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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[...] sequence-driven DNA structures may represent a new layer of regulatory information. [...] understanding how cells prevent the negative effects of R-loops yet allowing their positive effects is a challenge for the years to come.
R-loops and initiation of DNA replication in human cells: a missing link? Rodrigo Lombraña, Ricardo Almeida, Alba Álvarez and María Gómez* Front. Genet., 28 April 2015 | http://dx.doi.org/10.3389/fgene.2015.00158 http://journal.frontiersin.org/article/10.3389/fgene.2015.00158/abstract

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Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Eukaryotic cells rapidly duplicate their genome by initiating DNA replication at multiple origins. In multicellular eukaryotes, the rules for how certain genomic loci are selected to be active origins remain incompletely defined. It remains possible that other proteins bound to the amplicon NDRs prevent ORC access to DNA when the origin is not active. It remains an open question whether small changes to nucleosome position, or a change in the dynamic association of nucleosomes with origin DNA, contribute to the developmental activation of the origins. [...] other approaches will be needed to determine whether they are resident at amplicon origins and contribute to their activity. [...] intrinsic DNA architecture at DAFC-66D may help choreograph the interplay between ORC and origin nucleosomes. Important remaining questions include how HATs are recruited to the amplicons and how histone acetylation facilitates different steps of pre-RC assembly and activation. [...] high-resolution MNase-Seq maps, combined with other methods afforded by the model amplicon origins, will permit a further definition of how nucleosome position and modification promotes pre-RC assembly at a subclass of origins.
DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila Jun Liu, Kurt Zimmer, Douglas B. Rusch, Neha Paranjape, Ram Podicheti, Haixu Tang and Brian R. Calvi Nucl. Acids Res. 43 (18): 8746-8761. doi: 10.1093/nar/gkv766 http://nar.oxfordjournals.org/content/43/18/8746.full

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[...] the purpose for the initial increase in Tetrahymena ORC and MCM abundance awaits further investigation [...] [...] the dependence of ORC during endoreplication phase II is less clear. How might replication initiation be achieved with limiting amounts of ORC? Advances in genome-wide analysis, such as nascent strand-seq should provide fundamental insights in the underlying mechanism for ‘alternative’ DNA replication programs [...]
Lee P-H, Meng X, Kapler GM (2015) Developmental Regulation of the Tetrahymena thermophila Origin Recognition Complex. PLoS Genet 11(1): e1004875. doi:10.1371/journal.pgen.1004875 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004875

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The developmental oscillations in ORC and MCM protein levels that we uncovered suggest that the rules for DNA replication change at different stages of development. They are intriguing because ORC levels do not correlate with the amount of DNA that is synthesized at a given time.
Lee P-H, Meng X, Kapler GM (2015) Developmental Regulation of the Tetrahymena thermophila Origin Recognition Complex. PLoS Genet 11(1): e1004875. doi:10.1371/journal.pgen.1004875 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004875

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[...] elongation is the rate limiting step when ORC and MCM levels are reduced in this species. Whether this reflects how origins are distributed throughout the Tetrahymena genome (i.e. dispersed versus clustered origins), different requirements for ORC:MCM stoichiometry, or alternative mechanisms for replication initiation in the amitotic macronucleus awaits further studies.
Lee P-H, Meng X, Kapler GM (2015) Developmental Regulation of the Tetrahymena thermophila Origin Recognition Complex. PLoS Genet 11(1): e1004875. doi:10.1371/journal.pgen.1004875 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004875

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DNA replication initiates at specific sites in chromosomes, termed origins of replication. While the genomic architecture of replication initiation sites varies widely across the eukaryotic lineage, a conserved feature is their association with the six-subunit Origin Recognition Complex (ORC) [...] macronuclear DNA replication is governed by the same regulatory mechanisms that function in canonical (G1-S-G2-M) cell cycles. They include[:] [1] ORC-dependent, site-specific initiation of DNA replication, [2] cell cycle regulated pre-RC assembly, [3] S phase inactivation of ORC (to prevent re-replication) [4] and the presence of a robust ATR-mediated DNA damage/replication stress checkpoint response. The successive changes in ORC and MCMs protein levels that we uncovered indicate that developmentally regulated replication programs are more complex than previously imagined.
Lee P-H, Meng X, Kapler GM (2015) Developmental Regulation of the Tetrahymena thermophila Origin Recognition Complex. PLoS Genet 11(1): e1004875. doi:10.1371/journal.pgen.1004875 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004875

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Further studies are needed to determine the relative contribution of chromatin-associated and pre-deposition histones to the H3 acetylation profile in HU-arrested Tetrahymena. The underlying mechanism for replication initiation in ORC-depleted Tetrahymena awaits further studies. High-throughput mapping of replication origins should provide novel insights into underlying mechanism(s) for replication initiation site selection in Tetrahymena.
Sandoval PY, Lee P-H, Meng X, Kapler GM (2015) Checkpoint Activation of an Unconventional DNA Replication Program in Tetrahymena. PLoS Genet 11(7): e1005405. doi:10.1371/journal.pgen.1005405 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005405

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DNA damage and replication stress activate cell cycle checkpoint responses that protect the integrity of eukaryotic chromosomes. A major challenge of the cell cycle is to faithfully transmit chromosomes to daughter cells. This is accomplished through the replication and segregation of chromosomes during the respective S and M phases. The integrity of chromosomes is under constant assault from extrinsic and intrinsic sources that directly damage DNA or generate roadblocks for the replication machinery. The resulting DNA damage and replication stress can irreparably harm chromosomes. While the proteins that elicit checkpoint responses are conserved, there are fundamental differences in how eukaryotes deal with DNA damage.
Sandoval PY, Lee P-H, Meng X, Kapler GM (2015) Checkpoint Activation of an Unconventional DNA Replication Program in Tetrahymena. PLoS Genet 11(7): e1005405. doi:10.1371/journal.pgen.1005405 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005405

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[...] it is not clear that there is a kinesin isoform that autonomously targets specifically to the somatodendritic compartment [...] [...] a role for dynein in the localization of mRNA to dendrites is likely, and merits further investigation.
Actin and Myosin-Dependent Localization of mRNA to Dendrites Varuzhan Balasanyan, Don B. Arnold •DOI: 10.1371/journal.pone.0092349 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092349

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The axon is unique in its morphology and function and it contains several specialized structures and mechanisms that ensure proper axonal functioning. [...] comprehensive knowledge on the how the cytoskeleton organization relates to the function of specific axonal structures is limited. [...] it will be important to elucidate the currently ambiguous role of actin within the presynapse to understand the molecular mechanisms of presynaptic organization and functioning. Also, it will be important to examine the contribution of MTs in presynaptic functioning. In addition, unraveling the molecular mechanisms of the barrier function of the AIS and how the underlying cytoskeleton contributes to this function will increase our understanding of the mechanisms of polarized transport. Moreover, further identification of motor proteins, their adaptors, cargoes, and regulatory mechanisms will be essential to understand the precise molecular mechanisms underlying axonal transport. [...] fundamental knowledge about intracellular transport mechanisms and cytoskeleton organization will be important for the development of new therapeutic strategies.
The axonal cytoskeleton: from organization to function Josta T. Kevenaar and Casper C. Hoogenraad Front. Mol. Neurosci., http://dx.doi.org/10.3389/fnmol.2015.00044 http://journal.frontiersin.org/article/10.3389/fnmol.2015.00044/abstract

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Neurons are the basic cells that process information within the brain. They are compartmentalized into two morphologically, molecularly and functionally distinct domains; the axonal and the somatodendritic compartments. Multiple short and highly branched dendrites function in receiving and integrating electrical synaptic inputs from thousands of neurons. In contrast, only a single axon is responsible for transmitting this integrated information in the form of an action potential, an electrical excitation wave that travels along the axonal membrane. To ensure that information is transmitted properly, the axon has a unique cytoskeletal organization and contains several specialized structures, including the axon initial segment (AIS) and presynaptic buttons.
The axonal cytoskeleton: from organization to function Josta T. Kevenaar and Casper C. Hoogenraad Front. Mol. Neurosci., http://dx.doi.org/10.3389/fnmol.2015.00044 http://journal.frontiersin.org/article/10.3389/fnmol.2015.00044/abstract

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Emerging evidence suggest that the unique cytoskeleton organization in the axon is essential for its structure and integrity. In addition, the increasing number of neurodevelopmental and neurodegenerative diseases linked to defect in actin- and microtubule-dependent processes emphasizes the importance of a properly regulated cytoskeleton for normal axonal functioning.
The axonal cytoskeleton: from organization to function Josta T. Kevenaar and Casper C. Hoogenraad Front. Mol. Neurosci., http://dx.doi.org/10.3389/fnmol.2015.00044 http://journal.frontiersin.org/article/10.3389/fnmol.2015.00044/abstract

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High-affinity binding of the CAP-Gly domain to microtubules would enhance dynein's ability to pull one spindle pole to the cortex by a mechanism that has not yet been elucidated. It is likely that additional proteins are dephosphorylated to promote cortical anchoring by dynein. [...] it will be important to discover how acentriolar spindle rotation occurs in other organisms.
Dynactin-dependent cortical dynein and spherical spindle shape correlate temporally with meiotic spindle rotation in Caenorhabditis elegans Marina E. Crowder, Jonathan R. Flynn, Karen P. McNally, Daniel B. Cortes, Kari L. Price, Paul A. Kuehnert, Michelle T. Panzica, Armann Andaya, Julie A. Leary, and Francis J. McNally doi: 10.1091/mbc.E15-05-0290 Mol. Biol. Cell vol. 26 no. 17 3030-3046 http://www.molbiolcell.org/content/26/17/3030.full

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Dynein flexibility also raises new questions about the nature of the allosteric communication between the ATPase cycle in the head and the MT binding affinity of the stalkhead that is vital to dynein’s many cellular functions.
Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules Hiroshi Imai, Tomohiro Shima, Kazuo Sutoh, Matthew L. Walker, Peter J. Knight, Takahide Kon & Stan A. Burgess Nature Communications 6, Article number: 8179 doi:10.1038/ncomms9179 http://www.nature.com/ncomms/2015/150914/ncomms9179/full/ncomms9179.html

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It will therefore be a challenge to determine the structure of any dynein-MT complex at high resolution, since current methods for this all combine data from many molecules.
Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules Hiroshi Imai, Tomohiro Shima, Kazuo Sutoh, Matthew L. Walker, Peter J. Knight, Takahide Kon & Stan A. Burgess Nature Communications 6, Article number: 8179 doi:10.1038/ncomms9179 http://www.nature.com/ncomms/2015/150914/ncomms9179/full/ncomms9179.html

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Perhaps the most striking feature of stepping dynein is the great flexibility between the ATPase domain and the track binding domain [...]
Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules Hiroshi Imai, Tomohiro Shima, Kazuo Sutoh, Matthew L. Walker, Peter J. Knight, Takahide Kon & Stan A. Burgess Nature Communications 6, Article number: 8179 doi:10.1038/ncomms9179 http://www.nature.com/ncomms/2015/150914/ncomms9179/full/ncomms9179.html

Complex complexity Work in progress... stay tunedDionisio_{November 10, 2015
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What structural mechanisms could enhance processivity of the dimer over that of monomer to reduce the probability of both heads detaching simultaneously? [...] it is unclear why either motor would behave differently from a monomer, unless this is mediated by contacts between the two heads.
Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules Hiroshi Imai, Tomohiro Shima, Kazuo Sutoh, Matthew L. Walker, Peter J. Knight, Takahide Kon & Stan A. Burgess Nature Communications 6, Article number: 8179 doi:10.1038/ncomms9179 http://www.nature.com/ncomms/2015/150914/ncomms9179/full/ncomms9179.html

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An alternative which invites future investigation is flexion of the two linker subdomains away from the unprimed conformations that they adopt in the superposed dimer.
Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules Hiroshi Imai, Tomohiro Shima, Kazuo Sutoh, Matthew L. Walker, Peter J. Knight, Takahide Kon & Stan A. Burgess Nature Communications 6, Article number: 8179 doi:10.1038/ncomms9179 http://www.nature.com/ncomms/2015/150914/ncomms9179/full/ncomms9179.html

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Our cryo-EM of stepping dynein reveals a great diversity of structures. We deduce a value of 0.035?pN?nm?1 for the elastic spring constant of this head–head linkage. The molecular basis of this elastic linkage is unclear.
Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules Hiroshi Imai, Tomohiro Shima, Kazuo Sutoh, Matthew L. Walker, Peter J. Knight, Takahide Kon & Stan A. Burgess Nature Communications 6, Article number: 8179 doi:10.1038/ncomms9179 http://www.nature.com/ncomms/2015/150914/ncomms9179/full/ncomms9179.html

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Future studies promise exciting insights...
Yes! That's exactly right! That's why we should look forward, with increasing anticipation, to reading the research papers that might be published in the days, weeks, months ahead. Because they might shed more light on the elaborate cellular and molecular information-processing choreographies orchestrated within the biological systems. The more we know, the more we have to learn. Unending Revelation of the Ultimate Reality.Dionisio_{November 10, 2015
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It remains to be seen how this domain [dynein CT-cap] exerts its effects. Future studies promise exciting insights into the mechanisms by which the CT-cap regulates the dynein nanomachine.
Control of cytoplasmic dynein force production and processivity by its C-terminal domain Matthew P. Nicholas, Peter Höök, Sibylle Brenner, Caitlin L. Wynne, Richard B. Vallee & Arne Gennerich Nature Communications 6, Article number: 6206 doi:10.1038/ncomms7206 http://www.nature.com/ncomms/2015/150211/ncomms7206/full/ncomms7206.html

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The possibility that the CT-cap can alter stepping behaviour, in addition to its impact on force generation and processivity, requires further investigation.
Control of cytoplasmic dynein force production and processivity by its C-terminal domain Matthew P. Nicholas, Peter Höök, Sibylle Brenner, Caitlin L. Wynne, Richard B. Vallee & Arne Gennerich Nature Communications 6, Article number: 6206 doi:10.1038/ncomms7206 http://www.nature.com/ncomms/2015/150211/ncomms7206/full/ncomms7206.html

Complex complexity Work In progress... stay tunedDionisio_{November 10, 2015
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[...] dynein processivity can be controlled by elements within the motor itself. The relationship between such factors, and dynactin- and CT-cap-regulated processivity remains to be addressed in detail.
Control of cytoplasmic dynein force production and processivity by its C-terminal domain Matthew P. Nicholas, Peter Höök, Sibylle Brenner, Caitlin L. Wynne, Richard B. Vallee & Arne Gennerich Nature Communications 6, Article number: 6206 doi:10.1038/ncomms7206 http://www.nature.com/ncomms/2015/150211/ncomms7206/full/ncomms7206.html

Complex complexity Work In progress... stay tunedDionisio_{November 10, 2015
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Extending or shortening the duration of specific steps in the mechanochemical cycle could affect force-bearing states of the dynein cross-bridge cycle and consequently increase the motor’s stall force and processivity. Whether such changes prove valid remains to be tested.
Control of cytoplasmic dynein force production and processivity by its C-terminal domain Matthew P. Nicholas, Peter Höök, Sibylle Brenner, Caitlin L. Wynne, Richard B. Vallee & Arne Gennerich Nature Communications 6, Article number: 6206 doi:10.1038/ncomms7206 http://www.nature.com/ncomms/2015/150211/ncomms7206/full/ncomms7206.html

Complex complexity Work In progress... stay tunedDionisio_{November 10, 2015
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We speculate that the CT-cap may act as a target for regulatory factors and/or post-translational modifications responsible for modulating mammalian dynein processivity and force output for dynein’s numerous and diverse cellular functions.
Control of cytoplasmic dynein force production and processivity by its C-terminal domain Matthew P. Nicholas, Peter Höök, Sibylle Brenner, Caitlin L. Wynne, Richard B. Vallee & Arne Gennerich Nature Communications 6, Article number: 6206 doi:10.1038/ncomms7206 http://www.nature.com/ncomms/2015/150211/ncomms7206/full/ncomms7206.html

Complex complexity Work In progress... stay tunedDionisio_{November 10, 2015
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The molecular mechanism for the anisotropy remains to be elucidated [...] Because the behavior seen here under rearward force exhibits features of both slip bonding (at low force) and ideal bonding (at higher force), we term it slip–ideal bonding. The underlying mechanism is unclear; to our knowledge this is the first report of such behavior. Future studies should address how tension affects AAA1 ATP affinity. Although AAA3 plays an important role in controlling dynein–MT attachment, the details are just emerging. It is unclear how AAA3 gates AAA1 function and how linker- vs. C-terminal tension alters this regulation. Somewhat unexpectedly, ADP binding to AAA3 weakens MT binding and minimizes the asymmetry between forward and backward unbinding forces. [...] the AAA3 conformation itself is remarkably similar in both the apo and ADP-bound structures, raising the question of how ADP binding to AAA3 might physically exert its effects.
Cytoplasmic dynein regulates its attachment to microtubules via nucleotide state-switched mechanosensing at multiple AAA domains Matthew P. Nicholas, Florian Berger, Lu Rao, Sibylle Brenner, Carol Cho, and Arne Gennerich vol. 112 no. 20 > Matthew P. Nicholas, 6371–6376, doi: 10.1073/pnas.1417422112 http://www.pnas.org/content/112/20/6371

Somewhat unexpectedly? Why? What else did they expect? Complex complexity. Work in progress ... stay tuned. Some outstanding questions get answered while new questions are raised. The more we know, the more we have to learn. Unending Revelation of the Ultimate Reality.Dionisio_{November 9, 2015
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How basement membranes balance tissue support, type IV collagen cross-linking, and dramatic expansion during development remains an open question. Live imaging of cell–basement membrane interactions during development will also allow a clearer understanding of the roles basement membrane components, associated growth factors, proteases, and receptors have in regulating diverse cellular behaviors. [...] broad analysis of organismal development and physiology will continue to provide significant findings in cell–matrix biology. [...] technical advances, and a wide experimental net, will bring a more comprehensive understanding of the fascinating, fundamental, and ancient interactions of cells and their surrounding extracellular matrix.
A developmental biologist’s “outside-the-cell” thinking David R. Sherwood JCB vol. 210 no. 3 369-372 doi: 10.1083/jcb.201501083 http://jcb.rupress.org/content/210/3/369.full

Complex complexity Work in progress… stay tunedDionisio_{November 8, 2015
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Developmental studies are poised to address many remaining fundamental questions on the cell biology of basement membranes. Basement membrane structure, composition, and assembly are still poorly understood and are primarily inferred from indirect biochemical and reconstitution studies. [...] the complexity and regulation of basement membranes is likely vast.
A developmental biologist’s “outside-the-cell” thinking David R. Sherwood JCB vol. 210 no. 3 369-372 doi: 10.1083/jcb.201501083 http://jcb.rupress.org/content/210/3/369.full

Complex complexity Work in progress… stay tunedDionisio_{November 8, 2015
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Cell biology is an enormously broad discipline that examines cell structure and function, as well as interactions between the cell and its environment. Studying cell biology during development offers one of the most dynamic, process-rich, and physiologically relevant settings for understanding the functions of cells. Thus, many seminal findings on cell signaling, the cell cycle, cell migration, cell polarization, and programmed cell death have been discovered in developmental contexts.
A developmental biologist’s “outside-the-cell” thinking David R. Sherwood JCB vol. 210 no. 3 369-372 doi: 10.1083/jcb.201501083 http://jcb.rupress.org/content/210/3/369.full

Complex complexity Work in progress... stay tunedDionisio_{November 8, 2015
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A major gap in our understanding of cell biology is how cells generate and interact with their surrounding extracellular matrix. Studying this problem during development has been particularly fruitful. Recent work on the basement membrane in developmental systems is transforming our view of this matrix from one of a static support structure to that of a dynamic scaffold that is regularly remodeled to actively shape tissues and direct cell behaviors.
A developmental biologist’s “outside-the-cell” thinking David R. Sherwood JCB vol. 210 no. 3 369-372 doi: 10.1083/jcb.201501083 http://jcb.rupress.org/content/210/3/369.full

Complex complexity Work in progress... stay tunedDionisio_{November 8, 2015
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