BioEssays

Cover image for Vol. 35 Issue 5

May 2013

Volume 35, Issue 5

Pages 409–495

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Contents and highlights of this issue
    5. Idea revisited
    6. Insights & Perspectives
    7. Prospects & Overviews
    8. Meetings
    9. BiotecVisions
    10. Next Issue
    1. You have free access to this content
      BioEssays 5/2013

      Version of Record online: 12 APR 2013 | DOI: 10.1002/bies.201390017

      Computer simulations in 3D image-derived geometries provide a complementary tool for studying biological processes in space and time, as outlined by Ivo F. Sbalzarini on pages 482–490 of this issue. The cover art shows a computer visualization of the 3D structure of the endoplasmic reticulum of a VERO cell. The 3D shape of this organelle has been reconstructed from confocal microscopy images using computational image-processing methods. Computer simulations then allow the study of dynamic processes in such realistic biological shapes, such as the diffusion of fl uorescent marker proteins in a fl uorescence recovery experiment. This enables one to perturb parameters of the system that are experimentally not controllable (such as the shape of the organelle) and observe quantities that are experimentally not observable. Ivo F. Sbalzarini provides an introduction to the, to many unfamiliar, world of computational biology, explaining commonly used terms and highlighting prospects and pitfalls.

  2. Editorial

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Contents and highlights of this issue
    5. Idea revisited
    6. Insights & Perspectives
    7. Prospects & Overviews
    8. Meetings
    9. BiotecVisions
    10. Next Issue
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    2. You have free access to this content
  3. Contents and highlights of this issue

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Contents and highlights of this issue
    5. Idea revisited
    6. Insights & Perspectives
    7. Prospects & Overviews
    8. Meetings
    9. BiotecVisions
    10. Next Issue
    1. You have free access to this content
      BioEssays 5/2013 (pages 410–411)

      Version of Record online: 12 APR 2013 | DOI: 10.1002/bies.201390016

  4. Idea revisited

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Contents and highlights of this issue
    5. Idea revisited
    6. Insights & Perspectives
    7. Prospects & Overviews
    8. Meetings
    9. BiotecVisions
    10. Next Issue
    1. Idea revisited

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    2. You have free access to this content
      Back to the beginning: The initiation of cancer (page 413)

      Cesar Cobaleda and Isidro Sánchez-García

      Version of Record online: 2 APR 2013 | DOI: 10.1002/bies.201300024

  5. Insights & Perspectives

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Contents and highlights of this issue
    5. Idea revisited
    6. Insights & Perspectives
    7. Prospects & Overviews
    8. Meetings
    9. BiotecVisions
    10. Next Issue
    1. Ex laboratorio

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    2. Ideas & Speculations

      You have full text access to this OnlineOpen article
      Linguistic evidence supports date for Homeric epics (pages 417–420)

      Eric Lewin Altschuler, Andreea S. Calude, Andrew Meade and Mark Pagel

      Version of Record online: 18 FEB 2013 | DOI: 10.1002/bies.201200165

      Thumbnail image of graphical abstract

      The Homeric epics are among the greatest masterpieces of literature, but when they were produced is not known with certainty. Here we apply evolutionary-linguistic phylogenetic statistical methods to differences in Homeric, Modern Greek and ancient Hittite vocabulary items to estimate a date of approximately 710–760 BCE for these great works.

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      Modular genetic control of innate behaviors (pages 421–424)

      Xiaohong Xu

      Version of Record online: 11 MAR 2013 | DOI: 10.1002/bies.201200167

      Thumbnail image of graphical abstract

      Neural pathways underlying innate behaviors, such as stereotyped mating behaviors (raster plot), are genetically hardwired in the brain. Modular genomic information including cis-elements (colored boxes) and protein domains (gray shapes) dictates that the brain is anatomically and functionally modular. As a result, genetic control of innate behaviors is also modular.

  6. Prospects & Overviews

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Contents and highlights of this issue
    5. Idea revisited
    6. Insights & Perspectives
    7. Prospects & Overviews
    8. Meetings
    9. BiotecVisions
    10. Next Issue
    1. Recently in press

      Initiation of clathrin-mediated endocytosis: All you need is two? (pages 425–429)

      Laura E. Swan

      Version of Record online: 26 FEB 2013 | DOI: 10.1002/bies.201200129

      Thumbnail image of graphical abstract

      Coccuci et al. propose that clathrin coated pits (ccps) randomly nucleate via simultaneous arrival of two AP2 complexes and a clathrin triskelion at the plasma membrane. The nascent ccp stabilizes by incorporating more clathrin/AP2 complexes and early factors such as FCHo1/2, before integrating transmembrane cargoes and acquiring curvature.

    2. G protein-coupled receptors engage the mammalian Hippo pathway through F-actin : F-Actin, assembled in response to Galpha12/13 induced RhoA-GTP, promotes dephosphorylation and activation of the YAP oncogene (pages 430–435)

      Laura Regué, Fan Mou and Joseph Avruch

      Version of Record online: 1 MAR 2013 | DOI: 10.1002/bies.201200163

      Thumbnail image of graphical abstract

      The hippo pathway, a protein kinase cascade activated by cell contact, phosphorylates the YAP oncogene to inhibit proliferation. GPCRs like PAR1 that recruit Gα12/13 and activate RhoA can dephosphorylate and activate YAP through an inhibition of the hippo pathway. This requires F-actin assembly, which also activates YAP through hippo-independent mechanisms.

    3. From deep sequencing to viral tagging: Recent advances in viral metagenomics (pages 436–442)

      Dana Willner and Philip Hugenholtz

      Version of Record online: 1 MAR 2013 | DOI: 10.1002/bies.201200174

      Thumbnail image of graphical abstract

      Recent advances in viral metagenomics include techniques for sequencing limiting amounts of viral nucleic acids, the use of ultra-deep sequencing, and viral tagging to determine virus–host interactions. Mock communities should be used to rigorously evaluate new protocols, and special consideration must be given to the storage of metagenomic data.

    4. Review essays

      Cycling progenitors maintain epithelia while diverse cell types contribute to repair (pages 443–451)

      David P. Doupé and Philip H. Jones

      Version of Record online: 6 MAR 2013 | DOI: 10.1002/bies.201200166

      Thumbnail image of graphical abstract

      Epithelial homeostasis in tissues from mouse epidermis, oesophagus and intestine to Drosophila intestine is maintained by population self-renewal rather than individual, hard-wired asymmetric division. In wound healing stem, progenitor and even differentiated cells may all exhibit flexibility of fate without necessitating a quiescent stem cell reserve.

    5. Problems & Paradigms

      You have full text access to this OnlineOpen article
      Microtubule dynamic instability: A new model with coupled GTP hydrolysis and multistep catastrophe (pages 452–461)

      Hugo Bowne-Anderson, Marija Zanic, Monika Kauer and Jonathon Howard

      Version of Record online: 27 MAR 2013 | DOI: 10.1002/bies.201200131

      Thumbnail image of graphical abstract

      The mechanisms underlying microtubule dynamic instability are not well understood. We review the existing theoretical models, from single-protofilament to multiple-protofilament kinetic models utilizing a variety of hydrolysis mechanisms. We provide a novel model utilizing a coupled GTP hydrolysis mechanism, accounting for many experimental observations, including the multistep nature of catastrophe.

      Corrected by:

      Errata: Erratum

      Vol. 35, Issue 6, 579, Version of Record online: 3 MAY 2013

    6. You have full text access to this OnlineOpen article
      Multi-step down-regulation of the secretory pathway in mitosis: A fresh perspective on protein trafficking (pages 462–471)

      Foong May Yeong

      Version of Record online: 12 MAR 2013 | DOI: 10.1002/bies.201200144

      Thumbnail image of graphical abstract

      The molecular details of protein trafficking in interphase cells are well-studied. Here I highlight interesting data showing down-regulation of protein trafficking at various levels in mitosis by CDK1. I propose that a deeper understanding of the secretory pathway could emerge from studies with a perspective from the cell division cycle.

    7. Methods, Models & Techniques

      A simple model for the fate of the cytokinesis midbody remnant: Implications for remnant degradation by autophagy : Modeling remnant production and degradation enables re-interpretation of published data and improves design of future experiments (pages 472–481)

      Elizabeth Faris Crowell, Jean-Yves Tinevez and Arnaud Echard

      Version of Record online: 1 MAR 2013 | DOI: 10.1002/bies.201200132

      Thumbnail image of graphical abstract

      As cells divide, they produce bridges, which decay into remnants. Remnants are then thought to decay by autophagy. Defective remnant decay correlates with enhanced proliferation. We generated a model for remnant turnover, measured remnant lifetime, and simulated published experiments. We find that remnant decay can occur by autophagy-independent pathways.

    8. You have full text access to this OnlineOpen article
      Modeling and simulation of biological systems from image data (pages 482–490)

      Ivo F. Sbalzarini

      Version of Record online: 27 MAR 2013 | DOI: 10.1002/bies.201200051

      Thumbnail image of graphical abstract

      Computational modeling and simulation is a key technique in systems biology. It helps dissect complex dynamics in space and time. Spatiotemporal modeling using geometries reconstructed from quantitative images allows us to address questions of morphogenesis, growth, and shape. I outline the field of image-based modeling and simulation in biology.

  7. Meetings

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Contents and highlights of this issue
    5. Idea revisited
    6. Insights & Perspectives
    7. Prospects & Overviews
    8. Meetings
    9. BiotecVisions
    10. Next Issue
    1. Meetings

      Understanding phenotypic responses to global change : Report from the meeting “Global change in the Mediterranean: Learning from experiences worldwide” November 2012, Seville, Spain (pages 491–495)

      Laura Gangoso, Rocío Márquez-Ferrando, Francisco Ramírez, Ivan Gomez-Mestre and Jordi Figuerola

      Version of Record online: 6 MAR 2013 | DOI: 10.1002/bies.201300019

      Thumbnail image of graphical abstract

      The symposium “Global change in the Mediterranean: learning from experiences worldwide” held on 15–16 November 2012 in Seville, was funded by the EU's FP7 within the project ECOGENES. The contributions highlighted the need to incorporate environmentally-induced variations in organismal development and ecological interactions into the global change research program.

  8. BiotecVisions

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Contents and highlights of this issue
    5. Idea revisited
    6. Insights & Perspectives
    7. Prospects & Overviews
    8. Meetings
    9. BiotecVisions
    10. Next Issue
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      BiotecVisions 2013, April (pages A1-A8)

      Version of Record online: 12 APR 2013 | DOI: 10.1002/bies.201390018

  9. Next Issue

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Contents and highlights of this issue
    5. Idea revisited
    6. Insights & Perspectives
    7. Prospects & Overviews
    8. Meetings
    9. BiotecVisions
    10. Next Issue
    1. You have free access to this content
      BioEssays – Next Issue

      Version of Record online: 12 APR 2013 | DOI: 10.1002/bies.201390019

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