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Table of Contents

July 2009

Cover

The cicada Diceroprocta semicincta is host to a highly unusual bacterial symbiont.
Issue Image

Cicadas feed exclusively on plant xylem sap. To supplement their nutrient-poor diet, they have developed elaborate symbioses with bacteria. An article in this issue of PLoS Genetics (see McCutcheon et al., 10.1371/journal.pgen.1000565) describes the genomic properties of a remarkable bacterium that is symbiotic in cicadas. This α-Proteobacteria, called Hodgkinia cicadicola, has the smallest reported genome of any cellular organism, with only 188 genes in total. Although all other small bacterial genomes are guanine-cytosine (GC)-poor, this one is GC-rich, resulting in an unprecedented combination of genomic features. Additionally, Hodgkinia uses an alternative genetic code, in which UGA has been reassigned from stop to tryptophan.

Image Credit: Adam Fleishman (Cometmoth Sight and Sound, http://cometmoth.com).

Editorial

Scientists←Editors←Scientists: The Past, Present, and Future of PLoS Genetics

Gregory S. Barsh, Gregory P. Copenhaver

PLOS Genetics: published July 31, 2009 | https://doi.org/10.1371/journal.pgen.1000580

Interview

You Say You Want a Revolution: An Interview with Pat Brown

Jane Gitschier

PLOS Genetics: published July 17, 2009 | https://doi.org/10.1371/journal.pgen.1000560

Viewpoints

Prediction and Interaction in Complex Disease Genetics: Experience in Type 1 Diabetes

David G. Clayton

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000540

Perspective

PCH'ing Together an Understanding of Crossover Control

Drew Thacker, Scott Keeney

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000576

Related Articles

  1. Pch2 Links Chromosome Axis Remodeling at Future Crossover Sites and Crossover Distribution during Yeast Meiosis
  2. The pch2Δ Mutation in Baker's Yeast Alters Meiotic Crossover Levels and Confers a Defect in Crossover Interference

Research Articles

Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana

Cheng Zou, Melissa D. Lehti-Shiu, Michael Thomashow, Shin-Han Shiu

PLOS Genetics: published July 31, 2009 | https://doi.org/10.1371/journal.pgen.1000581

Statistical Power of Model Selection Strategies for Genome-Wide Association Studies

Zheyang Wu, Hongyu Zhao

PLOS Genetics: published July 31, 2009 | https://doi.org/10.1371/journal.pgen.1000582

Evolution of a Novel Appendage Ground Plan in Water Striders Is Driven by Changes in the Hox Gene Ultrabithorax

Abderrahman Khila, Ehab Abouheif, Locke Rowe

PLOS Genetics: published July 31, 2009 | https://doi.org/10.1371/journal.pgen.1000583

EPHA2 Is Associated with Age-Related Cortical Cataract in Mice and Humans

Gyungah Jun, Hong Guo, Barbara E. K. Klein, Ronald Klein, Jie Jin Wang, Paul Mitchell, Hui Miao, Kristine E. Lee, Tripti Joshi, Matthias Buck, Preeti Chugha, David Bardenstein, Alison P. Klein, Joan E. Bailey-Wilson, Xiaohua Gong, Tim D. Spector, Toby Andrew, Christopher J. Hammond, Robert C. Elston, Sudha K. Iyengar, Bingcheng Wang

PLOS Genetics: published July 31, 2009 | https://doi.org/10.1371/journal.pgen.1000584

Lack of CFTR in Skeletal Muscle Predisposes to Muscle Wasting and Diaphragm Muscle Pump Failure in Cystic Fibrosis Mice

Maziar Divangahi, Haouaria Balghi, Gawiyou Danialou, Alain S. Comtois, Alexandre Demoule, Sheila Ernest, Christina Haston, Renaud Robert, John W. Hanrahan, Danuta Radzioch, Basil J. Petrof

PLOS Genetics: published July 31, 2009 | https://doi.org/10.1371/journal.pgen.1000586

Pch2 Links Chromosome Axis Remodeling at Future Crossover Sites and Crossover Distribution during Yeast Meiosis

Neeraj Joshi, Aekam Barot, Christine Jamison, G. Valentin Börner

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000557

Related Articles

  1. The pch2Δ Mutation in Baker's Yeast Alters Meiotic Crossover Levels and Confers a Defect in Crossover Interference
  2. PCH'ing Together an Understanding of Crossover Control

Coevolution of Interacting Fertilization Proteins

Nathaniel L. Clark, Joe Gasper, Masashi Sekino, Stevan A. Springer, Charles F. Aquadro, Willie J. Swanson

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000570

The pch2Δ Mutation in Baker's Yeast Alters Meiotic Crossover Levels and Confers a Defect in Crossover Interference

Sarah Zanders, Eric Alani

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000571

Related Articles

  1. PCH'ing Together an Understanding of Crossover Control
  2. Pch2 Links Chromosome Axis Remodeling at Future Crossover Sites and Crossover Distribution during Yeast Meiosis

On Quality Control Measures in Genome-Wide Association Studies: A Test to Assess the Genotyping Quality of Individual Probands in Family-Based Association Studies and an Application to the HapMap Data

David W. Fardo, Iuliana Ionita-Laza, Christoph Lange

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000572

Circadian Clock Genes Contribute to the Regulation of Hair Follicle Cycling

Kevin K. Lin, Vivek Kumar, Mikhail Geyfman, Darya Chudova, Alexander T. Ihler, Padhraic Smyth, Ralf Paus, Joseph S. Takahashi, Bogi Andersen

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000573

Alternative Splicing of NURF301 Generates Distinct NURF Chromatin Remodeling Complexes with Altered Modified Histone Binding Specificities

So Yeon Kwon, Hua Xiao, Carl Wu, Paul Badenhorst

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000574

Inactivation of TIF1γ Cooperates with KrasG12D to Induce Cystic Tumors of the Pancreas

David F. Vincent, Kai-Ping Yan, Isabelle Treilleux, Fabien Gay, Vanessa Arfi, Bastien Kaniewsky, Julien C. Marie, Florian Lepinasse, Sylvie Martel, Sophie Goddard-Leon, Juan L. Iovanna, Pierre Dubus, Stéphane Garcia, Alain Puisieux, Ruth Rimokh, Nabeel Bardeesy, Jean-Yves Scoazec, Régine Losson, Laurent Bartholin

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000575

Related Articles

  1. Correction: Inactivation of TIF1γ Cooperates with KrasG12D to Induce Cystic Tumors of the Pancreas

Transcriptional Mutagenesis Induced by 8-Oxoguanine in Mammalian Cells

Damien Brégeon, Paul-Antoine Peignon, Alain Sarasin

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000577

Positive Epistasis Drives the Acquisition of Multidrug Resistance

Sandra Trindade, Ana Sousa, Karina Bivar Xavier, Francisco Dionisio, Miguel Godinho Ferreira, Isabel Gordo

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000578

A Missense Mutation in the SERPINH1 Gene in Dachshunds with Osteogenesis Imperfecta

Cord Drögemüller, Doreen Becker, Adrian Brunner, Bianca Haase, Patrick Kircher, Frank Seeliger, Michael Fehr, Ulrich Baumann, Kerstin Lindblad-Toh, Tosso Leeb

PLOS Genetics: published July 24, 2009 | https://doi.org/10.1371/journal.pgen.1000579

Evolutionary Dynamics of Human Toll-Like Receptors and Their Different Contributions to Host Defense

Luis B. Barreiro, Meriem Ben-Ali, Hélène Quach, Guillaume Laval, Etienne Patin, Joseph K. Pickrell, Christiane Bouchier, Magali Tichit, Olivier Neyrolles, Brigitte Gicquel, Judith R. Kidd, Kenneth K. Kidd, Alexandre Alcaïs, Josiane Ragimbeau, Sandra Pellegrini, Laurent Abel, Jean-Laurent Casanova, Lluís Quintana-Murci

PLOS Genetics: published July 17, 2009 | https://doi.org/10.1371/journal.pgen.1000562

The Epithelial Cell Adhesion Molecule EpCAM Is Required for Epithelial Morphogenesis and Integrity during Zebrafish Epiboly and Skin Development

Krasimir Slanchev, Thomas J. Carney, Marc P. Stemmler, Birgit Koschorz, Adam Amsterdam, Heinz Schwarz, Matthias Hammerschmidt

PLOS Genetics: published July 17, 2009 | https://doi.org/10.1371/journal.pgen.1000563

A Genome-Wide Association Study of Hypertension and Blood Pressure in African Americans

Adebowale Adeyemo, Norman Gerry, Guanjie Chen, Alan Herbert, Ayo Doumatey, Hanxia Huang, Jie Zhou, Kerrie Lashley, Yuanxiu Chen, Michael Christman, Charles Rotimi

PLOS Genetics: published July 17, 2009 | https://doi.org/10.1371/journal.pgen.1000564

Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

John P. McCutcheon, Bradon R. McDonald, Nancy A. Moran

PLOS Genetics: published July 17, 2009 | https://doi.org/10.1371/journal.pgen.1000565

Novel Secretion Apparatus Maintains Spore Integrity and Developmental Gene Expression in Bacillus subtilis

Thierry Doan, Cecile Morlot, Jeffrey Meisner, Monica Serrano, Adriano O. Henriques, Charles P. Moran Jr, David Z. Rudner

PLOS Genetics: published July 17, 2009 | https://doi.org/10.1371/journal.pgen.1000566

Two Chromatin Remodeling Activities Cooperate during Activation of Hormone Responsive Promoters

Guillermo Pablo Vicent, Roser Zaurin, A. Silvina Nacht, Ang Li, Jofre Font-Mateu, Francois Le Dily, Michiel Vermeulen, Matthias Mann, Miguel Beato

PLOS Genetics: published July 17, 2009 | https://doi.org/10.1371/journal.pgen.1000567

Evolution and Survival on Eutherian Sex Chromosomes

Melissa A. Wilson, Kateryna D. Makova

PLOS Genetics: published July 17, 2009 | https://doi.org/10.1371/journal.pgen.1000568

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

Timothy T. Perkins, Robert A. Kingsley, Maria C. Fookes, Paul P. Gardner, Keith D. James, Lu Yu, Samuel A. Assefa, Miao He, Nicholas J. Croucher, Derek J. Pickard, Duncan J. Maskell, Julian Parkhill, Jyoti Choudhary, Nicholas R. Thomson, Gordon Dougan

PLOS Genetics: published July 17, 2009 | https://doi.org/10.1371/journal.pgen.1000569

A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana

Paula X. Kover, William Valdar, Joseph Trakalo, Nora Scarcelli, Ian M. Ehrenreich, Michael D. Purugganan, Caroline Durrant, Richard Mott

PLOS Genetics: published July 10, 2009 | https://doi.org/10.1371/journal.pgen.1000551

Mre11-Rad50 Promotes Rapid Repair of DNA Damage in the Polyploid Archaeon Haloferax volcanii by Restraining Homologous Recombination

Stéphane Delmas, Lee Shunburne, Hien-Ping Ngo, Thorsten Allers

PLOS Genetics: published July 10, 2009 | https://doi.org/10.1371/journal.pgen.1000552

The Caenorhabditis elegans HNF4α Homolog, NHR-31, Mediates Excretory Tube Growth and Function through Coordinate Regulation of the Vacuolar ATPase

Annett Hahn-Windgassen, Marc R. Van Gilst

PLOS Genetics: published July 10, 2009 | https://doi.org/10.1371/journal.pgen.1000553

Rapid Response of a Marine Mammal Species to Holocene Climate and Habitat Change

Mark de Bruyn, Brenda L. Hall, Lucas F. Chauke, Carlo Baroni, Paul L. Koch, A. Rus Hoelzel

PLOS Genetics: published July 10, 2009 | https://doi.org/10.1371/journal.pgen.1000554

Distinct Roles of Non-Canonical Poly(A) Polymerases in RNA Metabolism

Salvatore San Paolo, Stepanka Vanacova, Luca Schenk, Tanja Scherrer, Diana Blank, Walter Keller, André P. Gerber

PLOS Genetics: published July 10, 2009 | https://doi.org/10.1371/journal.pgen.1000555

General Rules for Optimal Codon Choice

Ruth Hershberg, Dmitri A. Petrov

PLOS Genetics: published July 10, 2009 | https://doi.org/10.1371/journal.pgen.1000556

The Ups and Downs of Mutation Frequencies during Aging Can Account for the Apert Syndrome Paternal Age Effect

Song-Ro Yoon, Jian Qin, Rivka L. Glaser, Ethylin Wang Jabs, Nancy S. Wexler, Rebecca Sokol, Norman Arnheim, Peter Calabrese

PLOS Genetics: published July 10, 2009 | https://doi.org/10.1371/journal.pgen.1000558

Specific Loss of Histone H3 Lysine 9 Trimethylation and HP1γ/Cohesin Binding at D4Z4 Repeats Is Associated with Facioscapulohumeral Dystrophy (FSHD)

Weihua Zeng, Jessica C. de Greef, Yen-Yun Chen, Richard Chien, Xiangduo Kong, Heather C. Gregson, Sara T. Winokur, April Pyle, Keith D. Robertson, John A. Schmiesing, Virginia E. Kimonis, Judit Balog, Rune R. Frants, Alexander R. Ball Jr., Leslie F. Lock, Peter J. Donovan, Silvère M. van der Maarel, Kyoko Yokomori

PLOS Genetics: published July 10, 2009 | https://doi.org/10.1371/journal.pgen.1000559

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  1. The D4Z4 Macrosatellite Repeat Acts as a CTCF and A-Type Lamins-Dependent Insulator in Facio-Scapulo-Humeral Dystrophy

Defects in tRNA Modification Associated with Neurological and Developmental Dysfunctions in Caenorhabditis elegans Elongator Mutants

Changchun Chen, Simon Tuck, Anders S. Byström

PLOS Genetics: published July 10, 2009 | https://doi.org/10.1371/journal.pgen.1000561

Positional Cloning of Zinc Finger Domain Transcription Factor Zfp69, a Candidate Gene for Obesity-Associated Diabetes Contributed by Mouse Locus Nidd/SJL

Stephan Scherneck, Matthias Nestler, Heike Vogel, Matthias Blüher, Marcel-Dominique Block, Mauricio Berriel Diaz, Stephan Herzig, Nadja Schulz, Marko Teichert, Sina Tischer, Hadi Al-Hasani, Reinhart Kluge, Annette Schürmann, Hans-Georg Joost

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000541

Interactions between Cells with Distinct Mutations in c-MYC and Pten in Prostate Cancer

Jongchan Kim, Isam-Eldin A. Eltoum, Meejeon Roh, Jie Wang, Sarki A. Abdulkadir

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000542

Mitochondrial 2,4-dienoyl-CoA Reductase Deficiency in Mice Results in Severe Hypoglycemia with Stress Intolerance and Unimpaired Ketogenesis

Ilkka J. Miinalainen, Werner Schmitz, Anne Huotari, Kaija J. Autio, Raija Soininen, Emiel Ver Loren van Themaat, Myriam Baes, Karl-Heinz Herzig, Ernst Conzelmann, J. Kalervo Hiltunen

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000543

Defects in ErbB-Dependent Establishment of Adult Melanocyte Stem Cells Reveal Independent Origins for Embryonic and Regeneration Melanocytes

Keith A. Hultman, Erine H. Budi, Daniel C. Teasley, Andrew Y. Gottlieb, David M. Parichy, Stephen L. Johnson

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000544

Enhanced Disease Susceptibility 1 and Salicylic Acid Act Redundantly to Regulate Resistance Gene-Mediated Signaling

Srivathsa C. Venugopal, Rae-Dong Jeong, Mihir K. Mandal, Shifeng Zhu, A. C. Chandra-Shekara, Ye Xia, Matthew Hersh, Arnold J. Stromberg, DuRoy Navarre, Aardra Kachroo, Pradeep Kachroo

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000545

Run-Off Replication of Host-Adaptability Genes Is Associated with Gene Transfer Agents in the Genome of Mouse-Infecting Bartonella grahamii

Eva C. Berglund, A. Carolin Frank, Alexandra Calteau, Olga Vinnere Pettersson, Fredrik Granberg, Ann-Sofie Eriksson, Kristina Näslund, Martin Holmberg, Hillevi Lindroos, Siv G. E. Andersson

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000546

A Targeted Constitutive Mutation in the Apc Tumor Suppressor Gene Underlies Mammary But Not Intestinal Tumorigenesis

Claudia Gaspar, Patrick Franken, Lia Molenaar, Cor Breukel, Martin van der Valk, Ron Smits, Riccardo Fodde

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000547

Clustering of Codons with Rare Cognate tRNAs in Human Genes Suggests an Extra Level of Expression Regulation

Joanna L. Parmley, Martijn A. Huynen

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000548

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

Li-Jun Ma, Ashraf S. Ibrahim, Christopher Skory, Manfred G. Grabherr, Gertraud Burger, Margi Butler, Marek Elias, Alexander Idnurm, B. Franz Lang, Teruo Sone, Ayumi Abe, Sarah E. Calvo, Luis M. Corrochano, Reinhard Engels, Jianmin Fu, Wilhelm Hansberg, Jung-Mi Kim, Chinnappa D. Kodira, Michael J. Koehrsen, Bo Liu, Diego Miranda-Saavedra, Sinead O'Leary, Lucila Ortiz-Castellanos, Russell Poulter, Julio Rodriguez-Romero, José Ruiz-Herrera, Yao-Qing Shen, Qiandong Zeng, James Galagan, Bruce W. Birren, Christina A. Cuomo, Brian L. Wickes

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000549

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

Rob J. Kulathinal, Laurie S. Stevison, Mohamed A. F. Noor

PLOS Genetics: published July 3, 2009 | https://doi.org/10.1371/journal.pgen.1000550