Table of Contents: April 2009

The bacterial chaperonin GroEL is an ATP-regulated molecular machine. It assists misfolded or partially folded proteins to unfold and refold into the correct native structure. The molecule consists of two rings, each composed of seven subunits. A dominant mechanism of motion during this process, which is predicted by the elastic network model, is the concerted counter-rotation of the two rings. This image displays four successive snapshots, viewed from the top, corresponding to successive steps of this allosteric process (see Yang et al., doi:10.1371/journal.pcbi.1000360).

Image Credit: The image was created by Zheng Yang (University of Pittsburgh, United States of America).


Ten Simple Rules To Combine Teaching and Research

Quentin Vicens, Philip E. Bourne


Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article

David Shotton, Katie Portwin, Graham Klyne, Alistair Miles

Research Articles

Estimating the Location and Spatial Extent of a Covert Anthrax Release

Judith Legrand, Joseph R. Egan, Ian M. Hall, Simon Cauchemez, Steve Leach, Neil M. Ferguson

Spontaneous Local Gamma Oscillation Selectively Enhances Neural Network Responsiveness

Se-Bum Paik, Tribhawan Kumar, Donald A. Glaser

Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines

Xing Xu, Yongmei Ji, Gary D. Stormo

Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions

Claudiu A. Giurumescu, Paul W. Sternberg, Anand R. Asthagiri

Polymorphism Data Can Reveal the Origin of Species Abundance Statistics

Yosef E. Maruvka, Nadav M. Shnerb

The Role of Environmental Transmission in Recurrent Avian Influenza Epidemics

Romulus Breban, John M. Drake, David E. Stallknecht, Pejman Rohani

A Dynamic Network Approach for the Study of Human Phenotypes

César A. Hidalgo, Nicholas Blumm, Albert-László Barabási, Nicholas A. Christakis

Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum

Orland Gonzalez, Susanne Gronau, Friedhelm Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt

A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1)

Srinivas Ramachandran, Adrian W. R. Serohijos, Le Xu, Gerhard Meissner, Nikolay V. Dokholyan

A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases

Dipak Barua, James R. Faeder, Jason M. Haugh

Evolutionary Epidemiology of Drug-Resistance in Space

Florence Débarre, Thomas Lenormand, Sylvain Gandon

Information Flow Analysis of Interactome Networks

Patrycja Vasilyev Missiuro, Kesheng Liu, Lihua Zou, Brian C. Ross, Guoyan Zhao, Jun S. Liu, Hui Ge

The Homeostasis of Plasmodium falciparum-Infected Red Blood Cells

Jakob M. A. Mauritz, Alessandro Esposito, Hagai Ginsburg, Clemens F. Kaminski, Teresa Tiffert, Virgilio L. Lew

Amyloidogenesis Abolished by Proline Substitutions but Enhanced by Lipid Binding

Ping Jiang, Weixin Xu, Yuguang Mu

Maximal Extraction of Biological Information from Genetic Interaction Data

Gregory W. Carter, David J. Galas, Timothy Galitski

Natural Image Coding in V1: How Much Use Is Orientation Selectivity?

Jan Eichhorn, Fabian Sinz, Matthias Bethge

Dissociating Variability and Effort as Determinants of Coordination

Ian O'Sullivan, Etienne Burdet, Jörn Diedrichsen

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

James Robert White, Niranjan Nagarajan, Mihai Pop

Tumor-Immune Interaction, Surgical Treatment, and Cancer Recurrence in a Mathematical Model of Melanoma

Steffen Eikenberry, Craig Thalhauser, Yang Kuang

Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes

Curt Scharfe, Henry Horng-Shing Lu, Jutta K. Neuenburg, Edward A. Allen, Guan-Cheng Li, Thomas Klopstock, Tina M. Cowan, Gregory M. Enns, Ronald W. Davis

Design Principles for Riboswitch Function

Chase L. Beisel, Christina D. Smolke

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling

Bree B. Aldridge, Julio Saez-Rodriguez, Jeremy L. Muhlich, Peter K. Sorger, Douglas A. Lauffenburger

Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis

Gitanjali Yadav, Rajesh S. Gokhale, Debasisa Mohanty

An Analytically Solvable Model for Rapid Evolution of Modular Structure

Nadav Kashtan, Avi E. Mayo, Tomer Kalisky, Uri Alon