Mystery at the heart of life

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December 21, 2014

Cell biology, Intelligent Design, News

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Cell biology
Intelligent Design
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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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Comments

Although ROS metabolism is known to be involved in the control of the balance between cell proliferation and differentiation in plants and animals, the underlying mechanism remains to be elucidated. Identification of UPB1 signaling would stimulate further study of the mechanism linking ROS homeostasis with the transition from cell proliferation to differentiation via intercellular signaling.
Mobility of signaling molecules: the key to deciphering plant organogenesis Kensuke Kawade, Hirokazu Tanimoto 10.1007/s10265-014-0692-5 JPR Symposium Plasmodesmata: Function and Diversity in Plant Intercellular Communication Journal of Plant Research Volume 128, Issue 1, pp 17-25 http://link.springer.com/article/10.1007/s10265-014-0692-5/fulltext.html

Complex complexity.Dionisio_{September 7, 2015
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[...] our quantitative understanding of the spatiotemporal dynamics of intercellular signaling in plants is limited. It is difficult to fully elucidate the mechanism controlling the mobility of signaling molecules because of complex underlying processes [...] It is no doubt that these studies pioneer a new field to investigate the mechanism that mediates the morphogen gradient formation, however, the mechanism is not yet fully characterized.
Mobility of signaling molecules: the key to deciphering plant organogenesis Kensuke Kawade, Hirokazu Tanimoto 10.1007/s10265-014-0692-5 JPR Symposium Plasmodesmata: Function and Diversity in Plant Intercellular Communication Journal of Plant Research Volume 128, Issue 1, pp 17-25 http://link.springer.com/article/10.1007/s10265-014-0692-5/fulltext.html

Complex complexity.Dionisio_{September 7, 2015
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A developing organ comprises a heterogeneous field of individual cells that differ in terms of physical conditions, molecular constitution, structures, differentiation stages and other properties. Cells orchestrate* such variables using* cell-to-cell communication to achieve* normal organogenesis. The movement of signaling molecules between cells defines* their spatiotemporal distribution within a developing organ, and, thereafter, guides* developmental progression.
Mobility of signaling molecules: the key to deciphering plant organogenesis Kensuke Kawade, Hirokazu Tanimoto 10.1007/s10265-014-0692-5 JPR Symposium Plasmodesmata: Function and Diversity in Plant Intercellular Communication Journal of Plant Research Volume 128, Issue 1, pp 17-25 http://link.springer.com/article/10.1007/s10265-014-0692-5/fulltext.html

(*) how? Complex complexity.Dionisio_{September 7, 2015
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With the advent of next generation sequencing, our ability to generate biological data is rapidly outpacing our ability to store and make sense of it.
- http://beacon-center.org/ BEACON Researchers at Work: Bases vs Bytes- Bioinformaticians to the Rescue Posted on September 7, 2015 by Danielle Whittaker

Complex complexity.Dionisio_{September 7, 2015
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Mobility of signaling molecules: the key to deciphering plant organogenesis Kensuke Kawade, Hirokazu Tanimoto 10.1007/s10265-014-0692-5 JPR Symposium Plasmodesmata: Function and Diversity in Plant Intercellular Communication Journal of Plant Research Volume 128, Issue 1, pp 17-25 http://link.springer.com/article/10.1007/s10265-014-0692-5/fulltext.html
Signaling molecules move between cells to form a characteristic distribution pattern within a developing organ; thereafter, they spatiotemporally regulate organ development. A key question in this process is how the signaling molecules robustly form the precise distribution on a tissue scale in a reproducible manner. Despite of an increasing number of quantitative studies regarding the mobility of signaling molecules, the detail mechanism of organogenesis via intercellular signaling is still unclear.

Complex complexity. Work in progress... stay tuned.Dionisio_{September 7, 2015
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Salivary gland development: A template for regeneration Vaishali N. Patel, Matthew P. Hoffman doi:10.1016/j.semcdb.2013.12.001 Seminars in Cell & Developmental Biology Volumes 25–26, Pages 52–60 Development of Ectodermal Organs http://www.sciencedirect.com/science/article/pii/S1084952113001304
The mammalian salivary gland develops as a highly branched structure designed to produce and secrete saliva. There is some controversy within the literature about the developmental origin of the epithelium of the major salivary glands i.e. are they ectodermal or endodermal in origin? Salivary gland development involves the interaction of multiple cell types including epithelial, mesenchymal, endothelial and neuronal cells. there is still much to learn. the role of the vasculature during development remains to be elucidated. Little is known about the lineage relationships and the mechanisms that regulate the differentiation of salivary gland stem/progenitors cells.

designed ? What did they mean by designed in this case? Complex complexity. Work in progress... stay tuned.Dionisio_{September 7, 2015
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Integration of comprehensive 3D microCT and signaling analysis reveals differential regulatory mechanisms of craniofacial bone development Thach-Vu Ho, Junichi Iwata, Hoang Anh Ho, Weston C. Grimes, Shery Park, Pedro A. Sanchez-Lara, Yang Chai doi:10.1016/j.ydbio.2015.02.010 Developmental Biology Volume 400, Issue 2, Pages 180–190 http://www.sciencedirect.com/science/article/pii/S0012160615000688
Growth factor signaling regulates tissue–tissue interactions to control organogenesis and tissue homeostasis. [...] the relative involvement of canonical and non-canonical TGF? signaling in regulating specific craniofacial bone formation remains unclear. [...] the regulatory mechanisms of craniofacial bone morphogenesis remain poorly understood. The majority of the craniofacial bones, with the exception of the cranial base and parts of the mandible that arise from endochondral ossification, are formed by intramembranous ossification through a mechanism that remains poorly understood. [...] the extent to which canonical and non-canonical TGF? signaling cascades contribute to CNC–derived craniofacial bone formation is still unknown. [...] the underlying mechanisms of craniofacial bone development remain to be elucidated. Further studies are needed to test these hypotheses. 3D data and other biochemical data will aid our study to gain a better understanding of the regulatory mechanism and integrated function of craniofacial bones.

Complex complexity. Work in progress... stay tuned.Dionisio_{September 7, 2015
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The transcriptome of human pluripotent stem cells Kin Fai Au, Vittorio Sebastiano doi:10.1016/j.gde.2014.09.012 Current Opinion in Genetics & Development Volume 28, Pages 71–77 Cell reprogramming, regeneration and repair http://www.sciencedirect.com/science/article/pii/S0959437X14001075
[...] the transcriptome research of PSCs is still incomplete. [...] more efforts are needed to expand and optimize this method to more PSCs [...] As we complete transcriptome profiling of different PSCs and the transition stages between them, we will gain better understanding of pluripotency.

Complex complexity. Work in progress... stay tuned.Dionisio_{September 7, 2015
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Identification of the Common Origins of Osteoclasts, Macrophages, and Dendritic Cells in Human Hematopoietic Yanling Xiao, Sebastiaan Zijl, Liqin Wang, Daniel C. de Groot, Maarten J. van Tol, Arjan C. Lankester, Jannie Borst doi:10.1016/j.stemcr.2015.04.012 Stem Cell Reports Volume 4, Issue 6, Pages 984–994 http://www.sciencedirect.com/science/article/pii/S2213671115001241
Osteoclasts (OCs) originate from the myeloid cell lineage, but the successive steps in their lineage commitment are ill-defined, especially in humans. Although OCs are of key importance, their developmental pathway is largely unknown as testified by the striking absence of OCs in most depictions of the hematopoietic tree. The hematopoietic tree describes the developmental pathways of all blood cells emanating from the pluripotent hematopoietic stem cell (HSC). Future work should address the functionality of the culture-derived cells. Also, additional markers must be found to discern the MODP and proposed CDP. Understanding the development of OC, DC, and M? is important for clinical diagnostics, targeted drug-based therapy, and cellular therapy. Identification of the MODP will also facilitate generation of these cell types, with precursor stemness benefitting expansion and cell yield.

Complex complexity.Dionisio_{September 6, 2015
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Submandibular Parasympathetic Gangliogenesis Requires Sprouty-Dependent Wnt Signals from Epithelial Progenitors Wendy M. Knosp, Sarah M. Knox, Isabelle M.A. Lombaert, Candace L. Haddox, Vaishali N. Patel, Matthew P. Hoffman doi:10.1016/j.devcel.2015.01.023 Developmental Cell Volume 32, Issue 6, Pages 667–677 http://www.sciencedirect.com/science/article/pii/S1534580715000660
[...] signals that initiate gangliogenesis after the precursors differentiate into neurons are unknown. K5+ progenitors produce Wnt signals to establish the PSG-epithelial communication required for organ innervation and progenitor cell maintenance.

Dionisio_{September 6, 2015
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Investigating the principles of morphogen gradient formation: from tissues to cells Anna Kicheva, Tobias Bollenbach, Ortrud Wartlick, Frank Jülicher, Marcos Gonzalez-Gaitan doi:10.1016/j.gde.2012.08.004 Current Opinion in Genetics & Development Volume 22, Issue 6, Pages 527–532 Genetics of system biology http://www.sciencedirect.com/science/article/pii/S0959437X12000998
Morphogen gradients regulate the patterning and growth of many tissues, hence a key question is how they are established and maintained during development. [...] it remains challenging to conclusively distinguish between cellular mechanisms.

Complex complexity.Dionisio_{September 6, 2015
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Encoding and decoding of positional information in morphogen-dependent patterning Ken-ichi Hironaka Yoshihiro Morishita Current Opinion in Genetics & Development Volume 22, Issue 6, Pages 553–561 Genetics of system biology doi:10.1016/j.gde.2012.10.002 http://www.sciencedirect.com/science/article/pii/S0959437X12001268
Patterning during organogenesis is fundamentally realized through the interpretation of morphogen gradients by particular types of gene regulatory networks (GRNs). research on mechanisms for generating robust patterns in growing tissues with time-variant morphogen information is just beginning General principles for robust patterning adopted by real systems will be elucidated only by quantitatively analyzing the interdependent relationships among gradient dynamics, cell trajectory in growing tissues, and time series of cellular responses. mathematical modeling of spatial information coding and simulation studies, as well as advanced measurement techniques, will play crucial roles.

Complex complexity. Since this paper is around 3 years old, perhaps some of the issues it presented have been resolved in more recent papers?Dionisio_{September 6, 2015
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The very first cell fate decision made in the early mammalian embryo – the segregation of ICM and TE – remains a remarkably complex and little understood process. Although our knowledge on the mechanisms of the ICM/TE segregation has grown considerably, there are still many questions unanswered. How do the key transcription factors interact with epigenetic regulators (such as histone-modifying enzymes) to activate or suppress gene expression? Which miRNAs are essential for blastocyst development? What are the critical targets of these miRNAs? How do blastomeres transduce extracellular signal into the intracellular signaling pathways? How do the Ras-MAPK, Hippo, and PKC pathways coordinately regulate cell fate commitment? These central questions constitute the challenge for the future.
Molecular basis of the first cell fate determination in mouse embryogenesis Lingyi Chen, Dekun Wang, Zhaoting Wu, Liping Ma and George Q Daley Cell Research (2010) 20:982–993. doi: 10.1038/cr.2010.106; http://www.nature.com/cr/journal/v20/n9/full/cr2010106a.html

Since the referenced paper is around 5 years old, which is a long time in terms of the accelerated pace of current research, perhaps some of the questions in it have been answered by now? We'll keep looking into the most recent publications to see what has been answered and what still remains open. However, let's keep in mind that there were more questions that could have been asked I that paper. Also, answering some questions could generate newer questions. Work in progress... stay tuned. Complex complexity.Dionisio_{September 6, 2015
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Isoforms of protein kinase C (PKC) might also be involved in the TE/ICM segregation. However, the details of how PKC isotypes affect cell polarity remain unclear. In many other situations, signaling pathways coordinately induce cellular responses to environmental cues. It remains to be clarified whether and how the Ras-MAPK pathway, the Hippo pathway, and the PKC isotypes cross-regulate each other. Another important question is how the cell senses the outside/inside position and transduces this information to intracellular pathways.
Molecular basis of the first cell fate determination in mouse embryogenesis Lingyi Chen, Dekun Wang, Zhaoting Wu, Liping Ma and George Q Daley Cell Research (2010) 20:982–993. doi: 10.1038/cr.2010.106; http://www.nature.com/cr/journal/v20/n9/full/cr2010106a.html

Work in progress... stay tuned. Complex complexity.Dionisio_{September 6, 2015
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The differential epigenetic profiles of the ICM and the TE beg the question of which comes first: are the distinct epigenetic profiles a consequence of differentiation of the ICM and the TE, or do the differential epigenetic profiles precede lineage allocation and mediate the cell fate commitment? [...] epigenetic information precedes and dictates the ICM/TE cell fate determination, by acting on critical lineage-specific genes. How epigenetic marks are first initiated remains a central question.
Molecular basis of the first cell fate determination in mouse embryogenesis Lingyi Chen, Dekun Wang, Zhaoting Wu, Liping Ma and George Q Daley Cell Research (2010) 20:982–993. doi: 10.1038/cr.2010.106; http://www.nature.com/cr/journal/v20/n9/full/cr2010106a.html

Well, at least a "chicken-egg" question apparently got answered. Work in progress... stay tuned. Complex complexity.Dionisio_{September 6, 2015
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Certainly, complex events yet to be discovered are required to ensure proper TE and ICM differentiation. [...] less is known about the transcription network in TE cells. Other factors regulating the expression of these TE-specific factors remain to be identified. The different epigenetic marks in blastomeres at various stages orchestrate the developmental potential of these blastomeres. [...] histone modifications cooperate together to ensure the appropriate spatial and temporal expression of lineage-specific genes. [...] further substantiation is required before acknowledging AID as the long-sought demethylase. [...] how the paternal X chromosome is predominantly inactivated remains elusive. [...] little is known about the reactivation of the inactive paternal X chromosome in the ICM. More investigations are necessary to better understand the mechanism of Xi reactivation.
Molecular basis of the first cell fate determination in mouse embryogenesis Lingyi Chen, Dekun Wang, Zhaoting Wu, Liping Ma and George Q Daley Cell Research (2010) 20:982–993. doi: 10.1038/cr.2010.106; http://www.nature.com/cr/journal/v20/n9/full/cr2010106a.html

A few questions remained unanswered a few years ago, but perhaps some have been answered by now? Work in progress... stay tuned. Complex complexity.Dionisio_{September 6, 2015
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Regarding the formation of the blastocyst, several questions of great biological importance remain unanswered or controversial. When and how do the cells become different from each other in the embryo? When and how are the fates of cells determined? How is the developmental potential of cells regulated during the transition from the totipotent zygote to the pluripotent ICM cells and the multipotent TE cells?
Molecular basis of the first cell fate determination in mouse embryogenesis Lingyi Chen, Dekun Wang, Zhaoting Wu, Liping Ma and George Q Daley Cell Research (2010) 20:982–993. doi: 10.1038/cr.2010.106; http://www.nature.com/cr/journal/v20/n9/full/cr2010106a.html

Complex complexity.Dionisio_{September 6, 2015
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Molecular basis of the first cell fate determination in mouse embryogenesis Lingyi Chen1, Dekun Wang1, Zhaoting Wu1, Liping Ma1 and George Q Daley2 Cell Research (2010) 20:982–993. doi: 10.1038/cr.2010.106; http://www.nature.com/cr/journal/v20/n9/full/cr2010106a.html
Through proliferation and differentiation, a single cell, the zygote, can give rise to a complex organism composed of many types of cells. Up to the eight-cell embryo stage, the blastomeres are morphologically identical and distributed symmetrically in the mammalian embryo. Functionally, in some species, they are all totipotent. However, due to the compaction of blastomeres and the asymmetrical cell division at the late phase of the eight-cell embryo, the blastomeres of the morula are no longer identical. During the transition from morula to blastocyst, blastomeres differentiate, resulting in the first cell fate decision in embryogenesis, namely, the segregation of the inner cell mass and the trophectoderm. [...] regulatory mechanisms essential for the cell fate choice during blastocyst development, including transcriptional regulation, epigenetic regulation, microRNAs, and signal transduction.

decision? what are the spatiotemporal criteria and procedures underlying such decision process? Complex complexity.Dionisio_{September 6, 2015
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The Current State of Naïve Human Pluripotency Benjamin T. Dodsworth, Rowan Flynn and Sally A. Cowley DOI: 10.1002/stem.2085 http://onlinelibrary.wiley.com/doi/10.1002/stem.2085/full
There remain many challenges in the field of naïve pluripotency. All protocols for generating human naïve PSCs yield slightly different cellular states. It is still unclear which of these is closest to its in vivo counterpart. The in vivo naïve state is inherently transient, so continuous in vitro culture may be detrimental. In the near future, naïve hPSCs may be useful for accessing paths of differentiation which have been previously unreachable.

A few issues remain unresolved. Work in progress... stay tuned. Complex complexity.Dionisio_{September 5, 2015
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Structure and mechanism of the T-box riboswitches Jinwei Zhang and Adrian R. Ferré-D'Amaré WIREs RNA 2015, 6:419–433. doi: 10.1002/wrna.1285 http://onlinelibrary.wiley.com/doi/10.1002/wrna.1285/abstract
The unveiling of the structure and mechanism of the T-box system thus expands our appreciation of the range of capabilities and modes of action of structured noncoding RNAs, and hints at the existence of networks of noncoding RNAs that communicate through both, structural and sequence specificity. WIREs RNA 2015, 6:419–433. doi: 10.1002/wrna.1285

Dionisio_{September 5, 2015
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tRNA: Vast reservoir of RNA molecules with unexpected regulatory function Renaud Geslain and Tao Pan PNAS vol. 108 no. 40 Renaud Geslain, 16489–16490, doi: 10.1073/pnas.1113715108 http://www.pnas.org/content/108/40/16489.full
Transfer RNA (tRNA) is a ubiquitous class of housekeeping RNA required for reading the genetic code in protein synthesis. The involvement of tRNA in translation begins with the transfer of amino acids onto cognate tRNA catalyzed by specific aminoacyl-tRNA synthetases. Aminoacyl-tRNAs are then shuttled to the ribosome by elongation factors, where the amino acid is incorporated into the new polypeptide chain. Finding tRNA regulators and their RNA, protein or other molecular targets will present a heretofore unanticipated opportunity for the postgenomic era.

Unexpected? Unanticipated? What else did they expect?Dionisio_{September 5, 2015
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tRNAs: Cellular barcodes for amino acids Edited by Manuel Santos Rajat Banerjeea, Shawn Chend, Kiley Darea, Marla Gilreathc, Mette Praetorius-Ibbab, Medha Rainac, Noah M. Reynoldsa, Theresa Rogersa, Hervé Roya, Srujana S. Yadavallia, Michael Ibba doi:10.1016/j.febslet.2009.11.013 Volume 584, Issue 2, Pages 387–395 Transfer RNA http://www.sciencedirect.com/science/article/pii/S0014579309009065
Whether such a complex between AdT, aaRS and tRNA also forms during the indirect synthesis of Gln-tRNAGln remains an open question. [...] the exact nature of tRNA-dependent aa-AMP hydrolysis remains unclear and the precise mechanisms are unknown. The physiological significance of these multiple-specificity aaPGS activities remains an open question. Rare tRNAs are also important for biofilm formation and dispersal in E. coli, and it seems likely that still other roles remain to be discovered. Further exploration is now needed to more fully understand how tRNAs and their cleavage products function as regulatory RNAs. Possible roles for tRNAs and pseudo-tRNAs outside translation are also starting to emerge, for example as members of the broader class of regulatory RNAs. Overall, recent advances have expanded the functional repertoire of aa-tRNAs, tRNAs, and pseudo-tRNAs, and it seems likely that many more functions await discovery in the post-genomic era.

Complex complexityDionisio_{September 5, 2015
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Role of cell–cell adhesion complexes in embryonic stem cell biology Tim Pieters and Frans van Roy doi: 10.1242/?jcs.146720 J Cell Sci 127, 2603-2613. http://jcs.biologists.org/content/127/12/2603.long
Pluripotent embryonic stem cells (ESCs) can self-renew or differentiate into any cell type within an organism. precisely regulated levels and activities of several junctional proteins, in particular E-cadherin, safeguard naive pluripotency and are a prerequisite for complete somatic cell reprogramming. Stem cells can have different embryonic origins that coincide with their developmental potency (Box 1). A hallmark of pluripotent stem cells is their ability to generate cell types that descend from all three germ layers (ectoderm, mesoderm and ectoderm) in vitro and in vivo. Pluripotent stem cells can be divided into two categories, naive and primed, that have specific characteristics The role of the related protein p120ctn in ESCs has only been partly elucidated [...] Although our knowledge on the role of classic cadherins in embryonic stem cells is already vast, many subtleties still await discovery and exploration. These interesting observations indicate that further research on gap junction proteins in embryonic stem cells is warranted. Much still needs to be learned about how junctional proteins and their upstream regulators are causally involved in specific degrees of cell stemness.

Complex complexity. A few issues remain unresolved. Work in progress... stay tuned.Dionisio_{September 4, 2015
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Box @866 Yes, agree! Thanks for commenting on this. They keep dreaming in la-la-land, "pie-pie in the sky" wishful thinking. Too bad. Their awakening could be more shocking later. Just look at the example with morphogenesis: They wondered how in the world the right cells end up in the right place at the right time. Then the great eureka moment arrived: morphogen gradients! Hurrah! Champagne corks flew out everywhere... all night long celebration... finally we knew how it works... pop-sci mags went nuts with click-bait "mystery solved!" headlines Well, the next morning, after they were recovered from the hangovers, the realization that now they had to deal with new issues: (1) how in the world these morphogen gradients are formed and (2) how are they "read" and interpreted by the cells? Complex complexity. :)Dionisio_{September 4, 2015
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@863
Sadeghi: Understanding the mechanisms by which hundreds of diverse cell types develop from a single mammalian zygote has been a central challenge of developmental biology.
Without central command who has overview it cannot be done. IOW it can never be a bottom-up process.
Sadeghi: There are even more aspects of the cell biology that are critical for understanding development and differentiation. While gene-to-gene interactions are essential for the cells to differentiate, cell-to-cell communications are crucial for the embryo to balance the required quantity of each cell type, and to develop tissues and organs.
Imagine several millions of people “communicating” and building something as complicated as a human body. Without central command who has overview it cannot be done.
Sadeghi: In absence of signals and intercellular communication, development would terminate in a salt-and-pepper mixture of differentiated cell types without any pattern.
Sure, but “communication” isn’t enough. Orders are to be followed without question. And those orders have to be absolutely correct and coordinated. And without overview what or who can give correct orders?
Sadeghi: Cell division and epigenetic mechanisms such as DNA methylation and histone modifications are the other crucial factors that influence the starting point and shape of the epigenetic landscape for each cell.
Those “epigenetic mechanisms” lack the overview and authority to be the directors of the coordinated building process.Box_{September 4, 2015
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CDH2 and CDH11 act as regulators of stem cell fate decisions Stella Alimpertia, Stelios T. Andreadis doi:10.1016/j.scr.2015.02.002 Stem Cell Research Volume 14, Issue 3, Pages 270–282 http://www.sciencedirect.com/science/article/pii/S187350611500029X
Accumulating evidence suggests that the mechanical and biochemical signals originating from cell–cell adhesion are critical for stem cell lineage specification. Intercellular adhesion plays important role in tissue architecture and morphogenesis by controlling the assembly of individual cells into the three-dimensional tissues. [...] the mechanical and biochemical signals originating from cell–cell adhesion remain relatively unexplored in this context. Although many studies have focused on the effects of substrate stiffness on stem cell biology, the role of intercellular adhesion forces in guiding stem cell self-renewal or differentiation has been relatively unexplored. [...] more work is necessary to understand how intercellular adhesion affects MSC differentiation and reveals some of the molecular pathways guiding this process.

Dionisio_{September 3, 2015
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#863 follow up What are the spatiotemporal criteria and procedures for the decision-making mechanisms?Dionisio_{September 3, 2015
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Increased robustness of early embryogenesis through collective decision-making by key transcription factors Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkan, Hamid Pezeshk, Hamidreza Chitsaz and Mehdi Sadeghi BMC Systems Biology 2015, 9:23 doi:10.1186/s12918-015-0169-8 http://www.biomedcentral.com/1752-0509/9/23
Understanding the mechanisms by which hundreds of diverse cell types develop from a single mammalian zygote has been a central challenge of developmental biology. While the proposed hierarchical regulatory circuitry provides a basis for better understanding and analysis of developmental bifurcations, we do not exclude more complicated mechanisms such as the role of signaling networks and morphogens. There are even more aspects of the cell biology that are critical for understanding development and differentiation. While gene-to-gene interactions are essential for the cells to differentiate, cell-to-cell communications are crucial for the embryo to balance the required quantity of each cell type, and to develop tissues and organs. In absence of signals and intercellular communication, development would terminate in a salt-and-pepper mixture of differentiated cell types without any pattern. Cell division and epigenetic mechanisms such as DNA methylation and histone modifications are the other crucial factors that influence the starting point and shape of the epigenetic landscape for each cell. [...] this comprehensive approach to the Waddington landscape will provide new insights to the developmental biology. [...] any factor that has the potential to affect the expression or function of those TFs, such as genetic mutations, extrinsic stimuli and intrinsic noise, could deviate the corresponding cell fate decision.

Interesting paper. Complex complexity. Work in progress... stay tuned.Dionisio_{September 3, 2015
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Surrounding tissues canalize motile cardiopharyngeal progenitors towards collective polarity and directed migration Stephanie Gline, Nicole Kaplan, Yelena Bernadskaya, Yusuff Abdu* and Lionel Christiaen‡ doi: 10.1242/dev.115444 Development 142, 544-554. http://dev.biologists.org/content/142/3/544.full
Unequivocal identification of the TVC-inducing FGF ligand(s) will be necessary to formally establish the signaling mechanisms that govern TVC induction. Future studies combining dnSar1 expression in multiple tissues will be necessary Future studies will assay whether C6-like plays a role in the early mutual attraction of TVCs. Future studies will determine whether the integrins and/or other cell-matrix adhesion systems are involved in cell-cell and cell-matrix adhesions of TVCs during migration. Future studies will explore the causal relationships between the polarized migration of TVCs, and their subsequent oriented asymmetric cell divisions and fate specification events.

Complex complexity.Dionisio_{September 3, 2015
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Pom1 gradient buffering through intermolecular auto?phosphorylation Micha Hersch, Olivier Hachet, Sascha Dalessi, Pranav Ullal, Payal Bhatia, Sven Bergmann, Sophie G Martin DOI 10.15252/msb.20145996 Molecular Systems Biology (2015) 11: 818 http://msb.embopress.org/content/11/7/818
Concentration-dependent intermolecular autocatalysis may represent a simple, built-in control mechanism to buffer biological activities.

Interesting.Dionisio_{September 2, 2015
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