This parody of evo devo makes it sound a lot like ID

_{Denyse O'Leary

December 19, 2017

Cell biology, Evolution, Evolutionary biology}

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“This is how we go from single cells to people.” Hmmm.

See also: From Biology Direct: Darwinism, now thoroughly detached from its historical roots as a falsifiable theory, “must be abandoned”

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2351 typo correction evo devoDionisio_{January 31, 2018
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The whole eve devo enchilada: https://www.ncbi.nlm.nih.gov/pubmed?term=%22Evodevo%22[jour] :)Dionisio_{January 30, 2018
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Evolutionary biosemiotics and multilevel construction networks Alexei A. Sharon Biosemiotics. 9(3): 399–416. doi: 10.1007/s12304-016-9269-0 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5283393/pdf/nihms810857.pdfDionisio_{January 30, 2018
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Principles of constructivism are used here to explore how organisms develop tools, subagents, scaffolds, signs, and adaptations. Here I discuss reasons why organisms have composite nature and include diverse subagents that interact in partially cooperating and partially conflicting ways. Such modularity is necessary for efficient and robust functionality, including mutual construction and adaptability at various time scales. Subagents interact via material and semiotic relations, some of which force or prescribe actions of partners. Other interactions, which I call "guiding", do not have immediate effects and do not disrupt the evolution and learning capacity of partner agents. However, they modify the extent of learning and evolutionary possibilities of partners via establishment of scaffolds and constraints. As a result, subagents construct reciprocal scaffolding for each other to rebalance their communal evolution and learning. As an example, I discuss guiding interactions between the body and mind of animals, where the pain system adjusts mind-based learning to the physical and physiological constraints of the body. Reciprocal effects of mind and behaviors on the development and evolution of the body includes the effects of Lamarck and Baldwin. Composite Agency: Semiotics of Modularity and Guiding Interactions. Sharov AA1. Biosemiotics. 2017 Jul;10(2):157-178. doi: 10.1007/s12304-017-9301-z.Dionisio_{January 30, 2018
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Evolution of natural agents: preservation, advance, and emergence of functional information Alexei A. Sharov Biosemiotics. 9(1): 103–129. doi: 10.1007/s12304-015-9250-3 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978442/pdf/nihms773099.pdfDionisio_{January 30, 2018
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Analysis of gene function in complex organisms relies extensively on tools to detect the cellular and subcellular localization of gene products, especially proteins. Typically, immunostaining with antibodies provides these data. However, due to cost, time, and labor limitations, generating specific antibodies against all proteins of a complex organism is not feasible. Furthermore, antibodies do not enable live imaging studies of protein dynamics. Hence, tagging genes with standardized immunoepitopes or fluorescent tags that permit live imaging has become popular. Importantly, tagging genes present in large genomic clones or at their endogenous locus often reports proper expression, subcellular localization, and dynamics of the encoded protein. Moreover, these tagging approaches allow the generation of elegant protein removal strategies, standardization of visualization protocols, and permit protein interaction studies using mass spectrometry. Here, we summarize available genomic resources and techniques to tag genes and discuss relevant applications that are rarely, if at all, possible with antibodies. Gene Tagging Strategies To Assess Protein Expression, Localization, and Function in Drosophila. Kanca O1,2, Bellen HJ3,2,4,5,6, Schnorrer F7. Genetics. 2017 Oct;207(2):389-412. doi: 10.1534/genetics.117.199968.Dionisio_{January 30, 2018
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The role of protein localization along the apical-basal axis of polarized cells is difficult to investigate in vivo, partially due to lack of suitable tools. Despite of its importance, the role of protein localization and the effects of forced protein mislocalization have not been studied extensively and hence remain in many cases not well understood. A nanobody-based toolset to investigate the role of protein localization and dispersal in Drosophila Stefan Harmansa,1,† Ilaria Alborelli,1,† Dimitri Bieli,1 Emmanuel Caussinus,1,2 and Markus Affolter eLife. 2017; 6: e22549. doi: 10.7554/eLife.22549Dionisio_{January 30, 2018
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Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs). We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS). Most of REs hosting TFBS were highly diverged repeats, and for the evolutionary young (0–8% diverged) elements we identified only ~7% of all RE-linked TFBS. The gene-specific distributions of RE-linked TFBS generally correlated with the distributions for all TFBS. However, several groups of molecular processes were highly enriched in the RE-linked TFBS regulation. They were strongly connected with the immunity and response to pathogens, with the negative regulation of gene transcription, ubiquitination, and protein degradation, extracellular matrix organization, regulation of STAT signaling, fatty acids metabolism, regulation of GTPase activity, protein targeting to Golgi, regulation of cell division and differentiation, development and functioning of perception organs and reproductive system. By contrast, the processes most weakly affected by the REs were linked with the conservative aspects of embryo development. We also identified differences in the regulation features by the younger and older fractions of the REs. The regulation by the older fraction of the REs was linked mainly with the immunity, cell adhesion, cAMP, IGF1R, Notch, Wnt, and integrin signaling, neuronal development, chondroitin sulfate and heparin metabolism, and endocytosis. The younger REs regulate other aspects of immunity, cell cycle progression and apoptosis, PDGF, TGF beta, EGFR, and p38 signaling, transcriptional repression, structure of nuclear lumen, catabolism of phospholipids, and heterocyclic molecules, insulin and AMPK signaling, retrograde Golgi-ER transport, and estrogen signaling. The immunity-linked pathways were highly represented in both categories, but their functional roles were different and did not overlap. Our results point to the most quickly evolving molecular pathways in the recent and ancient evolution of human genome. (2018). Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins. Frontiers in Immunology. 9. . 10.3389/fimmu.2018.00030.Dionisio_{January 30, 2018
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Chondroitin sulfate (CS) is the most abundant glycosaminoglycan (GAG) in the central nervous system (CNS) matrix. Its sulfation and epimerization patterns give rise to different forms of CS, which enables it to interact specifically and with a significant affinity with various signalling molecules in the matrix including growth factors, receptors and guidance molecules. These interactions control numerous biological and pathological processes, during development and in adulthood. In this review, we describe the specific interactions of different families of proteins involved in various physiological and cognitive mechanisms with CSs in CNS matrix. A better understanding of these interactions could promote a development of inhibitors to treat neurodegenerative diseases. Djerbal, Linda & Lortat-Jacob, Hugues & Kwok, JCF. (2017). Chondroitin sulfates and their binding molecules in the central nervous system. Glycoconjugate Journal. 34. . 10.1007/s10719-017-9761-z.Dionisio_{January 30, 2018
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Chondroitin sulfate (CS)/dermatan sulfate (DS) proteoglycans are abundant on the cell surface and in the extracellular matrix and have important functions in matrix structure, cell-matrix interaction and signaling. The DS epimerases 1 and 2, encoded by Dse and Dsel, respectively, convert CS to a CS/DS hybrid chain, which is structurally and conformationally richer than CS, favouring interaction with matrix proteins and growth factors. We recently showed that Xenopus Dse is essential for the migration of neural crest cells by allowing cell surface CS/DS proteoglycans to adhere to fibronectin. Here we investigate the expression of Dse and Dsel in Xenopus embryos. We show that both genes are maternally expressed and exhibit partially overlapping activity in the eyes, brain, trigeminal ganglia, neural crest, adenohypophysis, sclerotome, and dorsal endoderm. Dse is specifically expressed in the epidermis, anterior surface ectoderm, spinal nerves, notochord and dermatome, whereas Dsel mRNA alone is transcribed in the spinal cord, epibranchial ganglia, prechordal mesendoderm and myotome. The expression of the two genes coincides with sites of cell differentiation in the epidermis and neural tissue. Several expression domains can be linked to previously reported phenotypes of knockout mice and clinical manifestations, such as the Musculocontractural Ehlers-Danlos syndrome and psychiatric disorders. Gouignard, Nadege & Schön, Tanja & Holmgren, Christian & Strate, Ina & Ta?öz, Emirhan & Wetzel, Franziska & Maccarana, Marco & Pera, Edgar. (2018). Gene expression of the two developmentally regulated dermatan sulfate epimerases in the Xenopus embryo. PLOS ONE. 13. e0191751. 10.1371/journal.pone.0191751.Dionisio_{January 30, 2018
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Presomitic mesoderm (PSM) cells are the precursors of the somites, which flank both sides of the neural tube and give rise to the musculo-skeletal system shaping the vertebrate body. WNT and FGF signaling control the formation of both the PSM and the somites and show a graded distribution with highest levels in the posterior PSM. The ability to generate PSM cells of either posterior or anterior PSM identity with high efficiency in vitro will promote the investigation of the gene regulatory networks controlling the formation of nascent PSM cells and their switch to differentiating/somitic paraxial mesoderm. Different Concentrations of FGF Ligands, FGF2 or FGF8 Determine Distinct States of WNT-Induced Presomitic Mesoderm. Sudheer S1,2, Liu J1, Marks M1, Koch F1, Anurin A1,3, Scholze M1, Senft AD1,4, Wittler L1, Macura K1, Grote P1,5, Herrmann BG1 Stem Cells. 2016 Jul;34(7):1790-800. doi: 10.1002/stem.2371. Epub 2016 Apr 18.Dionisio_{January 30, 2018
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How metabolism is rewired during embryonic development is still largely unknown, as it remains a major technical challenge to resolve metabolic activities or metabolite levels with spatiotemporal resolution. Combined, our approach identifies a gradient of glycolytic activity across the PSM, and we provide evidence that these spatiotemporal metabolic changes are intrinsically linked to PSM development and differentiation. [...] very little is known about the metabolic state in the context of mammalian embryonic development, particularly in organogenesis-stage mammalian embryos. The ability to reveal metabolite levels and potentially metabolic transitions with spatiotemporal resolution will be critical in future studies that will address how metabolic and signaling gradients are mechanistically and functionally linked within the context of embryonic development. Spatiotemporal Analysis of a Glycolytic Activity Gradient Linked to Mouse Embryo Mesoderm Development. Bulusu V1, Prior N2, Snaebjornsson MT2, Kuehne A3, Sonnen KF2, Kress J2, Stein F4, Schultz C4, Sauer U3, Aulehla A5. Dev Cell. 2017 Feb 27;40(4):331-341.e4. doi: 10.1016/j.devcel.2017.01.015.Dionisio_{January 30, 2018
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KF @338, Good comment. Thanks.Dionisio_{January 30, 2018
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DNA nanostructures represent the confluence of materials science, computer science, biology, and engineering. As functional assemblies, they are capable of performing mechanical and chemical work. In this study, we demonstrate global twisting of DNA nanorails made from two DNA origami six-helix bundles. Twisting was controlled using ethidium bromide or SYBR Green I as model intercalators. Our findings demonstrate that DNA nanorails: (i) twist when subjected to intercalators and the amount of twisting is concentration dependent, and (ii) twisting saturates at elevated concentrations. This study provides insight into how complex DNA structures undergo conformational changes when exposed to intercalators and may be of relevance when exploring how intercalating drugs interact with condensed biological structures such as chromatin and chromosomes, as well as chromatin analogous gene expression devices. Zadegan, Reza & G. Lindau, Elias & P. Klein, William & Green, Christopher & Graugnard, Elton & Yurke, Bernard & Kuang, Wan & L. Hughes, William. (2017). Twisting of DNA Origami from Intercalators. Scientific Reports. 7. . 10.1038/s41598-017-07796-3.Dionisio_{January 30, 2018
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DiEb, 311: Several times, you have raised the issue of search. I have pointed out that at base, it is tantamount to sampling from a configuration space. In the sense, blind search, by chance and/or mechanical necessity without intelligent direction or control or guidance or influence generally. This is directly relevant to the challenge of "finding" -- strictly, happening upon the shorelines of -- deeply isolated islands of function in config spaces of 500 - 1,000 bits or more of complexity. In these cases,
a: the atomic resources of the sol system or observed cosmos [10^57 to 10^80 atoms, more or less] b: treated as observers each sampling at fast chemical reaction rates [~10^14 samples or observations/sec] c: for 10^17 s (order of time since the typical projection to the singularity) will be __________________________________ d: utterly overwhelmed by the scope of search to plausibly sample enough of the space to credibly hit one or more shorelines of function.
This does not require any detailed probability assessment, but indicates that by many orders of magnitude the challenge overwhelms the search resources. As a direct result, blind search is not a plausible means of discovering zones exhibiting functionally specific complex organisation and/or associated information [FSCO/I] in sufficiently complex configuration spaces. Where, per search samples the space, it is a subset, so the set of possible searches is comparable to the power set. If the direct set is of magnitude n, the set of searches is comparable in magnitude to 2^n. Thus, search for a golden search is plausibly exponentially harder than direct search. Of course, typical discussions of fitness landscapes are about incremental hill-climbing within islands of function. They thus beg the question of arriving at shorelines of function. Where also, deep isolation is a direct result of FSCO/I requiring multiple, well matched components properly arranged and coupled to produce relevant results. And as a consequence of OOL requiring credibly 100k - 1,000 k bases and body plans 10 - 100 millions, we are well beyond the FSCO/I threshold in these cases. So, it is not plausible that the FSCO/I seen in life forms at origin or at basic body plan level, originated by blind search. Pausing, it is worth noting that the proposal that ability to reproduce leading to descent with incremental modification solves the problem typically overlooks that at OOL, there is need to account for the FSCO/I of the von Neumann kinematic self-replicator found in the living cell. Likewise, that for body plan origins, many co-ordinated changes (often, involving reproduction) will have to be accounted for. Natural selection of reproducing entities does not evade the origin of FSCO/I challenge. What, per Newton's vera causa principle, has right to be regarded as an observed effective cause of FSCO/I? Intelligently directed configuration, aka design. Indeed, we are well within our inductive logic, epistemic rights, to hold that FSCO/I is a well tested, highly reliable sign of design as materially relevant cause. On a trillion member observation base. KFkairosfocus_{January 30, 2018
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Most DNA processes are governed by molecular interactions that take place in a sequence-specific manner. Determining the sequence selectivity of DNA ligands is still a challenge, particularly for small drugs where labeling or sequencing methods do not perform well. Here, we present a fast and accurate method based on parallelized single molecule magnetic tweezers to detect the sequence selectivity and characterize the thermodynamics and kinetics of binding in a single assay. Mechanical manipulation of DNA hairpins with an engineered sequence is used to detect ligand binding as blocking events during DNA unzipping, allowing determination of ligand selectivity both for small drugs and large proteins with nearly base-pair resolution in an unbiased fashion. The assay allows investigation of subtle details such as the effect of flanking sequences or binding cooperativity. Unzipping assays on hairpin substrates with an optimized flat free energy landscape containing all binding motifs allows determination of the ligand mechanical footprint, recognition site, and binding orientation. Manosas, Maria & Camunas-Soler, Joan & Croquette, Vincent & Ritort, Felix. (2017). Single molecule high-throughput footprinting of small and large DNA ligands. Nature Communications. 8. . 10.1038/s41467-017-00379-w.Dionisio_{January 30, 2018
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Single-molecule approaches present a powerful way to obtain detailed kinetic information at the molecular level. However, the identification of small rate changes is often hindered by the considerable noise present in such single-molecule kinetic data. We present a general method to detect such kinetic change points in trajectories of motion of processive single molecules having Gaussian noise, with a minimum number of parameters and without the need of an assumed kinetic model beyond piece-wise linearity of motion. Kinetic change points are detected using a likelihood ratio test in which the probability of no change is compared to the probability of a change occurring, given the experimental noise. A predetermined confidence interval minimizes the occurrence of false detections. Applying the method recursively to all sub-regions of a single molecule trajectory ensures that all kinetic change points are located. The algorithm presented allows rigorous and quantitative determination of kinetic change points in noisy single molecule observations without the need for filtering or binning, which reduce temporal resolution and obscure dynamics. The statistical framework for the approach and implementation details are discussed. The detection power of the algorithm is assessed using simulations with both single kinetic changes and multiple kinetic changes that typically arise in observations of single-molecule DNA-replication reactions. Implementations of the algorithm are provided in ImageJ plugin format written in Java and in the Julia language for numeric computing, with accompanying Jupyter Notebooks to allow reproduction of the analysis presented here. R. Hill, Flynn & van Oijen, Antoine & Duderstadt, Karl. (2018). Detection of kinetic change points in piece-wise linear single molecule motion. The Journal of Chemical Physics. 148. 123317. 10.1063/1.5009387.Dionisio_{January 30, 2018
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The astonishing efficiency and accuracy of DNA replication has long suggested that refined rules enforce a single highly reproducible sequence of molecular events during the process. This view was solidified by early demonstrations that DNA unwinding and synthesis are coupled within a stable molecular factory, known as the replisome, which consists of conserved components that each play unique and complementary roles. However, recent single-molecule observations of replisome dynamics have begun to challenge this view, revealing that replication may not be defined by a uniform sequence of events. Instead, multiple exchange pathways, pauses, and DNA loop types appear to dominate replisome function. These observations suggest we must rethink our fundamental assumptions and acknowledge that each replication cycle may involve sampling of alternative, sometimes parallel, pathways. Here, we review our current mechanistic understanding of DNA replication while highlighting findings that exemplify multi-pathway aspects of replisome function and considering the broader implications. J. Scherr, Matthias & Safaric, Barbara & Duderstadt, Karl. (2017). Noise in the Machine: Alternative Pathway Sampling is the Rule During DNA Replication. BioEssays. 40. 1700159. 10.1002/bies.201700159.Dionisio_{January 30, 2018
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The replisome, the multiprotein system responsible for genome duplication, is a highly dynamic complex displaying a large number of different enzyme activities. Recently, the Saccharomyces cerevisiae minimal replication reaction has been successfully reconstituted in vitro. This provided an opportunity to uncover the enzymatic activities of many of the components in a eukaryotic system. Their dynamic behavior and interactions in the context of the replisome, however, remain unclear. We use a tethered-bead assay to provide real-time visualization of leading-strand synthesis by the S. cerevisiae replisome at the single-molecule level. The minimal reconstituted leading-strand replisome requires 24 proteins, forming the CMG helicase, the Pol ? DNA polymerase, the RFC clamp loader, the PCNA sliding clamp, and the RPA single-stranded DNA binding protein. We observe rates and product lengths similar to those obtained from ensemble biochemical experiments. At the single-molecule level, we probe the behavior of two components of the replication progression complex and characterize their interaction with active leading-strand replisomes. The Minichromosome maintenance protein 10 (Mcm10), an important player in CMG activation, increases the number of productive replication events in our assay. Furthermore, we show that the fork protection complex Mrc1-Tof1-Csm3 (MTC) enhances the rate of the leading-strand replisome threefold. The introduction of periods of fast replication by MTC leads to an average rate enhancement of a factor of 2, similar to observations in cellular studies. We observe that the MTC complex acts in a dynamic fashion with the moving replisome, leading to alternating phases of slow and fast replication. S. Lewis, Jacob & Spenkelink, Lisanne & D. Schauer, Grant & R. Hill, Flynn & E. Georgescu, Roxanna & E. O’Donnell, Michael & van Oijen, Antoine. (2017). Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome. Proceedings of the National Academy of Sciences. 114. 201711291. 10.1073/pnas.1711291114.Dionisio_{January 30, 2018
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Genetic recombination occurs in all organisms and is vital for genome stability. Indeed, in humans, aberrant recombination can lead to diseases such as cancer. Our understanding of homologous recombination is built upon more than a century of scientific inquiry, but achieving a more complete picture using ensemble biochemical and genetic approaches is hampered by population heterogeneity and transient recombination intermediates. Recent advances in single-molecule and super-resolution microscopy methods help to overcome these limitations and have led to new and refined insights into recombination mechanisms, including a detailed understanding of DNA helicase function and synaptonemal complex structure. The ability to view cellular processes at single-molecule resolution promises to transform our understanding of recombination and related processes. Kaniecki, Kyle & De Tullio, Luisina & C. Greene, Eric. (2017). A change of view: homologous recombination at single-molecule resolution. Nature Reviews Genetics. . 10.1038/nrg.2017.92.Dionisio_{January 30, 2018
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Single molecule microscopy techniques allow to visualize the translocation of single transport receptors and cargo molecules or particles through nuclear pore complexes. These data indicate that cargo molecule import into the nucleus takes less than 10 milliseconds and nuclear export of messenger RNA (mRNA) particles takes 50 to 350 milliseconds, up to several seconds for extremely bulky particles. This review summarizes and discusses experimental results on transport of nuclear transport factor 2 (NTF2), importin ? and mRNA particles. Putative regulatory functions of importin ? for the NPC transport mechanism and the RNA helicase Dbp5 for mRNA export kinetics are discussed. Kubitscheck, Ulrich & Siebrasse, Jan. (2017). Kinetics of transport through the nuclear pore complex. Seminars in Cell & Developmental Biology. . 10.1016/j.semcdb.2017.06.016.Dionisio_{January 30, 2018
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Force sensing and generation at the tissular and cellular scale is central to many biological events. There is a growing interest in modern cell biology for methods enabling force measurements in vivo Optical trapping allows non-invasive probing of pico-Newton forces and thus emerged as a promising mean for assessing biomechanics in vivo Nevertheless, the main obstacles rely in the accurate determination of the trap stiffness in heterogeneous living organisms, at any position where the trap is used. A proper calibration of the trap stiffness is thus required for performing accurate and reliable force measurements in vivo Here, we introduce a method that overcomes these difficulties by accurately measuring hemodynamic profiles in order to calibrate the trap stiffness. Doing so, and using numerical methods to assess the accuracy of the experimental data, we measured flow profiles and drag forces imposed to trapped red blood cells of living zebrafish embryos. Using treatments enabling blood flow tuning, we demonstrated that such method is powerful in measuring hemodynamic forces in vivo with accuracy and confidence. Altogether, this study demonstrates the power of optical tweezing in measuring low range hemodynamic forces in vivo and offers an unprecedented tool in both cell and developmental biology. Harlepp, Sebastien & Thalmann, Fabrice & Follain, Gautier & Goetz, Jacky. (2017). Hemodynamic forces can be accurately measured in vivo with optical tweezers. Molecular Biology of the Cell. 28. mbc.E17-06. 10.1091/mbc.E17-06-0382.Dionisio_{January 30, 2018
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Identifying the key structural and dynamical determinants that drive the association of biomolecules, whether in solution, or perhaps more importantly in a membrane environment, has critical implications for our understanding of cellular dynamics, processes, and signaling. With recent advances in high-resolution imaging techniques, from the development of new molecular labels to technical advances in imaging methodologies and platforms, researchers are now reaping the benefits of being able to directly characterize and quantify local dynamics, structures, and conformations in live cells and tissues. These capabilities are providing unique insights into association stoichiometries, interactions, and structures on sub-micron length scales. We previously examined the role of lipid headgroup chemistry and phase state in guiding the formation of pseudoisocyanine (PIC) dye J-aggregates on supported planar bilayers [Langmuir, 25, 10,719]. We describe here how these same J-aggregates can report on the in situ formation of organellar membrane domains in live cells. Live cell hyperspectral confocal microscopy using GFP-conjugated GTPase markers of early (Rab5) and late (Rab7) endosomes revealed that the PIC J-aggregates were confined to domains on either the limiting membrane or intralumenal vesicles (ILV) of late endosomes, known to be enriched in the anionic lipid bis(monoacylglycero)phosphate (BMP). Correlated confocal fluorescence - atomic force microscopy performed on endosomal membrane-mimetic supported planar lipid bilayers confirmed BMP-specific templating of the PIC J-aggregates. These data provide strong evidence for the formation of BMP-rich lipid domains during multivesicular body formation and portend the application of structured dye aggregates as markers of cellular membrane domain structure, size, and formation. C.H. Mo, Gary & M. Yip, Christopher. (2017). Structural Templating of J-aggregates: Visualizing Bis(monoacylglycero)phosphate domains in live cells. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1865. . 10.1016/j.bbapap.2017.07.019.Dionisio_{January 30, 2018
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With new approaches in imaging—from new tools or reagents to processing algorithms—come unique opportunities and challenges to our understanding of biological processes, structures, and dynamics. Although innovations in super-resolution imaging are affording novel perspectives into how molecules structurally associate and localize in response to, or in order to initiate, specific signaling events in the cell, questions arise as to how to interpret these observations in the context of biological function. Just as each neighborhood in a city has its own unique vibe, culture, and indeed density, recent work has shown that membrane receptor behavior and action is governed by their localization and association state. There is tremendous potential in developing strategies for tracking how the populations of these molecular neighborhoods change dynamically. Oreopoulos, John & D. Gray-Owen, Scott & Yip, Christopher. (2017). High Density or Urban Sprawl: What Works Best in Biology?. ACS Nano. 11. . 10.1021/acsnano.7b00061.Dionisio_{January 30, 2018
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Single-molecule manipulation and imaging techniques have become important elements of the biologist's toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components. Monachino, Enrico & Spenkelink, Lisanne & van Oijen, Antoine. (2016). Watching cellular machinery in action, one molecule at a time. The Journal of cell biology. 216. . 10.1083/jcb.201610025.Dionisio_{January 30, 2018
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Kinesin motors play central roles in establishing and maintaining the mitotic spindle during cell division. Unlike most other kinesins, Cin8, a kinesin-5 motor in Saccharomyces cerevisiae, can move bidirectionally along microtubules, switching directionality according to biochemical conditions, a behavior that remains largely unexplained. To this end, we used biochemical rate and equilibrium constant measurements as well as cryo-electron microscopy methodologies to investigate the microtubule interactions of the Cin8 motor domain. These experiments unexpectedly revealed that, while Cin8 ATPase kinetics fell within measured ranges for kinesins (especially kinesin-5 proteins), approximately four motors can unexpectedly bind each ab-tubulin dimer within the microtubule lattice. This result contrasted with those observations on other known kinesins, which can bind only a single "canonical" site per ab-tubulin dimer. Competition assays with human kinesin-5 (Eg5) only partially abrogated this behavior, indicating that Cin8 binds microtubules not only at the canonical site, but also one or more separate ("noncanonical") sites. Moreover, we found that deleting the large, class-specific insert in the microtubule-binding loop 8 reverts Cin8 to one motor per tubulin in the microtubule. The novel microtubule-binding mode of Cin8 identified here provides a potential explanation for Cin8 clustering along microtubules and potentially may contribute to the mechanism for direction reversal. M Bell, Kayla & Cha, Hyo Keun & Sindelar, Charles & C Cochran, Jared. (2017). The yeast kinesin-5 Cin8 interacts with the microtubule in a noncanonical manner. Journal of Biological Chemistry. 292. jbc.M117.797662. 10.1074/jbc.M117.797662Dionisio_{January 30, 2018
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The bipolar kinesin-5 motors perform essential functions in mitotic spindle dynamics. We previously demonstrated that phosphorylation of at least one of the Cdk1 sites in the catalytic domain of the Saccharomyces cerevisiae kinesin-5 Cin8 (S277, T285, S493) regulates its localization to the anaphase spindle. The contribution of these three sites to phospho-regulation of Cin8, as well as the timing of such contributions, remains unknown. Here, we examined the function and spindle localization of phospho-deficient (serine/threonine to alanine) and phospho-mimic (serine/threonine to aspartic acid) Cin8 mutants. In vitro, the three Cdk1 sites undergo phosphorylation by Clb2-Cdk1. In cells, phosphorylation of Cin8 affects two aspects of its localization to the anaphase spindle, translocation from the spindle-pole bodies (SPBs) region to spindle microtubules (MTs) and the midzone, and detachment from the mitotic spindle. We found that phosphorylation of S277 is essential for the translocation of Cin8 from SPBs to spindle MTs and the subsequent detachment from the spindle. Phosphorylation of T285 mainly affects the detachment of Cin8 from spindle MTs during anaphase, while phosphorylation at S493 affects both the translocation of Cin8 from SPBs to the spindle and detachment from the spindle. Only S493 phosphorylation affected the anaphase spindle elongation rate. We conclude that each phosphorylation site plays a unique role in regulating Cin8 functions and postulate a model in which the timing and extent of phosphorylation of the three sites orchestrates the anaphase function of Cin8. Goldstein, Alina & Siegler, Nurit & Goldman, Darya & Judah, Haim & Valk, Ervin & Kõivomägi, Mardo & Loog, Mart & Gheber, Larisa. (2017). Three Cdk1 sites in the kinesin-5 Cin8 catalytic domain coordinate motor localization and activity during anaphase. Cellular and Molecular Life Sciences. 74. . 10.1007/s00018-017-2523-z.Dionisio_{January 30, 2018
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Lazo, Pedro. (2017). Is Centrosomal Protein 70, a Centrosomal Protein with New Roles in Breast Cancer Dissemination and Metastasis, a Facilitator of Epithelial-Mesenchymal Transition?. The American Journal of Pathology. 187. . 10.1016/j.ajpath.2016.12.008. This commentary highlights the article by Shi et al that identified centrosomal protein 70 as a key mediator of breast cancer growth and metastasis.Dionisio_{January 30, 2018
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Chromosome stability is ensured by precisely fine-tuned dynamics of mitotic spindles, which are controlled by a network of various microtubule-associated and interacting proteins including the kinesin-13 family. The best characterized member of this family is the mitotic centromere-associated kinesin (MCAK). By efficiently depolymerizing microtubules, MCAK influences various key events during mitosis. MCAK itself is regulated by its interaction partners, its intrinsic conformation switch and the phosphorylation of mitotic kinases like Aurora A/B, cyclin-dependent kinase 1 and Polo-like kinase 1. Perturbing its regulation alters MCAK’s conformation, catalytic activity, subcellular localization and stability, leading further to mitotic defects in spindle formation and chromosome movement. Indeed, MCAK is aberrantly regulated in various cancer types, which is linked to increased invasiveness, metastasis and drug resistance. In the current review, we summarize recently published data concerning MCAK, correlate its conformation changes with its depolymerization activity and function, propose a model of its regulation by multiple mitotic kinases and highlight its potential involvement in oncogenesis and drug resistance. Ritter, Andreas & Kreis, Nina-Naomi & Louwen, Frank & Wordeman, Linda & Yuan, Juping. (2016). Molecular insight into the regulation and function of MCAK. Critical Reviews in Biochemistry and Molecular Biology. 51. 1-18. 10.1080/10409238.2016.1178705.Dionisio_{January 30, 2018
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Polo-like kinase 1 (Plk1) has been established as one of the most promising targets for molecular anticancer intervention. In fact, various Plk1 inhibitors have been identified and characterized. While the data derived from the bench are prospective, the clinical outcomes are less encouraging by showing modest efficacy. One of the explanations for this discrepancy could be unintendedly targeting of non-malignant cells by Plk1 inhibitors. In this work, we have addressed the effect of Plk1 inhibition in adipose tissue-derived mesenchymal stem cells (ASCs). We show that both visceral and subcutaneous ASCs display monopolar spindles, reduced viability and strong apoptosis induction upon treatment with BI 2536 and BI 6727, the Plk1 kinase domain inhibitors, and with Poloxin, the regulatory Polo-box domain inhibitor. While Poloxin triggers quickly apoptosis, BI 2536 and BI 6727 result in mitotic arrest in ASCs. Importantly, survived ASCs exhibit DNA damage and a pronounced senescent phenotype. In addition, Plk1 inhibition impairs ASCs' motility and homing ability. These results show that Plk1 inhibitors target slowly proliferating ASCs, an important population of anti-inflammation and immune modulation. The toxic effects on primary cells like ASCs could be partially responsible for the reported moderate antitumor activity in patients treated with Plk1 inhibitors. Ritter, Andreas & Friemel, Alexandra & Kreis, Nina-Naomi & Louwen, Frank & Yuan, Juping. (2016). Impact of Polo-like kinase 1 inhibitors on human adipose tissue-derived mesenchymal stem cells. Oncotarget. 7. . 10.18632/oncotarget.12482Dionisio_{January 30, 2018
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