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Table of Contents: October 2008

Top: observed distribution of auxin transporters (PIN proteins) in shoot apical meristem cells of Arabidopsis. The image was obtained by immunolabelling of the PIN1 auxin-carrier using confocal microscopy. Bottom left: Digitized version of the top image where the efflux carriers have been manually positioned. Bottom right: simulated distribution of efflux carriers (in red) emerging from a flux-based polarization hypothesis of auxin transport. This type of virtual experiment makes it possible to test in silico different hypotheses on mechanisms that are not fully accessible experimentally and to assess their plausibility by comparing predictions with experimental data (see Stoma et al., doi:10.1371/journal.pcbi.1000207).

Image Credit: Szymon Stoma (INRIA, Virtual Plants project team), Christophe Godin (INRIA, Virtual Plants project team), Jan Traas (ENS-Lyon, RDP)

Reviews

Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web

Duncan Hull, Steve R. Pettifer, Douglas B. Kell

Research Articles

A Learning Theory for Reward-Modulated Spike-Timing-Dependent Plasticity with Application to Biofeedback

Robert Legenstein, Dejan Pecevski, Wolfgang Maass

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes

Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda

Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data

Piers J. Ingram, Michael P. H. Stumpf, Jaroslav Stark

Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm

Jun Yan, Haifang Wang, Yuting Liu, Chunxuan Shao

Impact of Limited Solvent Capacity on Metabolic Rate, Enzyme Activities, and Metabolite Concentrations of S. cerevisiae Glycolysis

Alexei Vazquez, Marcio A. de Menezes, Albert-László Barabási, Zoltan N. Oltvai

Noise during Rest Enables the Exploration of the Brain's Dynamic Repertoire

Anandamohan Ghosh, Y. Rho, A. R. McIntosh, R. Kötter, V. K. Jirsa

Dose-to-Duration Encoding and Signaling beyond Saturation in Intracellular Signaling Networks

Marcelo Behar, Nan Hao, Henrik G. Dohlman, Timothy C. Elston

Biophysical Basis for Three Distinct Dynamical Mechanisms of Action Potential Initiation

Steven A. Prescott, Yves De Koninck, Terrence J. Sejnowski

Aggregation Propensity of the Human Proteome

Elodie Monsellier, Matteo Ramazzotti, Niccolò Taddei, Fabrizio Chiti

The Inactivation Principle: Mathematical Solutions Minimizing the Absolute Work and Biological Implications for the Planning of Arm Movements

Bastien Berret, Christian Darlot, Frédéric Jean, Thierry Pozzo, Charalambos Papaxanthis, Jean Paul Gauthier

Fusion and Fission of Genes Define a Metric between Fungal Genomes

Pascal Durrens, Macha Nikolski, David Sherman

An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution

Elhanan Borenstein, David C. Krakauer

Organization of Physical Interactomes as Uncovered by Network Schemas

Eric Banks, Elena Nabieva, Bernard Chazelle, Mona Singh

Cell Groups Reveal Structure of Stimulus Space

Carina Curto, Vladimir Itskov

Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development

Szymon Stoma, Mikael Lucas, Jérôme Chopard, Marianne Schaedel, Jan Traas, Christophe Godin

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

Jacek Puchałka, Matthew A. Oberhardt, Miguel Godinho, Agata Bielecka, Daniela Regenhardt, Kenneth N. Timmis, Jason A. Papin, Vítor A. P. Martins dos Santos