3ZZ nevertheless behaves abnormally: it does not further accumulate on kinetochores when microtubules are depolymerized; it reduces the rate of Mad1 recruitment; and it dominantly interferes with the dynein-mediated streaming of RZZ from attached kinetochores.

    These results suggest that the mutated residue of rodZ3 is required for normal RZZ kinetochore recruitment and function and moreover that the RZZ recruitment pathway may differ in syncytial stage embryos and post-embryonic somatic cells.


  197. 197
    Dionisio says:

    Dynamic kinetochore

    The kinetochore is a highly specialized structure that forms at centromeric chromatin during mitosis and meiosis to act as the chromosomal attachment site for the dynamic spindle microtubules that drive chromosome segregation.

    The hundred or more kinetochore proteins have a wide range of functions including localization to centromeric chromatin to specify the position of the kinetochore, binding to spindle microtubules, mediating chromosome movement, and sensing and correcting errors during chromosome segregation.

    The field is moving at a rapid pace and the objective is to bring together both senior and junior researchers in the field to present their latest work.

    Topics include:
    •Epigenetic centromere specification and dynamics
    •Regulation of kinetochore function
    •Kinetochore microtubule interactions
    •Spindle assembly checkpoint signaling
    •Error correction machinery


  198. 198
    Dionisio says:

    DNA methylation age of blood predicts all-cause mortality in later life


    DNA methylation levels change with age.

    Recent studies have identified biomarkers of chronological age based on DNA methylation levels.

    It is not yet known whether DNA methylation age captures aspects of biological age.

    Here we test whether differences between people’s chronological ages and estimated ages, DNA methylation age, predict all-cause mortality in later life.

    The difference between DNA methylation age and chronological age, (delta age), was calculated in four longitudinal cohorts of older people.

    Meta-analysis of proportional hazards models from the four cohorts was used to determine the association between delta age and mortality.

    A 5-year higher delta age is associated with a 21% higher mortality risk, adjusting for age and sex.

    After further adjustments for childhood IQ, education, social class, hypertension, diabetes, cardiovascular disease, and APOE e4 status, there is a 16% increased mortality risk for those with a 5-year higher delta age.

    A pedigree-based heritability analysis of delta age was conducted in a separate cohort.

    The heritability of delta age was 0.43.

    DNA methylation-derived measures of accelerated ageing are heritable traits that predict mortality independently of health status, lifestyle factors, and known genetic factors.


  199. 199
    Dionisio says:

    198 follow-up

    What factors determine the location(s) of the DNA Methylation? Assuming it is a stochastic process, what systemic configuration allows such stochastic process to produce the results it does? How does such structural configuration get setup to begin with?

  200. 200
    Dionisio says:

    OMICS Tutorial

    Feb 1, 2015 (Vol. 35, No. 3)

    Systems Biology Tools for Integrated Omics Analysis

    Understanding Disease Mechanisms through Multi-Omics Data Integration Pathway Analysis

    Advancements in next-generation sequencing (NGS) technologies have enabled researchers to generate genome-wide data of unprecedented quality and quantity.

    Genomics, expression, microRNA, chromatin IP, methylation, histone modification, and more recently chromosome confirmation capture are rapidly moving into the clinical setting.

    Projects like 1000 Genomes, Encode, Blueprint, and many smaller projects are providing a rich source of background information and understanding of the genome and the epigenome in relation to normal and disease states.

    With data generation growing at an exponential rate, the need for efficient analyses, data reduction, and comprehensible visualizations is critical for biomedical interpretation of NGS data.


  201. 201
    Dionisio says:

    What’s Next for Next-Gen Sequencing?

    A More Embedded, Pervasive Genomics Sets the Stage for Increasingly Ambitious Applications
    MaryAnn Labant


  202. 202
    Dionisio says:

    NR2F1 controls tumour cell dormancy via ?SOX9- and ?RAR?-driven quiescence programmers


    Metastases can originate from disseminated tumour cells (DTCs), which may be dormant for years before reactivation.

    Here we find that the orphan nuclear receptor ?NR2F1 is epigenetically upregulated in experimental head and neck squamous cell carcinoma (HNSCC) dormancy models and in DTCs from prostate cancer patients carrying dormant disease for 7–18 years.

    ?NR2F1-dependent dormancy is recapitulated by a co-treatment with the DNA-demethylating agent ?5-Aza-C and ?retinoic acid across various cancer types. ?

    NR2F1-induced quiescence is dependent on ?SOX9, ?RAR? and CDK inhibitors.

    Intriguingly, ?NR2F1 induces global chromatin repression and the pluripotency gene ?NANOG, which contributes to dormancy of DTCs in the bone marrow.

    When ?NR2F1 is blocked in vivo, growth arrest or survival of dormant DTCs is interrupted in different organs.

    We conclude that ?NR2F1 is a critical node in dormancy induction and maintenance by integrating epigenetic programmes of quiescence and survival in DTCs.


  203. 203
    Dionisio says:

    Postmitotic control of sensory area specification during neocortical development


    The mammalian neocortex is subdivided into cytoarchitectural areas with distinct connectivity, gene expression and neural functions.

    Areal identity is initially specified by rostrocaudal and mediolateral gene expression gradients in neuroepithelial and radial glial progenitors (the ‘protomap’).

    On further differentiation, distinct sets of gene expression gradients arise in intermediate progenitors and postmitotic neurons, and are necessary to implement areal specification.

    However, it is still unknown whether postmitotic gene expression gradients can determine areal identity independently of protomap gradients.

    Here we show, by cell type-restricted genetic loss- and gain-of-function, that high levels of postmitotic ?COUP-TFI (?Nr2f1) expression are necessary and sufficient for the development of sensory (caudal) areal identity.

    Our data indicate a crucial role for postmitotic patterning genes in areal specification and reveal an unexpected plasticity in this process, which may account for complex and evolutionarily novel structures characteristic of the mammalian neocortex.


  204. 204
    Dionisio says:

    How Cells Use Signaling Mechanisms to Control Interferon Production

    The immune system has a delicate balance to maintain.

    When certain infected cells detect an invader, they use a molecule called interferon to rally the body’s defenses.

    The immune system responds to this rallying cry by immediately boosting its general antiviral defenses and simultaneously initiating a more specialized secondary response.

    But interferon production must be finely tuned: Too much can provoke immune cells to attack the body’s own cells indiscriminately.

    Type I interferon plays such an important role in immune defense that the body has three known pathways to trigger its production in response to microbial infection.

    New research by Howard Hughes Medical Institute (HHMI) scientists has found that all three pathways use a common mechanism to communicate with the protein that switches on type I interferon-producing genes.

    “We have provided a mechanism that explains how this key transcription factor is activated by three distinct pathways known to induce type I interferons,” Chen says.

    Now, he says, his team plans to examine that mechanism in more detail, with further biochemical analyses and structural studies.


  205. 205
    Dionisio says:

    How Immune Cells Hone Skills to Fight Disease

    The last time you were in the doctor’s office for a vaccine booster shot, did you wonder why you needed one?

    Exactly how booster shots offer long-term protection from viruses has long been a mystery to scientists.

    Now, a new study from scientists at The Scripps Research Institute (TSRI) helps explain how booster shots prompt immune “memory” to improve, an important step toward the development of more effective, longer-lasting vaccines.

    “We can now see the evolution* of better protection in single memory cells as they respond to the boost,” said TSRI Professor Michael McHeyzer-Williams, senior author of the new study.

    Scientists have long known that memory B cells produce more effective antibodies each time they encounter a virus—that’s why most vaccines require “booster” shots.

    But until now, scientists didn’t know all the stages of training that take place in the lymph nodes.

    “You develop memory so that the next time you see it, you clear the infection more quickly,” explained McHeyzer-Williams. “But the cellular and molecular details of memory are not well understood.”

    The scientists also found that cells were undergoing different parts of the training process in an ordered progression of gene expression, showing new features of the training programing and how antibodies evolve after vaccine boosts.

    The training is actually ongoing; they keep on training and keep getting better at their task,” said TSRI Senior Scientific Associate Louise McHeyzer-Williams, who was co-first author of the paper with Pierre Milpied, a TSRI research associate at the time of the study.


    (*) this term ‘evolution’ seems correctly used in this context. Here it seems to refer to a particular cellular/molecular mechanism they can see happening. It’s not a gross extrapolation of an adaptability mechanism.

  206. 206
    Dionisio says:

    205 addendum

    Class-switched memory B cells remodel BCRs within secondary germinal centers


    Effective vaccines induce high-affinity memory B cells and durable antibody responses through accelerated mechanisms of natural selection. [built in the system a priori]

    Secondary changes in antibody repertoires after vaccine boosts suggest progressive rediversification of B cell receptors (BCRs), but the underlying mechanisms remain unresolved.

    Here, the integrated specificity and function of individual memory B cell progeny revealed ongoing evolution of polyclonal antibody specificities through germinal center (GC)-specific transcriptional activity. [a priori built in mechanisms]

    At the clonal and subclonal levels, single-cell expression of the genes encoding the costimulatory molecule CD83 and the DNA polymerase Pol? segregated the secondary GC transcriptional program into four stages that regulated divergent mechanisms of memory BCR evolution. [gradual improvements based on a priori built in mechanisms]

    Our studies demonstrate that vaccine boosts reactivate a cyclic program of GC function in class-switched memory B cells to remodel existing antibody specificities and enhance durable immunological protection.


  207. 207
    Dionisio says:

    #204 addendum

    Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation

    Science DOI: 10.1126/science.aaa2630

    During virus infection, the adaptor proteins MAVS and STING transduce signals from the cytosolic nucleic acid sensors RIG-I and cyclic guanosine monophosphate–adenosine monophosphate synthase, respectively, to induce type I interferons (IFNs) and other antiviral molecules.

    Here, we show that MAVS and STING harbor two conserved serine and threonine clusters that are phosphorylated by the kinases inhibitor of nuclear factor ?B subunit IKK and/or TBK1 in response to stimulation.

    Phosphorylated MAVS and STING then bind to a positively charged surface of interferon regulatory factor 3 (IRF3) and thereby recruit IRF3 for its phosphorylation and activation by TBK1.

    We further show that TRIF, an adaptor protein in Toll-like receptor signaling, activates IRF3 through a similar phosphorylation-dependent mechanism.

    These results reveal that phosphorylation of innate adaptor proteins is an essential and conserved mechanism that selectively recruits IRF3 to activate the type I IFN pathway.


  208. 208
    Dionisio says:

    Mitochondrial DNA stress primes the antiviral innate immune response

    Nature (2015) doi:10.1038/nature14156

    Mitochondrial DNA (mtDNA) is normally present at thousands of copies per cell and is packaged into several hundred higher-order structures termed nucleoids.

    The abundant mtDNA-binding protein TFAM (transcription factor A, mitochondrial) regulates nucleoid architecture, abundance and segregation.

    Complete mtDNA depletion profoundly impairs oxidative phosphorylation, triggering calcium-dependent stress signaling and adaptive metabolic responses.

    However, the cellular responses to mtDNA instability, a physiologically relevant stress observed in many human diseases and ageing, remain poorly defined.

    Here we show that moderate mtDNA stress elicited by TFAM deficiency engages cytosolic antiviral signalling to enhance the expression of a subset of interferon-stimulated genes.

    Mechanistically, we find that aberrant mtDNA packaging promotes escape of mtDNA into the cytosol, where it engages the DNA sensor cGAS (also known as MB21D1) and promotes STING (also known as TMEM173)–IRF3-dependent signalling to elevate interferon-stimulated gene expression, potentiate type I interferon responses and confer broad viral resistance.

    Furthermore, we demonstrate that herpesviruses induce mtDNA stress, which enhances antiviral signaling and type I interferon responses during infection.

    Our results further demonstrate that mitochondria are central participants in innate immunity, identify mtDNA stress as a cell-intrinsic trigger of antiviral signalling and suggest that cellular monitoring of mtDNA homeostasis cooperates with canonical virus sensing mechanisms to fully engage antiviral innate immunity.


  209. 209
    Dionisio says:

    “Biology is an open-ended system, way more complex and difficult to reduce than a computer engineering problem.” -Dale Yuzuki


  210. 210
    Dionisio says:

    How did these creatures appear to begin with?

    Is that explained anywhere?


  211. 211
    Dionisio says:

    Bacteria evolution is seem everyday. Ever heard of antibiotics resistance? But they remain bacteria, as far as I’m aware of.

    Isn’t there evolution within every species? But how did their complex development mechanisms evolve into the development mechanisms of another species?

    For the following paper, a question could be: how did these creatures appear to begin with? Is that explained anywhere? Did I miss that memo? 🙂


  212. 212
    Dionisio says:

    Dissecting affinity maturation: a model explaining selection of antibody-forming cells and memory B cells in the germinal centre.

    The Walter and Eliza Hall Institute for Medical Research, PO Royal Melbourne Hospital, Victoria 3050, Australia.
    Immunology Today (Impact Factor: 9.49). 10/2000; 21(9):436-41. DOI: 10.1016/S0167-5699(00)01687-X
    Source: PubMed

    Until recently, the relationship between apoptosis, selection in the germinal centre (GC) and production of high-affinity antibody-forming cells (AFCs) and memory B cells has been unclear.

    Here, Tarlinton and Smith present a model that accounts for the switch in GC production from high-affinity AFCs to memory B cells, and explain how Bcl-2, an inhibitor of apoptosis, can influence memory cells but not bone marrow AFCs.


  213. 213
    Dionisio says:

    Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition

    DOI: 10.1002/jmr.2394

    The concept of antibody specificity is analyzed and shown to reside in the ability of an antibody to discriminate between two antigens.

    Initially, antibody specificity was attributed to sequence differences in complementarity determining regions (CDRs), but as increasing numbers of crystallographic antibody-antigen complexes were elucidated, specificity was analyzed in terms of six antigen-binding regions (ABRs) that only roughly correspond to CDRs.

    It was found that each ABR differs significantly in its amino acid composition and tends to bind different types of amino acids at the surface of proteins.

    In spite of these differences, the combined preference of the six ABRs does not allow epitopes to be distinguished from the rest of the protein surface.

    These findings explain the poor success of past and newly proposed methods for predicting protein epitopes.

    Antibody polyspecificity refers to the ability of one antibody to bind a large variety of epitopes in different antigens, and this property explains how the immune system develops an antibody repertoire that is able to recognize every antigen the system is likely to encounter.

    Antibody heterospecificity arises when an antibody reacts better with another antigen than with the one used to raise the antibody.

    As a result, an antibody may sometimes appear to have been elicited by an antigen with which it is unable to react.

    The implications of antibody polyspecificity and heterospecificity in vaccine development are pointed out.

    Copyright © 2014 John Wiley & Sons, Ltd.


  214. 214
    Dionisio says:

    An Outdated Notion of Antibody Specificity is One of the Major Detrimental Assumptions of the Structure-Based Reverse Vaccinology Paradigm, Which Prevented It from Helping to Develop an Effective HIV-1 Vaccine.

    DOI: 10.3389/fimmu.2014.00593

    The importance of paradigms for guiding scientific research is explained with reference to the seminal work of Karl Popper and Thomas Kuhn.

    A prevalent paradigm, followed for more than a decade in HIV-1 vaccine research, which gave rise to the strategy known as structure-based reverse vaccinology is described in detail.

    Several reasons why this paradigm did not allow the development of an effective HIV-1 vaccine are analyzed.

    A major reason is the belief shared by many vaccinologists that antibodies possess a narrow specificity for a single epitope and are not polyspecific for a diverse group of potential epitopes.

    When this belief is abandoned, it becomes obvious that the one particular epitope structure observed during the crystallographic analysis of a neutralizing antibody-antigen complex does not necessarily reveal, which immunogenic structure should be used to elicit the same type of neutralizing antibody.

    In the physical sciences, scientific explanations are usually presented as logical deductions derived from a relevant law of nature together with certain initial conditions.

    In immunology, causal explanations in terms of a single cause acting according to a law of nature are not possible because numerous factors always play a role in bringing about an effect.

    The implications of this state of affairs for the rational design of HIV vaccines are outlined.

    An alternative approach to obtain useful scientific understanding consists in intervening empirically in the immune system and it is suggested that manipulating the system experimentally is needed to learn to control it and achieve protective immunity by vaccination.


  215. 215
    Dionisio says:

    Posts #9-13 in the thread “antibodies affinity maturation”
    are references to research papers, starting here:


  216. 216
  217. 217
    Dionisio says:

    How advances in immunology provide insight into improving vaccine efficacy

    doi: 10.1016/j.vaccine.2014.03.078

    Vaccines represent one of the most compelling examples of how biomedical research has improved society by saving lives and dramatically reducing the burden of infectious disease.

    Despite the importance of vaccinology, we are still in the early stages of understanding how the best vaccines work and how we can achieve better protective efficacy through improved vaccine design.

    Most successful vaccines have been developed empirically, but recent advances in immunology are beginning to shed new light on the mechanisms of vaccine-mediated protection and development of long-term immunity.

    Although natural infection will often elicit lifelong immunity, almost all current vaccines require booster vaccination in order to achieve durable protective humoral immune responses, regardless of whether the vaccine is based on infection with replicating live-attenuated vaccine strains of the specific pathogen or whether they are derived from immunization with inactivated, non-replicating vaccines or subunit vaccines.

    The form of the vaccine antigen (e.g., soluble or particulate/aggregate) appears to play an important role in determining immunogenicity and the interactions between dendritic cells, B cells and T cells in the germinal center are likely to dictate the magnitude and duration of protective immunity.

    By learning how to optimize these interactions, we may be able to elicit more effective and long-lived immunity with fewer vaccinations.


  218. 218
    Dionisio says:

    Mathematical modeling provides kinetic details of the human immune response to vaccination

    doi: 10.3389/fcimb.2014.00177

    With major advances in experimental techniques to track antigen-specific immune responses many basic questions on the kinetics of virus-specific immunity in humans remain unanswered.

    To gain insights into kinetics of T and B cell responses in human volunteers we combined mathematical models and experimental data from recent studies employing vaccines against yellow fever and smallpox.

    Yellow fever virus-specific CD8 T cell population expanded slowly with the average doubling time of 2 days peaking 2.5 weeks post immunization.

    Interestingly, we found that the peak of the yellow fever-specific CD8 T cell response was determined by the rate of T cell proliferation and not by the precursor frequency of antigen-specific cells as has been suggested in several studies in mice.

    We also found that while the frequency of virus-specific T cells increased slowly, the slow increase could still accurately explain clearance of yellow fever virus in the blood.

    Our additional mathematical model described well the kinetics of virus-specific antibody-secreting cell and antibody response to vaccinia virus in vaccinated individuals suggesting that most of antibodies in 3 months post immunization were derived from the population of circulating antibody-secreting cells.

    Taken together, our analysis provided novel insights into mechanisms by which live vaccines induce immunity to viral infections and highlighted challenges of applying methods of mathematical modeling to the current, state-of-the-art yet limited immunological data.


  219. 219
    Dionisio says:

    Estimating directional epistasis

    doi: 10.3389/fgene.2014.00198

    Epistasis, i.e., the fact that gene effects depend on the genetic background, is a direct consequence of the complexity of genetic architectures.

    Despite this, most of the models used in evolutionary and quantitative genetics pay scant attention to genetic interactions.

    For instance, the traditional decomposition of genetic effects models epistasis as noise around the evolutionarily-relevant additive effects.

    Such an approach is only valid if it is assumed that there is no general pattern among interactions—a highly speculative scenario.

    Systematic interactions generate directional epistasis, which has major evolutionary consequences.

    In spite of its importance, directional epistasis is rarely measured or reported by quantitative geneticists, not only because its relevance is generally ignored, but also due to the lack of simple, operational, and accessible methods for its estimation.


    Oops! Are they serious?

  220. 220
    Dionisio says:

    Identification of cardiovascular lineage descendants at single-cell resolution

    doi: 10.1242/dev.116897

    The transcriptional profiles of cardiac cells derived from murine embryos and from mouse embryonic stem cells (mESCs) have primarily been studied within a cell population.

    However, the characterization of gene expression in these cells at a single-cell level might demonstrate unique variations that cannot be appreciated within a cell pool.

    These results demonstrate that multiplex gene expression analysis in single cells is a powerful tool for examining the unique behaviors of individual embryo- or mESC- derived cardiac cells.


  221. 221
    Dionisio says:

    Asymmetric inheritance of the apical domain and self-renewal of retinal ganglion cell progenitors depend on Anillin function

    2015, doi: 10.1242/dev.118612

    Divisions that generate one neuronal lineage-committed and one self-renewing cell maintain the balance of proliferation and differentiation for the generation of neuronal diversity.

    The asymmetric inheritance of apical domains and components of the cell division machinery has been implicated in this process, and might involve interactions with cell fate determinants in regulatory feedback loops of an as yet unknown nature.

    Here, we report the dynamics of Anillin – an essential F-actin regulator and furrow component – and its contribution to progenitor cell divisions in the developing zebrafish retina.

    We find that asymmetrically dividing retinal ganglion cell progenitors position the Anillin-rich midbody at the apical domain of the differentiating daughter.

    anillin hypomorphic conditions disrupt asymmetric apical domain inheritance and affect daughter cell fate.

    Consequently, the retinal cell type composition is profoundly affected, such that the ganglion cell layer is dramatically expanded.

    This study provides the first in vivo evidence for the requirement of Anillin during asymmetric neurogenic divisions.

    It also provides insights into a reciprocal regulation between Anillin and the ganglion cell fate determinant Ath5, suggesting a mechanism whereby the balance of proliferation and differentiation is accomplished during progenitor cell divisions in vivo.


  222. 222
    Dionisio says:

    UMD Study Uncovers New Mechanism of Transgenerational RNAi

    While it is known that environmental changes in an organism can trigger changes in its progeny for three or more generations, the exact mechanisms behind such transgenerational epigenetic effects remain unclear.

    New research out of the University of Maryland, however, shows that RNAi-inducing double-stranded RNA molecules produced in the neurons of the model organisms Caenorhabditis elegans can be transmitted into the worm’s germline, resulting in a gene-silencing effect that can persist for over 25 generations.

    The findings demonstrate for the first time that a somatic tissue of an animal can influence a gene’s expression over multiple generations by transporting dsRNA to the germline, and point to a previously unknown epigenetic mechanism.

    “Thus, it remains unknown whether somatic cells in C. elegans can export signals for delivery into the germline to cause transgenerational gene silencing,” the UMD team wrote in its paper, which appeared in the Proceedings of the National Academy of Sciences.

    “For example, expression of some genes within the germline can affect longevity, and transgenerational silencing of such genes might underlie the longevity that results from ancestral starvation in C. elegans,” the investigators wrote in PNAS.

    “Thus, additional experiments are needed to determine the role of mobile RNAs, if any, in the transport of such experience-dependent information from somatic cells to subsequent generations in C. elegans.”



    Some interlocutors and their comrades strongly dislike the highlighting of certain words and phrases in the abstracts. Maybe they’ll get used to it, eventually. 🙂

  223. 223
    Dionisio says:

    Cross-talk and regulatory interactions between the essential response regulator RpaB and cyanobacterial circadian clock output.

    The response regulator RpaB (regulator of phycobilisome associated B), part of an essential two-component system conserved in cyanobacteria that responds to multiple environmental signals, has recently been implicated in the control of cell dimensions and of circadian rhythms of gene expression in the model cyanobacterium Synechococcus elongatus PCC 7942.

    However, little is known of the molecular mechanisms that underlie RpaB functions.

    In this study we show that the regulation of phenotypes by RpaB is intimately connected with the activity of RpaA (regulator of phycobilisome associated A), the master regulator of circadian transcription patterns.

    RpaB affects RpaA activity both through control of gene expression, a function requiring an intact effector domain, and via altering RpaA phosphorylation, a function mediated through the N-terminal receiver domain of RpaB.

    Thus, both phosphorylation cross-talk and coregulation of target genes play a role in the genetic interactions between the RpaA and RpaB pathways.

    In addition, RpaB?P levels appear critical for survival under light:dark cycles, conditions in which RpaB phosphorylation is environmentally driven independent of the circadian clock.

    We propose that the complex regulatory interactions between the essential and environmentally sensitive NblS-RpaB system and the SasA-RpaA clock output system integrate relevant extra- and intracellular signals to the circadian clock.


    Some interlocutors and their comrades strongly dislike the highlighting of certain words and phrases in the abstracts. Maybe they’ll get used to it, eventually. 🙂

  224. 224
    Dionisio says:

    Metabolic compensation and circadian resilience in prokaryotic cyanobacteria.

    doi: 10.1146/annurev-biochem-060713-035632.

    For a biological oscillator to function as a circadian pacemaker that confers a fitness advantage, its timing functions must be stable in response to environmental and metabolic fluctuations.

    One such stability enhancer, temperature compensation, has long been a defining characteristic of these timekeepers.

    However, an accurate biological timekeeper must also resist changes in metabolism, and this review suggests that temperature compensation is actually a subset of a larger phenomenon, namely metabolic compensation, which maintains the frequency of circadian oscillators in response to a host of factors that impinge on metabolism and would otherwise destabilize these clocks.

    The circadian system of prokaryotic cyanobacteria is an illustrative model because it is composed of transcriptional and nontranscriptional oscillators that are coupled to promote resilience.

    Moreover, the cyanobacterial circadian program regulates gene activity and metabolic pathways, and it can be manipulated to improve the expression of bioproducts that have practical value.


  225. 225
    Dionisio says:

    Genetic adaptation of the human circadian clock to day-length latitudinal variations and relevance for affective disorders


    The temporal coordination of biological processes into daily cycles is a common feature of most living organisms.

    In humans, disruption of circadian rhythms is commonly observed in psychiatric diseases, including schizophrenia, bipolar disorder, depression and autism.

    Light therapy is the most effective treatment for seasonal affective disorder and circadian-related treatments sustain antidepressant response in bipolar disorder patients.

    Day/night cycles represent a major circadian synchronizing signal and vary widely with latitude.

    Our results suggest that human populations adapted to life at different latitudes by tuning their circadian clock systems.

    This process also involves risk variants for neuropsychiatric conditions, suggesting possible genetic modulators for chronotherapies and candidates for interaction analysis with photoperiod-related environmental variables, such as season of birth, country of residence, shift-work or lifestyle habits.


  226. 226
    Dionisio says:

    An Integrated View of Cellular Systems

    FREE Webinar

    Thursday February 26, 2015
    2:30 – 4:00 p.m. Eastern Time

    By integrating information from the genome, transcriptome, proteome, and metabolome, dynamic interactions can be examined to decipher complex biological networks.

    This systems approach involves the integration of high-throughput technology and multiple interdisciplinary areas or fields, including molecular biology, cell biology, genomics, proteomics, metabolomics, and bioinformatics.

    The Scientist brings together a panel of experts to discuss emerging technologies for studying complex biological interactions.

    Attendees will have an opportunity to interact with the experts, ask questions, and seek advice on topics that are unique to their research.

    Topics to be covered:
    • Approaches and considerations for analyzing complex biological networks
    • Tools and strategies for integrating data to provide biological insights
    • How a systems approach can be used to understand disease phenotypes


  227. 227
    Dionisio says:

    Disruption of the head direction cell network impairs the parahippocampal grid cell signal

    DOI: 10.1126/science.1259591

    Navigation depends on multiple neural systems that encode the moment-to-moment changes in an animal’s direction and location in space.

    These include head direction (HD) cells representing the orientation of the head and grid cells that fire at multiple locations, forming a repeating hexagonal grid pattern.

    Computational models hypothesize that generation of the grid cell signal relies upon HD information that ascends to the hippocampal network via the anterior thalamic nuclei (ATN).

    We inactivated or lesioned the ATN and subsequently recorded single units in the entorhinal cortex and parasubiculum.

    ATN manipulation significantly disrupted grid and HD cell characteristics while sparing theta rhythmicity in these regions.

    These results indicate that the HD signal via the ATN is necessary for the generation and function of grid cell activity.


  228. 228
    Dionisio says:

    Multiscale Polar Theory of Microtubule and Motor-Protein Assemblies

    DOI: http://dx.doi.org/10.1103/PhysRevLett.114.048101

    Microtubules and motor proteins are building blocks of self-organized subcellular biological structures such as the mitotic spindle and the centrosomal microtubule array.

    These same ingredients can form new “bioactive” liquid-crystalline fluids that are intrinsically out of equilibrium and which display complex flows and defect dynamics.

    It is not yet well understood how microscopic activity, which involves polarity-dependent interactions between motor proteins and microtubules, yields such larger-scale dynamical structures.

    In our multiscale theory, Brownian dynamics simulations of polar microtubule ensembles driven by cross-linking motors allow us to study microscopic organization and stresses.

    Polarity sorting and cross-link relaxation emerge as two polar-specific sources of active destabilizing stress.

    On larger length scales, our continuum Doi-Onsager theory captures the hydrodynamic flows generated by polarity-dependent active stresses.

    The results connect local polar structure to flow structures and defect dynamics.


  229. 229
    Dionisio says:

    Atomic-Scale Nuclear Spin Imaging Using Quantum-Assisted Sensors in Diamond

    DOI: http://dx.doi.org/10.1103/PhysRevX.5.011001

    Nuclear spin imaging at the atomic level is essential for the understanding of fundamental biological phenomena and for applications such as drug discovery.

    The advent of novel nanoscale sensors promises to achieve the long-standing goal of single-protein, high spatial-resolution structure determination under ambient conditions.

    In particular, quantum sensors based on the spin-dependent photoluminescence of nitrogen-vacancy (NV) centers in diamond have recently been used to detect nanoscale ensembles of external nuclear spins.

    While NV sensitivity is approaching single-spin levels, extracting relevant information from a very complex structure is a further challenge since it requires not only the ability to sense the magnetic field of an isolated nuclear spin but also to achieve atomic-scale spatial resolution.

    Here, we propose a method that, by exploiting the coupling of the NV center to an intrinsic quantum memory associated with the nitrogen nuclear spin, can reach a tenfold improvement in spatial resolution, down to atomic scales.

    The spatial resolution enhancement is achieved through coherent control of the sensor spin, which creates a dynamic frequency filter selecting only a few nuclear spins at a time.

    We propose and analyze a protocol that would allow not only sensing individual spins in a complex biomolecule, but also unraveling couplings among them, thus elucidating local characteristics of the molecule structure.


  230. 230
    Dionisio says:

    Protein design algorithms predict viable resistance to an experimental antifolate

    doi: 10.1073/pnas.1411548112

    Computationally predicting drug resistance mutations early in the discovery phase would be an important breakthrough in drug development.

    The most meaningful predictions of target mutations will show reduced affinity for the drug while maintaining viability in the complex context of a cell.

    Here, the protein design algorithm K* in Osprey was used to predict a single-nucleotide polymorphism in the target dihydrofolate reductase that confers resistance to an experimental antifolate in the preclinical discovery phase.

    Excitingly, the mutation was also selected in bacteria under antifolate pressure, confirming the prediction of a viable molecular response to external stress.

    Methods to accurately predict potential drug target mutations in response to early-stage leads could drive the design of more resilient first generation drug candidates.

    In this study, a structure-based protein design algorithm (K* in the OSPREY suite) was used to prospectively identify single-nucleotide polymorphisms that confer resistance to an experimental inhibitor effective against dihydrofolate reductase (DHFR) from Staphylococcus aureus.

    Four of the top-ranked mutations in DHFR were found to be catalytically competent and resistant to the inhibitor.

    Selection of resistant bacteria in vitro reveals that two of the predicted mutations arise in the background of a compensatory mutation.

    Using enzyme kinetics, microbiology, and crystal structures of the complexes, we determined the fitness of the mutant enzymes and strains, the structural basis of resistance, and the compensatory relationship of the mutations.

    To our knowledge, this work illustrates the first application of protein design algorithms to prospectively predict viable resistance mutations that arise in bacteria under antibiotic pressure.


  231. 231
    Dionisio says:

    Polarized cells, polarized views: asymmetric cell division in hematopoietic cells

    doi: 10.3389/fimmu.2014.00026.

    It has long been recognized that alterations in cell shape and polarity play important roles in coordinating lymphocyte functions.

    In the last decade, a new aspect of lymphocyte polarity has attracted much attention, termed asymmetric cell division (ACD).

    ACD has previously been shown to dictate or influence many aspects of development in model organisms such as the worm and the fly, and to be disrupted in disease.

    Recent observations that ACD also occurs in lymphocytes led to exciting speculations that ACD might influence lymphocyte differentiation and function, and leukemia.

    Dissecting the role that ACD might play in these activities has not been straightforward, and the evidence to date for a functional role in lymphocyte fate determination has been controversial.

    In this review, we discuss the evidence to date for ACD in lymphocytes, and how it might influence lymphocyte fate.

    We also discuss current gaps in our knowledge, and suggest approaches to definitively test the physiological role of ACD in lymphocytes.


  232. 232
    Dionisio says:

    Normalized polarization ratios for the analysis of cell polarity.

    doi: 10.1371/journal.pone.0099885

    The quantification and analysis of molecular localization in living cells is increasingly important for elucidating biological pathways, and new methods are rapidly emerging.

    The quantification of cell polarity has generated much interest recently, and ratiometric analysis of fluorescence microscopy images provides one means to quantify cell polarity.

    However, detection of fluorescence, and the ratiometric measurement, is likely to be sensitive to acquisition settings and image processing parameters.

    Using imaging of EGFP-expressing cells and computer simulations of variations in fluorescence ratios, we characterized the dependence of ratiometric measurements on processing parameters.

    This analysis showed that image settings alter polarization measurements; and that clustered localization is more susceptible to artifacts than homogeneous localization.

    To correct for such inconsistencies, we developed and validated a method for choosing the most appropriate analysis settings, and for incorporating internal controls to ensure fidelity of polarity measurements.

    This approach is applicable to testing polarity in all cells where the axis of polarity is known.


    Interesting paper about the design of analytical tools for cell polarity.

  233. 233
    Dionisio says:

    When fate follows age: unequal centrosomes in asymmetric cell division

    DOI: 10.1098/rstb.2013.0466 .

    A strong correlation between centrosome age and fate has been reported in some stem cells and progenitors that divide asymmetrically.

    In some cases, such stereotyped centrosome behaviour is essential to endow stemness to only one of the two daughters, whereas in other cases causality is still uncertain.

    Here, we present the different cell types in which correlated centrosome age and fate has been documented, review current knowledge on the underlying molecular mechanisms and discuss possible functional implications of this process.

    Paraphrasing T. Dobzhansky archcited quote one could say: ‘nothing in cell biology makes sense except in the light of development’ [1].

    Admittedly an overstatement—like the original—this sentence does hold a great deal of truth.

    In Metazoa, cells have a time, a place and a function, and all cellular processes are orchestrated to fulfil the needs dictated by these critical coordinates.

    Metabolic pathways, the cell cycle, gene expression or cell shape cannot escape this principle; and, indeed, neither can centrosomes.

    Because the founding articles appeared only 7 years ago [16–18] and because the total count of articles published until now is still below 10 (four of which have been published in the last 12 months), it is fair to state offhand that the subject of centrosome asymmetry in SRAD is in its infancy: only a few cell types have been observed and the molecular details are still sketchy [19,20].

    Yet, the stereotyped behavior that mother and daughter centrosomes display in these cells, so markedly different and tightly linked to the unequal fate of the resulting daughter cells has caught the attention of cell and developmental biologists alike


  234. 234
    Dionisio says:

    Centrosomes back in the limelight

    DOI: 10.1098/rstb.2013.0452 .

    To appreciate the uncertain state of affairs in the 1970s, one can consider the thoughtful chapter of Chandler Fulton [1, p. 170], who started his contribution with these words: ‘If one wandered about asking biologists to complete the sentence “Centrioles are…” the answers might well range from “I don’t know” to “Centrioles are self-replicating organelles responsible for the synthesis and assembly of microtubules”.

    Although it is conceivable that the later reply contains a little truth, the “I don’t know” is more likely to be the reply of an expert’.

    How did we go from such uncertainty to the renaissance that this Theme Issue is heralding?

    The field has indeed experienced a rebirth as evidenced by comparing the few dozen articles on the centrosome published each year in the early 1980s with the over 400 contributions in the year 2013, or by considering the growing number of conferences in the field.

    Many novel avenues of research have been opened recently: the centrosome is back in the thinking of many cell and developmental biologists after a long eclipse during which even the term centrosome was neglected to the benefit of the acronym MTOC: Microtubule Organizing Centre


    “I don’t know” is more likely to be the reply of an expert’.
    -Chandler Fulton

  235. 235
    Dionisio says:

    #234 highlight

    “I don’t know” is more likely to be the reply of an expert’.
    -Chandler Fulton

    Many folks in this site may benefit from thinking about this seriously.

  236. 236
    Dionisio says:

    OT: clarification for some confused interlocutors in this or in other threads:

    I’m not an ID proponent, though I agree with their fundamental principle. I’m not a YEC, or an OEC, or any other ‘classification’ being used these days to label people. None of them apply to me.

    My identity is in Christ alone. When He created all or how He did it are unknown to me. I just believe He did it. Generally, that’s not what the ID proponents claim.

    The details about when and how He did it are not that important to me, though I would not mind knowing it. That’s not what the YEC/OEC folks state.

    I’m a sinner gracefully redeemed by the Savior of the world and thus eternally reconciled with our Maker. Christ is the King of kings, the Lord of lords, the Light, the Way, the Truth and the Life. Without Him there is no seeing, no going, no knowing, no living.

  237. 237
    Dionisio says:

    Centrosomes as signalling centers

    DOI: 10.1098/rstb.2013.0464 .

    Centrosomes—as well as the related spindle pole bodies (SPBs) of yeast—have been extensively studied from the perspective of their microtubule-organizing roles.

    Moreover, the biogenesis and duplication of these organelles have been the subject of much attention, and the importance of centrosomes and the centriole–ciliary apparatus for human disease is well recognized.

    Much less developed is our understanding of another facet of centrosomes and SPBs, namely their possible role as signalling centres.

    Yet, many signalling components, including kinases and phosphatases, have been associated with centrosomes and spindle poles, giving rise to the hypothesis that these organelles might serve as hubs for the integration and coordination of signalling pathways.

    In this review, we discuss a number of selected studies that bear on this notion.

    We cover different processes (cell cycle control, development, DNA damage response) and organisms (yeast, invertebrates and vertebrates), but have made no attempt to be comprehensive.

    This field is still young and although the concept of centrosomes and SPBs as signalling centres is attractive, it remains primarily a concept—in need of further scrutiny.

    We hope that this review will stimulate thought and experimentation.


  238. 238
    Dionisio says:


  239. 239
    Dionisio says:

    Polar ejection forces promote spindle assembly checkpoint satisfaction by generating intra-kinetochore stretch


  240. 240
    Dionisio says:

    Embryonic Stem Cell Specific “Master” Replication Origins at the Heart of the Loss of Pluripotency.

    doi: 10.1371/journal.pcbi.1003969

    Epigenetic regulation of the replication program during mammalian cell differentiation remains poorly understood.

    We performed an integrative analysis of eleven genome-wide epigenetic profiles at 100 kb resolution of Mean Replication Timing (MRT) data in six human cell lines.

    Compared to the organization in four chromatin states shared by the five somatic cell lines, embryonic stem cell (ESC) line H1 displays (i) a gene-poor but highly dynamic chromatin state (EC4) associated to histone variant H2AZ rather than a HP1-associated heterochromatin state (C4) and (ii) a mid-S accessible chromatin state with bivalent gene marks instead of a polycomb-repressed heterochromatin state.

    Plastic MRT regions (? 20% of the genome) are predominantly localized at the borders of U-shaped timing domains.

    Whereas somatic-specific U-domain borders are gene-dense GC-rich regions, 31.6% of H1-specific U-domain borders are early EC4 regions enriched in pluripotency transcription factors NANOG and OCT4 despite being GC poor and gene deserts.

    Silencing of these ESC-specific “master” replication initiation zones during differentiation corresponds to a loss of H2AZ and an enrichment in H3K9me3 mark characteristic of late replicating C4 heterochromatin.

    These results shed a new light on the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency and lineage commitment.


  241. 241
    Dionisio says:

    Ubiquitous human ‘master’ origins of replication are encoded in the DNA sequence via a local enrichment in nucleosome excluding energy barriers.

    doi: 10.1088/0953-8984/27/6/064102

    As the elementary building block of eukaryotic chromatin, the nucleosome is at the heart of the compromise between the necessity of compacting DNA in the cell nucleus and the required accessibility to regulatory proteins.

    The recent availability of genome-wide experimental maps of nucleosome positions for many different organisms and cell types has provided an unprecedented opportunity to elucidate to what extent the DNA sequence conditions the primary structure of chromatin and in turn participates in the chromatin-mediated regulation of nuclear functions, such as gene expression and DNA replication.

    In this study, we use in vivo and in vitro genome-wide nucleosome occupancy data together with the set of nucleosome-free regions (NFRs) predicted by a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix, to investigate the role of intrinsic nucleosome occupancy in the regulation of the replication spatio-temporal programme in human.

    We focus our analysis on the so-called replication U/N-domains that were shown to cover about half of the human genome in the germline (skew-N domains) as well as in embryonic stem cells, somatic and HeLa cells (mean replication timing U-domains).

    The ‘master’ origins of replication (MaOris) that border these megabase-sized U/N-domains were found to be specified by a few hundred kb wide regions that are hyper-sensitive to DNase I cleavage, hypomethylated, and enriched in epigenetic marks involved in transcription regulation, the hallmarks of localized open chromatin structures.

    Here we show that replication U/N-domain borders that are conserved in all considered cell lines have an environment highly enriched in nucleosome-excluding-energy barriers, suggesting that these ubiquitous MaOris have been selected during evolution.

    In contrast, MaOris that are cell-type-specific are mainly regulated epigenetically and are no longer favoured by a local abundance of intrinsic NFRs encoded in the DNA sequence.

    At the smaller few hundred bp scale of gene promoters, CpG-rich promoters of housekeeping genes found nearby ubiquitous MaOris as well as CpG-poor promoters of tissue-specific genes found nearby cell-type-specific MaOris, both correspond to in vivo NFRs that are not coded as nucleosome-excluding-energy barriers.

    Whereas the former promoters are likely to correspond to high occupancy transcription factor binding regions, the latter are an illustration that gene regulation in human is typically cell-type-specific.


  242. 242
    Dionisio says:

    Large replication skew domains delimit GC-poor gene deserts in human.

    doi: 10.1016/j.compbiolchem.2014.08.020

    Besides their large-scale organization in isochores, mammalian genomes display megabase-sized regions, spanning both genes and intergenes, where the strand nucleotide composition asymmetry decreases linearly, possibly due to replication activity.

    These so-called skew-N domains cover about a third of the human genome and are bordered by two skew upward jumps that were hypothesized to compose a subset of “master” replication origins active in the germline.

    Skew-N domains were shown to exhibit a particular gene organization.

    Genes with CpG-rich promoters likely expressed in the germline are over represented near the master replication origins, with large genes being co-oriented with replication fork progression, which suggests some coordination of replication and transcription.

    In this study, we describe another skew structure that covers ?13% of the human genome and that is bordered by putative master replication origins similar to the ones flanking skew-N domains.

    These skew-split-N domains have a shape reminiscent of a N, but split in half, leaving in the center a region of null skew whose length increases with domain size.

    These central regions (median size ?860 kb) have a homogeneous composition, i.e. both a null and constant skew and a constant and low GC content.

    They correspond to heterochromatin gene deserts found in low-GC isochores with an average gene density of 0.81 promoters/Mb as compared to 7.73 promoters/Mb genome wide.

    The analysis of epigenetic marks and replication timing data confirms that, in these late replicating heterochomatic regions, the initiation of replication is likely to be random.

    This contrasts with the transcriptionally active euchromatin state found around the bordering well positioned master replication origins.

    Altogether skew-N domains and skew-split-N domains cover about 50% of the human genome.


  243. 243
    Dionisio says:

    Human Genome Replication Proceeds through Four Chromatin States

    •DOI: 10.1371/journal.pcbi.1003233

    Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions.

    Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in response to the environment.

    Paradoxically, the molecular mechanisms that regulate the initiation and the maintenance of the spatio-temporal replication program in higher eukaryotes, and in particular their links to epigenetic modifications, still remain elusive. [even after this paper?]

    Understanding the role of chromatin structure and dynamics in the regulation of the nuclear functions including transcription and replication, is a major challenge of current research in genomics and epigenomics.

    This new segmentation sheds a new light on the epigenetic regulation of the spatio-temporal replication program in human and provides a framework for further studies in different cell types, in both health and disease.

    This constitutes the first evidence of epigenetic compartmentalization of the human genome into replication domains likely corresponding to autonomous units in the 3D chromatin architecture.

    This opens new perspectives in the study of chromatin-mediated epigenetic regulation of transcription and replication in mammalian genomes in both health and disease.


    Some interlocutors and their comrades strongly dislike the highlighting of certain words and phrases in the referenced papers. Maybe they’ll get used to it, eventually. 🙂

  244. 244
    Dionisio says:

    Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation


    DNA methylation is an epigenetic modification associated with transcriptional repression of promoters and is essential for mammalian development.

    Establishment of DNA methylation is mediated by the de novo DNA methyltransferases DNMT3A and DNMT3B, whereas DNMT1 ensures maintenance of methylation through replication.

    Absence of these enzymes is lethal, and somatic mutations in these genes have been associated with several human diseases.

    How genomic DNA methylation patterns are regulated remains poorly understood, as the mechanisms that guide recruitment and activity of DNMTs in vivo are largely unknown.

    To gain insights into this matter we determined genomic binding and site-specific activity of the mammalian de novo DNA methyltransferases DNMT3A and DNMT3B.

    We show that both enzymes localize to methylated, CpG-dense regions in mouse stem cells, yet are excluded from active promoters and enhancers.

    By specifically measuring sites of de novo methylation, we observe that enzymatic activity reflects binding.

    De novo methylation increases with CpG density, yet is excluded from nucleosomes.

    Notably, we observed selective binding of DNMT3B to the bodies of transcribed genes, which leads to their preferential methylation.

    This targeting to transcribed sequences requires SETD2-mediated methylation of lysine 36 on histone H3 and a functional PWWP domain of DNMT3B.

    Together these findings reveal how sequence and chromatin cues guide de novo methyltransferase activity to ensure methylome integrity.


    Some interlocutors and their comrades strongly dislike the highlighting of certain words and phrases in the referenced papers. Maybe they’ll get used to it, eventually. 🙂

  245. 245
    Dionisio says:

    Function and information content of DNA methylation


    Cytosine methylation is a DNA modification generally associated with transcriptional silencing.

    Factors that regulate methylation have been linked to human disease, yet how they contribute to malignances remains largely unknown.

    Genomic maps of DNA methylation have revealed unexpected dynamics at gene regulatory regions, including active demethylation by TET proteins at binding sites for transcription factors.

    These observations indicate that the underlying DNA sequence largely accounts for local patterns of methylation.

    As a result, this mark is highly informative when studying gene regulation in normal and diseased cells, and it can potentially function as a biomarker.

    Although these findings challenge the view that methylation is generally instructive for gene silencing, several open questions remain, including how methylation is targeted and recognized and in what context it affects genome readout.


  246. 246
    Dionisio says:

    Crystal structure of the CRISPR RNA–guided surveillance complex from Escherichia coli

    DOI: 10.1126/science.1256328

    Clustered regularly interspaced short palindromic repeats (CRISPRs) are essential components of RNA-guided adaptive immune systems that protect bacteria and archaea from viruses and plasmids.

    In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble into a 405-kilodalton multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense).

    Here we present the 3.24 angstrom resolution x-ray crystal structure of Cascade.

    Eleven proteins and a 61-nucleotide crRNA assemble into a seahorse-shaped architecture that binds double-stranded DNA targets complementary to the crRNA-guide sequence.

    Conserved sequences on the 3? and 5? ends of the crRNA are anchored by proteins at opposite ends of the complex, whereas the guide sequence is displayed along a helical assembly of six interwoven subunits that present five-nucleotide segments of the crRNA in pseudo–A-form configuration.

    The structure of Cascade suggests a mechanism for assembly and provides insights into the mechanisms of target recognition.


  247. 247
    Dionisio says:

    Interkinetic Nuclear Migration Is Centrosome Independent and Ensures Apical Cell Division to Maintain Tissue Integrity


    Pseudostratified epithelia are widespread during animal development and feature elongated cells whose nuclei adopt various positions along the apicobasal cell axis.

    Before mitosis, nuclei migrate toward the apical surface, and subsequent divisions occur apically.

    So far, the exact purpose of this nuclear migration remained elusive.

    One hypothesis was that apical migration ensures that nuclei and centrosomes meet for mitosis.

    We here demonstrate that in zebrafish neuroepithelia apical nuclear migration occurs independently of centrosome position or integrity.

    It is a highly reproducible phenomenon linked to the cell cycle via CDK1 activity. [how?]

    We propose that the robustness of bringing nuclei apically for mitosis ensures that cells are capable of reintegrating into the epithelium after division.

    Nonapical divisions lead to cell delamination and formation of cell clusters that subsequently interfere with neuronal layering.

    Therefore, positioning divisions apically in pseudostratified neuroepithelia could serve to safeguard epithelial integrity and enable proper proliferation and maturation.


  248. 248
    Dionisio says:

    The Centrosome and Its Duplication Cycle

    doi: 10.1101/cshperspect.a015800.

    The centrosome was discovered in the late 19th century when mitosis was first described.

    Long recognized as a key organelle of the spindle pole, its core component, the centriole, was realized more than 50 or so years later also to comprise the basal body of the cilium.

    Here, we chart the more recent acquisition of a molecular understanding of centrosome structure and function.

    The strategies for gaining such knowledge were quickly developed in the yeasts to decipher the structure and function of their distinctive spindle pole bodies.

    Only within the past decade have studies with model eukaryotes and cultured cells brought a similar degree of sophistication to our understanding of the centrosome duplication cycle and the multiple roles of this organelle and its component parts in cell division and signaling.

    Now as we begin to understand these functions in the context of development, the way is being opened up for studies of the roles of centrosomes in human disease.


  249. 249
    Dionisio says:

    The centriole duplication cycle

    doi: 10.1098/rstb.2013.0460.

    Centrosomes are the main microtubule-organizing centre of animal cells and are important for many critical cellular and developmental processes from cell polarization to cell division.

    At the core of the centrosome are centrioles, which recruit pericentriolar material to form the centrosome and act as basal bodies to nucleate formation of cilia and flagella.

    Defects in centriole structure, function and number are associated with a variety of human diseases, including cancer, brain diseases and ciliopathies.

    In this review, we discuss recent advances in our understanding of how new centrioles are assembled and how centriole number is controlled.

    We propose a general model for centriole duplication control in which cooperative binding of duplication factors defines a centriole ‘origin of duplication’ that initiates duplication, and passage through mitosis effects changes that license the centriole for a new round of duplication in the next cell cycle. [how?]

    We also focus on variations on the general theme in which many centrioles are created in a single cell cycle, including the specialized structures associated with these variations, the deuterosome in animal cells and the blepharoplast in lower plant cells.


  250. 250
    Dionisio says:

    Polo-like kinases: structural variations lead to multiple functions


    Members of the polo-like kinase (PLK) family are crucial regulators of cell cycle progression, centriole duplication, mitosis, cytokinesis and the DNA damage response.

    PLKs undergo major changes in abundance, activity, localization and structure at different stages of the cell cycle.

    They interact with other proteins in a tightly controlled spatiotemporal manner as part of a network that coordinates key cell cycle events.

    Their essential roles are highlighted by the fact that alterations in PLK function are associated with cancers and other diseases.

    Recent knowledge gained from PLK crystal structures, evolution and interacting molecules offers important insights into the mechanisms that underlie their regulation and activity, and suggests novel functions unrelated to cell cycle control for this family of kinases.


  251. 251
    Dionisio says:

    Cep126 is required for pericentriolar satellite localisation to the centrosome and for primary cilium formation

    doi: 10.1111/boc.201300087

    The centrosome is the primary microtubule-organising centre of animal cells and it has crucial roles in several fundamental cellular functions, including cell division, cell polarity, and intracellular transport.

    The mechanisms responsible for this are not completely understood.


  252. 252
    Dionisio says:

    Positive and Negative Regulation of Vertebrate Separase by Cdk1-Cyclin B1 Might Explain why Securin Is Dispensable

    doi: 10.1074/jbc.M114.615310


    Could this be a case of reliability and robustness through redundancy?

    Isn’t that a commonly seen approach in engineering and computing?

    How did each variant come to be to begin with?

  253. 253
    Dionisio says:

    Identification of non-Ser/Thr-Pro consensus motifs for Cdk1 and their roles in mitotic regulation of C2H2 zinc finger proteins and Ect2


    The cyclin B-dependent protein kinase Cdk1 is a master regulator of mitosis and phosphorylates numerous proteins on the minimal consensus motif Ser/Thr-Pro (S/T-P).

    At least in several proteins, however, not well-defined motifs lacking a Pro in the +1 position, referred herein to as non-S/T-P motifs, have been shown to be phosphorylated by Cdk1.

    Here we show that non-S/T-P motifs in fact form consensus sequences for Cdk1 and probably play roles in mitotic regulation of physiologically important proteins.

    First, we show, by in vitro kinase assays, that previously identified non-S/T-P motifs all harbour one or more C-terminal Arg/Lys residues essential for their phosphorylation by Cdk1.

    Second, using Arg/Lys-scanning oriented peptide libraries, we demonstrate that Cdk1 phosphorylates a minimal sequence S/T-X-X-R/K and more favorable sequences (P)-X-S/T-X-[R/K]2–5 as its non-S/T-P consensus motifs.

    Third, on the basis of these results, we find that highly conserved linkers (typically, T-G-E-K-P) of C2H2 zinc finger proteins and a nuclear localization signal-containing sequence (matching P-X-S-X-[R/K]5) of the cytokinesis regulator Ect2 are inhibitorily phosphorylated by Cdk1, well accounting for the known mitotic regulation and function of the respective proteins.

    We suggest that non-S/T-P Cdk1 consensus motifs identified here may function to regulate many other proteins during mitosis.


  254. 254
    Dionisio says:

    Mammalian Polo-like Kinase 1 (Plk1) Promotes Proper Chromosome Segregation by Phosphorylating and Delocalizing the PBIP1-CENP-Q Complex from Kinetochore

    doi: 10.1074/jbc.M114.623546

    Mammalian polo-like kinase 1 (Plk1) is critically required for proper M-phase progression.

    Plk1 is self-recruited to prekinetochores/kinetochores by phosphorylating and binding to the T78 motif of a kinetochore scaffold protein, PBIP1 (also called CENP-U/50), which forms a stable complex with another kinetochore component, CENP-Q.

    However, the mechanism underlying how Plk1 localization to this site is regulated remains largely unknown.

    Thus, we propose that Plk1 regulates the timing of the delocalization and ultimate destruction of the PBIP1-CENP-Q complex, and that these processes are important not only for promoting Plk1-dependent mitotic progression, but also for resetting the timing of Plk1 recruitment to prekinetochores in the next cell cycle.


  255. 255
    Dionisio says:

    Lentivirus?mediated silencing of spindle and kinetochore?associated protein 1 inhibits the proliferation and invasion of neuronal glioblastoma cells.

    doi: 10.3892/mmr.2015.3175

    Spindle and kinetochore?associated protein 1 (SKA1) is an important component of the human kinetochore, which plays a key role in mitosis.

    The resent study was designed to investigate the role of SKA1 in human glioblastoma.

    The results of the present study demonstrated that SKA1 was expressed in human glioblastoma cells.

    In addition, the knockdown of SKA1 expression in the A172 and U251 human glioblastoma cell lines was accomplished using a lentivirus infection method.

    An MTT assay demonstrated that downregulation of SKA1 may inhibit cell proliferation, without affecting the cell cycle.

    Furthermore, knockdown of SKA1 expression resulted in reduced cell invasion.

    The results of the present study indicated that SKA1 may be a potential target protein for antiproliferative and anti?invasive therapeutic strategies of human glioblastoma.


  256. 256
    Dionisio says:

    Meikin is a conserved regulator of meiosis-I-specific kinetochore function.

    doi: 10.1038/nature14097

    The kinetochore is the crucial apparatus regulating chromosome segregation in mitosis and meiosis.

    Particularly in meiosis I, unlike in mitosis, sister kinetochores are captured by microtubules emanating from the same spindle pole (mono-orientation) and centromeric cohesion mediated by cohesin is protected in the following anaphase.

    Although meiotic kinetochore factors have been identified only in budding and fission yeasts, these molecules and their functions are thought to have diverged earlier.

    Therefore, a conserved mechanism for meiotic kinetochore regulation remains elusive.

    Our integrative analysis indicates that the long-awaited key regulator of meiotic kinetochore function is Meikin, which is conserved from yeasts to humans.


    Are there other factors besides meikin?
    How exactly does meikin get into this and how does it work?
    Are there any timing issues?
    Why does in work in one meiosis but not in the other? why not in mitosis?
    How is it produced? how much of it? why?

  257. 257
    Dionisio says:

    Cell division: Hold on and let go


    The discovery and functional analysis of the protein MEIKIN in mice leads to an evolutionarily conserved model of how chromosome segregation is regulated during a specialized type of cell division called meiosis I.

    During the first of the meiotic cell divisions that generate germ cells, sister kinetochores are captured by microtubules from the same spindle pole so that sister chromatids can be segregated into the same daughter cell.

    Yoshinori Watanabe and colleagues have now identified MEIKIN as the long-sought-after meiosis-specific kinetochore factor that ensures mono-orientation and protects sister chromatid cohesion during the first meiotic division in mouse germ cells.

    It functions mainly by recruiting the kinase PLK1 to kinetochores.

    Previously identified budding and fission yeast proteins, Spo13 and Moa1, respectively, are shown to be functional homologues of MEIKIN, and the authors propose that together they form the ‘Meikin’ family of meiosis-I-specific kinetochore factors.


  258. 258
  259. 259
    Dionisio says:

    Autoimmunity and antibody affinity maturation are modulated by genetic variants on mouse chromosome 12.

    doi: 10.1016/j.jaut.2015.01.007

    Autoimmune diseases result from a break in immune tolerance leading to an attack on self-antigens.

    Autoantibody levels serve as a predictive tool for the early diagnosis of many autoimmune diseases, including type 1 diabetes.

    We find that a genetic locus on mouse chromosome 12 influences the affinity maturation of antibodies as well as autoantibody production.


    Together, these results demonstrate that a genetic variant(s) present within the Chr12 locus plays a global role in modulating antibody affinity maturation.


  260. 260
    Dionisio says:

    Idd13 is involved in determining immunoregulatory DN T-cell number in NOD mice.

    doi: 10.1038/gene.2013.65.

    Immunoregulatory T cells have been identified as key modulators of peripheral tolerance and participate in preventing autoimmune diseases.

    Together, our results show that the regulation of DN T-cell number in NOD mice is at least partially conferred by alleles at the Idd13 locus.


  261. 261
    Dionisio says:

    An Integrated View of Cellular Systems

    By integrating information from the genome, transcriptome, proteome, and metabolome, dynamic interactions can be examined to decipher complex biological networks.

    This systems approach involves the integration of high-throughput technology and multiple interdisciplinary areas or fields, including molecular biology, cell biology, genomics, proteomics, metabolomics, and bioinformatics.


  262. 262
    Dionisio says:

    Measuring Extracellular Vesicle Stability: A New Frontier in Analytical Technology

    The study of extracellular vesicles is an area that has recently become the subject of intense interest.

    These vesicles are apparently ubiquitous in prokaryotic and eukaryotic organisms and it is believed they have a wide role to play in many physiological and pathological processes.

    They are typically described either as exosomes, which are produced from the cell endosome, or microvesicles, produced by cell membrane budding.

    Despite increased academic and commercial interest, much of the understanding of their cellular origin, structure, functions and size is still the subject of debate, as are the preferred methods of isolation and characterization.


  263. 263
    Dionisio says:

    Local and macroscopic electrostatic interactions in single ?-helices


    The noncovalent forces that stabilize protein structures are not fully understood.

    One way to address this is to study equilibria between unfolded states and ?-helices in peptides.

    Electrostatic forces—which include interactions between side chains, the backbone and side chains, and side chains and the helix macrodipole—are believed to contribute to these equilibria.

    Here we probe these interactions experimentally using designed peptides.

    We find that both terminal backbone–side chain and certain side chain–side chain interactions (which include both local effects between proximal charges and interatomic contacts) contribute much more to helix stability than side chain–helix macrodipole electrostatics, which are believed to operate at larger distances.

    This has implications for current descriptions of helix stability, the understanding of protein folding and the refinement of force fields for biomolecular modeling and simulations.

    In addition, this study sheds light on the stability of rod-like structures formed by single ?-helices, which are common in natural proteins such as non-muscle myosins.


  264. 264
    Dionisio says:

    #263 addendum

    Dr. Emily Baker conducted the research in the laboratory of Prof. Dek Woolfson.

    She explains:

    “The amide bonds can be thought of as tiny bar magnets.

    When an a-helix is formed these all line up.

    For almost 40 years it was thought that the smaller bar magnets, which are known as dipoles, add up to give one large effective magnet, called the helix macrodipole.”

    As Prof. Woolfson puts it:

    “We are not saying that the helix macrodipole doesn’t exist, it is just that it is very weak and its influence is far less than previously thought.

    Indeed, it is trumped by the local effects that we studied.

    In short, we do not need to use the macrodipole concept anymore to explain the vast majority of phenomena that have been attributed to it in the past, including in textbooks.”


  265. 265
    Dionisio says:

    Shedding light on structure of key cellular “gatekeeper”

    Facing a challenge akin to solving a 1,000-piece jigsaw puzzle while blindfolded—and without touching the pieces—many structural biochemists thought it would be impossible to determine the atomic structure of a massive cellular machine called the nuclear pore complex (NPC), which is vital for cell survival.

    But after 10 years of attacking the problem, a team led by André Hoelz, assistant professor of chemistry, recently solved almost a third of the puzzle.

    “This is an incredibly important structure to study,” he says, “but because it is so large and complex, people thought it was crazy to work on it. But 10 years ago, we hypothesized that we could solve the atomic structure with a divide-and-conquer approach—basically breaking the task into manageable parts—and we’ve shown that for a major section of the NPC, this actually worked.”

    Still, he adds, “My dream actually goes much farther. I don’t really want to have a static image of the pore. What I really would like—and this is where people look at me with a bit of a smile on their face, like they’re laughing a little bit—is to get an image of how the pore is moving, how the machine actually works. The pore is not a static hole, it can open up like the iris of a camera to let something through that’s much bigger. How does it do it?

    To understand that machine in motion, he adds, “you don’t just need one snapshot, you need multiple snapshots. But once you have one, you can infer the other ones much quicker, so that’s the ultimate goal. That’s the dream.”


    Can’t wait to see their dream become real. It should be fascinating to understand how that complex machinery functions.

  266. 266
    Dionisio says:

    #265 addendum

    Architecture of the nuclear pore complex coat

    DOI: 10.1126/science.aaa4136

    The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport.

    Despite half a century of structural characterization, the architecture of the NPC remains unknown.

    Here, we present the crystal structure of a reconstituted ~400 kDa coat nucleoporin complex (CNC) from S. cerevisiae at a 7.4-Å resolution.

    The crystal structure revealed a curved Y-shaped architecture and the molecular details of the coat nucleoporin interactions forming the central “triskelion” of the Y.

    A structural comparison of the yeast CNC with an electron microscopy reconstruction of its human counterpart suggested the evolutionary conservation of the elucidated architecture.

    Moreover, 32 copies of the CNC crystal structure docked readily into a cryoelectron tomographic reconstruction of the fully-assembled human NPC, thereby accounting for ~16 MDa of its mass.


  267. 267
    Dionisio says:

    Bacterial armor holds clues for self-assembling nanostructures


  268. 268

    The real marvel on display is the capacity of Darwinists to stare at the unveiling of the most sophisticated software/engineering/technology ever witnessed, beyond what has ever been imagined, and resolutely insist that it all occurred completely undirected by any intelligence whatsoever.

    Religious zealotry is blinding Darwinists to the mounting evidence before their eyes.

  269. 269
    gpuccio says:

    William J Murray:

    You are perfectly right. Observing intelligent people who force their cognitive “creativity” to defend what is utterly indefensible is an experience at the same time funny and sad.

    Unable to explain the origin of one single functional protein, they happily accept the dogma that complex and irreducible systems implying that coordinated and controlled interactions of hundreds of proteins and structures certainly originated by the same mythical mechanism which exists only in their imagination and faith

  270. 270
    Dionisio says:

    Structural basis for RNA replication by the hepatitis C virus polymerase

    DOI: 10.1126/science.1259210

    Nucleotide analog inhibitors have shown clinical success in the treatment of hepatitis C virus (HCV) infection, despite an incomplete mechanistic understanding of NS5B, the viral RNA-dependent RNA polymerase.

    Here we study the details of HCV RNA replication by determining crystal structures of stalled polymerase ternary complexes with enzymes, RNA templates, RNA primers, incoming nucleotides, and catalytic metal ions during both primed initiation and elongation of RNA synthesis.

    Our analysis revealed that highly conserved active-site residues in NS5B position the primer for in-line attack on the incoming nucleotide.

    A ? loop and a C-terminal membrane–anchoring linker occlude the active-site cavity in the apo state, retract in the primed initiation assembly to enforce replication of the HCV genome from the 3? terminus, and vacate the active-site cavity during elongation.

    We investigated the incorporation of nucleotide analog inhibitors, including the clinically active metabolite formed by sofosbuvir, to elucidate key molecular interactions in the active site.


  271. 271
    Dionisio says:

    A unique chromatin complex occupies young ?-satellite arrays of human centromeres

    DOI: 10.1126/sciadv.1400234

    The intractability of homogeneous ?-satellite arrays has impeded understanding of human centromeres.

    Artificial centromeres are produced from higher-order repeats (HORs) present at centromere edges, although the exact sequences and chromatin conformations of centromere cores remain unknown.

    We use high-resolution chromatin immunoprecipitation (ChIP) of centromere components followed by clustering of sequence data as an unbiased approach to identify functional centromere sequences.

    We find that specific dimeric ?-satellite units shared by multiple individuals dominate functional human centromeres.

    We identify two recently homogenized ?-satellite dimers that are occupied by precisely positioned CENP-A (cenH3) nucleosomes with two ~100–base pair (bp) DNA wraps in tandem separated by a CENP-B/CENP-C–containing linker, whereas pericentromeric HORs show diffuse positioning.

    Precise positioning is largely maintained, whereas abundance decreases exponentially with divergence, which suggests that young ?-satellite dimers with paired ~100-bp particles mediate evolution of functional human centromeres.

    Our unbiased strategy for identifying functional centromeric sequences should be generally applicable to tandem repeat arrays that dominate the centromeres of most eukaryotes.


  272. 272
    Dionisio says:

    F-actin flow drives affinity maturation and spatial organization of LFA-1 at the immunological synapse

    doi: 10.1083/jcb.201406121

    Integrin-dependent interactions between T cells and antigen-presenting cells are vital for proper T cell activation, effector function, and memory.

    Regulation of integrin function occurs via conformational change, which modulates ligand affinity, and receptor clustering, which modulates valency.

    Here, we show that conformational intermediates of leukocyte functional antigen 1 (LFA-1) form a concentric array at the immunological synapse.

    Using an inhibitor cocktail to arrest F-actin dynamics, we show that organization of this array depends on F-actin flow and ligand mobility.

    Furthermore, F-actin flow is critical for maintaining the high affinity conformation of LFA-1, for increasing valency by recruiting LFA-1 to the immunological synapse, and ultimately for promoting intracellular cell adhesion molecule 1 (ICAM-1) binding.

    Finally, we show that F-actin forces are opposed by immobilized ICAM-1, which triggers LFA-1 activation through a combination of induced fit and tension-based mechanisms.

    Our data provide direct support for a model in which the T cell actin network generates mechanical forces that regulate LFA-1 activity at the immunological synapse.


  273. 273
    Dionisio says:

    Actin works both sides of the immunological synapse

    doi: 10.1083/jcb.2084if

    The cytoskeleton of both T cells and antigen-presenting cells promotes mechanical signaling during T cell activation.

    Antigen-presenting cells (APCs) activate T cells by forming a specialized contact site called the immunological synapse (IS).

    The T cell receptor (TCR) and its downstream signaling molecules cluster in the center of the IS, surrounded by a ring of integrin molecules such as LFA-1, which lower the threshold for T cell priming by both tightly adhering to ligands on the surface of the APC and by activating downstream signaling pathways of their own.

    The next questions, says Burkhardt, are how the adhesion and signaling activities of active LFA-1 promote T cell priming, and how mechanical forces at the IS affect T cell functions in vivo.


  274. 274
    Dionisio says:

    The dendritic cell cytoskeleton promotes T cell adhesion and activation by constraining ICAM-1 mobility

    doi: 10.1083/jcb.201406120

    Integrity of the dendritic cell (DC) actin cytoskeleton is essential for T cell priming, but the underlying mechanisms are poorly understood.

    We show that the DC F-actin network regulates the lateral mobility of intracellular cell adhesion molecule 1 (ICAM-1), but not MHCII.

    ICAM-1 mobility and clustering are regulated by maturation-induced changes in the expression and activation of moesin and ?-actinin-1, which associate with actin filaments and the ICAM-1 cytoplasmic domain.

    Constrained ICAM-1 mobility is important for DC function, as DCs expressing a high-mobility ICAM-1 mutant lacking the cytoplasmic domain exhibit diminished antigen-dependent conjugate formation and T cell priming.

    These defects are associated with inefficient induction of leukocyte functional antigen 1 (LFA-1) affinity maturation, which is consistent with a model in which constrained ICAM-1 mobility opposes forces on LFA-1 exerted by the T cell cytoskeleton, whereas ICAM-1 clustering enhances valency and further promotes ligand-dependent LFA-1 activation.

    Our results reveal an important new mechanism through which the DC cytoskeleton regulates receptor activation at the immunological synapse.


  275. 275
    Dionisio says:

    Solving the centriole disengagement puzzle


    The microcephaly protein, Cep215, contributes to the engagement of duplicated centrioles in interphase.

    Now two distinct pools of Cep215 at centrosomes are identified, one bound to Cep68 and the other to pericentrin.

    Plk1-mediated degradation of Cep68 and separase-mediated cleavage of pericentrin release both pools of Cep215, thereby promoting centriole disengagement.


  276. 276
    Dionisio says:

    Myosin II controls cellular branching morphogenesis and migration in three dimensions by minimizing cell-surface curvature


    In many cases, cell function is intimately linked to cell shape control.

    We used endothelial cell branching morphogenesis as a model to understand the role of myosin II in shape control of invasive cells migrating in 3D collagen gels.

    We applied principles of differential geometry and mathematical morphology to 3D image sets to parameterize cell branch structure and local cell-surface curvature.

    We find that Rho/ROCK-stimulated myosin II contractility minimizes cell-scale branching by recognizing and minimizing local cell-surface curvature.

    Using microfabrication to constrain cell shape identifies a positive feedback mechanism in which low curvature stabilizes myosin II cortical association, where it acts to maintain minimal curvature.

    The feedback between regulation of myosin II by curvature and control of curvature by myosin II drives cycles of localized cortical myosin II assembly and disassembly.

    These cycles in turn mediate alternating phases of directionally biased branch initiation and retraction to guide 3D cell migration.


  277. 277
    Dionisio says:

    Cdk1-dependent mitotic enrichment of cortical myosin II promotes cell rounding against confinement


    Actomyosin-dependent mitotic rounding occurs in both cell culture and tissue, where it is involved in cell positioning and epithelial organization.

    How actomyosin is regulated to mediate mitotic rounding is not well understood.

    Here we characterize the mechanics of single mitotic cells while imaging actomyosin recruitment to the cell cortex.

    At mitotic onset, the assembly of a uniform ?DIAPH1-dependent F-actin cortex coincides with initial rounding.

    Thereafter, cortical enrichment of F-actin remains stable while myosin II progressively accumulates at the cortex, and the amount of myosin at the cortex correlates with intracellular pressure.

    Whereas F-actin provides only short-term (<10 s) resistance to mechanical deformation, myosin sustains intracellular pressure for a longer duration (>60 s).

    Our data suggest that progressive accumulation of myosin II to the mitotic cell cortex probably requires the ?Cdk1 activation of both ?p21-activated kinases, which inhibit myosin recruitment, and of Rho kinase, which stimulates myosin recruitment to the cortex.


  278. 278
    Dionisio says:

    Actin depolymerisation and crosslinking join forces with myosin II to contract actin coats on fused secretory vehicles

    doi: 10.1242/?jcs.165571

    In many secretory cells actin and myosin are specifically recruited to the surface of secretory granules following their fusion with the plasma membrane.

    Actomyosin-dependent compression of fused granules is essential to promote active extrusion of cargo.

    Yet, little is known about molecular mechanisms regulating actin coat formation and contraction.

    Here we provide a detailed kinetic analysis of the molecules regulating actin coat contraction on fused lamellar bodies (LBs) in primary alveolar type II cells.

    We demonstrate that Rock1 and myosin light chain kinase (MLCK) translocate to fused LBs and activate myosin II on actin coats.

    Yet, myosin II activity is not sufficient for efficient actin coat contraction. In addition, cofilin-1 and ?-actinin translocate to actin coats.

    Rock1-dependent, regulated actin depolymerisation by cofilin-1 in cooperation with actin crosslinking by ?-actinin is essential for complete coat contraction.

    In summary, our data suggest a complementary role for regulated actin depolymerisation/crosslinking and myosin II activity to contract actin coats and drive secretion.


  279. 279
    Dionisio says:

    Trip6 Promotes Dendritic Morphogenesis through Dephosphorylated GRIP1-Dependent Myosin VI and F-Actin Organization

    doi: 10.1523/JNEUROSCI.2125-14.2015

    Thyroid receptor-interacting protein 6 (Trip6), a multifunctional protein belonging to the zyxin family of LIM proteins, is involved in various physiological and pathological processes, including cell migration and tumorigenesis.

    However, the role of Trip6 in neurons remains unknown.

    Here, we show that Trip6 is expressed [why? how?] in mouse hippocampal neurons and promotes dendritic morphogenesis.

    Through interaction with the glutamate receptor-interacting protein 1 (GRIP1) and myosin VI, Trip6 is crucial for the total dendritic length and the number of primary dendrites in cultured hippocampal neurons.

    Trip6 depletion reduces F-actin content and impairs dendritic morphology, and this phenocopies GRIP1 or myosin VI knockdown.

    Furthermore, phosphorylation of GRIP1956T by AKT1 inhibits the interaction between GRIP1 and myosin VI, but facilitates GRIP1 binding to 14-3-3 protein, which is required for regulating F-actin organization and dendritic morphogenesis.

    Thus, the Trip6–GRIP1–myosin VI interaction and its regulation on F-actin network play a significant role in dendritic morphogenesis.


  280. 280
    Dionisio says:

    #279 addendum

    Trip6 protein localizes to focal adhesion sites and along actin stress fibers. [why?] [how?]

    Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner and it regulates LPA-induced cell migration.


  281. 281
    Dionisio says:

    Regulation of T Cell Motility In Vitro and In Vivo by LPA and LPA2

    •DOI: 10.1371/journal.pone.0101655

    Lysophosphatidic acid (LPA) and the LPA-generating enzyme autotaxin (ATX) have been implicated in lymphocyte trafficking and the regulation of lymphocyte entry into lymph nodes.

    High local concentrations of LPA are thought to be present in lymph node high endothelial venules, suggesting a direct influence of LPA on cell migration.

    However, little is known about the mechanism of action of LPA, and more work is needed to define the expression and function of the six known G protein-coupled receptors (LPA 1–6) in T cells.

    Taken together, these data highlight a previously unsuspected and non-redundant role for LPA2 in intranodal T cell motility, and suggest that specific functions of LPA may be manipulated by targeting T cell LPA receptors.

    Although LPA2 appears to regulate T cell dynamics within lymph nodes at early stages after adoptive transfer, the fact that we recovered similar numbers of lpa2?/? and wild-type CD4+ T cells 42 hours after adoptive transfer (Figure 6) indicates that this receptor does not control steady-state T cell recirculation over time.

    We cannot exclude the possibility that deficiency of LPA2 compromises T cell localization or migratory behavior within lymph nodes at later stages after adoptive transfer, even if bulk recirculation patterns are unaffected.

    Future studies will be needed to determine if other LPA receptors compensate for the lack of lpa2 over time, or if T cells were simply able to catch up over time independent of the influence of other receptors.

    What are the consequences of delayed migration of naïve CD4+ T cells within lymph nodes?

    The answer to this question will require further study, but the kinetics of T cell entry into secondary lymphoid organs could affect the quality or intensity of the effector response.

    Our discovery of a non-redundant role for LPA2 in T cell migration is important, since naïve CD4+ T cells express multiple LPA receptors.

    Future studies using gene-targeted mice and specific receptor inhibitors will help to dissect the individual roles of each LPA receptor on CD4+ T cell immune responses.

    There is likely cross-talk between the different LPA receptors in a cell-type specific manner, as well as interactions with other G-protein coupled receptors that regulate T cell migration [68].

    Our results add to the growing body of literature documenting an important role for LPA in the immune system, and suggest that future studies of LPA generation and action in vivo will enhance our understanding of initiation of immune responses.


  282. 282
    Dionisio says:

    Manipulating the Selection Forces during Affinity Maturation to Generate Cross-Reactive HIV Antibodies

    DOI: http://dx.doi.org/10.1016/j.cell.2015.01.027

    Generation of potent antibodies by a mutation-selection process called affinity maturation is a key component of effective immune responses.

    Antibodies that protect against highly mutable pathogens must neutralize diverse strains.

    Developing effective immunization strategies to drive their evolution requires understanding how affinity maturation happens in an environment where variants of the same antigen are present.

    We present an in silico model of affinity maturation driven by antigen variants which reveals that induction of cross-reactive antibodies often occurs with low probability because conflicting selection forces, imposed by different antigen variants, can frustrate affinity maturation.

    We describe how variables such as temporal pattern of antigen administration influence the outcome of this frustrated evolutionary process.

    Our calculations predict, and experiments in mice with variant gp120 constructs of the HIV envelope protein confirm, that sequential immunization with antigen variants is preferred over a cocktail for induction of cross-reactive antibodies focused on the shared CD4 binding site epitope.


  283. 283
    Dionisio says:

    Structural Damage in the C. elegans Epidermis Causes Release of STA-2 and Induction of an Innate Immune Response

    DOI: http://dx.doi.org/10.1016/j.immuni.2015.01.014

    The epidermis constantly encounters invasions that disrupt its architecture, yet whether the epidermal immune system utilizes damaged structures as danger signals to activate self-defense is unclear.

    Here, we used a C. elegans epidermis model in which skin-penetrating infection or injury activates immune defense and antimicrobial peptide (AMP) production.

    By systemically disrupting each architectural component, we found that only disturbance of the apical hemidesmosomes triggered an immune response and robust AMP expression.

    The epidermis recognized structural damage through hemidesmosomes associated with a STAT-like protein, whose disruption led to detachment of STA-2 molecules from hemidesmosomes and transcription of AMPs.

    This machinery enabled the epidermis to bypass certain signaling amplification and directly trigger AMP production when subjected to extensive architectural damage.

    Together, our findings uncover an evolutionarily conserved mechanism for the epithelial barriers to detect danger and activate immune defense.


  284. 284
    Dionisio says:

    Simulating the Entropic Collapse of Coarse-Grained Chromosomes

    DOI: http://dx.doi.org/10.1016/j.bpj.2014.12.032

    Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse.

    We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants.

    These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres.

    By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality.

    The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition.

    Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition.


  285. 285
    Dionisio says:

    Self-Restrained B Cells Arise following Membrane IgE Expression

    DOI: http://dx.doi.org/10.1016/j.celrep.2015.01.023

    Among immunoglobulins (Igs), IgE can powerfully contribute to antimicrobial immunity and severe allergy despite its low abundance.

    IgE protein and gene structure resemble other Ig classes, making it unclear what constrains its production to thousand-fold lower levels.

    Whether class-switched B cell receptors (BCRs) differentially control B cell fate is debated, and study of the membrane (m)IgE class is hampered by its elusive in vivo expression.

    Here, we demonstrate a self-controlled mIgE+ B cell stage.

    Primary or transfected mIgE+ cells relocate the BCRs into spontaneously internalized lipid rafts, lose mobility to chemokines, and change morphology.

    We suggest that combined proapoptotic mechanisms possibly involving Hax1 prevent mIgE+ memory lymphocyte accumulation.

    By uncoupling in vivo IgE switching from cytokine and antigen stimuli, we show that these features are independent from B cell stimulation and instead result from mIgE expression per se.

    Consequently, few cells survive IgE class switching, which might ensure minimal long-term IgE memory upon differentiation into plasma cells.


  286. 286
    Dionisio says:

    The NAD+-Dependent SIRT1 Deacetylase Translates a Metabolic Switch into Regulatory Epigenetics in Skeletal Muscle Stem Cells

    DOI: http://dx.doi.org/10.1016/j.stem.2014.12.004

    Stem cells undergo a shift in metabolic substrate utilization during specification and/or differentiation, a process that has been termed metabolic reprogramming.

    Here, we report that during the transition from quiescence to proliferation, skeletal muscle stem cells experience a metabolic switch from fatty acid oxidation to glycolysis.

    This reprogramming of cellular metabolism decreases intracellular NAD+ levels and the activity of the histone deacetylase SIRT1, leading to elevated H4K16 acetylation and activation of muscle gene transcription.

    Selective genetic ablation of the SIRT1 deacetylase domain in skeletal muscle results in increased H4K16 acetylation and deregulated activation of the myogenic program in SCs.

    Moreover, mice with muscle-specific inactivation of the SIRT1 deacetylase domain display reduced myofiber size, impaired muscle regeneration, and derepression of muscle developmental genes.

    Overall, these findings reveal how metabolic cues can be mechanistically translated into epigenetic modifications that regulate skeletal muscle stem cell biology.


  287. 287
    Dionisio says:

    The formation of the zygote
    The zygote, the first cell of a new organism with an individual genome (2n4C) is created by the alignment of the maternal chromosomes together with the paternal ones on a common spindle apparatus.


    From Wikipedia:
    A zygote […] is the initial cell formed when two gamete cells are joined by means of sexual reproduction.
    Zygotes are usually produced by a fertilization event between two haploid cells—an ovum (female gamete) and a sperm cell (male gamete)—which combine to form the single diploid cell.

  288. 288
    Dionisio says:

    Integrative analysis of 111 reference human epigenomes


    The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference.

    To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues.

    Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.

    We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors.

    We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease.

    Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.


  289. 289
    Dionisio says:

    Annotation of the non-coding genome


    Reference epigenomes enable comprehensive annotations of dynamic non-coding regulatory and transcribed elements across hundreds of human cell types and tissues


  290. 290
    Dionisio says:

    Regulatory models: networks, motifs, modules, sequence drivers and predictive models


    Integrative analyses of reference epigenomes reveal context-specific regulatory motifs, factors, modules, pathways and networks


  291. 291
    Dionisio says:

    Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs


    Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs.

    Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation for 3,753 (69% examined) lincRNAs, with 54% active in one of the 14 cell/tissue clusters and an additional 15% in two or three clusters.

    A larger fraction of lincRNA TSSs is marked in a tissue-specific manner by H3K4me1 than by H3K4me3.

    The tissue-specific lincRNAs are strongly linked to tissue-specific pathways and undergo distinct chromatin state transitions during cellular differentiation.

    Polycomb-regulated lincRNAs reside in the bivalent state in embryonic stem cells and many of them undergo H3K27me3-mediated silencing at early stages of differentiation.

    The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes.


  292. 292
    Dionisio says:

    Maternal-zygotic knockout reveals a critical role of Cdx2 in the morula to blastocyst transition


    The first lineage segregation in the mouse embryo generates the inner cell mass (ICM), which gives rise to the pluripotent epiblast and therefore the future embryo, and the trophectoderm (TE), which will build the placenta.

    The TE lineage depends on the transcription factor Cdx2.

    However, when Cdx2 first starts to act remains unclear.

    Embryos with zygotic deletion of Cdx2 develop normally until the late blastocyst stage leading to the conclusion that Cdx2 is important for the maintenance but not specification of the TE.

    In contrast, down-regulation of Cdx2 transcripts from the early embryo stage results in defects in TE specification before the blastocyst stage.

    Here, to unambiguously address at which developmental stage Cdx2 becomes first required, we genetically deleted Cdx2 from the oocyte stage using a Zp3-Cre/loxP strategy.

    Careful assessment of a large cohort of Cdx2 maternal-zygotic null embryos, all individually filmed, examined and genotyped, reveals an earlier lethal phenotype than observed in Cdx2 zygotic null embryos that develop until the late blastocyst stage.

    The developmental failure of Cdx2 maternal-zygotic null embryos is associated with cell death and failure of TE specification, starting at the morula stage.

    These results indicate that Cdx2 is important for the correct specification of TE from the morula stage onwards and that both maternal and zygotic pools of Cdx2 are required for correct pre-implantation embryogenesis.


  293. 293
    Dionisio says:

    Deciphering the genetic programme triggering timely and spatially-regulated chitin deposition

    doi: 10.1371/journal.pgen.1004939

    Organ and tissue formation requires a finely tuned temporal and spatial regulation of differentiation programmes.

    This is necessary to balance sufficient plasticity to undergo morphogenesis with the acquisition of the mature traits needed for physiological activity.

    Here we addressed this issue by analysing the deposition of the chitinous extracellular matrix of Drosophila, an essential element of the cuticle (skin) and respiratory system (tracheae) in this insect.

    Chitin deposition requires the activity of the chitin synthase Krotzkopf verkehrt (Kkv).

    Our data demonstrate that this process equally requires the activity of two other genes, namely expansion (exp) and rebuf (reb).

    We found that Exp and Reb have interchangeable functions, and in their absence no chitin is produced, in spite of the presence of Kkv.

    Conversely, when Kkv and Exp/Reb are co-expressed in the ectoderm, they promote chitin deposition, even in tissues normally devoid of this polysaccharide.

    Therefore, our results indicate that both functions are not only required but also sufficient to trigger chitin accumulation.

    We show that this mechanism is highly regulated in time and space, ensuring chitin accumulation in the correct tissues and developmental stages.

    Accordingly, we observed that unregulated chitin deposition disturbs morphogenesis, thus highlighting the need for tight regulation of this process.

    In summary, here we identify the genetic programme that triggers the timely and spatially regulated deposition of chitin and thus provide new insights into the extracellular matrix maturation required for physiological activity.



  294. 294
    Dionisio says:

    The extracellular matrix: Structure, composition, age-related differences, tools for analysis and applications for tissue engineering.

    doi: 10.1177/2041731414557112

    The extracellular matrix is a structural support network made up of diverse proteins, sugars and other components.

    It influences a wide number of cellular processes including migration, wound healing and differentiation, all of which is of particular interest to researchers in the field of tissue engineering.

    Understanding the composition and structure of the extracellular matrix will aid in exploring the ways the extracellular matrix can be utilised in tissue engineering applications especially as a scaffold.

    This review summarises the current knowledge of the composition, structure and functions of the extracellular matrix and introduces the effect of ageing on extracellular matrix remodelling and its contribution to cellular functions.

    Additionally, the current analytical technologies to study the extracellular matrix and extracellular matrix-related cellular processes are also reviewed.


  295. 295
    Dionisio says:

    B10 Cells: A Functionally Defined Regulatory B Cell Subset.

    DOI: 10.4049/jimmunol.1401329

    B cells are commonly thought to enhance inflammatory immune responses.

    However, specific regulatory B cell subsets recently were identified that downregulate adaptive and innate immunity, inflammation, and autoimmunity through diverse molecular mechanisms.

    In both mice and humans, a rare, but specific, subset of regulatory B cells is functionally characterized by its capacity to produce IL-10, a potent inhibitory cytokine.

    For clarity, this regulatory B cell subset has been labeled as B10 cells, because their ability to downregulate immune responses and inflammatory disease is fully attributable to IL-10, and their absence or loss exacerbates disease symptoms in mouse models.

    This review preferentially focuses on what is known about mouse B10 cell development, phenotype, and effector function, as well as on mechanistic studies that demonstrated their functional importance during inflammation, autoimmune disease, and immune responses.

    Copyright © 2015 by The American Association of Immunologists, Inc.



  296. 296
    Dionisio says:

    Application of metabolomics in autoimmune diseases: Insight into biomarkers and pathology

    DOI: 10.1016/j.jneuroim.2015.01.001

    Metabolomics has recently become a new technology using mass spectrometry (MS) and high-resolution proton nuclear magnetic resonance (NMR) to access metabolite profiles in biofluids or tissue extracts for the detection of biomarker molecules and biochemical effects induced by a disease or its therapeutic intervention.

    This review outlines recent advances in the use of metabolomic techniques to study autoimmune diseases (ADs), including multiple sclerosis (MS), rheumatoid arthritis (RA), inflammatory bowel diseases (IBD), autoimmune diabetes et al.

    Many studies have demonstrated that AD patients including subtypes of some diseases, and healthy individuals can be distinguished using metabolic profiling accompanied with well-established data analysis tools including principal component analysis (PCA) and partial least squares (PLS).

    These metabolites not only affect glucose, amino acid and lipid metabolism, but also involve alteration of neurotransmitters, nucleotides, immune responses and anti-inflammatory responses.

    Knowledge of unique metabolomic fingerprint in ADs could be useful for diagnosis, treatment, and detection mechanisms of diseases.




    So many things can mess up the delicate biological systems. How can they function at all?

  297. 297
    Dionisio says:

    Pathogen manipulation of B cells: the best defence is a good offence

    DOI: 10.1038/nrmicro3415

    B cells have long been regarded as simple antibody production units, but are now becoming known as key players in both adaptive and innate immune responses.

    However, several bacteria, viruses and parasites have evolved the ability to manipulate B cell functions to modulate immune responses.

    Pathogens can affect B cells indirectly, by attacking innate immune cells and altering the cytokine environment, and can also target B cells directly, impairing B cell-mediated immune responses.

    In this Review, we provide a summary of recent advances in elucidating direct B cell-pathogen interactions and highlight how targeting this specific cell population benefits different pathogens.



  298. 298
    Dionisio says:

    B cell TLR1/2, TLR4, TLR7 and TLR9 interact in induction of class switch DNA recombination: modulation by BCR and CD40, and relevance to T-independent antibody responses.

    doi: 10.3109/08916934.2014.993027.


  299. 299
    Dionisio says:

    Epigenetic function of activation-induced cytidine deaminase and its link to lymphomagenesis.

    doi: 10.3389/fimmu.2014.00642

    Activation-induced cytidine deaminase (AID) is essential for somatic hypermutation and class switch recombination of immunoglobulin (Ig) genes during B cell maturation and immune response.

    Expression of AID is tightly regulated due to its mutagenic and recombinogenic potential, which is known to target not only Ig genes, but also non-Ig genes, contributing to lymphomagenesis.

    In recent years, a new epigenetic function of AID and its link to DNA demethylation came to light in several developmental systems.

    In this review, we summarize existing evidence linking deamination of unmodified and modified cytidine by AID to base-excision repair and mismatch repair machinery resulting in passive or active removal of DNA methylation mark, with the focus on B cell biology.

    We also discuss potential contribution of AID-dependent DNA hypomethylation to lymphomagenesis.

  300. 300
    Dionisio says:

    Regulation of Immunoglobulin Class-Switch Recombination: Choreography of Noncoding Transcription, Targeted DNA Deamination, and Long-Range DNA Repair


    Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default C? constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as “Ch genes”, e.g., C?, C?, or C?).

    The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction.

    CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor S? and acceptor S regions.

    CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining.

    In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs.

    Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations.

    Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming.



    Did they say ‘choreography’? 🙂

    Pretty simple, isn’t it?

    Sometimes I highlight text that I might have further questions on, but this time I would have to highlight almost the entire article.

  301. 301
    Dionisio says:

    AIDing chromatin and transcription-coupled orchestration of immunoglobulin class-switch recombination


    Secondary diversification of the antibody repertoire upon antigenic challenge, in the form of immunoglobulin heavy chain (IgH) class-switch recombination (CSR) endows mature, naïve B cells in peripheral lymphoid organs with a limitless ability to mount an optimal humoral immune response, thus expediting pathogen elimination.

    CSR replaces the default constant (CH) region exons (C?) of IgH with any of the downstream CH exons (C?, C?, or C?), thereby altering effector functions of the antibody molecule.

    This process depends on, and is orchestrated by, activation-induced deaminase (AID), a DNA cytidine deaminase that acts on single-stranded DNA exposed during transcription of switch (S) region sequences at the IgH locus.

    DNA lesions thus generated are processed by components of several general DNA repair pathways to drive CSR.

    Given that AID can instigate DNA lesions and genomic instability, stringent checks are imposed that constrain and restrict its mutagenic potential.

    In this review, we will discuss how AID expression and substrate specificity and activity is rigorously enforced at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and how the DNA-damage response is choreographed with precision to permit targeted activity while limiting bystander catastrophe.


    Did they write ‘orchestrated’ and ‘choreographed’ ?


  302. 302
    Dionisio says:

    Chromatin and Transcriptional Tango on the Immune Dance Floor

    doi: 10.3389/fimmu.2014.00631


    The process of generating differentiated cell types performing specific effector functions from their respective undifferentiated precursors is dictated by extracellular signals, which alter the host cell’s capacity to perform cellular functions.

    One major mechanism for bringing about such changes is at the level of transcription.

    Thus, the transcription-related induction of previously silent genes and suppression of active genes in response to extracellular signals can result in the acquisition of new functions by the cells.

    The general transcriptional machinery, which comprised of RNA Polymerase II and associated initiation factors, assemble into preinitiation complexes at the core promoters of eukaryotic protein coding genes in response to the signal-dependent activation of corresponding regulatory factors that bind to promoter and enhancer elements (1).

    The rate of formation and/or stability of these complexes, which can be modulated both by enhancer–promoter interactions and by chromatin structural modifications, dictate the transcriptional regulation of the corresponding gene.

    Such coordinated temporal and spatial regulation of gene expression in response to specific signals determines lineage differentiation, cellular proliferation, and development (2).

    It takes two to tango, but apparently there are more dancers in the center of the ballroom. 🙂

  303. 303
    Dionisio says:

    Engineering the extracellular matrix for clinical applications: endoderm, mesoderm, and ectoderm.

    doi: 10.1002/biot.201300120

    Tissue engineering is rapidly progressing from a research-based discipline to clinical applications.

    Emerging technologies could be utilized to develop therapeutics for a wide range of diseases, but many are contingent on a cell scaffold that can produce proper tissue ultrastructure.

    The extracellular matrix, which a cell scaffold simulates, is not merely a foundation for tissue growth but a dynamic participant in cellular crosstalk and organ homeostasis.

    Cells change their growth rates, recruitment, and differentiation in response to the composition, modulus, and patterning of the substrate on which they reside.

    Cell scaffolds can regulate these factors through precision design, functionalization, and application.

    The ideal therapy would utilize highly specialized cell scaffolds to best mimic the tissue of interest.

    This paper discusses advantages and challenges of optimized cell scaffold design in the endoderm, mesoderm, and ectoderm for clinical applications in tracheal transplant, cardiac regeneration, and skin grafts, respectively.


    Do they have to ‘design’ something in order to imitate the functioning of biological components that allegedly were not designed?

  304. 304
    Dionisio says:

    Ectosomes and exosomes: shedding the confusion between extracellular vesicles

    DOI: http://dx.doi.org/10.1016/j.tcb.2015.01.004

    Long- and short-distance communication can take multiple forms.

    Among them are exosomes and ectosomes, extracellular vesicles (EVs) released from the cell to deliver signals to target cells.

    While most of our understanding of how these vesicles are assembled and work comes from mechanistic studies performed on exosomes, recent studies have begun to shift their focus to ectosomes.

    Unlike exosomes, which are released on the exocytosis of multivesicular bodies (MVBs), ectosomes are ubiquitous vesicles assembled at and released from the plasma membrane.


    Several ‘how?’ and’ why?’ questions come to mind, don’t they? 🙂

  305. 305
    Dionisio says:

    Human Promoters Are Intrinsically Directional

    DOI: http://dx.doi.org/10.1016/j.molcel.2014.12.029

    Divergent transcription, in which reverse-oriented transcripts occur upstream of eukaryotic promoters in regions devoid of annotated genes, has been suggested to be a general property of active promoters.

    Here we show that the human basal RNA polymerase II transcriptional machinery and core promoter are inherently unidirectional and that reverse-oriented transcripts originate from their own cognate reverse-directed core promoters.

    In vitro transcription analysis and mapping of nascent transcripts in HeLa cells revealed that sequences at reverse start sites are similar to those of their forward counterparts.

    The use of DNase I accessibility to define proximal promoter borders revealed that about half of promoters are unidirectional and that unidirectional promoters are depleted at their upstream edges of reverse core promoter sequences and their associated chromatin features.

    Divergent transcription is thus not an inherent property of the transcription process but rather the consequence of the presence of both forward- and reverse-directed core promoters.


  306. 306
    Dionisio says:

    Pervasive and Essential Roles of the Top3-Rmi1 Decatenase Orchestrate Recombination and Facilitate Chromosome Segregation in Meiosis

    DOI: http://dx.doi.org/10.1016/j.molcel.2015.01.021

    The Bloom’s helicase ortholog, Sgs1, plays central roles to coordinate the formation and resolution of joint molecule intermediates (JMs) during meiotic recombination in budding yeast.

    Sgs1 can associate with type-I topoisomerase Top3 and its accessory factor Rmi1 to form a conserved complex best known for its unique ability to decatenate double-Holliday junctions.

    Contrary to expectations, we show that the strand-passage activity of Top3-Rmi1 is required for all known functions of Sgs1 in meiotic recombination, including channeling JMs into physiological crossover and noncrossover pathways, and suppression of non-allelic recombination.

    We infer that Sgs1 always functions in the context of the Sgs1-Top3-Rmi1 complex to regulate meiotic recombination.

    In addition, we reveal a distinct late role for Top3-Rmi1 in resolving recombination-dependent chromosome entanglements to allow segregation at anaphase.

    Surprisingly, Sgs1 does not share this essential role of Top3-Rmi1.

    These data reveal an essential and pervasive role for the Top3-Rmi1 decatenase during meiosis.


    Did they say ‘orchestrate’? 🙂

    Contrary to expectations,? what expectations?

    Surprisingly, ? why? did they expect something else?

  307. 307
    Dionisio says:

    Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

    DOI: 10.1126/science.aaa1934

    Normal brain function relies on a diverse set of differentiated cell types, including neurons, glia, and vasculature.

    Across the diversity of cortical cell types, transcription factors formed a complex, layered regulatory code, suggesting a mechanism for the maintenance of adult cell type identity.


    complex, layered regulatory code?

    Hmmm… where did that come from? FUCA, LUCA? how?

  308. 308
    Dionisio says:

    NIH-Supported Researchers Map Epigenome of More than 100 Tissue, Cell Types

    “This represents a major advance in the ongoing effort to understand how the 3 billion letters of an individual’s DNA instruction book are able to instruct vastly different molecular activities, depending on the cellular context,” said NIH Director Francis Collins, M.D., Ph.D. “This outpouring of data-rich publications, produced by a remarkable team of creative scientists, provides powerful momentum for the rapidly growing field of epigenomics.”

    “What the Roadmap Epigenomics Program has delivered is a way to look at the human genome in its living, breathing nature from cell type to cell type,” said Manolis Kellis, Ph.D., professor of computer science at the Massachusetts Institute of Technology, Cambridge, and senior author of the paper.

    “Today, sequencing the human genome can be done rapidly and cheaply, but interpreting the genome remains a challenge,” said Bing Ren, Ph.D., professor of cellular and molecular medicine at the University of California, San Diego, and co-author of the Nature paper and several of the associated papers. “These 111 reference epigenome maps are essentially a vocabulary book that helps us decipher each DNA segment in distinct cell and tissue types. These maps are like snapshots of the human genome in action.”

    “This is the most comprehensive catalog of epigenomic data from primary human cells and tissues to date,” said Lisa Helbling Chadwick, Ph.D., project team leader and a program director at the National Institute of Environmental Health Sciences (NIEHS), part of NIH. “This coordinated effort, along with uniform data processing, makes it much easier for researchers to make direct comparisons across the entire data set.”

    “Researchers from the 88 projects supported by the program, including those from this recent series of papers, have propelled the development of new epigenomic technologies,” said John Satterlee, Ph.D., co-coordinator of the Roadmap Epigenomics Program, and program director at the National Institute on Drug Abuse (NIDA), part of NIH. Satterlee added that the work of this program has served as a foundation for continued exploration of the human epigenome through the International Human Epigenome Consortium External Web Site Policy.

    “With this increased understanding of the full epigenome, and the datasets available to the entire scientific community, the NIH Common Fund is striving to catalyze future research, to aid the understanding of how epigenomics plays a role in human diseases, with the expectation that further studies will identify early indications of disease and targets for therapeutics,” said James Anderson, M.D., Ph.D., director of NIH Division of Program Coordination, Planning, and Strategic Initiatives that oversees the NIH Common Fund.


  309. 309
    Dionisio says:

    Basic components of connective tissues and extracellular matrix: elastin, fibrillin, fibulins, fibrinogen, fibronectin, laminin, tenascins and thrombospondins.

    doi: 10.1007/978-94-007-7893-1_3.

    Collagens are the most abundant components of the extracellular matrix and many types of soft tissues.

    Elastin is another major component of certain soft tissues, such as arterial walls and ligaments.

    Many other molecules, though lower in quantity, function as essential components of the extracellular matrix in soft tissues.



  310. 310
    Dionisio says:

    The time allotted for the current learning phase is about to end. Next moving on to another phase in the project. Will try to stop by and keep an eye on what’s going on here -specially the interesting discussions.

  311. 311
    Dionisio says:

    Embryo engineering alarm:

    A prudent path forward for genomic engineering and germline gene modification


  312. 312
    Dionisio says:

    Remaining Mysteries of the Cytoplasm

    Timothy J. Mitchison

    Department of Systems Biology, Systems Biology, Harvard Medical School, Boston, MA 02115

    Nothing epitomizes the mystery of life more than the spatial organization and dynamics of the cytoplasm. How can a bunch of molecules, no matter how sophisticated, generate spatially complex behavior on a scale that is much larger than the molecules themselves?


  313. 313
    Dionisio says:

    How Far Will We See in the Future?

    Kim Nasmyth

    University of Oxford, Department of Biochemistry, Oxford OX1 3QU, United Kingdom

    Crucially, because previous discoveries have revealed more ignorance than understanding, we are paradoxically more ignorant than we have ever been.


  314. 314
    Dionisio says:

    Cell Biology: The Endless Frontier

    Bruce Alberts

    University of California, San Francisco, San Francisco, CA 94143

    Cell biology has come a very long way since my early days as a scientist. It seems very safe to predict that the more we learn about cells and organisms, the more intriguing will be the new mysteries that remain to be solved. Our view of the cell today is certain to seem incredibly simplistic to anyone rereading these brief essays on the 100th anniversary of ASCB, in 2060. To me, there is nothing more grand about science than this, its “endless frontier.”


  315. 315
    Dionisio says:

    Nat Rev Mol Cell Biol. doi: 10.1038/nrm3187

    PMCID: PMC3282063
    NIHMSID: NIHMS355294

    Asifa Akhtar, Elaine Fuchs, Tim Mitchison, Reuben J. Shaw, Daniel St Johnston, Andreas Strasser, Susan Taylor, Claire Walczak, and Marino Zerial

    A.A. The dynamics and quantitative nature of how various pathways and macromolecular complexes function remain poorly understood.
    We are also beginning to appreciate that spatial and temporal control contribute important regulatory steps in gene regulation.
    The same molecule in different cellular compartments may have very different regulatory functions, which could be missed during biochemical analyses.
    If we can gear our research to go from qualitative to quantitative biology and understand the real dynamics of our favourite molecules in vivo, we will make a great leap in our understanding of various cellular pathways.

    E.F. The most pressing questions in my field are in many ways no different than they were 20–30 years ago, but the answers are closer at hand.
    How do stem cells build tissues during normal homeostasis and wound repair, and how does this go awry in human diseases, including cancers?
    And how can we exploit this information to understand the bases of these different diseases and develop new and improved therapies for the treatment of these disorders? With the recombinant DNA technology revolution of the early 1980s and the human genome revolution at the turn of the century, the interface between basic science and medicine is closing at a pace we never imagined possible as students.
    The tools and technologies available to address fundamental biological questions are advancing at a ferocious rate.
    The challenge ahead will be to ask the right questions and creatively develop strategies that exploit these tools to bridge this gap and revolutionize medicine.

    R.J.S. A big challenge going forward comes out of this explosion of data from different systems: bridging the omics studies (RNAi screens, ChIP–seq, phosphoproteomes and mass spectrometry interactomes) to define what the key rate-limiting proteins in any biological process are.
    The world still needs careful mechanistic dissection of individual proteins and functions, which sometimes gets lost amidst the push for larger and larger datasets.
    Taking the findings in cellular systems and then bridging that to the physiology and pathology of diseases in the intact higher organism also remains a key challenge.

    D. St J. Most recent cell biology has focused on a relatively small number of cell types (most often, unpolarized, transformed tissue culture cells) and has largely overlooked the astonishing array of different cell types with specialized functions that occur in vivo.
    I think that one of the key challenges for the future is to develop better ways of performing in vivo cell biology to examine cellular behaviours in the context of organs and tissues.
    The ability to induce iPS cells to form organs in culture will be an enormous help for this type of work.

    A.S. One challenge is elucidating the precise definition of how cellular differentiation and functional activation are controlled; that is, how the many transcriptional regulators, modifications to the genome (for example, through methylation) and posttranscriptional regulatory processes (for example, through the impact of miRNAs) interact to regulate stepwise changes towards a differentiated state.
    Another is defining the mechanisms that regulate non-apoptotic, but still genetically programmed, cell death pathways and the definition of their role in normal physiology (for example, during embryonic development and tissue homeostasis in adulthood).

    S.T. The biggest challenge for biology is always to ask the right question, and this is even more important now as technologies advance so rapidly.
    In our frenzy to collect more and more data, we need to learn how to ask the right questions and how to extract useful information from that data.
    In parallel with systems biology, we must have a mechanistic understanding of biology.
    Without understanding the underlying biochemical principles, the data mean little.
    Just as we need classical physiology to understand how molecules work in whole animals, we need biochemistry to have a true mechanistic understanding of biological events.

    C.E.W. While the genomic revolution has provided us with a wealth of potentially important molecules, the large-scale functional genomics screens only scratch the surface of understanding the mechanisms by which these proteins act.
    The challenge is to develop creative approaches to answer the most fundamental biological questions.
    For example, although proteomic approaches have identified all of the components of the mitotic spindle and genome-wide screens have identified an array of molecules that affect the mitotic spindle, we still do not understand the fundamental mechanism by which each chromosome moves to the spindle equator and then is partitioned to the daughter cells.

    M.Z. Cell biology must move to tissues and organisms.
    An outstanding problem is bridging between scales.
    Understanding how cellular components form complexes, how these assemble into organelles and how organelles form cells, which build organs and organisms, poses enormous technical and conceptual challenges.

    The integration of biological processes is one of the most difficult problems we face.
    Solving these problems requires trespassing across the traditional borders between fields and developing new experimental and analytical methods.
    At present, we can explain only small parts of biological mechanisms: we see a few pieces of a puzzle, but for the whole picture we must draw in complexity.
    There are no current solutions at the modelling or computational level.
    This problem requires the development of new theories.


  316. 316
    Dionisio says:

    Nat Rev Mol Cell Biol.
    doi: 10.1038/nrm3775

    PMCID: PMC4211427

    NIHMSID: NIHMS604041

    Organization and execution of the epithelial polarity programme

    Enrique Rodriguez-Boulan and Ian G. Macara

    Epithelial cells require apical–basal plasma membrane polarity to perform crucial vectorial transport functions and cytoplasmic polarity to generate different cell progenies for tissue morphogenesis.

    The establishment and maintenance of a polarized epithelial cell with apical, basolateral and ciliary surface domains is guided by an epithelial polarity programme (EPP) that is controlled by a network of protein and lipid regulators.

    The EPP is organized in response to extracellular cues and is executed through the establishment of an apical-basal axis, intercellular junctions, epithelial–specific cytoskeletal rearrangements and a polarized trafficking machinery.

    Recent studies have provided insight on the interactions of the EPP with the polarized trafficking machinery and how they regulate epithelial polarization and depolarization.

    The EPP integrates numerous processes and touches on almost every aspect of cell biology.

    Many of the mechanistic details of this integration remain to be identified.

    One complication is that the execution of the EPP may vary markedly in different locations or physiological contexts, often using the same components but in cell-type specific ways.

    For example, in Drosophila, Crb is only essential for apical specification during morphogenesis when adherens junctions are rapidly expanding or turning over 15.

    Moreover, basolateral polarity proteins such as Lgl are not essential for the maintenance of polarity in late-stage embryogenesis, but are required during gastrulation.

    As an example from mammalian cells, the initial landmark for the apical domain in single cells grown in 3D culture is the site of abscission during cytokinesis, but this is unlikely to be true during development, when single cells are probably not isolated from each other, and neighboring cells will provide spatial information through cadherin-based adhesion.

    An important future goal, therefore, will be to understand how the EPP operates in specific, biologically relevant contexts.

    It will also be central to gain better temporal and spatial resolution of the initial stages of epithelial polarization.

    We do not know which proteins first arrive at the presumptive membrane domains, or at the tight junctions that form between the apical and lateral domains.

    We also need to learn more about the interconnected signaling between sensors, such as the primary cilium, integrins and cadherins, and the EPP.

    Our knowledge of the links between the effectors of the EPP, particularly the vesicle trafficking machinery and the polarity proteins, is also still very superficial.

    A comprehensive understanding of these links will surely inform our knowledge of human disease, which so often involves epithelial cells.


  317. 317
    Dionisio says:

    Small Cells—Big Future

    Mol Biol Cell. doi: 10.1091/mbc.E10-05-0399
    PMCID: PMC2982112

    Bonnie L. Bassler

    Every living organism—including Earth’s simplest life form, the bacterium—is loaded with molecular devices that are breathtaking in their design, complexity, and efficiency.

    Bacteria invented the rules for cellular organization.


    say what?


    invented the rules?

  318. 318
    Dionisio says:

    Unsolved mysteries in NLR biology

    Christopher Lupfer and Thirumala-Devi Kanneganti

    Front. Immunol. doi: 10.3389/fimmu.2013.00285

    NOD-like receptors (NLRs) are a class of cytoplasmic pattern-recognition receptors.

    Although most NLRs play some role in immunity, their functions range from regulating antigen presentation (NLRC5, CIITA) to pathogen/damage sensing (NLRP1, NLRP3, NLRC1/2, NLRC4) to suppression or modulation of inflammation (NLRC3, NLRP6, NLRP12, NLRX1).

    However, NLRP2, NLRP5, and NLRP7 are also involved in non-immune pathways such as embryonic development.

    In this review, we highlight some of the least well-understood aspects of NLRs, including the mechanisms by which they sense pathogens or damage.

    NLRP3 recognizes a diverse range of stimuli and numerous publications have presented potential unifying models for NLRP3 activation, but no single mechanism proposed thus far appears to account for all possible NLRP3 activators.

    Additionally, NLRC3, NLRP6, and NLRP12 inhibit NF-?B activation, but whether direct ligand sensing is a requirement for this function is not known.

    Herein, we review the various mechanisms of sensing and activation proposed for NLRP3 and other inflammasome activators.

    We also discuss the role of NLRC3, NLRP6, NLRP12, and NLRX1 as inhibitors and how they are activated and function in their roles to limit inflammation.

    Finally, we present an overview of the emerging roles that NLRP2, NLRP5, and NLRP7 play during embryonic development and postulate on the potential pathways involved.

    The role of NLRs in immune function is unequivocal. However, there is much molecular, biochemical and structural research which remains to be done to better understand how NLRs are activated and regulated.

    The fact that after a decade of research, new inflammasome activators are still being discovered may indicate that more NLRs fill this function than those previously described.

    Furthermore, recent studies have also validated roles for NLRP5 in embryonic development, although the exact mechanisms underlying these observations have not been elucidated (123–125).

    With more than 10 NLRs unstudied, it will be of interest to determine the function of these remaining NLRs in inflammation and development.


  319. 319
    Dionisio says:

    …the biggest mystery of the cell cycle resolved?

    Journal of Physics: Condensed Matter


    Spindle checkpoint regulated by nonequilibrium collective spindle-chromosome interaction; relationship to single DNA molecule force-extension formula

    The spindle checkpoint, which blocks segregation until all sister chromatid pairs have been stably connected to the two spindle poles, is perhaps the biggest mystery of the cell cycle.

    The main reason seems to be that the spatial correlations imposed by microtubules between stably attached kinetochores and the nonlinear dependence of the system on the increasing number of such kinetochores have been disregarded in earlier spindle checkpoint studies.

    From these missing parts a non-equilibrium collective spindle–chromosome interaction is obtained here for budding yeast (Saccharomyces cerevisiae) cells.

    The interaction, which is based on a non-equilibrium statistical mechanics, can sense and count the number of stably attached kinetochores and sense the threshold for segregation.

    It blocks segregation until all sister chromatids pairs have been bi-oriented and regulates tension such that segregation becomes synchronized, thus explaining how the cell might decide to segregate replicated chromosomes.

    The model also predicts kinetochore oscillations at a frequency which agrees well with observation.

    Finally, a relationship between this spindle–chromosome dynamics and the force-extension formula obtained in a single DNA molecule experiment is obtained.


    Read the whole paper and see the detailed mathematical description of the physical model describing this complex machinery. Very simple… Really cool! 🙂

  320. 320
    Dionisio says:

    Combinatorial code governing cellular responses to complex stimuli

    Nature Communications 6, Article number: 6847 doi:10.1038/ncomms7847

    Cells adapt to their environment through the integration of complex signals. Multiple signals can induce synergistic or antagonistic interactions, currently considered as homogenous behaviours. Here, we use a systematic theoretical approach to enumerate the possible interaction profiles for outputs measured in the conditions 0 (control), signals X, Y, X+Y. Combinatorial analysis reveals 82 possible interaction profiles, which we biologically and mathematically grouped into five positive and five negative interaction modes. To experimentally validate their use in living cells, we apply an original computational workflow to transcriptomics data of innate immune cells integrating physiopathological signal combinations. Up to 9 of the 10 defined modes coexisted in context-dependent proportions. Each interaction mode was preferentially used in specific biological pathways, suggesting a functional role in the adaptation to multiple signals. Our work defines an exhaustive map of interaction modes for cells integrating pairs of physiopathological and pharmacological stimuli.


  321. 321
    Dionisio says:

    Transcriptional and epigenetic networks of helper T and innate lymphoid cells

    DOI: 10.1111/imr.12208

    The discovery of the specification of CD4+ helper T cells to discrete effector ‘lineages’ represented a watershed event in conceptualizing mechanisms of host defense and immunoregulation.

    However, our appreciation for the actual complexity of helper T-cell subsets continues unabated.

    Just as the Sami language of Scandinavia has 1000 different words for reindeer, immunologists recognize the range of fates available for a CD4+ T cell is numerous and may be underestimated.

    Added to the crowded scene for helper T-cell subsets is the continuously growing family of innate lymphoid cells (ILCs), endowed with common effector responses and the previously defined ‘master regulators’ for CD4+ helper T-cell subsets are also shared by ILC subsets.

    Within the context of this extraordinary complexity are concomitant advances in the understanding of transcriptomes and epigenomes.

    So what do terms like ‘lineage commitment’ and helper T-cell ‘specification’ mean in the early 21st century?

    How do we put all of this together in a coherent conceptual framework?

    It would be arrogant to assume that we have a sophisticated enough understanding to seriously answer these questions.

    Instead, we review the current status of the flexibility of helper T-cell responses in relation to their genetic regulatory networks and epigenetic landscapes.

    Recent data have provided major surprises as to what master regulators can or cannot do, how they interact with other transcription factors and impact global genome-wide changes, and how all these factors come together to influence helper cell function.


  322. 322
    Dionisio says:

    Toll-like receptor mediated regulation of cancer: a case of mixed blessings

    doi: 10.3389/fimmu.2014.00224

    Discovery of the role of TLRs in cancer biology have paved the way for development of new therapies targeting TLRs.

    There is a lot of interest to study the relation between inflammation and cancer as it has been termed as the seventh hallmark of cancer.

    TLRs play an important role in inflammation mediated cancers as well as cancer related inflammation.

    Activation of TLRs for therapy may be an exciting proposition, but one has to be careful as over activation of TLRs can also lead to development of tumors (Figure 1).

    Thus, regulatory mechanisms should also be taken into account before using TLRs for cancer therapy.

    Furthermore, molecular and genetic analysis of breast cancer sub-types should be considered before deciding the course of therapy with TLRs.

    There are some reports on the role of genetic polymorphisms in TLRs in the outcome of breast cancer therapy.

    More studies need to be conducted to determine whether the loss or gain of function polymorphisms in TLRs is an indicator of disease outcome or therapy.


  323. 323
    Dionisio says:

    Toll-like receptor activation in immunity vs. tolerance

    doi: 10.3389/fimmu.2015.00146

    After the discovery of Toll-like receptors (TLR) in the late 1990s, initial investigations were focused on understanding their role, stimulating immune responses against infectious agents.

    The mechanisms that underlie the immune regulatory properties of TLRs are not well understood.


    Let’s look forward, with much anticipation, to reading future research reports shedding more light on this important subject.

  324. 324
    Dionisio says:

    Amazing orchestration:
    “Embryonic development has its own tempo—from the thumping rock beat of early cell division to something more like modern minimalism, where you have cells working together while still doing their own thing, making the music more melodious and complex. Finally, as nerves start working and sending impulses, it moves to something more syncopated and rhythmic.”
    Professor Hazel Sive, MIT.

  325. 325
    Dionisio says:

    Outstanding development questions?

    This was said 4 years ago in official lectures at a very prestigious educational institution by a scientific authority in the given subject. This is serious stuff.

    However, maybe by now some (or all) of those raised questions have been answered? Research is advancing fast these days, hence recent discoveries could have resolved the issues presented in these two video lectures?

    Please, note that the below indicated time marks may not be exact, therefore start a little earlier and keep listening until the professor changes the subject and moves on to the next topic. You may just listen to the marked comments. Each takes just a couple of minutes or less. Enjoy it!

    Development 1:

    @23:21 beginning of life?
    @23:31 magically get together?
    @23:51 zygote – magical single cell?
    @24:00 two dying cells…?

    @43:00 how this works is not well understood, it’s complex?


    Development 2:

    @21:11 still not known how the kidney gets built? There’s no organ where we can say “these are all the steps to build it. it’s incredibly complex?

    @24:20 this is an engineering problem?
    @25:01 it’s really amazing?

    @30:15 a student asked how do cells know where to go?
    The lecturer’s answer is interesting. She mentions possible plans, instructions, somehow somewhere they unfold as organs are built, but she concludes it’s really a fascinating question?


  326. 326
    Dionisio says:

    Co-regulation of translation in protein complexes
    Marlena Siwiak and Piotr Zielenkiewicz

    Co-regulation of gene expression has been known for many years, and studied widely both globally and for individual genes.

    Nevertheless, most analyses concerned transcriptional control, which in case of physically interacting proteins and protein complex subunits may be of secondary importance.

    In case of translational co-regulation, however, there is still much to be discovered.

    This research is the first quantitative analysis that provides global-scale evidence for translation co-regulation among associated proteins.

    […]the phenomenon of translational co-regulation applies to the variety of living organisms and concerns many complex constituents.

    […]translational regulation of a protein should always be studied with respect to the expression of its primary interacting partners.

    Apparently the main purpose of translational co-regulation is to prevent waste of resources during synthesis of building blocks of stoichiometric complexes and guarantee their on time production


    Let’s look forward, with much anticipation, to reading future research reports shedding more light on this important subject.

  327. 327
    Dionisio says:

    Totally Tubular: The Mystery behind Function and Origin of the Brain Ventricular System

    doi: 10.1002/bies.200800207

    Laura Anne Lowery and Hazel Siva

    A unique feature of the vertebrate brain is the brain ventricular system, a series of connected cavities which are filled with cerebrospinal fluid (CSF) and surrounded by neuroepithelium.

    While CSF is critical for both adult brain function and embryonic brain development, neither development nor function of the brain ventricular system is fully understood.

    In this review, we discuss the mystery of why vertebrate brains have ventricles, and whence they originate.

    Neither development nor function of the vertebrate brain ventricular system is fully understood in any animal system, and a long list of unanswered questions remains.

    One significant future challenge is to understand the molecular connection between brain patterning and brain morphogenesis, including ventricle shaping.

    The precise role of epithelial junctional complexes and the ECM during brain morphogenesis and ventricle formation remain unclear.

    The connection between cell proliferation and brain morphogenesis is also not understood.

    The extent to which eCSF governs neuroepithelial fate remains an area of key interest.

    What is the role of eCSF flow and pressure?

    What are the roles of the many factors in the eCSF?

    Does the eCSF primarily govern cell division/proliferation in the brain, or is its primary role to direct formation of specific neuronal or glial subtypes?


    We want those questions answered ASAP, don’t we? Perhaps some of them are already answered by NW, since the paper is kind of old (2009?).

    Sorry, no time left for OOL discussions. 🙂

  328. 328
    Dionisio says:

    Embryonic blood-cerebrospinal fluid barrier formation and function

    doi: 10.3389/fnins.2014.00343

    Just as most civilizations develop along riverbanks and seashores, using the fluid medium that is immediately available to them to promote cohesion and transport, and to enhance the chances of survival of the people who live at the edge of the liquid medium, so the brain is also organized, from its embryonic beginnings and throughout adult life, around an extraordinarily dynamic, and complex fluid: the CSF. Continuing this simile, as civilizations build harbors from which to ship goods and control transport that becomes ever more complex as they develop, so the brain has evolved barrier mechanisms, which start to form very early in brain development and change their morphology and physiology in accordance with the changing developmental stages.


    Really? How?

  329. 329
    Dionisio says:

    The Extreme Anterior Domain Is an Essential Craniofacial Organizer Acting through Kinin-Kallikrein Signaling

    DOI: http://dx.doi.org/10.1016/j.celrep.2014.06.026


    the mechanisms that direct the cranial NC into the face primordium, and the identity of localized guidance signals that facilitate this migration are not known.

    …the embryonic pathway in Xenopus functions through a signaling sequence similar to that described for the adult mammalian pathway, and conservation is present in zebrafish.

    …nitric oxide (NO) production is an outcome of the pathway and is necessary for mouth and neural crest (NC) development.

    …the extreme anterior domain (EAD) functions as a craniofacial organizer and facilitates migration of first arch cranial NC into the face via Kinin-Kallikrein signaling.

    These findings add insight into localized signaling essential for craniofacial development.

    suggesting that different downstream receptors or alternate forms of peptide processing may be available to the NC.

    The demonstration that the EAD is necessary for migration of the first arch NC into the facial region addresses the long-standing question of what region might guide the migratory cranial NC into the face.

    …but identify cpn locally expressed in the EAD as required for NC ingress, possibly through processing of Kng-derived peptides.

    …highlighting complex spatiotemporal requirements for Kinin-Kallikrein signaling during NC development.

    suggesting that the Kinin-Kallikrein pathway may indirectly regulate mouth opening through the NC.

    raising the question of whether activity of this pathway during craniofacial development is conserved.

    It is also possible that redundant genes or another pathway such as endothelin signaling work together with Kinin-Kallikrein signaling.

    important future directions, including mechanistic studies addressing a putative NC guidance function for xBdk and other EAD-derived activities, and the relationship between NC migration and mouth formation.


    Let’s look forward, with much anticipation, to reading future research reports shedding more light on this important subject.

  330. 330
    Dionisio says:

    Assessing the translational landscape of myogenic differentiation by ribosome profiling

    doi: 10.1093/nar/gkv281

    The formation of skeletal muscles is associated with drastic changes in protein requirements known to be safeguarded by tight control of gene transcription and mRNA processing.

    The contribution of regulation of mRNA translation during myogenesis has not been studied so far.

    This study demonstrates that differential mRNA translation controls protein expression of specific subsets of genes during myogenesis.

    Ribosome footprints derived from coding and non-coding genes

    …a relative high proportion of reads mapped to long intergenic non-coding RNAs (lincRNAs) (between 5 and 10% in average) and small RNAs (between 10 and 20% in average).

    Subsets of mRNAs primarily regulated at translational level during myoblasts differentiation

    In addition to the nature of the transcribed protein, the efficiency of translation seems to be tightly controlled.

    …translation initiation represent a layer of regulation of protein expression in myogenesis for specific subsets of functionally correlated genes.

    Cellular processes controlled by selective mRNA translation in myogenesis

    …a percentage of footprints derived from non-coding transcripts.

    Whether they lead to active translation is still debated,…

    These changes are highly reproducible between replicates, they are cell specific and tightly controlled during differentiation and therefore they likely represent a regulatory mechanism with relevance for muscle differentiation.

    The mechanisms regulating alternative TISs usage in myogenesis remain to be investigated.

    Previous studies have shown that proteins involved in the translation machinery are autoregulated and their synthesis is mainly controlled at the level of translation.

    Due to the many regulatory potential of uORFs, a full understanding of the translational control of these genes may be relevant for clinical purposes.

    The contribution of mRNA translation in myogenesis

    …we also observed a dampening effect of translational regulation. The causes of this dampening effect remain to be elucidated. Translation can be regulated by many different mechanisms.

    …the transcription of genes from distinct promoters, and the translation initiation from distinct start codons, seem to be two complementary mechanisms to control gene and protein expression in myogenesis.

    Our analysis might therefore underestimate the number of alternative TSSs which are in very close proximity and therefore overestimate the number of switches in TIS usage exclusively dependent on the translational control. It remains to be investigated to which extent this phenomenon may alter our results.

    suggesting a likely stronger regulatory potential.


    Let’s look forward, with much anticipation, to reading future research reports shedding more light on this important subject.

  331. 331
    Dionisio says:

    Translational reprogramming in cellular stress response

    DOI: 10.1002/wrna.1212

    Cell survival in changing environments requires appropriate regulation of gene expression, including translational control.

    Multiple stress signaling pathways converge on several key translation factors, such as eIF4F and eIF2, and rapidly modulate messenger RNA (mRNA) translation at both the initiation and the elongation stages.

    Repression of global protein synthesis is often accompanied with selective translation of mRNAs encoding proteins that are vital for cell survival and stress recovery.

    The past decade has seen significant progress in our understanding of translational reprogramming in part due to the development of technologies that allow the dissection of the interplay between mRNA elements and corresponding binding proteins.

    Recent genome?wide studies using ribosome profiling have revealed unprecedented proteome complexity and flexibility through alternative translation, raising intriguing questions about stress?induced translational reprogramming.

    Many surprises emerged from these studies, including wide?spread alternative translation initiation, ribosome pausing during elongation, and reversible modification of mRNAs.

    Elucidation of the regulatory mechanisms underlying translational reprogramming will ultimately lead to the development of novel therapeutic strategies for human diseases.


    Significant progress! We like that, don’t we?
    The sooner science will fill the outstanding gaps in biological understanding, the greater possibilities to get better medicines and health maintenance treatments for all.
    Also, every new discovery sheds more light on the elaborate cellular and molecular choreographies orchestrated within the biological systems. And doubtless many of us -specially those with information technology background- enjoy that kind of stuff, right?
    Best regards to all.

  332. 332
    Dionisio says:

    Engineering design quality assurance procedures for testing different possible scenarios before the product is implemented or released to final customers have been known for many years. Also, some organizations test products available in the market, in order to check how they function and publish reports for potential consumers. Those tests may try to cover as many situations as possible.

    Now, is that what they call “evolutionary approach” in this recent paper?


    Also, regarding the actual objects being tested, are they showing anything besides elaborate built-in adaptation mechanisms in action?

    Did I get this wrong? Please correct me. Thanks.

  333. 333
    Dionisio says:

    Poly(A)-tail profiling reveals an embryonic switch in translational control

    doi: 10.1038/nature13007

    Poly(A) tails enhance the stability and translation of most eukaryotic mRNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function.

    Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos.

    Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other ‘housekeeping’ proteins tending to have shorter tails.

    As expected, tail lengths were coupled to translational efficiencies in early zebrafish and frog embryos.

    However, this strong coupling diminished at gastrulation and was absent in non-embryonic samples, indicating a rapid developmental switch in the nature of translational control.

    This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA-mediated deadenylation concurrently shifts from translational repression to mRNA destabilization.


  334. 334
    Dionisio says:

    Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation


    Tissue-specific RNA plasticity broadly impacts the development, tissue identity and adaptability of all organisms, but changes in composition, expression levels and its impact on gene regulation in different somatic tissues are largely unknown.

    We have identified thousands of novel genes and isoforms differentially expressed between these three tissues.

    Active promoter regions in all three tissues reveal both known and novel enriched tissue-specific elements, along with putative transcription factors, suggesting novel tissue-specific modes of transcription initiation

    For the first time, PAT-Seq allowed us to directly study tissue specific gene expression changes in an in vivo setting and compare these changes between three somatic tissues from the same organism at single-base resolution within the same experiment.

    We pinpoint precise tissue-specific transcriptome rearrangements and for the first time link tissue-specific alternative polyadenylation to miRNA regulation, suggesting novel and unexplored tissue-specific post-transcriptional regulatory networks in somatic cells.


    This is exciting news.

    Let’s look forward, with much anticipation, to reading future research reports shedding more light on this important subject.

  335. 335
    Dionisio says:

    Alternative mRNA transcription, processing, and translation: insights from RNA sequencing

    DOI: http://dx.doi.org/10.1016/j.tig.2015.01.001

    .RNA sequencing uncovers mechanisms regulating gene expression.

    •Use of alternative TSSs, PASs, and exons is the rule.

    •Alternative translation initiation at 5?-UTRs and downstream codons is widespread.

    •Transcription, RNA processing, and translation are often interdependent processes.

    The human transcriptome comprises >80?000 protein-coding transcripts and the estimated number of proteins synthesized from these transcripts is in the range of
    250?000 to 1 million.

    These transcripts and proteins are encoded by less than
    20?000 genes, suggesting extensive regulation at the transcriptional, post-transcriptional, and translational level.

    Here we review how RNA sequencing (RNA-seq) technologies have increased our understanding of the mechanisms that give rise to alternative transcripts and their alternative translation.

    We highlight four different regulatory processes: alternative transcription initiation, alternative splicing, alternative polyadenylation, and alternative translation initiation.

    We discuss their transcriptome-wide distribution, their impact on protein expression, their biological relevance, and the possible molecular mechanisms 0leading to their alternative regulation.

    We conclude with a discussion of the coordination and the interdependence of these four regulatory layers.



    This is exciting news.

    Let’s look forward, with much anticipation, to reading future research reports shedding more light on this important subject.

  336. 336
    Dionisio says:

    Identification of the optic recess region as a morphogenetic entity in the zebrafish forebrain

    The 3D reconstruction and segmentation of the secondary prosencephalon in zebrafish revealed the unexpected complexity of the ventricular morphology, in particular that of the optic recess.

    The morphogenetic organization of the secondary prosencephalon is thus very difficult to interpret without 3D analysis of the data at cellular resolution.

    Its spatial organization directly derives from the ventricle-to-mantle orientation of the proliferation and differentiation stages of neural progenitors over time.

    A systematic application of these procedures will allow building a 3D atlas of the zebrafish forebrain at different time points during development, providing a powerful and comprehensive tool to analyze in detail morphogenesis, neurogenesis, and regionalization in the zebrafish brain, in a comparative perspective.


  337. 337
    Dionisio says:

    Morphomechanics: transforming tubes into organs


    After decades focusing on the molecular and genetic aspects of organogenesis, researchers are showing renewed interest in the physical mechanisms that create organs.

    This review deals with the mechanical processes involved in constructing the heart and brain, concentrating primarily on cardiac looping, shaping of the primitive brain tube, and folding of the cerebral cortex.

    Recent studies suggest that differential growth drives large-scale shape changes in all three problems, causing the heart and brain tubes to bend and the cerebral cortex to buckle.

    Relatively local changes in form involve other mechanisms such as differential contraction.

    Understanding the mechanics of organogenesis is central to determining the link between genetics and the biophysical creation of form and structure.


    Glad to see more interest in that important aspect of development.

  338. 338
    Dionisio says:

    Morphogenesis on the Multicellular Level: Patterns of Mechanical Stresses and Main Modes of Collective Cell Behavior


    Regular patterns of mechanical stresses are perfectly expressed on the macromorphological level in the embryos of all taxonomic groups studied in this respect.

    Stress patterns are characterized by the topological invariability retained during prolonged time periods and drastically changing in between.

    After explanting small pieces of embryonic tissues, they are restored within several dozens minutes.

    Disturbance of stress patterns in developing embryos irreversibly breaks the long-range order of subsequent development.

    Morphogenetically important stress patterns are established by three geometrically different modes of cell alignment: parallel, perpendicular, and oblique.

    The first of them creates prolonged files of actively elongated cells.

    The second is responsible for segregation of an epithelial layer to the domains of columnar and flattened cells.

    The model of this process, demonstrating its scaling capacities, is described.

    The third mode which follows the previous one is responsible for making the curvatures.

    It is associated with formation of “cell fans,” the universal devices for shapes formation due to slow relaxation of the stored elastic energy.


    Morphomechanical Feedbacks


    An attempt is made to reconstruct the natural successions of the developmental events on the basis of a common mechanically based trend.

    It is formulated in terms of a hyper-restoration (HR) hypothesis claiming that embryonic tissue responds to any external deforming force by generating its own one, directed toward the restoration of the initial stress value, but as a rule overshooting it in the opposite side.

    We give a mathematical formulation of this model, present a number of supporting evidences, and describe several HR-driven feedbacks which may drive forth morphogenesis.

    We use this approach for reconstructing in greater detail the gastrulation of the embryos from different taxonomic groups.

    Also, we discuss the application of this model to cytotomy, ooplasmic segregation, and shape complication of tubular rudiments (taking hydroid polyps as examples).

    In addition, we review the perspectives for applying morphomechanical approach to the problem of cell differentiation.


    There yet? 🙂

  339. 339
    Dionisio says:

    Segment-Specific Adhesion as a Driver of Convergent Extension

    •DOI: 10.1371/journal.pcbi.1004092

    Convergent extension, the simultaneous extension and narrowing of tissues, is a crucial event in the formation of the main body axis during embryonic development.

    It involves processes on multiple scales: the sub-cellular, cellular and tissue level, which interact via explicit or intrinsic feedback mechanisms.

    Computational modelling studies play an important role in unravelling the multiscale feedbacks underlying convergent extension.

    Convergent extension usually operates in tissue which has been patterned or is currently being patterned into distinct domains of gene expression.

    How such tissue patterns are maintained during the large scale tissue movements of convergent extension has thus far not been investigated

    […] in future work we aim to investigate the dynamic interplay between sequential segmentation and convergent extension.

    Considering such bidirectional feedback between patterning and morphogenesis may bring to light important principles of coordinating growth and patterning.


    Work in progress…

  340. 340
    Dionisio says:

    The Rho GTPase Cdc42 regulates hair cell planar polarity and cellular patterning in the developing cochlear

    doi: 10.1242/?bio.20149753

    Hair cells of the organ of Corti (OC) of the cochlea exhibit distinct planar polarity, both at the tissue and cellular level.

    Planar polarity at tissue level is manifested as uniform orientation of the hair cell stereociliary bundles

    […] an intriguing possibility remains that Cdc42 is an effector of nectins in hair cells, similar as shown in other types of epithelial cells […]

    This may indicate functional compensation between the two Rho GTPases, a possibility that would explain why defects were not manifested in all recombined OHCs in the Cdc42 mutant[…]

    Our results suggest that Cdc42 is involved in OHC stereociliogenesis early postnatally, likely through the regulation of actin dynamics […]


  341. 341
    Querius says:

    Dionisio @ 325,

    I watched the complete lecture. First off, the complexity is truly astounding. Naming the processes facilitates categorization, but it also makes them sound ordinary, even inevitable, which is of course not the case.

    Yes, the professor did imply that the 3D structural instructions were sequential rather than located in a comprehensive “master plan” (which of course doesn’t obviate a master plan), and she indicated that she didn’t have *enough time* to explore this further. But she just couldn’t bring herself to say that researchers are utterly clueless on how the cells are made to respond in order to assemble themselves in an organ by a method other than simply forming sheets by preferential adhesion.

    The film showing a cell moving was amazing!

    How can students just sit there? How can they learn without asking questions?


  342. 342
    Dionisio says:

    A Balance of Form and Function: Planar Polarity and Development of the Vestibular Macular

    doi: 10.1016/j.semcdb.2013.03.


    An outstanding question is the identity of this motor protein because its identification may show how subcellular planar polarity is coupled to PCP and tissue polarity.

    Although this does not rule out a function for Fat/Dachsous signaling in HC development, it strongly suggests that the core PCP proteins have a more significant role in HCs.

    […] the significance of bundle rotation has not been established for development of tissue polarity in the maculae.

    Remarkably the abrupt change in stereociliary bundle orientation that occurs at the LPR does not require corresponding changes in the subcellular distribution of core PCP proteins.

    An interesting possibility is that…

    An alternative possibility is that…

    Despite these possibilities, mechanisms regulating tissue polarity and patterning the LPR in conjunction with the core PCP proteins have not been identified.

    Several lines of evidence, including […] support a hypothesis that […]

    However the cellular events enacting this coordination and whether these events are genetically encoded or activity dependent have not been determined.

    It is also important to understand how planar polarity is coordinated with other tissue-specific aspects of organ development.

    For example within the maculae, what prevents afferent neurons from contacting multiple HCs located on opposite sides of the LPR?

    And how is planar polarity influenced by the rapid and dynamic processes of inner ear morphogenesis?

    […] this problem should be resolved in the near future through the study of conditional mutants and the application of Cre/LoxP technologies.

    When this limitation is removed, many of these outstanding questions of planar polarity will be addressed, and studying the vestibular maculae is likely to advance our understanding of planar polarity mechanisms in the auditory system and other developmental processes.

    It seems like there are more new questions after they answered some outstanding ones?

    Apparently it ain’t easy to figure all that out. Is it?

    Let’s stay tuned… more to come.

  343. 343
    Dionisio says:

    Querius @341

    You have made very important observations and raised interesting questions.
    Thank you.

  344. 344
    Dionisio says:

    Subunit determination of the conductance of hair-cell mechanotransducer channels

    doi: 10.1073/pnas.1420906112

    Cochlear hair cells are sensory receptors of the inner ear that detect sound via opening of mechanically sensitive transduction channels at the tips of the eponymous hairs.

    The conductance of the channel increases two-fold along the cochlea, but neither its molecular structure nor mechanism of tonotopic variation is known.

    The molecular identity of this ion channel is still unclear, […]

    Our present hypothesis is that the reverse-polarity current represents the pore-forming subunit of the native channel, but a number of important questions remain with regard to this current.

    What connects these disparate processes and what might be the common signal to induce the channel response?

    […]the location of the underlying channels is not precisely known,[…]

    More experiments are needed to address the significance and localization of these channels.


    Almost there…

  345. 345
    Dionisio says:

    The physiology of mechanoelectrical transduction channels in hearing.

    doi: 10.1152/physrev.00038.2013.

    Much is known about the mechanotransducer (MT) channels mediating transduction in hair cells of the vertrbrate inner ear.

    However, the MT channel protein is still not firmly identified, nor is it known whether the channel is activated by force delivered through accessory proteins or by deformation of the lipid bilayer.


  346. 346
    Dionisio says:

    Adrenocortical zonation, renewal, and remodeling

    doi: 10.3389/fendo.2015.00027

    The mechanisms involved in adrenocortical remodeling are complex and redundant so as to fulfill the offsetting goals of organ homeostasis and stress adaptation.

    The regulation of adrenocortical development and homeostasis has been the subject of intensive investigation over the past decade

    The continual remodeling of the zones of the adrenal cortex requires the precise control of cell growth and differentiation.

    The pathways involved are complex and redundant so as to fulfill the offsetting goals of organ homeostasis and stress adaptation.

    Disruption of these pathways can lead to neoplasia.

    Although much has been learned about the regulation of adrenocortical homeostasis and regeneration, there are still many unanswered questions.

    It has proven difficult to isolate and characterize adrenocortical stem cell populations, and we do not know how these populations vary with age.

    Nor do we understand the relative contributions of the hedgehog, DLK1, FGF, and WNT/?-catenin signaling pathways to adrenocortical differentiation, or how these pathways interface with classic endocrine signaling systems, such as the RAAS and the HPA axis.

    The positional cues that mediate differentiation during centripetal (or centrifugal) migration also remain enigmatic.

    To date, there has been little progress in the development of in vitro models to study adrenocortical differentiation.

    Hopefully, such techniques will emerge in the coming years and help drive the field forward.


    Let’s look forward, with much anticipation, to reading future research reports shedding more light on this important subject.

  347. 347
    Dionisio says:

    DOI: 10.1002/dvdy.24257

    Organogenesis, the process of organ formation and homeostasis, relies on a symphony of interactions between different cells and tissues that collectively operate to maintain bodily function.

    Despite incredibly diverse architecture, size, shape, and tissue composition, the formation of distinct organs is remarkably similar.

    While it has long been appreciated that development is directed by information contained within the genome, and influenced by the maternal environment and epigenome, it is less well understood how variations in the fetal and maternal genome and epigenome interact with environmental factors and how this affects organogenesis.

    […] organogenesis is a tremendously robust process that integrates many diverse cellular and molecular processes.

    The end result of this precise coordination is highly complex functional organ systems that carry out essential functions, act in concert to maintain to homeostasis, and continually adapt to ever challenging external environments.



  348. 348
    Dionisio says:

    Tissue stiffness dictates development, homeostasis, and disease progression.

    Tissue development is orchestrated by the coordinated activities of both chemical and physical regulators.

    While much attention has been given to the role that chemical regulators play in driving development, researchers have recently begun to elucidate the important role that the mechanical properties of the extracellular environment play.

    For instance, the stiffness of the extracellular environment has a role in orienting cell division, maintaining tissue boundaries, directing cell migration, and driving differentiation.


  349. 349
    Querius says:

    What occurs to me is that it would not be unreasonable to use analogy to predict the amount of information and complexity required to control the described organogenesis. One could map out the control systems and the mechanisms employed to activate, monitor, and deactivate these processes. Anticipating this information is already being done of course, but the volume of interdependent information might be able to fine-tune investigation. This is an excellent example of the utility of the ID paradigm in my opinion, and it once again falsifies the incrementalism required for the theory of evolution.

    There’s also the design behind organ. Specifically regarding cochlear operation, in addition to sensitivity to a frequency band and logarithmic amplitude, it’s my understanding that it also acts as a comb filter, which provides additional spatial feedback. Genius!


  350. 350
    Dionisio says:

    Cell shape and the microenvironment regulate nuclear translocation of NF??B […]

    DOI 10.15252/msb.20145644

    We speculate that shape?mediated differences in NF??B shuttling could therefore have profound effects on how healthy, wounded, and pathological tissues respond to cytokines.

    While some models of oscillation have been proposed which take morphology into account, more work is needed to determine how cell shape impacts NF??B cycling.

    Further high?content studies that incorporate live cell GFP?p65 and shape measurements will overcome the acyclic nature of Bayesian networks and elucidate whether a feedback exists from NF??B to cell shape and provide insight into these mechanisms.


  351. 351
    Dionisio says:

    Querius @349

    Interesting comment. Thank you.

  352. 352
    Dionisio says:

    […]a master regulator gene of thymic epithelial development program[…]

    | doi: 10.3389/fimmu.2013.00187

    […]many issues regarding the transcriptional regulation of the TECs specification and homeostasis still remain to be solved.

    The development in vitro of cellular models of TEC lineage differentiation, by using the technology of nuclear reprograming, will be certainly useful to better characterize the discrete stages of the TECs differentiation and the molecular mechanism involved in the process.


  353. 353
    Dionisio says:

    Developing stratified epithelia: lessons from the epidermis and thymus

    doi: 10.1002/wdev.146.

    Stratified squamous epithelial cells are found in a number of organs, including the skin epidermis and the thymus.

    The progenitor cells of the developing epidermis form a multi-layered epithelium and appendages, like the hair follicle, to generate an essential barrier to protect against water loss and invasion of foreign pathogens.

    In contrast, the thymic epithelium forms a three-dimensional mesh of keratinocytes that are essential for positive and negative selection of self-restricted T cells.

    While these distinct stratified epithelial tissues derive from distinct embryonic germ layers, both tissues instruct immunity, and the epithelial differentiation programs and molecular mechanisms that control their development are remarkably similar.


  354. 354
    Dionisio says:

    Promiscuous gene expression in the thymus: a matter of epigenetics, miRNA, and more?

    doi: 10.3389/fimmu.2015.00093

    It is unclear whether this regulation occurs in human or mouse mTECs in vivo, and no conserved miRNA target sites in Aire mRNA have been predicted in silico by the currently available target prediction tools.

    Further investigation of the mTEC-specific miRNA and their targets will be needed to comprehend the miRNA-dependent regulation of pGE.

    […]further studies on miRNA function in the thymus should reveal whether a similar network determines turnover, maintenance, and function of mTECs.

    Though it is unclear by which precise means the antigens are shared, exosome transfer is a possible route.

    Whether transfer of miRNA from mTECs to dendritic cells indeed takes place via exosomes and the functional significance of this exchange will be clarified in future studies.

    Promiscuous expression of peripheral antigens in the thymus keeps autoimmunity at bay; grasping its exact molecular mechanism will lead to a better understanding of how central tolerance is established and maintained.

    The future challenge lies in finding out how exactly mTECs utilize ubiquitous epigenetic and post-transcriptional mechanisms to achieve and maintain their extraordinarily broad expression profiles.

    Will pGE eventually turn out to employ a unique scenario of gene regulatory modes for the sake of preserving tolerance?


  355. 355
    Dionisio says:

    Homeodomain-interacting protein kinase 2, a novel autoimmune regulator interaction partner, modulates promiscuous gene expression in medullary thymic epithelial cells.

    doi: 10.4049/jimmunol.1402694

    Promiscuous expression of a plethora of tissue-restricted Ags (TRAs) by medullary thymic epithelial cells (mTECs) plays an essential role in T cell tolerance.

    Although the cellular mechanisms by which promiscuous gene expression (pGE) imposes T cell tolerance have been well characterized, the underlying molecular mechanisms remain poorly understood.

    How AIRE and its partners mediate these various effects at the molecular level is still largely unclear.

    Unexpectedly, most differentially expressed genes were confined to […]


    Let’s look forward, with much anticipation, to reading future research reports shedding more light on the elaborate cellular and molecular choreographies orchestrated within the biological systems.

  356. 356
    Dionisio says:

    The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs

    doi: 10.1093/nar/gkv138

    […] the exact mechanism of microRNA regulation by TRIM32 during neuronal differentiation has yet to be elucidated.

    The dynamic expression pattern of miRNAs necessitates their tight regulation during the course of differentiation. However, little is known about the upstream regulators of miRNAs.

    […] the exact mechanism by which TRIM32 regulates microRNAs to promote neuronal differentiation remains elusive.

    In summary, we present here a novel protein–protein interaction network centered on the RNA-regulating proteins TRIM32 and DDX6, which is involved in the process of NSC differentiation.

    […] the exact mechanism of microRNA-regulation by TRIM32 during neuronal differentiation has yet to be elucidated.

    […] the two RNA-regulating proteins TRIM32 and DDX6 cooperate in the regulation of microRNAs to promote neuronal differentiation.

    However, all conclusion drawn from newly identified proteins that were not verified in additional assays obviously have a lower degree of confidence and remain to be confirmed.

    In future studies, it would be interesting to map the interaction surfaces of DDX6 and TRIM32 and to analyze the influence of abrogating their interaction on miRNA activity and neuronal differentiation.


  357. 357
    Dionisio says:

    Building a plant: cell fate specification in the early Arabidopsis embryo

    doi: 10.1242/dev.111500

    Embryogenesis is the beginning of plant development, yet the cell fate decisions and patterning steps that occur during this time are reiterated during development to build the post-embryonic architecture.

    In Arabidopsis, embryogenesis follows a simple and predictable pattern, making it an ideal model with which to understand how cellular and tissue developmental processes are controlled.

    Here, we review the early stages of Arabidopsis embryogenesis, focusing on the globular stage, during which time stem cells are first specified and all major tissues obtain their identities.

    We discuss four different aspects of development: the formation of outer versus inner layers; the specification of vascular and ground tissues; the determination of shoot and root domains; and the establishment of the first stem cells.


    Fascinating choreographies orchestrated within the biological systems.

  358. 358
    Dionisio says:

    Roles for noncoding RNAs in cell-fate determination and regeneration


    Cellular fate is determined* by transcriptional networks and epigenetic states.

    In addition to protein factors, noncoding RNAs (ncRNAs), particularly microRNAs and long ncRNAs, are able to remodel* transcriptional circuits and reshape* epigenetic landscapes.

    Here we draw upon recent findings to discuss the emerging roles of these ncRNAs in cellular reprogramming, transdifferentiation and organ regeneration.


    (*) how?

  359. 359
    Dionisio says:

    Notch is a direct negative regulator of the DNA-damage response


    The DNA-damage response (DDR) ensures* genome stability and proper inheritance of genetic information, both of which are essential to survival.

    It is presently unclear to what extent other signaling pathways modulate DDR function.


    (*) how?

  360. 360
    Dionisio says:

    #359 DDR?


    One funny thing about this contextual acronym: before 1990 there was a country in Europe that was identified by that same acronym (in their own language).
    Back then DDR = RDA = NRD = GDR.

  361. 361
    Dionisio says:

    Transcriptional regulation through noncoding RNAs and epigenetic modifications


    The recognition that substantial portions of the “noncoding (nc)” regions of metazoan genomes are transcribed has generated intense interest in the potential biological roles of ncRNAs.

    Although the extents to which these mechanisms are used remains to be established, the identification of highly conserved ncRNAs and the presence of RNA binding domains in a large number of transcriptional co-regulators raise the possibility that ncRNA/coregulator interactions play broad roles in the regulation of gene expression.


  362. 362
    Dionisio says:

    Promoter Targeting RNAs: Unexpected Contributors to the Control of HIV-1 Transcription


    It is well known that noncoding RNAs (ncRNAs) are implicated in a wide variety of cellular processes through posttranscriptional regulation of protein expression.

    In addition, there is increasing evidence pointing to their role in transcriptional gene regulation.

    High-throughput sequencing technology which allows analysis of the global transcriptome has revealed that over 90% of genomic DNA is utilized for transcription.

    Out of the total transcriptome, only a small portion (~2%) is translated into proteins.

    Therefore, ncRNAs represent a large portion of the transcriptome in mammals, and there is growing evidence that these transcripts function to regulate gene expression, especially in developmental pathways and in response to environmental stressors, such as viral infection.

    However, the expression levels of these ncRNAs are extremely low compared to mRNAs, perhaps consistent with their involvement in regulatory processes.

    NcRNAs can be categorized as infrastructural and regulatory.

    Ribosomal and transfer RNAs belong to infrastructural ncRNAs, while regulatory ncRNAs are broadly divided into two classes: small ncRNAs (200 nucleotides).

    The small ncRNAs are further classified into several subcategories: microRNA (miRNAs), 19–24 nucleotides in length, short interfering RNAs (siRNAs, ~22 nucleotides), and antisense RNAs (asRNAs, <200 nucleotides).

    The long noncoding RNA (lncRNA) category includes intergenic ncRNA, pseudogene transcripts, and long antisense RNAs (long asRNA, >200 nucleotides), which are also known as long antisense noncoding RNAs (antisense lncRNAs)


    Nicely compacted ncRNA review. Kudos to the authors!

    BTW, Unexpected Contributors? Why unexpected? What did they expect? Nothing? Something else?

    Do expressions like “being open-minded” and “thinking out of the box” come to mind? 🙂

  363. 363
    Dionisio says:

    […] new factors influencing centromeric heterochromatin integrity […]


    Thus far, over 50 proteins have been found to contribute to heterochromatin assembly at fission yeast centromeres.

    However, previous studies have not been exhaustive, and it is therefore likely that further factors remain to be identified.

    The molecular mechanisms underpinning the targeting and regulation of RNAi-directed heterochromatin formation are still not well understood,[…]

    Recent evidence suggests that alternative, RNAi-independent pathways can also promote heterochromatin assembly at centromeres, although the mechanisms and significance of these are as yet unclear.

    Although the precise function of Epe1 is unclear, it appears to antagonise heterochromatin formation, in particular suppressing the invasion of heterochromatin into euchromatic domains.

    However, a systematic genome-wide analysis has not yet been reported. Here we describe just such a genome-wide genetic screen […]

    Together these observations suggest that the heterochromatin defects observed in csn1? and csn2? mutant cells can be partially explained by defects in the regulation of Epe1, likely via the Cul4-Ddb1Cdt2 complex.

    Thus Csn1 and Csn2 appear to contribute to heterochromatin integrity by facilitating the Cul4-Ddb1Cdt2-dependent regulation of Epe1.

    They may also potentially regulate one or more other, as yet unidentified, heterochromatin proteins that are substrates for Cul4-dependent ubiquitin ligase complexes.

    How Epe1 antagonises heterochromatin is unclear, since although it has sequence similarity with histone demethylases, no demethylase activity has been detected in vitro.


  364. 364
    Dionisio says:

    A new transcription factor for mitosis: in Schizosaccharomyces pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression

    doi: 10.1093/nar/gkv274

    Mitotic genes are one of the most strongly oscillating groups of genes in the eukaryotic cell cycle.

    Understanding the regulation of mitotic gene expression is a key issue in cell cycle control but is poorly understood in most organisms.

    Critical amongst the cell cycle regulated genes are those needed for mitosis, arguably the most complex cell cycle event.

    Forkhead transcription factors have likewise been implicated in mitotic gene expression in other organisms, from the yeast Schizosaccharomyces pombe to mammals, but other components of the system are different, and the basis of regulation is not understood.

    The mechanisms of mitotic gene control are partly understood in S. cerevisiae, but not elsewhere.

    […] several acute issues remain:

    1. are there still additional proteins involved?

    2. why do the genes targeted by Sep1 apparently need two activators, Sep1 and Sak1?

    3. does Fkh2, though on its own a repressor, play some role in the formation or assembly of the ultimate activator?

    […] we cannot be certain that the levels of mitotic expression achieved in the fkh2 deletion are as high or as sharp as in the WT.

    4. […] how is the transition from repression to activation achieved and how is this regulated by CDK activity?

    Even though Sak1 can bind in the absence of fkh2, we cannot be certain whether the strength of binding is equivalent to WT.

  365. 365
    Dionisio says:

    Telomere-associated proteins add deoxynucleotides to terminal proteins during replication of the telomeres of linear chromosomes and plasmids in Streptomyces

    doi: 10.1093/nar/gkv302

    The discovery we made in this study was surprising, because it was totally unexpected.

    It is amazing that such unorthodox systems have evolved independently and convergently in different kingdoms.


    Hmm… 🙂

  366. 366
    Dionisio says:

    The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA recognition motifs

    doi: 10.1093/nar/gku277

    The crystal structure of the SHARP–RRM fragment, together with the associated RNA-binding studies, extend the repertoire of nucleic acid binding properties of RRM domains suggesting a new hypothesis for a better understanding of SPEN protein functions.

    With the increasing amount of structural information on multidomain proteins, it has become clear that proteins with multiple RRMs generally adopt unique architectures

    We identified an unexpected and stable interaction between RRM3 and RRM4.

    Our structural and biochemical studies unravelled a new architecture for a protein containing multi-RRM,…

    Although the exact function of the SHARP protein is still the subject of intense research, we would like to speculate that the key to understanding its various reported interacting partners lies in the highly atypical nucleic acid binding properties presently observed


    Work in progress…

  367. 367
    Dionisio says:

    The Yeast Histone Chaperone Hif1p Functions with RNA in Nucleosome Assembly

    •DOI: 10.1371/journal.pone.0100299

    specific RNA species may function in concert with histone chaperones to assemble chromatin

    Our understanding of chromatin assembly has grown rapidly in the past several years.

    While many proteins have been found to participate in chromatin assembly, it is likely that additional factors have yet to be identified.

    there are clearly multiple pathways of chromatin assembly that can, at least partially, compensate in the absence of other pathways.

    Surprisingly, our data suggest that histone chaperones can function in conjunction with RNA to accomplish chromatin assembly.

    the cytosolic extract contains a factor (or factors) that function in conjunction with rHif1p in the deposition of histones.

    the cytosolic extract might contain a novel chromatin assembly factor

    Based on our results, we would like to argue that the prevailing view should be challenged…

    our understanding of the breadth of functions that are performed in the cell by RNA has exploded in the decades since RNA was first shown to mediate chromatin assembly in vitro.


    Interesting statement:

    Based on our results, we would like to argue that the prevailing view should be challenged…

  368. 368
    Dionisio says:

    Maintenance of epigenetic information: a noncoding RNA perspective

    doi: 10.1007/s10577-013-9385-5.

    Along the lines of established players like chromatin modifiers and transcription factors, noncoding RNA (ncRNA) are now widely accepted as one of the key regulatory molecules in epigenetic regulation of transcription.

    With increasing evidence of ncRNAs in the establishment of gene silencing through their ability to interact with major chromatin modifiers, in the current review, we discuss their prospective role in the area of inheritance and maintenance of these established silenced states which can be reversible or irreversible in nature.

    In addition, we attempt to understand and speculate how these RNA dependent or independent maintenance mechanisms differ between each other in a developmental stage, tissue, and gene-specific manner in different biological contexts by utilizing known/unknown regulatory factors.


  369. 369
    Dionisio says:

    Epigenome engineering in cancer: fairytale or a realistic path to the clinic?

    Front. Oncol., 06 February 2015 | http://dx.doi.org/10.3389/fonc.2015.00022


    Epigenetic mechanisms including histone modifications, DNA methylation, and non-coding RNAs (ncRNAs) are essential for the mitotic maintenance of gene expression.

    Non-coding RNAs (ncRNAs) have emerged as important epigenetic regulators in crucial biological processes such as differentiation and development

  370. 370
    Dionisio says:

    Conditional targeting of MAD1 to kinetochores is sufficient to reactivate the spindle assembly checkpoint in metaphase

    Biology of the Nucleus
    © The Author(s) 2014

    Key unresolved issues are the nature and spatiotemporal regulation of these pathways and their relation to kinetochore-microtubule interactions.

    How some aspects of MPS1 function are maintained so as to assure SAC reactivation if required but some are repressed so as to allow MAD1 removal is an interesting challenge for further research.


    Getting closer… almost there… 🙂

  371. 371
    Dionisio says:

    DNA Damage Response and Spindle Assembly Checkpoint Function throughout the Cell Cycle to Ensure Genomic Integrity

    •DOI: 10.1371/journal.pgen.1005150

    We propose that the DDR and SAC function together in response to metaphase defects, most likely through DDR phosphorylation of SAC components, as has been previously reported in high throughput screens and other studies [18,19,55–57]; however, the specific role of these phosphorylation events await future studies.

    A DNA-damage-associated histone variant, similar to-H2AX in yeast and mammals, has yet to be identified in C. elegans […]


  372. 372
    Dionisio says:

    DNA Methylation, Its Mediators and Genome Integrity

    Meng H, Cao Y, Qin J, Song X, Zhang Q, Shi Y, Cao L. DNA Methylation, Its Mediators and Genome Integrity. Int J Biol Sci 2015; 11(5):604-617.


    […] understanding functional genetic mutations and aberrant expression of these DNA methylation mediators is critical to deciphering the crosstalk between concurrent genetic and epigenetic alterations in specific cancer types and to the development of new therapeutic strategies.

    Almost all MeCPs have been demonstrated to associate with transcriptional repressors, implying an additional layer of regulation between DNA methylation and transcription.

    […] further investigations are required to test the possibility that conversion of 5mC to 5hmC inhibits potentially the binding to MeCPs.

    Because numerous proteins containing zinc-fingers or SRA domains are encoded in mammalian genomes, novel classes of 5hmC-binding proteins with distinct binding specificities may be identified in future studies.

    […]precise global and gene-specific mechanisms of DNA demethylation have not been demonstrated in mammals[…]

    […] further investigations of putative 5mC glycosylase co-factors and/or post-translational modifications are required to define these mechanisms.

    […] data indicated a prospective functional link between interactions of DNA methylation mediators and BRCA1-associated genome instability via the p53 DDR pathway, alluding to possible epigenetic roles in transformation and aggression of BRCA1-deficient cancers.

    Further experiments are required to examine the roles of these functional protein complexes in the propagation and preservation of epigenetic signatures and in cellular surveillance systems that respond to intrinsic and extrinsic DDR signals.

    […] the precise mechanisms by which DNA methylation affects chromatin structure remain elusive, […]

    Some epigenetic factors including demethylase complexes have been implicated at these open chromatic sites, but their functional roles in coordinating DNA replication and transcription for genome stability have not been resolved.

    A better understanding of the significance of DNA methylation machinery and chromatin structure in maintaining genome integrity will facilitate future investigations to target DNA methylation and its mediators for novel drugs and chemotherapeutic combinations.

    Functional characterisation of the associated proteins continues to be an area of high interest,…

    A few questions remain.

  373. 373
    Dionisio says:

    Misexpression of BRE gene in the developing chick neural tube affects neurulation and somitogenesis

    doi: 10.1091/mbc.E14-06-1144

    The brain and reproductive expression (BRE) gene is expressed in numerous adult tissues and especially in the nervous and reproductive systems.

    However, little is known about BRE expression in the developing embryo or about its role in embryonic development.

    Cell proliferation is an essential process found in every aspect of embryo development, especially during the early developmental stages.


  374. 374
    Dionisio says:

    Spatiotemporal regulation of the anaphase-promoting complex in meiosis


    The appropriate timing of events that lead to chromosome segregation during mitosis and cytokinesis is essential to prevent aneuploidy,…


  375. 375
    Dionisio says:

    The spindle and kinetochore–associated (Ska) complex enhances binding of the anaphase-promoting complex/cyclosome (APC/C) to chromosomes and promotes mitotic exit

    doi: 10.1091/mbc.E13-07-0421

    […] it is simplistic to contend that the APC/C is simply “activated” at the metaphase–anaphase transition,[…]

    Thus regulation of APC/C activity in mitosis is complex.

    We do not know the detailed mechanism by which kinetochore accumulation of Ska promotes APC/C concentration on chromosomes.

    Its role may be direct or indirect and may involve other components of the kinetochore interacting with spindle microtubules.


    Almost there… getting closer. 🙂

  376. 376
    Dionisio says:

    Spatiotemporal organization of Aurora-B by APC/CCdh1 after mitosis coordinates cell spreading through FHOD1

    doi: 10.1242/?jcs.123232

    We have observed that the duration and size of this pool are sensitive to the surface on which AurB–Venus cells are cultured (N.W. and C.L., unpublished observations) leading us to speculate that AurB could modulate responses to external cues.

    We are currently working to establish an in vivo degradation assay for AurB that will allow us to test whether the rate or timing of AurB proteolysis by APC/CCdh1 is influenced by parameters affecting cell adhesion after division.

    Coordination of MT and F-actin networks may thus emerge as a central biological property of FHOD1.

    Understanding further how these components interact with each other both physically and functionally will be critical to understanding how daughter cell identity is established at the beginning of interphase.


    Work in progress… [that was a little over two years ago, maybe concluded by now?]

  377. 377
    Dionisio says:

    Cdk1 Inactivation Terminates Mitotic Checkpoint Surveillance and Stabilizes Kinetochore Attachments in Anaphase

    DOI: http://dx.doi.org/10.1016/j.cub.2014.01.034

    How do eukaryotic cells avoid the potentially catastrophic action of these pathways during sister chromatid segregation at anaphase?

    Eukaryotic cells may have solved this “anaphase problem” by entirely disabling these surveillance mechanisms at anaphase onset.

    Mitotic checkpoint proteins in early mitosis mark unattached kinetochores or kinetochores that lack tension.

    When stable bipolar attachments are formed at metaphase, mitotic checkpoint proteins dissociate from kinetochores and subsequently become undetectable at this location in anaphase.

    In the future, it will be important to identify these additional substrates whose phosphoregulation confers direct or indirect Cdk1 control over mitotic checkpoint surveillance and the stability of kinetochore-microtubule attachments.


    Those are really intelligent cells, aren’t they? 🙂

  378. 378
    Dionisio says:

    Dependency of the Spindle Assembly Checkpoint on Cdk1 Renders the Anaphase Transition Irreversible

    DOI: http://dx.doi.org/10.1016/j.cub.2014.01.033

    Establishing how Cdk1 promotes the SAC will be a challenge for future studies.

    Possible mechanisms include activation of Mps1, promoting the interaction between Cdc20 and Mad2, or aiding localization of the chromosomal passenger complex at kinetochores


    Work in progress…

  379. 379
    Dionisio says:

    Slow Checkpoint Activation Kinetics as a Safety Device in Anaphase



    we observe that checkpoint activation can still occur for a considerable time after the anaphase-promoting complex/cyclosome (APC/C) becomes active, raising the question whether the checkpoint is indeed completely inactivated by the time of anaphase under physiologic conditions.

    […] whether kinetochore recruitment indeed creates a signal sufficient to inhibit the anaphase-promoting complex/cyclosome (APC/C) has remained unclear […]

    when with respect to anaphase these mechanisms inactivate the checkpoint is largely unclear

    attachment remains stable despite the presence of Aurora B on centromeres, strengthening previous hints that an additional mechanism supports chromosome attachment stability in anaphase

    This needs to be corroborated by visualizing checkpoint proteins, which technical difficulties have so far rendered impossible for us.

    We asked whether such slow checkpoint activation is at all consistent with the timing of mitosis.

    Apparently, this timing is set by checkpoint-independent mechanisms controlling APC/C activity, because deletions of checkpoint genes do not accelerate mitosis

    We can envision two possibilities why slow checkpoint activation nevertheless exists and is evolutionary conserved: either there is a biochemical constraint, which makes faster inhibition of the APC/C impossible, or the slowness has been evolutionary conserved because it provides a safety mechanism in anaphase


    A few questions remain…

  380. 380
    Dionisio says:

    Hey, encouraging news!!!

    We’re almost there!!! 🙂

    Check this out:

    Cell Division: SACing the Anaphase Problem



    Three new studies provide clues to how cells cope with this problem.

    The various elegant studies on the anaphase problem have started to scratch the surface of the fundamental changes that occur during the transition from metaphase to anaphase.

    Deeper understanding will require answers to the following questions:

    how do Cdk1-dependent phosphorylation events functionally contribute to SAC activity, error-correction and stability of kinetochore–microtubule interactions?

    What level of reduction in Cdk1 activity is required to repress any of these processes?

    When, in relation to anaphase onset and completion of securin and cyclin degradation, is that level reached?

    What is the molecular basis of the slow SAC response and

    how do differences in the speed of the response between early embryonic divisions and somatic cell mitosis come about?

    Getting to the heart of this may require live biosensors to probe the kinetics of the various processes.

    Finally, how are genome integrity, cell-cycle progression and cell viability affected when the APC/C has been unable to fully degrade its anaphase substrates?

    If the current pace of discovery continues, the moment when the beautiful process of anaphase will have revealed its secrets may not be far away.


  381. 381
    Dionisio says:

    Spatial-temporal model for silencing of the mitotic spindle assembly checkpoint

    Nature Communications 5, Article number: 4795

    Jing Chen & Jian Liu

    Previous models attribute the high sensitivity of SAC signaling to a biochemical bistable switch that arises from mutual inhibition between cyclin B, SAC proteins, and APC/C.

    However, recent findings indicate that reversible and irreversible SAC silencing processes coexist.

    This intriguing observation indicates that additional factors, not yet incorporated into existing models, are important for irreversible SAC silencing.

    experiments demonstrated extremely high precision of anaphase onset, which occurs only after the last kinetochore-spindle attachment becomes stable

    Future experimental findings can help improve the model with more realistic details, […]

    A more realistic model requires future experiments […]

    Future efforts will explore […]

    How did the cell determine the spindle pole threshold signal?

    We do not have an answer, but we will use future experimental findings to develop more hypotheses.

    This model thus provided a unique solution to the robustness problem of SAC silencing in mitosis.

    It underscored the functional role of spatiotemporal regulation of SAC activity, and established a conceptual framework for understanding the mechanism that controls fidelity of mitosis.



    Serious work. Interesting study material.

  382. 382
    Dionisio says:

    Mechanisms of thymus organogenesis and morphogenesis

    doi: 10.1242/dev.059998

    Understanding the developmental processes that build correct thymus structure is important because defects in thymus structure and function can result in serious health consequences, including immunodeficiency or autoimmunity.

    The details of the patterning and morphogenetic events are not fully understood and, therefore, not surprisingly, the molecular mechanisms regulating these tightly coordinated processes remain, for the most part, poorly defined.

    The existence and identity of this TEC stem cell, and whether it is present in both fetal and postnatal thymus, remains a topic of much debate and investigation in the field.

    […] definitive functional data identifying the molecular mechanisms responsible for specification of thymus fate remain elusive.

    […] there appears to be a `missing link’ that establishes thymus fate […]

    the links between the pathways and the transcription factors responsible for establishing initial thymus fate have still not been defined.

    We are now beginning to have a detailed picture of the events that occur during normal early thymus organogenesis and morphogenesis,[…]

    Perhaps the most glaring gap in our knowledge of thymus organogenesis is that we have not identified the molecular mechanisms responsible for specifying thymus, and parathyroid, fate.

    what signaling pathways and transcription factors do establish these organ fates?

    how early are organ fates specified?

    what is the cellular origin of the cervical thymus?

    Do the same mechanisms control thoracic and cervical thymus development and, if so, how are they induced and deployed at different times during development?

    how early and by what mechanisms are the cTEC and mTEC lineages established?

    What cellular processes (e.g. adhesion, migration) and specific pathways are required?


  383. 383
    Dionisio says:

    Dynamics of thymus organogenesis and colonization in early human development

    doi: 10.1242/dev.087320

    The thymus is the central site of T-cell development and thus is of fundamental importance to the immune system, but little information exists regarding molecular regulation of thymus development in humans.

    The data presented above address the current profound gap in understanding of human thymus development.

    […] it is also possible that other, as yet unknown mechanisms, limiting the time of onset of TEC differentiation are initiated or repressed with different kinetics to FOXN1 in the human.


  384. 384
    Dionisio says:

    Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1)

    •DOI: 10.1371/journal.pone.0123380


    Genetic studies have placed the Fgfr1 gene at the top of major ontogenic pathways that enable gastrulation, tissue development and organogenesis.

    This investigation reveals the role of nuclear FGFR1 as a global genomic programmer of cell, neural and muscle development.

    Development of a multicellular organism from a single cell is regulated by myriads of TFs and requires the coordinated regulation of multi-gene programs.

    nFGFR1 has been proposed to act as a gate-opening factor in the feed-forward-and-gate module for control of CBP.

    Feed-forward loops are common in biological networks, serving as pulse generators, response-delaying circuits, signal-to-noise enhancers and signal integrators.

    nFGFR1-controlled feed-forward-and-gate loops are positioned at several strategic nodes that may increase the efficiency and reproducibility of ontogenic pathways.

  385. 385
    Dionisio says:

    Nuclear FGF Receptor-1 and CREB Binding Protein:
    An Integrative Signaling Module

    DOI: 10.1002/jcp.24879

    Whether nuclear FGFR1 targets these genes directly or only a subset of genes that initiate a cascade of downstream gene programs is under investigation.



    The jury is still out… stay tuned… 🙂

  386. 386
    Dionisio says:

    The Role of Epigenetic Mechanisms in Notch Signaling During Development

    DOI: 10.1002/jcp.24851

    The Notch pathway is a highly conserved cell–cell communication pathway in metazoan involved in numerous processes during embryogenesis, development, and adult organisms.

    Ligand-receptor interaction of Notch components on adjacent cells facilitates controlled sequential proteolytic cleavage resulting in the nuclear translocation of the intracellular domain of Notch (NICD).

    There it binds to the Notch effector protein RBP-J, displaces a corepressor complex and enables the induction of target genes by recruitment of coactivators in a cell-context dependent manner.

    Both, the gene-specific repression and the context dependent activation require an intense communication with the underlying chromatin of the regulatory regions.

    Since the epigenetic landscape determines the function of the genome, processes like cell fate decision, differentiation, and self-renewal depend on chromatin structure and its remodeling during development.

    In this review, structural features enabling the Notch pathway to read these epigenetic marks by proteins interacting with RBP-J/Notch will be discussed.

    Furthermore, mechanisms of the Notch pathway to write and erase chromatin marks like histone acetylation and methylation are depicted as well as ATP-dependent chromatin remodeling during the activation of target genes.

    An additional fine-tuning of transcriptional regulation upon Notch activation seems to be controlled by the commitment of miRNAs.

    Since cells within an organism have to react to environmental changes, and developmental and differentiation cues in a proper manner, different signaling pathways have to crosstalk to each other.

    The chromatin status may represent one major platform to integrate these different pathways including the canonical Notch signaling.

    J. Cell. Physiol. 230: 969–981, 2015. © 2014 Wiley Periodicals, Inc., A Wiley Company


  387. 387
    Dionisio says:

    Membrane and Integrative Nuclear Fibroblastic Growth Factor Receptor (FGFR) Regulation of FGF-23

    doi: 10.1074/jbc.M114.609230

    Fibroblastic growth factor receptor 1 (FGFR1) signaling pathways are implicated in the regulation of FGF-23 gene transcription, but the molecular pathways remain poorly defined.


  388. 388
    Dionisio says:

    The Mysterious Ways of ErbB2/HER2 Trafficking


    Among the receptors, ErbB2 is special in several ways.

    The reason(s) why ErbB2 is resistant to down-regulation are the subject of debate.

    The reason why ErbB2 is resistant to down-regulation remains unclear, and several discrepancies are reported.

    There can be many reasons for these discrepancies.

    It is suggested that multiple mechanisms collectively regulate endocytosis of the EGFR.

    This may also be the case for other receptors like ErbB2.

    A fascinating aspect is the suggestion that ErbB2 directly regulates the formation of coated pits.

    A conceptual question that remains is what role Hsp90 plays in inhibiting down-regulation of ErbB2.


  389. 389
    Dionisio says:

    EGFR Modulates DNA Synthesis and Repair through Tyr Phosphorylation of Histone H4


    Posttranslational modifications of histones play fundamental roles in many biological functions.

    Specifically, histone H4-K20 methylation is critical for DNA synthesis and repair.

    However, little is known about how these functions are regulated by the upstream stimuli.

    These findings uncover a mechanism by which EGFR transduces signal to chromatin to regulate DNA synthesis and repair.


  390. 390
    Dionisio says:

    Non-histone protein methylation as a regulator of cellular signaling and function

    Nature Reviews Molecular Cell Biology 16, 5–17 (2015) doi:10.1038/nrm3915


    Methylation of Lys and Arg residues on non-histone proteins has emerged as a prevalent post-translational modification and as an important regulator of cellular signal transduction mediated by the MAPK, WNT, BMP, Hippo and JAK–STAT signaling pathways.

    Crosstalk between methylation and other types of post-translational modifications, and between histone and non-histone protein methylation frequently occurs and affects cellular functions such as chromatin remodeling, gene transcription, protein synthesis, signal transduction and DNA repair.

    With recent advances in proteomic techniques, in particular mass spectrometry, the stage is now set to decode the methylproteome and define its functions in health and disease.

    Look forward, with much anticipation, to reading future research papers on this and related subjects, shedding more light on the elaborate cellular and molecular choreographies orchestrated within the biological systems.


  391. 391
    Dionisio says:

    DNA double strand break repair pathway choice: A chromatin based decision?

    Nucleus Volume 6, Issue 2, 2015, Pages 107-113

    DOI: 10.1080/19491034.2015.1010946


    DNA double-strand breaks (DSBs) are highly toxic lesions that can be rapidly repaired by 2 main pathways, namely Homologous Recombination (HR) and Non Homologous End Joining (NHEJ).

    The choice between these pathways is a critical, yet not completely understood, aspect of DSB repair.

    We recently found that distinct DSBs induced across the genome are not repaired by the same pathway.

    Indeed, DSBs induced in active genes, naturally enriched in the trimethyl form of histone H3 lysine 36 (H3K36me3), are channeled to repair by HR, in a manner depending on SETD2, the major H3K36 trimethyltransferase.

    Here, we propose that these findings may be generalized to other types of histone modifications and repair machineries thus defining a “DSB repair choice histone code”.

    This “decision making” function of preexisting chromatin structure in DSB repair could connect the repair pathway used to the type and function of the damaged region, not only contributing to genome stability but also to its diversity.

    © T Clouaire and G Legube.

  392. 392
    Dionisio says:

    Non-histone protein methylation as a regulator of cellular signaling and function

    Nature Reviews Molecular Cell Biology 16, 5–17 (2015)

    Methylation of Lys and Arg residues on non-histone proteins has emerged as a prevalent post-translational modification and as an important regulator of cellular signal transduction mediated by the MAPK, WNT, BMP, Hippo and JAK–STAT signaling pathways.

    Crosstalk between methylation and other types of post-translational modifications, and between histone and non-histone protein methylation frequently occurs and affects cellular functions such as chromatin remodeling, gene transcription, protein synthesis, signal transduction and DNA repair.

    With recent advances in proteomic techniques, in particular mass spectrometry, the stage is now set to decode the methylproteome and define its functions in health and disease.


  393. 393
    Dionisio says:

    The cranberry flavonoids PAC DP-9 and quercetin aglycone induce cytotoxicity and cell cycle arrest and increase cisplatin sensitivity in ovarian cancer cells

    DOI: 10.3892/ijo.2015.2931


    Cranberry flavonoids (flavonols and flavan-3-ols), in addition to their antioxidant properties, have been shown to possess potential in vitro activity against several cancers.

    Overall, this study demonstrates promising in vitro cytotoxic and anti-proliferative properties of two newly characterized cranberry flavonoids, quercetin aglycone and PAC DP-9, against ovarian cancer cells.

  394. 394
    Dionisio says:

    Multiple roles for HOXA3 in regulating thymus and parathyroid differentiation and morphogenesis

    doi: 10.1242/dev.110833

    HOX proteins are a highly conserved family of transcription factors that play essential roles in defining axial identity during metazoan development.

    Hoxa3 has multiple complex and tissue-specific functions during patterning, differentiation and morphogenesis of the thymus and parathyroids.

    HOXA3 function is primarily restricted to early organogenesis […]

    Hoxa3 regulates parathyroid differentiation and survival in a cell-autonomous manner

    it is unclear at this point how HOXA3 differentially affects the expression of a single gene in the dorsal versus ventral pouch

    the transcriptional initiator of the thymus program remains unknown.

    The identity of this pro-apoptotic signal is unclear – both SHH and inhibition of FGF signaling have been implicated in promoting this cell death;

    it is also unclear how these signaling pathways interact in this process

    although these signaling pathways might be involved in this aspect of the Hoxa3 mutant phenotype, the structure of the network that mediates this function has yet to be definitively identified.


    A few questions remain… stay tuned…

  395. 395
    Dionisio says:

    HOXA genes cluster: clinical implications of the smallest deletion

    Lidia Pezzani, Donatella Milani, Francesca Manzoni, Marco Baccarin, Rosamaria Silipigni, Silvana Guerneri and Susanna Esposito

    Italian Journal of Pediatrics 2015, 41:31 doi:10.1186/s13052-015-0137-3


    HOXA genes cluster plays a fundamental role in embryologic development.

    It is notable that in 2004 Lehoczky et al. demonstrated that EVX1, HIBADH, TAX1BP, JAZF1 and CREB5 show embryonic distal limb and genital bud expression, but at this time it is not known whether they have a role in their development. [10 years later still unknown?]

    In conclusion, this report improves our understanding of the genotype-phenotype correlations of HOXA genes cluster deletions via the identification and characterization of the smallest deletion (as well as critical region) reported to date, furthermore opening new discussion and interpretation cues on the unusual findings outlined.

  396. 396
    Dionisio says:

    Binding of transcription factors adapts to resolve information-energy trade-off

    arXiv:1505.01215 [q-bio.GN]

    the binding of transcription factors to DNA in terms of an information transfer problem.

    The input of the noisy channel is the biophysical signal of a factor bound to a DNA site, and the output is a distribution of probable DNA sequences at this site.

    This task involves an inherent tradeoff between the information gain and the energetics of the binding interaction – high binding energies provide higher information gain but hinder the dynamics of the system as factors are bound too tightly.

    We show that adaptation of the binding interaction towards increasing information transfer under energy constraints implies that the information gain per specific binding energy at each base-pair is maximized.

    We analyze hundreds of prokaryote and eukaryote transcription factors from various organisms to evaluate the discrimination energies.

    We find that, in accordance with our theoretical argument, binding energies nearly maximize the information gain per energy.

    This work suggests the adaptation of information gain as a generic design principle of molecular recognition systems.


    design principle ?

  397. 397
    Dionisio says:

    Nature presents multiple intriguing examples of processes which proceed at high precision and regularity.


  398. 398
    Dionisio says:

    Unraveling the mystery of cancer by secretory microRNA: horizontal microRNA transfer between living cells


    the secretory mechanism and biological function, as well as the significance of extracellular miRNAs, remain largely unclear.

    not only exosomal miRNAs but also other types of secretory miRNAs could control the state of cellular phenotypes to the benefit of cancer cells within their niche.

    they have not provided evidence of the molecules species that take part in the modulation of the distal site of metastasis.

    To reveal the exact function of miRNA targeting sites that are distant from the primary organ, we should identify the molecular mechanisms of the tropism of secretory miRNA transported by carriers.

    The research field of secretory miRNAs has just begun.

    To use the knowledge of secretory miRNAs for human health, we should unveil the mystery of secretory RNA as follows.

    First, we need to know all the kinds of secretory RNA species.

    Second, secretory machinery of miRNAs and other types of RNA should be clarified.

    Last point is to know the function of secretory miRNAs in more detail, […]

    Reports on the function of secretory miRNAs in physiological conditions, such as embryogenesis, organogenesis, and maintaining tissue and organ homeostasis, are not available*.

    Clarifying the species, mechanisms and roles of secretory miRNA, and other secretory ncRNAs in both pathological and physiological conditions would unveil the mystery of “secretory miRNAs-mediated disease”


    (*) 2012

  399. 399
    Dionisio says:

    Post-transcriptional processing of genetic information and its relation to cancer


    During the development, progression and dissemination of neoplastic lesions, cancer cells hijack normal pathways and mechanisms, especially those involved in repair and embryologic development.

    These pathways include those involved in intercellular communication, control of transcription, post-transcriptional regulation of protein production including translation of mRNAs, post-translational protein modifications, e.g., acetylation of proteins, and protein degradation.



    doi: 10.3109/10520295.2012.730152

  400. 400
    Dionisio says:

    Molecular Mechanisms of Podocyte Development Revealed by Zebrafish Kidney Research

    Miceli R, Kroeger PT, Wingert RA (2014) Molecular Mechanisms of Podocyte Development Revealed by Zebrafish Kidney Research. Cell Dev Biol 3:138. doi: 10.4172/2168-9296.1000138

    there is still a rather limited understanding about the molecular pathways that control podocyte formation.

    In recent years, however, studies of podocyte development using the zebrafish embryonic kidney, or pronephros, have been an expanding area of nephrology research.

    These results suggest the ratio of these factors is important in the regulation of podocytes during development.

    Taken together, these biochemical studies reveal previously unknown physical interactions […]

    different physical interactions of these proteins are capable of binding genomic targets, […]

    switches in the complex components over time may orchestrate transcriptional alterations that proceed during podocyte differentiation.

    additional podocyte research with the zebrafish model is poised to make useful contributions to this area of nephrology in the years ahead.

    Continued work to identify Wt1 targets [34] and to ascertain the full transcriptional profile of podocytes [35,36], is necessary to solve the remaining enigmas of Wt1 function in podocyte ontogeny and identify players in podocyte gene regulatory networks,


  401. 401
    Dionisio says:

    PRC2 during vertebrate organogenesis: A complex in transición


    Recent years have witnessed tremendous progress in our understanding of the contribution of PRC2 to differentiation and cell fate specification, yet much remains to be explored.

    […] remaining questions associated with its regulation and mechanisms of action.

    […] the full spectrum of PRC2 alternative roles has not been explored.

    These studies highlight the need for a re-examination of the subcellular localization of PRC2 components, and for a proper dissection of its functional activities during the progression from proliferation to differentiation.


    This was 3 years ago… maybe these questions are answered now?

  402. 402
    Dionisio says:

    Repression of the soma-specific transcriptome by Polycomb-repressive complex 2 promotes male germ cell development

    doi: 10.1101/gad.246124.114
    Genes Dev. 2014 Sep 15; 28(18): 2056–2069.

    Polycomb-repressive complex 2 (PRC2) catalyzes the methylation of histone H3 Lys27 (H3K27) and functions as a critical epigenetic regulator of both stem cell pluripotency and somatic differentiation, but its role in male germ cell development is unknown.

    Transcriptional profiling has revealed the dynamic changes to gene expression in differentiating germ cells, yet regulators of this program remain largely unidentified.

    PRC2 is a critical regulator of mammalian spermatogenesis, with essential roles in both the meiotic and mitotic compartments of the male germline.

    We hypothesize that* the ectopic expression of developmental genes in the absence of PRC2 compromises germ cell-specific transcription.

    PRC2 may control** spermatogonial maintenance through repression of developmental genes.


    (*) look forward to reading newer papers confirming this hypothesis

    (**) look forward to reading newer papers changing this term “may control” to just “control(s)”. Basically removing the word “may” so that the statement becomes a sure affirmation.

  403. 403
    Dionisio says:

    In situ histone landscape of nephrogenesis


    Epigenetic mechanisms have been implicated in impacting cell fate decisions during nephrogenesis; however, the chromatin landscape of nephron progenitors and daughter differentiating cells are largely unknown.

    We conclude that combinatorial histone signatures correlate with cell fate decisions during nephrogenesis.

    The present study examined the spatiotemporal distribution of histone modifications and modifiers during nephrogenesis.

    The potential significance of histone arginine methylation in nephrogenesis remains to be determined, since relatively little is known about the functions of these chromatin marks.

    The findings of the present study provide a general descriptive view of the histone landscape of the developing nephron but do not address other “epigenetic” marks such as DNA methylation and microRNA-based mechanisms.

    The data presented in this study are best interpreted within the context of functional data derived from existing and future ChIP-Seq data in nephron progenitors.

    In the future, it will be interesting to elucidate the effects of embryonic stressors on the epigenetic landscape of nephron progenitors in vivo.


    Work in progress… not there yet. A few* questions remain to be answered.

    (*) 🙂

  404. 404
    Dionisio says:

    Back to the future: transgenerational transmission of xenobiotic-induced epigenetic remodeling

    Epigenetics Volume 10, Issue 4, 2015
    DOI:10.1080/15592294.2015.1020267Josep C Jiménez-Chillaróna, Mark J Nijlandb, António A Ascensãoc, Vilma A Sardãod, José Magalhãesc, Michael J Hitchlere, Frederick E Domannf & Paulo J Oliveirad*

    pages 259-273

    Epigenetics, or regulation of gene expression independent of DNA sequence, is the missing link between genotype and phenotype.

    Epigenetic memory, mediated by histone and DNA modifications, is controlled by a set of specialized enzymes, metabolite availability, and signaling pathways.

    A mostly unstudied subject is how sub-toxic exposure to several xenobiotics during specific developmental stages can alter the epigenome and contribute to the development of disease phenotypes later in life.

    Furthermore, it has been shown that exposure to low-dose xenobiotics can also result in further epigenetic remodeling in the germ line and contribute to increase disease risk in the next generation (multigenerational and transgenerational effects).

    We here offer a perspective on current but still incomplete knowledge of xenobiotic-induced epigenetic alterations, and their possible transgenerational transmission.

    We also propose several molecular mechanisms by which the epigenetic landscape may be altered by environmental xenobiotics and hypothesize how diet and physical activity may counteract epigenetic alterations.


  405. 405
    Dionisio says:

    Targeting the Stress Chaperome in Cancer: A Chemical Biology Approach

    […] chaperones are expressed in all cells. They are one of the most abundant proteins. Therefore it has been really overlooked for many years until early ‘90s when serendipitous discovery of a small molecule has started what […]


  406. 406
    Dionisio says:

    The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues

    Epigenetics Volume 10, Issue 4, 2015
    DOI:10.1080/15592294.2014.1003744Robert Lowea*, Greg Slodkowiczb, Nick Goldmanb & Vardhman K Rakyana*
    pages 274-281

    In mammals, DNA methylation profiles vary substantially between tissues.

    Recent genome-scale studies report that blood displays a highly distinctive methylomic profile from other somatic tissues.

    In this study, we sought to understand why blood DNA methylation state is so different to the one found in other tissues.

    We found that whole blood contains approximately twice as many tissue-specific differentially methylated positions (tDMPs) than any other somatic tissue examined.

    Furthermore, a large subset of blood tDMPs showed much lower levels of methylation than tDMPs for other tissues.

    Surprisingly, these regions of low methylation in blood show no difference regarding genomic location, genomic content, evolutionary rates, or histone marks when compared to other tDMPs.

    Our results reveal why blood displays a distinctive methylation profile relative to other somatic tissues.

    In the future, it will be important to study how these blood specific tDMPs are mechanistically involved in blood-specific functions.



  407. 407
    Dionisio says:

    DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

    Kaie Lokk, Vijayachitra Modhukur, Balaji Rajashekar, Kaspar Märtens, Reedik Mägi, Raivo Kolde, Marina Koltšina, Torbjörn K Nilsson, Jaak Vilo, Andres Salumets* and Neeme Tõnisson*

    Genome Biology 2014, 15:r54

    This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues.

    Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions.

    Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms.

    hypomethylation, and not hypermethylation, was more likely to be associated with the tissue-specific functions.

    Our study also provoked the question, of how tDMRs mechanistically contribute to the tissue-specific functions, especially for the numerous methylation regions that were found in gene body areas.

    Still, it remains unclear, however, how the gene body tDMRs may function as regulators of gene expression, and this question should be addressed in the future epigenetic studies.



    Work in progress… a few questions remain unanswered.

    Stay tuned.

  408. 408
    Dionisio says:

    DNA methylation of the LIN28 pseudogene family

    Aaron P Davis, Abby D Benninghoff*, Aaron J Thomas, Benjamin R Sessions and Kenneth L White*

    BMC Genomics 2015, 16:287

    […] little is known about how pseudogenes are targeted for methylation or how methylation levels are maintained in different tissues.

    Non-CpG methylation has been observed to occur with higher frequency in non-dividing cells and gametes, although its function remains unknown.

    […] examination of more pseudogene families will be required to determine whether the same observation is consistent for other integrated pseudogenes

    Future [research] work should focus on these CpG sites and would further help determine how DNA methylation is targeted to specific genomic regions.

    […] this observation does not rule out the possibility that CpG-rich pseudogenes could serve as sites for regulation of gene expression by methylation, a hypothesis that may also be addressed by survey of other pseudogene families.

    New knowledge on the regulation of pseudogenes via DNA methylation could contribute to greater understanding of the maintenance of global and/or regional patterns of methylation.

    Future work on this topic should focus on characterizing methylation patterns for other pseudogene families to determine whether all pseudogenes are maintained in a similar manner or whether sequence specific patterns can be identified through analysis of pseudogenes.


  409. 409
    Dionisio says:

    [Pseudogenes: structure conservation, expression, and functions].

    Evgeniy Balakirev
    Francisco J Ayala

    Zhurnal obshche? biologii

    We describe some unexpected features of pseudogenes in diverse organisms that are inconsistent with this widely accepted point of view.

    Pseudogenes are often evolutionary conserved and transcriptionally active.

    Moreover, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene regulation, generation of genetic diversity, and other features that are expected in genes or DNA sequences that have functional roles.

    A review of the evidence leads to the conclusion that pseudogenes are important components of genomes, representing a repertoire of sequences available for functional evolution and subject to non-neutral evolutionary changes.

    Pseudogenes might be considered as potogenes, i.e. DNA sequences with a potentiality for becoming new genes or acquire new functions.

    Furthermore we conjecture that some pseudogenes along with their parental sequences may constitute sets of indivisible functionally interacting entities (intergenic complexes or “intergenes”), in which all the component elements are required in order to fulfill a collective functional role.

    [Pseudogenes: structure conservation, expression, and functions]. – ResearchGate. Available from: http://www.researchgate.net/pu....._functions

    Over 10 years old paper.

  410. 410
    Dionisio says:

    #409 follow-up?

    About 7 years after @409?

    Pseudogenes: Pseudo-functional or key regulators in health and disease?

    Ryan Charles Pink,
    Kate Wicks,
    Daniel Paul Caley,
    Emma Kathleen Punch,
    Laura Jacobs and
    David Raul Francisco Carter

    doi: 10.1261/rna.2658311
    RNA 2011. 17: 792-798

    Pseudogenes have long been labeled as “junk” DNA, failed copies of genes that arise during the evolution of genomes.

    However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins.

    Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation.

    Pseudogene transcripts can be processed into short interfering RNAs that regulate coding genes through the RNAi pathway.

    In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes by acting as microRNA decoys.

    The finding that pseudogenes are often deregulated during cancer progression warrants further investigation into the true extent of pseudogene function.

    In this review, we describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation.


  411. 411
    Dionisio says:

    Pseudogenes: Pseudo or Real Functional Elements?


    Although broadly existed, pseudogenes used to be considered as junk or relics of genomes which have not drawn enough attentions of biologists until recent years.

    growing lines of evidence have strongly suggested that some pseudogenes possess special functions, including regulating parental gene expression and participating in the regulation of many biological processes.

    pseudogenes are not purely dead fossils of genomes, but warrant further exploration in their distribution, expression regulation and functions.

    A new nomenclature is desirable for the currently called ‘pseudogenes’ to better describe their functions.


  412. 412
    Dionisio says:

    Pseudogene-derived lncRNAs: emerging regulators of gene expression

    Front. Genet., 04 February 2015 | http://dx.doi.org/10.3389/fgene.2014.00476

    In the more than one decade since the completion of the Human Genome Project, the prevalence of non-protein-coding functional elements in the human genome has emerged as a key revelation in post-genomic biology.

    Pseudogene transcription and function remain insufficiently understood.

    Redefining the Human Gene Count

    The fact that non-coding genes are so ubiquitous makes it reasonable to hypothesize that their ncRNA products may be extensively involved in the regulation of protein-coding genes.

    In fact, evidence in favor of specific lncRNAs’ regulatory inputs into particular protein-coding genes is emerging

    Long Non-Coding RNA: Structure, Identification, and Function

    the vast majority of individual lncRNA mechanisms remain unknown.

    Pseudogene Structure and Function

    Recently, Gencode has developed a distinct and hierarchical set of biotypes describing pseudogenes and differentiating them from protein-coding genes

    comprehensive comparisons of lncRNA promoter and exon conservation genomewide in other lineages have still not been performed.

    lncRNA Transcription Regulating Pseudogenes

    the still-emerging lncRNA-pseudogene regulation field is marked by a paucity of experimentally validated examples

    synergistic gene regulation by pseudogenes and lncRNAs needs to be considered as a novel regulatory mechanism.

    Despite this evidence for lncRNA and pseudogene function on a case by case basis, there is still a generalized dearth of expressed pseudogene functional support, particularly within the genomewide context of pseudogene overlaps with lncRNA genes.

    lncRNAs overlapping with pseudogenes are also a potential contributor to both the magnitude and the directionality of this regulation.

    numerous additional examples of joint lncRNA- and pseudogene-driven regulation of protein-coding genes are waiting to be discovered in post-genomic datasets.

    The rapidly growing datasets of significantly disease-associated SNPs from Genome-Wide Association Studies, a resource that has empowered the realization that most trait-associated loci are not protein-coding, are likely to provide a goldmine of intrapseudogenic and lncRNA exonic disease-associated SNPs which can then pave the way to functional studies for decades to come.


  413. 413
    Dionisio says:

    Junk DNA and the long non-coding RNA twist in cancer genetics

    Oncogene. 2015 Jan 26. doi: 10.1038/onc.2014.456

    The central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein. However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). More recently, long non-coding RNAs (lncRNAs) have attracted much attention due to their large number and biological significance. Many lncRNAs have been identified as mapping to regulatory elements including gene promoters and enhancers, ultraconserved regions and intergenic regions of protein-coding genes. Yet, the biological function and molecular mechanisms of lncRNA in human diseases in general and cancer in particular remain largely unknown. Data from the literature suggest that lncRNA, often via interaction with proteins, functions in specific genomic loci or use their own transcription loci for regulatory activity. In this review, we summarize recent findings supporting the importance of DNA loci in lncRNA function and the underlying molecular mechanisms via cis or trans regulation, and discuss their implications in cancer. In addition, we use the 8q24 genomic locus, a region containing interactive SNPs, DNA regulatory elements and lncRNAs, as an example to illustrate how single-nucleotide polymorphism (SNP) located within lncRNAs may be functionally associated with the individual’s susceptibility to cancer.Oncogene advance online publication, 26 January 2015; doi:10.1038/onc.2014.456.


  414. 414
    Dionisio says:

    The Long Noncoding RNA Pnky Regulates Neuronal Differentiation of Embryonic and Postnatal Neural Stem Cells


    While thousands of long noncoding RNAs (lncRNAs) have been identified, few lncRNAs that control neural stem cell (NSC) behavior are known.

    Here, we identify Pinky (Pnky) as a neural-specific lncRNA that regulates neurogenesis from NSCs in the embryonic and postnatal brain.

    Pnky is evolutionarily conserved and expressed in NSCs of the developing human brain.

    In the embryonic mouse cortex, Pnky knockdown increases neuronal differentiation and depletes the NSC population.

    Pnky interacts with the splicing gregulator PTBP1, and PTBP1 knockdown also enhances neurogenesis.

    In NSCs, Pnky and PTBP1 regulate the expression and alternative splicing of a core set of transcripts that relates to the cellular phenotype.

    These data thus unveil Pnky as a conserved lncRNA that interacts with a key RNA processing factor and regulates neurogenesis from embryonic and postnatal NSC populations.


  415. 415
    Dionisio says:

    The lncRNA Pnky in the Brain


    Long noncoding RNAs (lncRNAs) influence diverse cellular processes and have been implicated in regulating stem cell properties.

    Now in Cell Stem Cell, Ramos et al. (2015) demonstrate that the neural-specific lncRNA Pnky regulates neuronal differentiation from neural stem cells and mediates RNA splicing through interactions with polypyrimidine tract-binding protein 1 (PTBP1).


  416. 416
    Dionisio says:

    Long Non-Coding RNAs Control Hematopoietic Stem Cell Function


    Hematopoietic stem cells (HSCs) possess unique gene expression programs that enforce their identity and regulate lineage commitment.

    Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression and cell fate decisions, although their functions in HSCs are unclear.

    Together, these results demonstrate that lncRNAs play important roles in regulating HSCs, providing an additional layer to the genetic circuitry controlling HSC function.


  417. 417
    Dionisio says:

    An Epigenomic Road Map for Endoderm Development


    While studies of organ development have traditionally relied on model organisms, recent advances in embryonic stem cell (ESC) culture allow investigation of organogenesis in human cells.

    Wang et al. (2015) employ this system to map the dynamic enhancer landscape during ESC differentiation to the endoderm derivatives pancreas and liver.


  418. 418
    Dionisio says:

    Junk DNA and the long non-coding RNA twist in cancer genetics

    Oncogene , (26 January 2015)

    H Ling, K Vincent, M Pichler, R Fodde, I Berindan-Neagoe, F J Slack and G A Calin

    The central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein.

    However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs).

    More recently, long non-coding RNAs (lncRNAs) have attracted much attention due to their large number and biological significance.

    Many lncRNAs have been identified as mapping to regulatory elements including gene promoters and enhancers, ultraconserved regions and intergenic regions of protein-coding genes.

    Yet, the biological function and molecular mechanisms of lncRNA in human diseases in general and cancer in particular remain largely unknown.

    Data from the literature suggest that lncRNA, often via interaction with proteins, functions in specific genomic loci or use their own transcription loci for regulatory activity.

    In this review, we summarize recent findings supporting the importance of DNA loci in lncRNA function and the underlying molecular mechanisms via cis or trans regulation, and discuss their implications in cancer.

    In addition, we use the 8q24 genomic locus, a region containing interactive SNPs, DNA regulatory elements and lncRNAs, as an example to illustrate how single-nucleotide polymorphism (SNP) located within lncRNAs may be functionally associated with the individual’s susceptibility to cancer.


  419. 419
    Dionisio says:

    Integration of Genome-wide Approaches Identifies lncRNAs of Adult Neural Stem Cells and Their Progeny In Vivo


    Long noncoding RNAs (lncRNAs) have been described in cell lines and various whole tissues, but lncRNA analysis of development in vivo is limited.

    lncRNAs can play key roles in the glial-neuronal lineage specification of multipotent adult stem cells.

    Taken together, our genome-wide analysis and functional data further support the notion that lncRNAs and homeobox gene neighbors function cooperatively

    A recent model of lncRNA action suggests that lineage-specific lncRNAs become activated during differentiation and guide histone modifications that create cell type-specific transcriptional programs

    our data raise the possibility that lncRNA loci, like protein-coding genes, are targeted by chromatin-modifying factors that have critical roles in development.

    While this study attempted to be as comprehensive as possible, it i