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Table of Contents: March 2009

COVER

Nearing the structure of the human huntingtin protein.

Image Credit: Cartoon created using Google SketchUp and BiasViz by Miguel Andrade-Navarro (Max Delbrück Center for Molecular Medicine, Germany).
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For many years, it has been known that mutations in the human huntingtin protein are responsible for Huntington chorea, a neurodegenerative disease. However, very little is known about the structure and function of this long protein. Using a computational method on a sequence alignment of huntingtin with its orthologs (output shown in the background), we have predicted that this protein contains three elongated domains (alpha-rods, yellow cylinders) that are involved in intramolecular (left) and intermolecular (right) interactions (see Palidwor et al., doi:10.1371/journal.pcbi.1000304). This work opens avenues for further characterization of huntingtin and other proteins with alpha-rods.

Review

A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale

Jason W. Bohland, Caizhi Wu, Helen Barbas, Hemant Bokil, Mihail Bota, Hans C. Breiter, Hollis T. Cline, John C. Doyle, Peter J. Freed, Ralph J. Greenspan, Suzanne N. Haber, Michael Hawrylycz, Daniel G. Herrera, Claus C. Hilgetag, Z. Josh Huang, Allan Jones, Edward G. Jones, Harvey J. Karten, David Kleinfeld, Rolf Kötter, Henry A. Lester, John M. Lin, Brett D. Mensh, Shawn Mikula, Jaak Panksepp, Joseph L. Price, Joseph Safdieh, Clifford B. Saper, Nicholas D. Schiff, Jeremy D. Schmahmann, Bruce W. Stillman, Karel Svoboda, Larry W. Swanson, Arthur W. Toga, David C. Van Essen, James D. Watson, Partha P. Mitra

Research Articles

Biomedical Discovery Acceleration, with Applications to Craniofacial Development

Sonia M. Leach, Hannah Tipney, Weiguo Feng, William A. Baumgartner Jr., Priyanka Kasliwal, Ronald P. Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter

Hypertrophy and/or Hyperplasia: Dynamics of Adipose Tissue Growth

Junghyo Jo, Oksana Gavrilova, Stephanie Pack, William Jou, Shawn Mullen, Anne E. Sumner, Samuel W. Cushman, Vipul Periwal

BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis

Allen W. Bryan Jr., Matthew Menke, Lenore J. Cowen, Susan L. Lindquist, Bonnie Berger

Accurate Prediction of Peptide Binding Sites on Protein Surfaces

Evangelia Petsalaki, Alexander Stark, Eduardo García-Urdiales, Robert B. Russell

Broadband Criticality of Human Brain Network Synchronization

Manfred G. Kitzbichler, Marie L. Smith, Søren R. Christensen, Ed Bullmore

Computational Model of the Insect Pheromone Transduction Cascade

Yuqiao Gu, Philippe Lucas, Jean-Pierre Rospars

Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis

Matthew A. Hibbs, Chad L. Myers, Curtis Huttenhower, David C. Hess, Kai Li, Amy A. Caudy, Olga G. Troyanskaya

A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis

Gabriel Krouk, Daniel Tranchina, Laurence Lejay, Alexis A. Cruikshank, Dennis Shasha, Gloria M. Coruzzi, Rodrigo A. Gutiérrez

T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules

Aidan MacNamara, Ulrich Kadolsky, Charles R. M. Bangham, Becca Asquith

Positional Information Generated by Spatially Distributed Signaling Cascades

Javier Muñoz-García, Zoltan Neufeld, Boris N. Kholodenko

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors

Manu, Svetlana Surkova, Alexander V. Spirov, Vitaly V. Gursky, Hilde Janssens, Ah-Ram Kim, Ovidiu Radulescu, Carlos E. Vanario-Alonso, David H. Sharp, Maria Samsonova, John Reinitz

Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin

Gareth A. Palidwor, Sergey Shcherbinin, Matthew R. Huska, Tamas Rasko, Ulrich Stelzl, Anup Arumughan, Raphaele Foulle, Pablo Porras, Luis Sanchez-Pulido, Erich E. Wanker, Miguel A. Andrade-Navarro

Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis

Wolfram Stacklies, M. Cristina Vega, Matthias Wilmanns, Frauke Gräter

Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations

Vanessa Leone, Gianluca Lattanzi, Carla Molteni, Paolo Carloni

Cortical Factor Feedback Model for Cellular Locomotion and Cytofission

Shin I. Nishimura, Masahiro Ueda, Masaki Sasai

Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter

Boian S. Alexandrov, Vladimir Gelev, Sang Wook Yoo, Alan R. Bishop, Kim Ø. Rasmussen, Anny Usheva

Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome

Stella Veretnik, Christopher Wills, Philippe Youkharibache, Ruben E. Valas, Philip E. Bourne

Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis

Jessica H. Fong, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Michail Y. Lobanov, Oxana V. Galzitskaya, Anna R. Panchenko

Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data

Minghui Wang, Xiaohua Hu, Gang Li, Lindsey J. Leach, Elena Potokina, Arnis Druka, Robbie Waugh, Michael J. Kearsey, Zewei Luo

Robustness in Glyoxylate Bypass Regulation

Guy Shinar, Joshua D. Rabinowitz, Uri Alon

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery

Schraga Schwartz, Nurit Gal-Mark, Nir Kfir, Ram Oren, Eddo Kim, Gil Ast

Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation

Emili Balaguer-Ballester, Nicholas R. Clark, Martin Coath, Katrin Krumbholz, Susan L. Denham

The Modulation Transfer Function for Speech Intelligibility

Taffeta M. Elliott, Frédéric E. Theunissen