Table of Contents

July 2011

Neocortical L5 pyramidal cells generate dendritic Ca2+ spikes in distal apical region (top red region and corresponding voltage trace) as well as Na+ spikes in perisomatic region (bottom red region and voltage trace). The two spiking zones interact electrically in a complex "ping-pong"-like manner. This study provides detailed conductance-based models that faithfully replicate these important spiking properties together with their variability, as measured experimentally. This was achieved using multi-objective evolutionary optimization algorithm and experimentally measured statistics of both Ca2+ and Na+ spiking features. The study highlights the candidate key biophysical mechanisms underlying these active electrical properties of L5 pyramidal cells. (see Hay et al., doi:10.1371/journal.pcbi.1002107).

Image Credit: Ariel Chai, Brisbane, Australia


Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

Marc A. Marti-Renom, Leonid A. Mirny

Research Articles

Decelerating Spread of West Nile Virus by Percolation in a Heterogeneous Urban Landscape

Krisztian Magori, Waheed I. Bajwa, Sarah Bowden, John M. Drake

Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties

Etay Hay, Sean Hill, Felix Schürmann, Henry Markram, Idan Segev

Indirect Reciprocity under Incomplete Observation

Mitsuhiro Nakamura, Naoki Masuda

The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics

Qian Wang, Kao-Chen Liang, Arkadiusz Czader, M. Neal Waxham, Margaret S. Cheung

A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells

Tian Hong, Jianhua Xing, Liwu Li, John J. Tyson

The Dynamical Mechanism of Auto-Inhibition of AMP-Activated Protein Kinase

Cheng Peng, Teresa Head-Gordon

The Eps8/IRSp53/VASP Network Differentially Controls Actin Capping and Bundling in Filopodia Formation

Federico Vaggi, Andrea Disanza, Francesca Milanesi, Pier Paolo Di Fiore, Elisabetta Menna, Michela Matteoli, Nir S. Gov, Giorgio Scita, Andrea Ciliberto

Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models

Iulian Pruteanu-Malinici, Daniel L. Mace, Uwe Ohler

Modelling the Effects of Population Structure on Childhood Disease: The Case of Varicella

Romain Silhol, Pierre-Yves Boëlle

In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans

Christoph Kaleta, Luís F. de Figueiredo, Sarah Werner, Reinhard Guthke, Michael Ristow, Stefan Schuster

Proteins with Complex Architecture as Potential Targets for Drug Design: A Case Study of Mycobacterium tuberculosis

Bálint Mészáros, Judit Tóth, Beáta G. Vértessy, Zsuzsanna Dosztányi, István Simon

MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets

Kristen M. Naegle, Roy E. Welsch, Michael B. Yaffe, Forest M. White, Douglas A. Lauffenburger

In vivo Conditions Induce Faithful Encoding of Stimuli by Reducing Nonlinear Synchronization in Vestibular Sensory Neurons

Adam D. Schneider, Kathleen E. Cullen, Maurice J. Chacron

Stimulus-Dependent State Transition between Synchronized Oscillation and Randomly Repetitive Burst in a Model Cerebellar Granular Layer

Takeru Honda, Tadashi Yamazaki, Shigeru Tanaka, Soichi Nagao, Tetsuro Nishino

Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity

Daniel J. Cole, Eeson Rajendra, Meredith Roberts-Thomson, Bryn Hardwick, Grahame J. McKenzie, Mike C. Payne, Ashok R. Venkitaraman, Chris-Kriton Skylaris

Prediction of Cell Penetrating Peptides by Support Vector Machines

William S. Sanders, C. Ian Johnston, Susan M. Bridges, Shane C. Burgess, Kenneth O. Willeford

Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases

Michael D. Daily, George N. Phillips Jr., Qiang Cui

Does the Potential for Chaos Constrain the Embryonic Cell-Cycle Oscillator?

R. Scott McIsaac, Kerwyn Casey Huang, Anirvan Sengupta, Ned S. Wingreen

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

Dongjun Chung, Pei Fen Kuan, Bo Li, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin Dewey, Sündüz Keleş

Optimal Stimulus Shapes for Neuronal Excitation

Daniel B. Forger, David Paydarfar, John R. Clay

A Dynamical Model Reveals Gene Co-Localizations in Nucleus

Jing Kang, Bing Xu, Ye Yao, Wei Lin, Conor Hennessy, Peter Fraser, Jianfeng Feng