March 2010

The cytoplasm of the gram-negative bacterium Escherichia coli is very densely packed with macromolecules, and this highly crowded environment is expected to have a significant impact on the diffusive and thermodynamic properties of its constituents. Continuing progress in the field of structural biology now allows molecular simulations of the cytoplasm to be performed with structurally detailed models, providing a new, computational view of macromolecular behavior in vivo (see McGuffee, Elcock, doi:10.1371/journal.pcbi.1000694).

Image Credit: Adrian H Elcock (University of Iowa)

Message from ISCB

Getting Started in Gene Orthology and Functional Analysis

Gang Fang, Nitin Bhardwaj, Rebecca Robilotto, Mark B. Gerstein

PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000703

Research Articles

Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance

Bernie J. Daigle Jr, Alicia Deng, Tracey McLaughlin, Samuel W. Cushman, Margaret C. Cam, Gerald Reaven, Philip S. Tsao, Russ B. Altman

PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000718

Specialization Can Drive the Evolution of Modularity

Carlos Espinosa-Soto, Andreas Wagner

PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000719

Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV

Max von Kleist, Stephan Menz, Wilhelm Huisinga

PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000720

The Impact of Contact Tracing in Clustered Populations

Thomas House, Matt J. Keeling

PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000721

Investigating Homology between Proteins using Energetic Profiles

James O. Wrabl, Vincent J. Hilser

PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000722

Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction

Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov

PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000723

A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions

Chuan-Yun Li, Yong Zhang, Zhanbo Wang, Yan Zhang, Chunmei Cao, Ping-Wu Zhang, Shu-Juan Lu, Xiao-Mo Li, Quan Yu, Xiaofeng Zheng, Quan Du, George R. Uhl, Qing-Rong Liu, Liping Wei

PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000734

Tumor Growth Rate Determines the Timing of Optimal Chronomodulated Treatment Schedules

Samuel Bernard, Branka Čajavec Bernard, Francis Lévi, Hanspeter Herzel

PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000712

Estimating the Stoichiometry of HIV Neutralization

Carsten Magnus, Roland R. Regoes

PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000713

Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm

Timothy Nugent, David T. Jones

PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000714

Patient Referral Patterns and the Spread of Hospital-Acquired Infections through National Health Care Networks

Tjibbe Donker, Jacco Wallinga, Hajo Grundmann

PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000715

Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation

Carey D. Nadell, Kevin R. Foster, João B. Xavier

PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000716

Predicted Auxiliary Navigation Mechanism of Peritrichously Flagellated Chemotactic Bacteria

Nikita Vladimirov, Dirk Lebiedz, Victor Sourjik

PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000717

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function

Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt

PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000700

Non-Linear Neuronal Responses as an Emergent Property of Afferent Networks: A Case Study of the Locust Lobula Giant Movement Detector

Sergi Bermúdez i Badia, Ulysses Bernardet, Paul F. M. J. Verschure

PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000701

Effects of Transcriptional Pausing on Gene Expression Dynamics

Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro

PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000704

Detailed Simulations of Cell Biology with Smoldyn 2.1

Steven S. Andrews, Nathan J. Addy, Roger Brent, Adam P. Arkin

PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000705

A Multiscale Model to Investigate Circadian Rhythmicity of Pacemaker Neurons in the Suprachiasmatic Nucleus

Christina Vasalou, Michael A. Henson

PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000706

Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells

Jun Cai, Dan Xie, Zhewen Fan, Hiram Chipperfield, John Marden, Wing H. Wong, Sheng Zhong

PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000707

Slower Visuomotor Corrections with Unchanged Latency are Consistent with Optimal Adaptation to Increased Endogenous Noise in the Elderly

Michael Sherback, Francisco J. Valero-Cuevas, Raffaello D'Andrea

PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000708

Comparing Families of Dynamic Causal Models

Will D. Penny, Klaas E. Stephan, Jean Daunizeau, Maria J. Rosa, Karl J. Friston, Thomas M. Schofield, Alex P. Leff

PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000709

Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response

Muyoung Heo, Eugene I. Shakhnovich

PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000710

Neocortical Axon Arbors Trade-off Material and Conduction Delay Conservation

Julian M. L. Budd, Krisztina Kovács, Alex S. Ferecskó, Péter Buzás, Ulf T. Eysel, Zoltán F. Kisvárday

PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000711

Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ_9-40 Peptide: A Comparison to Agitated Fibrils

Chun Wu, Michael T. Bowers, Joan-Emma Shea

PLOS Computational Biology: published March 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000693

Cover

A molecular model of the bacterial cytoplasm.