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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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The process of collective cell migration that occurs during Drosophila oogenesis is a highly regulated, complex system. A future research interest is to integrate more molecular signaling data into the biophysical model in an effort to recapitulate additional in vivo behaviors.
A Mathematical Model of Collective Cell Migration in a Three-Dimensional, Heterogeneous Environment David P. Stonko, Lathiena Manning, Michelle Starz-Gaiano, Bradford E. Peercy PLOS •DOI: 10.1371/journal.pone.0122799 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122799
Complex complexity.Dionisio
September 20, 2015
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In vivo, the border cell cluster has been shown to rotate or rock while moving, with different cells taking turns as the leading cell. It is not clear if this behavior requires cell-to-cell signaling, or if is an emergent property of the interplay of the physical forces of movement. In addition, while egg chambers with too many or too few border cells do not develop properly, and the number of motile cells is generally consistent, it is not known if this number is required due to the physical forces or if it is specified for other reasons.
A Mathematical Model of Collective Cell Migration in a Three-Dimensional, Heterogeneous Environment David P. Stonko, Lathiena Manning, Michelle Starz-Gaiano, Bradford E. Peercy PLOS •DOI: 10.1371/journal.pone.0122799 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122799
Complex complexity.Dionisio
September 20, 2015
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A Mathematical Model of Collective Cell Migration in a Three-Dimensional, Heterogeneous Environment David P. Stonko, Lathiena Manning, Michelle Starz-Gaiano, Bradford E. Peercy PLOS •DOI: 10.1371/journal.pone.0122799 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122799
Cell migration is essential in animal development, homeostasis, and disease progression, but many questions remain unanswered about how this process is controlled. it is not entirely known how underlying mechanisms orchestrate cell movements. new questions arise upon consideration of cells moving coordinately, or through varied environments. it is not well-known if collectively moving cells must signal to one another during the migratory process It is also unclear how the forces generated between the cluster and its surroundings result in coordinated movements.
Complex complexity.Dionisio
September 20, 2015
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Leading and trailing cells cooperate in collective migration of the zebrafish posterior lateral line primordium Damian Dalle Nogare, Katherine Somers, Swetha Rao, Miho Matsuda, Michal Reichman-Fried, Erez Raz and Ajay B. Chitnis doi: 10.1242/dev.106690 http://dev.biologists.org/content/141/16/3188.full
[...] a chemokine-independent mechanism, not accounted for in our models, is responsible for this behavior. [...] )simple yet elegant manner in which leading and trailing cells coordinate migration while leading cells steer PLLp migration by following chemokine cues, cells further back play follow-the-leader as they migrate toward FGFs produced by leading cells. The mechanism by which FGF signals polarize migratory behavior remains unclear this aspect of the model is an over simplification. the mechanisms that define cohesive migration in the PLLp remain poorly understood. Future studies will determine how mechanical tension mediated by adhesion molecules, or by chemo attractants operating at short range, contribute to cohesive migration. The iterative construction of such in silico models coupled with rigorous experimental validation promises a progressively deeper understanding of collective migration of the zebrafish PLLp system.
Complex complexity. Work in progress... stay tuned.Dionisio
September 20, 2015
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How common are navigation strategies of sperm across phyla? It is quite remarkable that a signalling pathway can encompass these computational features in a single cell. chemoattractant landscapes around an egg in a natural habitat are not known and are expected to be rather complex. To emulate these native conditions and to study how sperm, and any other microswimmers, cruise in such complex chemical landscapes is the next frontier of enquiry.
Sperm navigation along helical paths in 3D chemoattractant landscapes Jan F. Jikeli, Luis Alvarez, Benjamin M. Friedrich, Laurence G. Wilson, René Pascal, Remy Colin, Magdalena Pichlo, Andreas Rennhack, Christoph Brenker & U. Benjamin Kaupp Nature Communications 6, Article number: 7985 doi:10.1038/ncomms8985 http://www.nature.com/ncomms/2015/150817/ncomms8985/full/ncomms8985.html#t
Complex complexity. Work in progress... stay tuned.Dionisio
September 20, 2015
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What might be the cellular signalling mechanisms underlying dynamic feedback strength? Future work needs to combine holographic microscopy with fluorescence imaging techniques to monitor the signalling events in single cells during 3D chemotaxis. How similar are 2D and 3D navigation mechanisms? Future work needs to address the behavioural ‘off response’ under 2D conditions
Sperm navigation along helical paths in 3D chemoattractant landscapes Jan F. Jikeli, Luis Alvarez, Benjamin M. Friedrich, Laurence G. Wilson, René Pascal, Remy Colin, Magdalena Pichlo, Andreas Rennhack, Christoph Brenker & U. Benjamin Kaupp Nature Communications 6, Article number: 7985 doi:10.1038/ncomms8985 http://www.nature.com/ncomms/2015/150817/ncomms8985/full/ncomms8985.html#t
Complex complexity. Work in progress... stay tuned.Dionisio
September 20, 2015
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steering responses of sperm are deterministic rather than stochastic sperm survey a chemical landscape on two different timescales simultaneously the swimming path organizes the temporal stimulus pattern perceived by sperm, a principle known as information self-structuring The rapid stimulus oscillations provide a sense of direction, whereas the baseline slope controls the response strength. regulation of response strength allows sperm to tune klinotaxis behavior
Sperm navigation along helical paths in 3D chemoattractant landscapes Jan F. Jikeli, Luis Alvarez, Benjamin M. Friedrich, Laurence G. Wilson, René Pascal, Remy Colin, Magdalena Pichlo, Andreas Rennhack, Christoph Brenker & U. Benjamin Kaupp Nature Communications 6, Article number: 7985 doi:10.1038/ncomms8985 http://www.nature.com/ncomms/2015/150817/ncomms8985/full/ncomms8985.html#t
Complex complexity.Dionisio
September 19, 2015
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Many motile sperm rely on chemical and physical cues to locate the egg. A beating hair-like filament, called the flagellum, serves both as an antenna that gathers sensory cues and as a motor that propels the cell. Receptors on the flagellar surface transduce these sensory cues into cellular signals. Ultimately, these signals modulate the wave-like beating of the flagellum that steers a sperm’s swimming path.
Sperm navigation along helical paths in 3D chemoattractant landscapes Jan F. Jikeli, Luis Alvarez, Benjamin M. Friedrich, Laurence G. Wilson, René Pascal, Remy Colin, Magdalena Pichlo, Andreas Rennhack, Christoph Brenker & U. Benjamin Kaupp Nature Communications 6, Article number: 7985 doi:10.1038/ncomms8985 http://www.nature.com/ncomms/2015/150817/ncomms8985/full/ncomms8985.html#t
Does this flagellum description seem more complex than Dr. Behe's description? Complex complexity.Dionisio
September 19, 2015
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Sperm navigation along helical paths in 3D chemoattractant landscapes Jan F. Jikeli, Luis Alvarez, Benjamin M. Friedrich, Laurence G. Wilson, René Pascal, Remy Colin, Magdalena Pichlo, Andreas Rennhack, Christoph Brenker & U. Benjamin Kaupp Nature Communications 6, Article number: 7985 doi:10.1038/ncomms8985 http://www.nature.com/ncomms/2015/150817/ncomms8985/full/ncomms8985.html#t
Sperm require a sense of direction to locate the egg for fertilization. They follow gradients of chemical and physical cues provided by the egg or the oviduct. However, the principles underlying three-dimensional (3D) navigation in chemical landscapes are unknown. These findings highlight the computational sophistication by which sperm sample gradients for deterministic klinotaxis.
Complex complexity.Dionisio
September 19, 2015
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Chemokine-guided cell migration and motility inzebrafish development Jeroen Bushman & Erez Raz DOI 10.15252/embj.201490105 https://www.academia.edu/11406952/Chemokine-guided_cell_migration_and_motility_in_zebrafish_development
chemokines are at the focus of studies in developmental biology An interesting open question relates to the mechanisms responsible for the migration of neutrophils away from their migration target following wound healing. it would be informative to characterize the distribution and levels of the signals that attracted the cells to sites of injury and correlate these data with the behavior of the neutrophils. It would thus be interesting to determine the role other non-signaling chemokine receptors play in controlling chemokine-guided migration in other contexts. The coupling between directed signaling and the motility machinery is still poorly understood and constitutes a key question in the field. it would be interesting to determine the similarity and difference between the mechanism facilitating the motility and directional migration of single cells guided by chemokines and cells that respond to those signals as a group.
Complex complexity.Dionisio
September 19, 2015
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it is not known if cytonemes allow the exchange of signal molecules between cells involved in the formation of other structures needed for flight. A future challenge will be to understand how individual cytonemes are able to connect to specific cells. Exchange of signals at synapses may be a universal mechanism of paracrine signaling.
Myoblast cytonemes mediate Wg signaling from the wing imaginal disc and Delta-Notch signaling to the air sac primordium Hai Huang, Thomas B Kornberg DOI: http://dx.doi.org/10.7554/eLife.06114 eLife 2015;4:e06114 http://elifesciences.org/content/4/e06114
Complex complexity.Dionisio
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Myoblast cytonemes mediate Wg signaling from the wing imaginal disc and Delta-Notch signaling to the air sac primordium Hai Huang, Thomas B Kornberg DOI: http://dx.doi.org/10.7554/eLife.06114 eLife 2015;4:e06114 http://elifesciences.org/content/4/e06114
The flight muscles, dorsal air sacs, wing blades, and thoracic cuticle of the Drosophila adult function in concert, and their progenitor cells develop together in the wing imaginal disc. The wing disc orchestrates dorsal air sac development by producing decapentaplegic and fibroblast growth factor that travel via specific cytonemes in order to signal to the air sac primordium (ASP).
function in concert? orchestrates? biology's music! Complex complexity.Dionisio
September 19, 2015
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[...] it remains unclear how these regulators coordinate to maintain homeostasis. [...] the implication of this to crypt stability and homeostasis, which is the topic of this investigation, is relatively less understood. These results paint a somewhat different picture of small intestinal crypt homeostasis from the existing view.
The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis Huijing Du, Qing Nie, William R. Holmes •DOI: 10.1371/journal.pcbi.1004285 http://www.ploscompbiol.org/article/metrics/info:doi/10.1371/journal.pcbi.1004285
Complex complexity.Dionisio
September 19, 2015
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[...] other signals along with choreographed motion of cells are responsible for [...]
The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis Huijing Du, Qing Nie, William R. Holmes •DOI: 10.1371/journal.pcbi.1004285 http://www.ploscompbiol.org/article/metrics/info:doi/10.1371/journal.pcbi.1004285
choreographed ? Wikipedia:
Choreography is the art or practice of designing sequences of movements of physical bodies (or their depictions) in which motion, form, or both are specified. Choreography may also refer to the design itself.
Did anybody say "design"? Complex complexity.Dionisio
September 19, 2015
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The small intestinal epithelium, like our skin, is constantly being renewed. In the intestine however, this epithelium is exposed to the harsh digestive environment, necessitating much more rapid renewal. Remarkably, the entire epithelium is renewed every 4–5 days. This raises the question, how can the size and structure of this tissue be maintained given this pace.
The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis Huijing Du, Qing Nie, William R. Holmes •DOI: 10.1371/journal.pcbi.1004285 http://www.ploscompbiol.org/article/metrics/info:doi/10.1371/journal.pcbi.1004285
Complex complexity.Dionisio
September 19, 2015
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The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis Huijing Du, Qing Nie, William R. Holmes •DOI: 10.1371/journal.pcbi.1004285 http://www.ploscompbiol.org/article/metrics/info:doi/10.1371/journal.pcbi.1004285
The epithelium of the small intestinal crypt, which has a vital role in protecting the underlying tissue from the harsh intestinal environment, is completely renewed every 4–5 days by a small pool of stem cells at the base of each crypt. How is this renewal controlled and homeostasis maintained, particularly given the rapid nature of this process?
Complex complexity.Dionisio
September 19, 2015
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Critical waves and the length problem of biology Robert B. Laughlin vol. 112 no. 33 10371–10376, doi: 10.1073/pnas.1422855112 http://www.pnas.org/content/112/33/10371.full
a fundamental piece of the machinery of life is probably invisible to present-day biochemical methods because they are too slow. It is not known how living things measure their lengths. No one knows why cells are the size they are, why plants and animals are the size they are, how organs grow maintaining their proportions, and how some animal bodies regenerate lost limbs. On the matter of length determination, per se, very little progress has been made beyond Thompson’s 1917 treatise on biological form.
Complex complexity.Dionisio
September 18, 2015
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@962
Comments not required, are they?
Well, except to say that apparently the author does not understand evolution. How can anyone dare to associate the word 'mystery' with biology in the middle of the second decade of the 21st century? Doesn't science have (or is about to figure out) the answers to all fundamental questions? ;)Dionisio
September 16, 2015
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“How can collections of cells each of which is able to take only one of two states, on and off, allow human minds to think complex, meaningful thoughts?” or “How do the various organic and inorganic players in an ecosystem interact so as to produce long-term stability?” or “How do embryos acquire their increasingly complex and elegant forms?” These are profound mysteries.
How computational models can help unlock biological systems G. Wayne Brodland doi:10.1016/j.semcdb.2015.07.001 http://www.sciencedirect.com/science/article/pii/S1084952115001287
Comments not required, are they?Dionisio
September 16, 2015
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Few things in the universe are as inspiring to behold as living systems, and one of the recurring mysteries about them is how their remarkable characteristics arise from interactions between relatively simple building blocks.
How computational models can help unlock biological systems G. Wayne Brodland doi:10.1016/j.semcdb.2015.07.001 http://www.sciencedirect.com/science/article/pii/S1084952115001287
Dionisio
September 16, 2015
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How computational models can help unlock biological systems G. Wayne Brodland doi:10.1016/j.semcdb.2015.07.001 http://www.sciencedirect.com/science/article/pii/S1084952115001287
Models cannot replace experiments nor can they prove that particular mechanisms are at work in a given situation. But they can demonstrate whether or not a proposed mechanism is sufficient to produce an observed phenomenon.
Complex complexity. Work in progress... stay tuned.Dionisio
September 16, 2015
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[...] need to develop powerful new modelling approaches to build these diverse data types into meaningful theoretical models that can provide insights into normal development. Bringing together stochasticity, geometry, physics and chemical regulation in a single analytic model is probably beyond hopeless, but doing so on a computer is surely not.
Towards understanding the roles of position and geometry on cell fate decisions during preimplantation development John S. Biggins, Christophe Royer, Tomoko Watanabe, Shankar Srinivas doi:10.1016/j.semcdb.2015.09.006 Seminars in Cell & Developmental Biology http://www.sciencedirect.com/science/article/pii/S1084952115001652
Complex complexity. Work in progress... stay tuned.Dionisio
September 16, 2015
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[...] it remains relatively unexplored whether mechanical cues also participate in their regulation [...] raising the question of whether YAP/TAZ may also play a role in mechanotransduction in the preimplantation embryo [...] it remains unclear which subcellular actin structures are directly involved in the mechanosensory properties of YAP/TAZ [...] it will be important to establish whether a link exists between cortical tensions and the Hippo pathway in this context. [...] it remains unclear how these F-actin-containing rings or cap structures at the apical membrane may be involved in mechanosensing [...] Recent studies have further highlighted this level of complexity, [...] Applying this type of approach to the preimplantation embryo may prove to be challenging, [...] [...] it is unclear whether the resistive forces are elastic, viscous or surface tension or indeed important at all. [...] accurate measurements of the osmotic pressure, elastic modulus and and surface tension will need to be taken [...] Testing the importance of mechanosensing and the specific magnitude of forces in the preimplantation embryo is not trivial and the tools are not readily available.
Towards understanding the roles of position and geometry on cell fate decisions during preimplantation development John S. Biggins, Christophe Royer, Tomoko Watanabe, Shankar Srinivas doi:10.1016/j.semcdb.2015.09.006 Seminars in Cell & Developmental Biology http://www.sciencedirect.com/science/article/pii/S1084952115001652
Complex complexity. Work in progress... stay tuned.Dionisio
September 16, 2015
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[...] in addition to apical–basolateral polarity, other mechanisms are in place to define cell position and determine cell fate within the preimplantation embryo. [...] it remains unclear how Notch signalling is activated in TE cells and future studies will establish the role of ICM cells for instance in this mechanism.
Towards understanding the roles of position and geometry on cell fate decisions during preimplantation development John S. Biggins, Christophe Royer, Tomoko Watanabe, Shankar Srinivas doi:10.1016/j.semcdb.2015.09.006 Seminars in Cell & Developmental Biology http://www.sciencedirect.com/science/article/pii/S1084952115001652
Complex complexity. Work in progress... stay tuned.Dionisio
September 16, 2015
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Our data sets were not large enough to meaningfully test stochastic models. For this reason, we look forward to full linage trees for much larger numbers of embryos in the future.
Towards understanding the roles of position and geometry on cell fate decisions during preimplantation development John S. Biggins, Christophe Royer, Tomoko Watanabe, Shankar Srinivas doi:10.1016/j.semcdb.2015.09.006 Seminars in Cell & Developmental Biology http://www.sciencedirect.com/science/article/pii/S1084952115001652
Complex complexity. Work in progress... stay tuned.Dionisio
September 16, 2015
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Towards understanding the roles of position and geometry on cell fate decisions during preimplantation development John S. Biggins, Christophe Royer, Tomoko Watanabe, Shankar Srinivas doi:10.1016/j.semcdb.2015.09.006 Seminars in Cell & Developmental Biology http://www.sciencedirect.com/science/article/pii/S1084952115001652
The first lineage segregation event in mouse embryos produces two separate cell populations: inner cell mass and trophectoderm. This is understood to be brought about by cells sensing their position within the embryo and differentiating accordingly. The cellular and molecular underpinnings of this process remain under investigation and have variously been considered to be completely stochastic or alternately, subject to some predisposition set up at fertilisation or before.
Complex complexity. Work in progress... stay tuned.Dionisio
September 16, 2015
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Models for patterning primary embryonic body axes: The role of space and time Hans Meinhardt doi:10.1016/j.semcdb.2015.06.005 Seminars in Cell & Developmental Biology Volume 42, Pages 103–117 Claudins and Time, Space and the Vertebrate Body Axis
Crucial for [the generation and interpretation of spatial patterns] is an intimate link between self-enhancing and antagonistic reactions. For spatial patterning, long-ranging antagonistic reactions are required that restrict the self-enhancing reactions to generate organizing regions. Self-enhancement is also required for a permanent switch-like activation of genes. This self-enhancement is antagonized by the mutual repression of genes, making sure that in a particular cell only one gene of a set of possible genes become activated – a long range inhibition in the ‘gene space’. To activate a specific gene at particular concentration of morphogenetic gradient, observations are compatible with a systematic and time-requiring ‘promotion’ from one gene to the next until the local concentration is insufficient to accomplish a further promotion. The achieved determination is stable against a fading of the morphogen, as required to allow substantial growth. Minor modifications lead to a purely time-dependent activation of genes; both mechanisms are involved to pattern the anteroposterior axis. A mutual activation of cell states that locally exclude each other accounts for many features of the segmental patterning of the trunk.
Complex complexity.Dionisio
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A time space translation hypothesis for vertebrate axial patterning A.J. Durston, K. Zhu doi:10.1016/j.semcdb.2015.06.001 Seminars in Cell & Developmental Biology Volume 42, Pages 86–93 Claudins and Time, Space and the Vertebrate Body Axis
How vertebrates generate their anterior–posterior axis is a >90-year-old unsolved probem. [...] a timer in the gastrula's non organiser mesoderm (NOM) undergoes sequential timed interactions with the Spemann organiser (SO) during gastrulation to generate the spatial axial pattern. [...] this mechanism works via Hox collinearity and that it requires Hox functionality. The NOM timer is putatively Hox temporal collinearity. This generates a spatially collinear axial Hox pattern in the emerging dorsal central nervous system and dorsal paraxial mesoderm. The interactions with the organiser are mediated by a BMP–anti BMP dependent mechanism. [...] weaknesses, questions, uncertainties and holes in the evidence [...]
Complex ComplexityDionisio
September 16, 2015
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Spatial and temporal aspects of Wnt signaling and planar cell polarity during vertebrate embryonic development Sergei Y. Sokol doi:10.1016/j.semcdb.2015.05.002 Seminars in Cell & Developmental Biology Volume 42, Pages 78–85 Claudins and Time, Space and the Vertebrate Body Axis
Wnt signaling pathways act at multiple locations and developmental stages to specify cell fate and polarity in vertebrate embryos. A long-standing question is how the same molecular machinery can be reused to produce different outcomes. Whereas both cell fate and cell polarity are modulated by spatially- and temporally-restricted Wnt activity, the downstream signaling mechanisms are very diverse.
Complex ComplexityDionisio
September 16, 2015
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Claudin switching: Physiological plasticity of the Tight Junction Christopher T. Capaldo, Asma Nusrat doi:10.1016/j.semcdb.2015.04.003 Seminars in Cell & Developmental Biology Volume 42, Pages 22–29 Claudins and Time, Space and the Vertebrate Body Axis
Tight Junctions (TJs) are multi-molecular complexes in epithelial tissues that regulate paracellular permeability. Within the TJ complex, claudins proteins span the paracellular space to form a seal between adjacent cells. This seal allows regulated passage of ions, fluids, and solutes, contingent upon the complement of claudins expressed. With as many as 27 claudins in the human genome, the TJ seal is complex indeed. physiologic Tight Junction plasticity involves both the adaptability of claudin expression and gene specific retention in the TJ
Complex complexity.Dionisio
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