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Table of Contents | January 2010

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The checkerboard strategy.

Many experiments suggest that the sustainability of an ecosystem depends on its spatial structure; when a local subpopulation goes extinct the empty habitat patch is "rescued" by immigrants from nearby patches. Trying to protect endangered species via the construction of conservation corridors, the engineer faces a Goldilocks problem: weak migration does not allow for the rescue of empty patches; strong migration leads to spatial coherence and global extinction. In this work, the authors show that maximum sustainability is achieved when the migration rate is tuned to the value that yields a checkerboard spatial pattern (see Ben Zion et al., doi:10.1371/journal.pcbi.1000643).

Image Credit: Gur Yaari (Yale University)

 
 

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Perspective

Live Coverage of Scientific Conferences Using Web Technologies

Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider

 

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Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances

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Axonal Velocity Distributions in Neural Field Equations

Ingo Bojak, David T. J. Liley

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Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells

Shakti Gupta, Mano Ram Maurya, Shankar Subramaniam

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FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model

Dennis L. Chao, M. Elizabeth Halloran, Valerie J. Obenchain, Ira M. Longini Jr

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A Reaction-Diffusion Model of ROS-Induced ROS Release in a Mitochondrial Network

Lufang Zhou, Miguel A. Aon, Tabish Almas, Sonia Cortassa, Raimond L. Winslow, Brian O'Rourke

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Acute Effects of Sex Steroid Hormones on Susceptibility to Cardiac Arrhythmias: A Simulation Study

Pei-Chi Yang, Junko Kurokawa, Tetsushi Furukawa, Colleen E. Clancy

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Protein Interaction Networks—More Than Mere Modules

Stefan Pinkert, Jörg Schultz, Jörg Reichardt

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Recombination Rate and Selection Strength in HIV Intra-patient Evolution

Richard A. Neher, Thomas Leitner

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Automatic Assignment of EC Numbers

Volker Egelhofer, Ida Schomburg, Dietmar Schomburg

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Optimizing Metapopulation Sustainability through a Checkerboard Strategy

Yossi Ben Zion, Gur Yaari, Nadav M. Shnerb

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SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

Aroop Sircar, Jeffrey J. Gray

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Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

Isabella Daidone, Hannes Neuweiler, Sören Doose, Markus Sauer, Jeremy C. Smith

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A Neurophysiologically Plausible Population Code Model for Feature Integration Explains Visual Crowding

Ronald van den Berg, Jos B. T. M. Roerdink, Frans W. Cornelissen

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Quantitative Modeling of GRK-Mediated β2AR Regulation

Sharat J. Vayttaden, Jacqueline Friedman, Tuan M. Tran, Thomas C. Rich, Carmen W. Dessauer, Richard B. Clark

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A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology

Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, J. Andrew McCammon

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Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local

Wee Siong Goh, Yuriy Orlov, Jingmei Li, Neil D. Clarke

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How Synchronization Protects from Noise

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Knots: Attractive Places with High Path Tortuosity in Mouse Open Field Exploration

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An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

Rod K. Nibbe, Mehmet Koyutürk, Mark R. Chance

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Associating Genes and Protein Complexes with Disease via Network Propagation

Oron Vanunu, Oded Magger, Eytan Ruppin, Tomer Shlomi, Roded Sharan

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A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules

Wei Zhang, Jun Zhu, Eric E. Schadt, Jun S. Liu

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Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

Daniel Seeliger, Bert L. de Groot

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Network-Free Inference of Knockout Effects in Yeast

Tal Peleg, Nir Yosef, Eytan Ruppin, Roded Sharan

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Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families

Marc Röttig, Christian Rausch, Oliver Kohlbacher

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Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach

Christiaan Klijn, Jan Bot, David J. Adams, Marcel Reinders, Lodewyk Wessels, Jos Jonkers

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Modeling Mitochondrial Bioenergetics with Integrated Volume Dynamics

Jason N. Bazil, Gregery T. Buzzard, Ann E. Rundell

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Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

Lukas Burger, Erik van Nimwegen

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