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Table of Contents: August 2011

COVER

A male and female of the African cichlids Lithochromis rubripinnis and their karyotypes.

Image Credit: Kohta Yoshida (Tokyo Institute of Technology)
Issue Image

Lithochromis rubripinnis is one species of Lake Victoria cichlids. Lake Victoria cichlids are a well-known model system for the study of speciation. Although the evolution of the sex-determination system may drive speciation, sex determination is not well-analyzed in the cichlids. In this issue of PLoS Genetics, Yoshida et al. report that L. rubripinnis have a unique sex-determination system. In this species, B chromosomes have a function in sex determination. B chromosomes are additional chromosomes known as selfish genetic elements. The image shows that the female karyotype includes two B chromosomes, while the male has none.

Research Articles

Global Chromosomal Structural Instability in a Subpopulation of Starving Escherichia coli Cells

Dongxu Lin, Ian B. Gibson, Jessica M. Moore, P. C. Thornton, Suzanne M. Leal, P. J. Hastings

Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection

Yongsheng Huang, Aimee K. Zaas, Arvind Rao, Nicolas Dobigeon, Peter J. Woolf, Timothy Veldman, N. Christine Øien, Micah T. McClain, Jay B. Varkey, Bradley Nicholson, Lawrence Carin, Stephen Kingsmore, Christopher W. Woods, Geoffrey S. Ginsburg, Alfred O. Hero III

Regulation of Caenorhabditis elegans p53/CEP-1–Dependent Germ Cell Apoptosis by Ras/MAPK Signaling

Rachael Rutkowski, Robin Dickinson, Graeme Stewart, Ashley Craig, Marianne Schimpl, Stephen M. Keyse, Anton Gartner

Specification of Drosophila Corpora Cardiaca Neuroendocrine Cells from Mesoderm Is Regulated by Notch Signaling

Sangbin Park, Erika L. Bustamante, Julie Antonova, Graeme W. McLean, Seung K. Kim

Predisposition to Cancer Caused by Genetic and Functional Defects of Mammalian Atad5

Daphne W. Bell, Nilabja Sikdar, Kyoo-young Lee, Jessica C. Price, Raghunath Chatterjee, Hee-Dong Park, Jennifer Fox, Masamichi Ishiai, Meghan L. Rudd, Lana M. Pollock, Sarah K. Fogoros, Hassan Mohamed, Christin L. Hanigan, Suiyuan Zhang, Pedro Cruz, Gabriel Renaud, Nancy F. Hansen, Praveen F. Cherukuri, Bhavesh Borate, Kirk J. McManus, Jan Stoepel, Payal Sipahimalani, Andrew K. Godwin, Dennis C. Sgroi, Maria J. Merino, Gene Elliot, Abdel Elkahloun, Charles Vinson, Minoru Takata, James C. Mullikin, Tyra G. Wolfsberg, Philip Hieter, Dae-Sik Lim, Kyungjae Myung , NISC Comparative Sequencing Program

Mutations in fam20b and xylt1 Reveal That Cartilage Matrix Controls Timing of Endochondral Ossification by Inhibiting Chondrocyte Maturation

B. Frank Eames, Yi-Lin Yan, Mary E. Swartz, Daniel S. Levic, Ela W. Knapik, John H. Postlethwait, Charles B. Kimmel

Increased RPA1 Gene Dosage Affects Genomic Stability Potentially Contributing to 17p13.3 Duplication Syndrome

Emily Outwin, Gillian Carpenter, Weimin Bi, Marjorie A. Withers, James R. Lupski, Mark O'Driscoll

A Pre-mRNA–Associating Factor Links Endogenous siRNAs to Chromatin Regulation

Kirk B. Burkhart, Shouhong Guang, Bethany A. Buckley, Lily Wong, Aaron F. Bochner, Scott Kennedy

Distinct Cdk1 Requirements during Single-Strand Annealing, Noncrossover, and Crossover Recombination

Camilla Trovesi, Marco Falcettoni, Giovanna Lucchini, Michela Clerici, Maria Pia Longhese

B Chromosomes Have a Functional Effect on Female Sex Determination in Lake Victoria Cichlid Fishes

Kohta Yoshida, Yohey Terai, Shinji Mizoiri, Mitsuto Aibara, Hidenori Nishihara, Masakatsu Watanabe, Asato Kuroiwa, Hirohisa Hirai, Yuriko Hirai, Yoichi Matsuda, Norihiro Okada

An EMT–Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype

Irina M. Shapiro, Albert W. Cheng, Nicholas C. Flytzanis, Michele Balsamo, John S. Condeelis, Maja H. Oktay, Christopher B. Burge, Frank B. Gertler

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

Julien Guglielmini, Leonor Quintais, Maria Pilar Garcillán-Barcia, Fernando de la Cruz, Eduardo P. C. Rocha

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Joelle Amselem, Christina A. Cuomo, Jan A. L. van Kan, Muriel Viaud, Ernesto P. Benito, Arnaud Couloux, Pedro M. Coutinho, Ronald P. de Vries, Paul S. Dyer, Sabine Fillinger, Elisabeth Fournier, Lilian Gout, Matthias Hahn, Linda Kohn, Nicolas Lapalu, Kim M. Plummer, Jean-Marc Pradier, Emmanuel Quévillon, Amir Sharon, Adeline Simon, Arjen ten Have, Bettina Tudzynski, Paul Tudzynski, Patrick Wincker, Marion Andrew, Véronique Anthouard, Ross E. Beever, Rolland Beffa, Isabelle Benoit, Ourdia Bouzid, Baptiste Brault, Zehua Chen, Mathias Choquer, Jérome Collémare, Pascale Cotton, Etienne G. Danchin, Corinne Da Silva, Angélique Gautier, Corinne Giraud, Tatiana Giraud, Celedonio Gonzalez, Sandrine Grossetete, Ulrich Güldener, Bernard Henrissat, Barbara J. Howlett, Chinnappa Kodira, Matthias Kretschmer, Anne Lappartient, Michaela Leroch, Caroline Levis, Evan Mauceli, Cécile Neuvéglise, Birgitt Oeser, Matthew Pearson, Julie Poulain, Nathalie Poussereau, Hadi Quesneville, Christine Rascle, Julia Schumacher, Béatrice Ségurens, Adrienne Sexton, Evelyn Silva, Catherine Sirven, Darren M. Soanes, Nicholas J. Talbot, Matt Templeton, Chandri Yandava, Oded Yarden, Qiandong Zeng, Jeffrey A. Rollins, Marc-Henri Lebrun, Marty Dickman

A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans

Chip Stewart, Deniz Kural, Michael P. Strömberg, Jerilyn A. Walker, Miriam K. Konkel, Adrian M. Stütz, Alexander E. Urban, Fabian Grubert, Hugo Y. K. Lam, Wan-Ping Lee, Michele Busby, Amit R. Indap, Erik Garrison, Chad Huff, Jinchuan Xing, Michael P. Snyder, Lynn B. Jorde, Mark A. Batzer, Jan O. Korbel, Gabor T. Marth , 1000 Genomes Project

Genome-Wide Gene-Environment Study Identifies Glutamate Receptor Gene GRIN2A as a Parkinson's Disease Modifier Gene via Interaction with Coffee

Taye H. Hamza, Honglei Chen, Erin M. Hill-Burns, Shannon L. Rhodes, Jennifer Montimurro, Denise M. Kay, Albert Tenesa, Victoria I. Kusel, Patricia Sheehan, Muthukrishnan Eaaswarkhanth, Dora Yearout, Ali Samii, John W. Roberts, Pinky Agarwal, Yvette Bordelon, Yikyung Park, Liyong Wang, Jianjun Gao, Jeffery M. Vance, Kenneth S. Kendler, Silviu-Alin Bacanu, William K. Scott, Beate Ritz, John Nutt, Stewart A. Factor, Cyrus P. Zabetian, Haydeh Payami

Variance of Gene Expression Identifies Altered Network Constraints in Neurological Disease

Jessica C. Mar, Nicholas A. Matigian, Alan Mackay-Sim, George D. Mellick, Carolyn M. Sue, Peter A. Silburn, John J. McGrath, John Quackenbush, Christine A. Wells

Gamma-Tubulin Is Required for Bipolar Spindle Assembly and for Proper Kinetochore Microtubule Attachments during Prometaphase I in Drosophila Oocytes

Stacie E. Hughes, J. Scott Beeler, Angela Seat, Brian D. Slaughter, Jay R. Unruh, Elisabeth Bauerly, Heinrich J. G. Matthies, R. Scott Hawley

Discovery of Sexual Dimorphisms in Metabolic and Genetic Biomarkers

Kirstin Mittelstrass, Janina S. Ried, Zhonghao Yu, Jan Krumsiek, Christian Gieger, Cornelia Prehn, Werner Roemisch-Margl, Alexey Polonikov, Annette Peters, Fabian J. Theis, Thomas Meitinger, Florian Kronenberg, Stephan Weidinger, Heinz Erich Wichmann, Karsten Suhre, Rui Wang-Sattler, Jerzy Adamski, Thomas Illig

Suppression of Scant Identifies Endos as a Substrate of Greatwall Kinase and a Negative Regulator of Protein Phosphatase 2A in Mitosis

Hélène Rangone, Eva Wegel, Melanie K. Gatt, Eirene Yeung, Alexander Flowers, Janusz Debski, Michal Dadlez, Veerle Janssens, Adelaide T. C. Carpenter, David M. Glover

Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation

Jason Gertz, Katherine E. Varley, Timothy E. Reddy, Kevin M. Bowling, Florencia Pauli, Stephanie L. Parker, Katerina S. Kucera, Huntington F. Willard, Richard M. Myers

Ku Must Load Directly onto the Chromosome End in Order to Mediate Its Telomeric Functions

Christopher R. Lopez, Albert Ribes-Zamora, Sandra M. Indiviglio, Christopher L. Williams, Svasti Haricharan, Alison A. Bertuch

Celsr3 Is Required for Normal Development of GABA Circuits in the Inner Retina

Alaron Lewis, Neil Wilson, George Stearns, Nicolas Johnson, Ralph Nelson, Susan E. Brockerhoff

Pervasive Sharing of Genetic Effects in Autoimmune Disease

Chris Cotsapas, Benjamin F. Voight, Elizabeth Rossin, Kasper Lage, Benjamin M. Neale, Chris Wallace, Gonçalo R. Abecasis, Jeffrey C. Barrett, Timothy Behrens, Judy Cho, Philip L. De Jager, James T. Elder, Robert R. Graham, Peter Gregersen, Lars Klareskog, Katherine A. Siminovitch, David A. van Heel, Cisca Wijmenga, Jane Worthington, John A. Todd, David A. Hafler, Stephen S. Rich, Mark J. Daly , on behalf of the FOCiS Network of Consortia

Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex Phenotype Converge on Intermediate Genes, with a Major Role for the HLA

Rudolf S. N. Fehrmann, Ritsert C. Jansen, Jan H. Veldink, Harm-Jan Westra, Danny Arends, Marc Jan Bonder, Jingyuan Fu, Patrick Deelen, Harry J. M. Groen, Asia Smolonska, Rinse K. Weersma, Robert M. W. Hofstra, Wim A. Buurman, Sander Rensen, Marcel G. M. Wolfs, Mathieu Platteel, Alexandra Zhernakova, Clara C. Elbers, Eleanora M. Festen, Gosia Trynka, Marten H. Hofker, Christiaan G. J. Saris, Roel A. Ophoff, Leonard H. van den Berg, David A. van Heel, Cisca Wijmenga, Gerard J. te Meerman, Lude Franke

Genome-Wide Association Analysis of Incident Coronary Heart Disease (CHD) in African Americans: A Short Report

Maja Barbalic, Alex P. Reiner, Chunyuan Wu, James E. Hixson, Nora Franceschini, Charles B. Eaton, Gerardo Heiss, David Couper, Thomas Mosley, Eric Boerwinkle

Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency

Jared W. Wenger, Jeffrey Piotrowski, Saisubramanian Nagarajan, Kami Chiotti, Gavin Sherlock, Frank Rosenzweig

FUS and TARDBP but Not SOD1 Interact in Genetic Models of Amyotrophic Lateral Sclerosis

Edor Kabashi, Valérie Bercier, Alexandra Lissouba, Meijiang Liao, Edna Brustein, Guy A. Rouleau, Pierre Drapeau

Genome-Wide Association Analysis of Autoantibody Positivity in Type 1 Diabetes Cases

Vincent Plagnol, Joanna M. M. Howson, Deborah J. Smyth, Neil Walker, Jason P. Hafler, Chris Wallace, Helen Stevens, Laura Jackson, Matthew J. Simmonds, Polly J. Bingley, Stephen C. Gough, John A. Todd , Type 1 Diabetes Genetics Consortium

Identification of Functional Toxin/Immunity Genes Linked to Contact-Dependent Growth Inhibition (CDI) and Rearrangement Hotspot (Rhs) Systems

Stephen J. Poole, Elie J. Diner, Stephanie K. Aoki, Bruce A. Braaten, Claire t'Kint de Roodenbeke, David A. Low, Christopher S. Hayes

Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping

Adam N. Famoso, Keyan Zhao, Randy T. Clark, Chih-Wei Tung, Mark H. Wright, Carlos Bustamante, Leon V. Kochian, Susan R. McCouch