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Table of Contents

October 2016

The mammalian genome is partitioned into submegabase-sized chromatin domains. Gene expression is highly regulated within domains, depending on their structure, whereas the chromatin itself is highly dynamic. We observed the movement of single nucleosomes using fluorescent labels (H2B-PA-mCherry; red spots in the background) in nuclei of living human cells. By modeling chromatin as a polymer with a fractal domain structure (lumps of fiber), the movement of nucleosomes was shown to depend on the domain structure they belong to. This means that the measured movement can provide information on how the fiber is packed in living cells. Shinkai et al.

Image Credit: Shinkai et al.

Editorials

Ten Simple Rules for Developing a MOOC

David T. Manallack, Elizabeth Yuriev

Ten Simple Rules for Digital Data Storage

Edmund M. Hart, Pauline Barmby, David LeBauer, François Michonneau, Sarah Mount, Patrick Mulrooney, Timothée Poisot, Kara H. Woo, Naupaka B. Zimmerman, Jeffrey W. Hollister

Education

A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution

C. Brandon Ogbunugafor, Daniel L. Hartl

Research Articles

SARAH Domain-Mediated MST2-RASSF Dimeric Interactions

Goar Sánchez-Sanz, Bartłomiej Tywoniuk, David Matallanas, David Romano, Lan K. Nguyen, Boris N. Kholodenko, Edina Rosta, Walter Kolch, Nicolae-Viorel Buchete

Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein

Jianhui Tian, Cesar A. López, Cynthia A. Derdeyn, Morris S. Jones, Abraham Pinter, Bette Korber, S. Gnanakaran

Mechano-chemical Interactions in Cardiac Sarcomere Contraction: A Computational Modeling Study

Lauren J. Dupuis, Joost Lumens, Theo Arts, Tammo Delhaas

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters

René Dreos, Giovanna Ambrosini, Philipp Bucher

Functional Connectivity’s Degenerate View of Brain Computation

Guillaume Marrelec, Arnaud Messé, Alain Giron, David Rudrauf

Eco-evolutionary Model of Rapid Phenotypic Diversification in Species-Rich Communities

Paula Villa Martín, Jorge Hidalgo, Rafael Rubio de Casas, Miguel A. Muñoz

Identifying Anatomical Origins of Coexisting Oscillations in the Cortical Microcircuit

Hannah Bos, Markus Diesmann, Moritz Helias

How Do Efficient Coding Strategies Depend on Origins of Noise in Neural Circuits?

Braden A. W. Brinkman, Alison I. Weber, Fred Rieke, Eric Shea-Brown

Genetic Redundancies Enhance Information Transfer in Noisy Regulatory Circuits

Guillermo Rodrigo, Juan F. Poyatos

Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates

Jumpei F Yamagishi, Nen Saito, Kunihiko Kaneko

Likelihood-Based Inference of B Cell Clonal Families

Duncan K. Ralph, Frederick A. Matsen IV

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern

Unsupervised Learning in an Ensemble of Spiking Neural Networks Mediated by ITDP

Yoonsik Shim, Andrew Philippides, Kevin Staras, Phil Husbands

Optimized Treatment Schedules for Chronic Myeloid Leukemia

Qie He, Junfeng Zhu, David Dingli, Jasmine Foo, Kevin Zox Leder

Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells

Soya Shinkai, Tadasu Nozaki, Kazuhiro Maeshima, Yuichi Togashi

The Spatial Dynamics of Predators and the Benefits and Costs of Sharing Information

Matthieu Barbier, James R. Watson

Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways

Beibei Wang, Joshua Francis, Monika Sharma, Sean M. Law, Alexander V. Predeus, Michael Feig

PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse

Kerstin Reuter, Alexander Biehl, Laurena Koch, Volkhard Helms

Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency

Max Schelker, Caroline Maria Mair, Fabian Jolmes, Robert-William Welke, Edda Klipp, Andreas Herrmann, Max Flöttmann, Christian Sieben

Apparent Motion Suppresses Responses in Early Visual Cortex: A Population Code Model

Nathalie Van Humbeeck, Tom Putzeys, Johan Wagemans

Glucose Oscillations Can Activate an Endogenous Oscillator in Pancreatic Islets

Joseph P. McKenna, Raghuram Dhumpa, Nikita Mukhitov, Michael G. Roper, Richard Bertram

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

Alexander T. Dilthey, Pierre-Antoine Gourraud, Alexander J. Mentzer, Nezih Cereb, Zamin Iqbal, Gil McVean

Structural Identifiability of Dynamic Systems Biology Models

Alejandro F. Villaverde, Antonio Barreiro, Antonis Papachristodoulou

Probabilistic Learning by Rodent Grid Cells

Allen Cheung

Catecholaminergic Regulation of Learning Rate in a Dynamic Environment

Marieke Jepma, Peter R. Murphy, Matthew R. Nassar, Mauricio Rangel-Gomez, Martijn Meeter, Sander Nieuwenhuis

MD/DPD Multiscale Framework for Predicting Morphology and Stresses of Red Blood Cells in Health and Disease

Hung-Yu Chang, Xuejin Li, He Li, George Em Karniadakis

Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements

Samuel M. D. Oliveira, Antti Häkkinen, Jason Lloyd-Price, Huy Tran, Vinodh Kandavalli, Andre S. Ribeiro