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Table of Contents: November 2014

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Recombination hotspots are subject to an evolutionary process, called biased gene conversion (BGC), which favors mutations suppressing their recombination activity. The analysis of an archaic human genome (Denisovan) showed that this self-destructive process is extremely fast, as the life expectancy of most active hotspots is less than 100,000 generations. This suggests that the turnover of recombination hotspots might be the consequence of a Red Queen process: the activity of recombination hotspots leads to their rapid loss by BGC, and the genes that determine the location of hotspots are therefore regularly under selective pressure to switch to new targets. See Lesecque et al.

Interview

Review

Regularized Machine Learning in the Genetic Prediction of Complex Traits

Sebastian Okser, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Samuli Ripatti, Tero Aittokallio

Research Articles

Natural Polymorphisms in Human APOBEC3H and HIV-1 Vif Combine in Primary T Lymphocytes to Affect Viral G-to-A Mutation Levels and Infectivity

Eric W. Refsland, Judd F. Hultquist, Elizabeth M. Luengas, Terumasa Ikeda, Nadine M. Shaban, Emily K. Law, William L. Brown, Cavan Reilly, Michael Emerman, Reuben S. Harris

SAS-1 Is a C2 Domain Protein Critical for Centriole Integrity in C. elegans

Lukas von Tobel, Tamara Mikeladze-Dvali, Marie Delattre, Fernando R. Balestra, Simon Blanchoud, Susanne Finger, Graham Knott, Thomas Müller-Reichert, Pierre Gönczy

HAM-5 Functions As a MAP Kinase Scaffold during Cell Fusion in Neurospora crassa

Wilfried Jonkers, Abigail C. Leeder, Charles Ansong, Yuexi Wang, Feng Yang, Trevor L. Starr, David G. Camp II, Richard D. Smith, N. Louise Glass

The Protein O-glucosyltransferase Rumi Modifies Eyes Shut to Promote Rhabdomere Separation in Drosophila

Amanda R. Haltom, Tom V. Lee, Beth M. Harvey, Jessica Leonardi, Yi-Jiun Chen, Yang Hong, Robert S. Haltiwanger, Hamed Jafar-Nejad

Three RNA Binding Proteins Form a Complex to Promote Differentiation of Germline Stem Cell Lineage in Drosophila

Di Chen, Chan Wu, Shaowei Zhao, Qing Geng, Yu Gao, Xin Li, Yang Zhang, Zhaohui Wang

Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

Zhihao Ding, Yunyun Ni, Sander W. Timmer, Bum-Kyu Lee, Anna Battenhouse, Sandra Louzada, Fengtang Yang, Ian Dunham, Gregory E. Crawford, Jason D. Lieb, Richard Durbin, Vishwanath R. Iyer, Ewan Birney

A Systems Genetics Approach Identifies CXCL14, ITGAX, and LPCAT2 as Novel Aggressive Prostate Cancer Susceptibility Genes

Kendra A. Williams, Minnkyong Lee, Ying Hu, Jonathan Andreas, Shashank J. Patel, Suiyuan Zhang, Peter Chines, Abdel Elkahloun, Settara Chandrasekharappa, J. Silvio Gutkind, Alfredo A. Molinolo, Nigel P. S. Crawford

The Complex I Subunit NDUFA10 Selectively Rescues Drosophila pink1 Mutants through a Mechanism Independent of Mitophagy

Joe H. Pogson, Rachael M. Ivatt, Alvaro Sanchez-Martinez, Roberta Tufi, Emma Wilson, Heather Mortiboys, Alexander J. Whitworth

A Thermolabile Aldolase A Mutant Causes Fever-Induced Recurrent Rhabdomyolysis without Hemolytic Anemia

Asmaa Mamoune, Michel Bahuau, Yamina Hamel, Valérie Serre, Michele Pelosi, Florence Habarou, Marie-Ange Nguyen Morel, Bertrand Boisson, Sabrina Vergnaud, Mai Thao Viou, Luc Nonnenmacher, Monique Piraud, Patrick Nusbaum, Joseph Vamecq, Norma Romero, Chris Ottolenghi, Jean-Laurent Casanova, Pascale de Lonlay

Genetic Analysis of a Novel Tubulin Mutation That Redirects Synaptic Vesicle Targeting and Causes Neurite Degeneration in C. elegans

Jiun-Min Hsu, Chun-Hao Chen, Yen-Chih Chen, Kent L. McDonald, Mark Gurling, Albert Lee, Gian Garriga, Chun-Liang Pan

Systematic Comparison of the Effects of Alpha-synuclein Mutations on Its Oligomerization and Aggregation

Diana F. Lázaro, Eva F. Rodrigues, Ramona Langohr, Hedieh Shahpasandzadeh, Thales Ribeiro, Patrícia Guerreiro, Ellen Gerhardt, Katharina Kröhnert, Jochen Klucken, Marcos D. Pereira, Blagovesta Popova, Niels Kruse, Brit Mollenhauer, Silvio O. Rizzoli, Gerhard H. Braus, Karin M. Danzer, Tiago F. Outeiro

The Talin Head Domain Reinforces Integrin-Mediated Adhesion by Promoting Adhesion Complex Stability and Clustering

Stephanie J. Ellis, Emily Lostchuck, Benjamin T. Goult, Mohamed Bouaouina, Michael J. Fairchild, Pablo López-Ceballos, David A. Calderwood, Guy Tanentzapf

The COP9 Signalosome Converts Temporal Hormone Signaling to Spatial Restriction on Neural Competence

Yi-Chun Huang, Yu-Nung Lu, June-Tai Wu, Cheng-Ting Chien, Haiwei Pi

Functional Diversity of Carbohydrate-Active Enzymes Enabling a Bacterium to Ferment Plant Biomass

Magali Boutard, Tristan Cerisy, Pierre-Yves Nogue, Adriana Alberti, Jean Weissenbach, Marcel Salanoubat, Andrew C. Tolonen

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response

Erin A. Becker, Phillip M. Seitzer, Andrew Tritt, David Larsen, Megan Krusor, Andrew I. Yao, Dongying Wu, Dominique Madern, Jonathan A. Eisen, Aaron E. Darling, Marc T. Facciotti

Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization

Danelle K. Seymour, Daniel Koenig, Jörg Hagmann, Claude Becker, Detlef Weigel

The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes

Yann Lesecque, Sylvain Glémin, Nicolas Lartillot, Dominique Mouchiroud, Laurent Duret

ATPase-Independent Type-III Protein Secretion in Salmonella enterica

Marc Erhardt, Max E. Mertens, Florian D. Fabiani, Kelly T. Hughes

Pseudoautosomal Region 1 Length Polymorphism in the Human Population

Martin A. Mensah, Matthew S. Hestand, Maarten H. D. Larmuseau, Mala Isrie, Nancy Vanderheyden, Matthias Declercq, Erika L. Souche, Jeroen Van Houdt, Radka Stoeva, Hilde Van Esch, Koen Devriendt, Thierry Voet, Ronny Decorte, Peter N. Robinson, Joris R. Vermeesch

Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability

Ayesha Hasan, Cristina Cotobal, Caia D. S. Duncan, Juan Mata

Coordinate Regulation of Stem Cell Competition by Slit-Robo and JAK-STAT Signaling in the Drosophila Testis

Rachel R. Stine, Leah J. Greenspan, Kapil V. Ramachandran, Erika L. Matunis

Genome-Wide Associations between Genetic and Epigenetic Variation Influence mRNA Expression and Insulin Secretion in Human Pancreatic Islets

Anders H. Olsson, Petr Volkov, Karl Bacos, Tasnim Dayeh, Elin Hall, Emma A. Nilsson, Claes Ladenvall, Tina Rönn, Charlotte Ling

Rad59-Facilitated Acquisition of Y′ Elements by Short Telomeres Delays the Onset of Senescence

Dmitri Churikov, Ferose Charifi, Marie-Noëlle Simon, Vincent Géli

The Role of cis Regulatory Evolution in Maize Domestication

Zachary H. Lemmon, Robert Bukowski, Qi Sun, John F. Doebley

A Germline Polymorphism of Thymine DNA Glycosylase Induces Genomic Instability and Cellular Transformation

Ashley Sjolund, Antonia A. Nemec, Nicolas Paquet, Aishwarya Prakash, Patrick Sung, Sylvie Doublié, Joann B. Sweasy

The CSN/COP9 Signalosome Regulates Synaptonemal Complex Assembly during Meiotic Prophase I of Caenorhabditis elegans

Heather Brockway, Nathan Balukoff, Martha Dean, Benjamin Alleva, Sarit Smolikove

Stress Granule-Defective Mutants Deregulate Stress Responsive Transcripts

Xiaoxue Yang, Yi Shen, Elena Garre, Xinxin Hao, Daniel Krumlinde, Marija Cvijović, Christina Arens, Thomas Nyström, Beidong Liu, Per Sunnerhagen

A Functional Portrait of Med7 and the Mediator Complex in Candida albicans

Faiza Tebbji, Yaolin Chen, Julien Richard Albert, Kearney T. W. Gunsalus, Carol A. Kumamoto, André Nantel, Adnane Sellam, Malcolm Whiteway

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

Alan O. Bergland, Emily L. Behrman, Katherine R. O'Brien, Paul S. Schmidt, Dmitri A. Petrov

ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing

Justin R. Pritchard, Michael C. Chao, Sören Abel, Brigid M. Davis, Catherine Baranowski, Yanjia J. Zhang, Eric J. Rubin, Matthew K. Waldor

24-Hour Rhythms of DNA Methylation and Their Relation with Rhythms of RNA Expression in the Human Dorsolateral Prefrontal Cortex

Andrew S. P. Lim, Gyan P. Srivastava, Lei Yu, Lori B. Chibnik, Jishu Xu, Aron S. Buchman, Julie A. Schneider, Amanda J. Myers, David A. Bennett, Philip L. De Jager

Formal Comments

Glutamate Receptor Gene GRIN2A, Coffee, and Parkinson Disease

Taye H. Hamza, Erin M. Hill-Burns, William K. Scott, Jeffrey M. Vance, Stewart A. Factor, Cyrus P. Zabetian, Haydeh Payami

Lack of Replication of the GRIN2A-by-Coffee Interaction in Parkinson Disease

Ismaïl Ahmed, Pei-Chen Lee, Christina M. Lill, Susan Searles Nielsen, Fanny Artaud, Lisa G. Gallagher, Marie-Anne Loriot, Claire Mulot, Magali Nacfer, Tian Liu, Joanna M. Biernacka, Sebastian Armasu, Kari Anderson, Federico M. Farin, Christina Funch Lassen, Johnni Hansen, Jørgen H. Olsen, Lars Bertram, Demetrius M. Maraganore, Harvey Checkoway, Beate Ritz, Alexis Elbaz

Let's Face It—Complex Traits Are Just Not That Simple

Benedikt Hallgrimsson, Washington Mio, Ralph S. Marcucio, Richard Spritz