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Table of Contents

May 2010

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Endophytic colonization.

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Many endophytic bacteria have demonstrated plant-growth promoting abilities that are currently being exploited to improve productivity of food and feedstocks. In this issue of PLoS Genetics, Taghavi et al. identify functions essential for the successful colonization and endophytic association of Enterobacter sp. 638 with its poplar host, with the endophyte responsible for the production of a phytohormone, and a precursor for another, which poplar is unable to synthesize, and where the production of the plant-growth promoting compounds depended on the presence of plant-synthesized compounds, such as sucrose, in the growth medium.

Image Credit: Safiyh Taghavi and Dmytro Nykypanchuk (Brookhaven National Laboratory; image taken at the Center for Functional Nanomaterials)

Interview

All About Mitochondrial Eve: An Interview with Rebecca Cann

Jane Gitschier

PLOS Genetics: published May 27, 2010 | https://doi.org/10.1371/journal.pgen.1000959

Research Articles

Shelterin-Like Proteins and Yku Inhibit Nucleolytic Processing of Saccharomyces cerevisiae Telomeres

Diego Bonetti, Michela Clerici, Savani Anbalagan, Marina Martina, Giovanna Lucchini, Maria Pia Longhese

PLOS Genetics: published May 27, 2010 | https://doi.org/10.1371/journal.pgen.1000966

The Proprotein Convertase Encoded by amontillado (amon) Is Required in Drosophila Corpora Cardiaca Endocrine Cells Producing the Glucose Regulatory Hormone AKH

Jeanne M. Rhea, Christian Wegener, Michael Bender

PLOS Genetics: published May 27, 2010 | https://doi.org/10.1371/journal.pgen.1000967

The Use of Orthologous Sequences to Predict the Impact of Amino Acid Substitutions on Protein Function

Nicholas J. Marini, Paul D. Thomas, Jasper Rine

PLOS Genetics: published May 27, 2010 | https://doi.org/10.1371/journal.pgen.1000968

Affecting Rhomboid-3 Function Causes a Dilated Heart in Adult Drosophila

Lin Yu, Teresa Lee, Na Lin, Matthew J. Wolf

PLOS Genetics: published May 27, 2010 | https://doi.org/10.1371/journal.pgen.1000969

Epistasis of Transcriptomes Reveals Synergism between Transcriptional Activators Hnf1α and Hnf4α

Sylvia F. Boj, Dimitri Petrov, Jorge Ferrer

PLOS Genetics: published May 27, 2010 | https://doi.org/10.1371/journal.pgen.1000970

Aging and Chronic Sun Exposure Cause Distinct Epigenetic Changes in Human Skin

Elke Grönniger, Barbara Weber, Oliver Heil, Nils Peters, Franz Stäb, Horst Wenck, Bernhard Korn, Marc Winnefeld, Frank Lyko

PLOS Genetics: published May 27, 2010 | https://doi.org/10.1371/journal.pgen.1000971

Manipulation of Behavioral Decline in Caenorhabditis elegans with the Rag GTPase raga-1

Matthew A. Schreiber, Jonathan T. Pierce-Shimomura, Stefan Chan, Dianne Parry, Steven L. McIntire

PLOS Genetics: published May 27, 2010 | https://doi.org/10.1371/journal.pgen.1000972

Sgs1 and Exo1 Redundantly Inhibit Break-Induced Replication and De Novo Telomere Addition at Broken Chromosome Ends

John R. Lydeard, Zachary Lipkin-Moore, Suvi Jain, Vinay V. Eapen, James E. Haber

PLOS Genetics: published May 27, 2010 | https://doi.org/10.1371/journal.pgen.1000973

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  1. Extensive DNA End Processing by Exo1 and Sgs1 Inhibits Break-Induced Replication
  2. Defective Resection at DNA Double-Strand Breaks Leads to De Novo Telomere Formation and Enhances Gene Targeting

A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editing

Alexander Wait Zaranek, Erez Y. Levanon, Tomer Zecharia, Tom Clegg, George M. Church

PLOS Genetics: published May 20, 2010 | https://doi.org/10.1371/journal.pgen.1000954

Ablation of Whirlin Long Isoform Disrupts the USH2 Protein Complex and Causes Vision and Hearing Loss

Jun Yang, Xiaoqing Liu, Yun Zhao, Michael Adamian, Basil Pawlyk, Xun Sun, D. Randy McMillan, M. Charles Liberman, Tiansen Li

PLOS Genetics: published May 20, 2010 | https://doi.org/10.1371/journal.pgen.1000955

Mutation in Archain 1, a Subunit of COPI Coatomer Complex, Causes Diluted Coat Color and Purkinje Cell Degeneration

Xinjie Xu, Rajendra Kedlaya, Hitoshi Higuchi, Sakae Ikeda, Monica J. Justice, Vijayasaradhi Setaluri, Akihiro Ikeda

PLOS Genetics: published May 20, 2010 | https://doi.org/10.1371/journal.pgen.1000956

Integration of Light Signals by the Retinoblastoma Pathway in the Control of S Phase Entry in the Picophytoplanktonic Cell Ostreococcus

Mickael Moulager, Florence Corellou, Valérie Vergé, Marie-Line Escande, François-Yves Bouget

PLOS Genetics: published May 20, 2010 | https://doi.org/10.1371/journal.pgen.1000957

The Polyproline Site in Hinge 2 Influences the Functional Capacity of Truncated Dystrophins

Glen B. Banks, Luke M. Judge, James M. Allen, Jeffrey S. Chamberlain

PLOS Genetics: published May 20, 2010 | https://doi.org/10.1371/journal.pgen.1000958

GC-Biased Evolution Near Human Accelerated Regions

Sol Katzman, Andrew D. Kern, Katherine S. Pollard, Sofie R. Salama, David Haussler

PLOS Genetics: published May 20, 2010 | https://doi.org/10.1371/journal.pgen.1000960

The Mating Type Locus (MAT) and Sexual Reproduction of Cryptococcus heveanensis: Insights into the Evolution of Sex and Sex-Determining Chromosomal Regions in Fungi

Banu Metin, Keisha Findley, Joseph Heitman

PLOS Genetics: published May 20, 2010 | https://doi.org/10.1371/journal.pgen.1000961

Genome-Wide Copy Number Variation in Epilepsy: Novel Susceptibility Loci in Idiopathic Generalized and Focal Epilepsies

Heather C. Mefford, Hiltrud Muhle, Philipp Ostertag, Sarah von Spiczak, Karen Buysse, Carl Baker, Andre Franke, Alain Malafosse, Pierre Genton, Pierre Thomas, Christina A. Gurnett, Stefan Schreiber, Alexander G. Bassuk, Michel Guipponi, Ulrich Stephani, Ingo Helbig, Evan E. Eichler

PLOS Genetics: published May 20, 2010 | https://doi.org/10.1371/journal.pgen.1000962

Caenorhabditis elegans SMA-10/LRIG Is a Conserved Transmembrane Protein that Enhances Bone Morphogenetic Protein Signaling

Tina L. Gumienny, Lesley MacNeil, Cole M. Zimmerman, Huang Wang, Lena Chin, Jeffrey L. Wrana, Richard W. Padgett

PLOS Genetics: published May 20, 2010 | https://doi.org/10.1371/journal.pgen.1000963

FACT Prevents the Accumulation of Free Histones Evicted from Transcribed Chromatin and a Subsequent Cell Cycle Delay in G1

Macarena Morillo-Huesca, Douglas Maya, Mari Cruz Muñoz-Centeno, Rakesh Kumar Singh, Vincent Oreal, Gajjalaiahvari Ugander Reddy, Dun Liang, Vincent Géli, Akash Gunjan, Sebastián Chávez

PLOS Genetics: published May 20, 2010 | https://doi.org/10.1371/journal.pgen.1000964

Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae

Jared W. Wenger, Katja Schwartz, Gavin Sherlock

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000942

Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

Safiyh Taghavi, Daniel van der Lelie, Adam Hoffman, Yian-Biao Zhang, Michael D. Walla, Jaco Vangronsveld, Lee Newman, Sébastien Monchy

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000943

The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution

Jean-François Gout, Daniel Kahn, Laurent Duret, Paramecium Post-Genomics Consortium

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000944

Related Articles

  1. Correction: The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution

Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana

Daniela Vlad, Fabrice Rappaport, Matthieu Simon, Olivier Loudet

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000945

A Comprehensive Genome-Wide Map of Autonomously Replicating Sequences in a Naive Genome

Ivan Liachko, Anand Bhaskar, Chanmi Lee, Shau Chee Claire Chung, Bik-Kwoon Tye, Uri Keich

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000946

Common Genetic Variants near the Brittle Cornea Syndrome Locus ZNF469 Influence the Blinding Disease Risk Factor Central Corneal Thickness

Yi Lu, David P. Dimasi, Pirro G. Hysi, Alex W. Hewitt, Kathryn P. Burdon, Tze'Yo Toh, Jonathan B. Ruddle, Yi Ju Li, Paul Mitchell, Paul R. Healey, Grant W. Montgomery, Narelle Hansell, Timothy D. Spector, Nicholas G. Martin, Terri L. Young, Christopher J. Hammond, Stuart Macgregor, Jamie E. Craig, David A. Mackey

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000947

Defective Resection at DNA Double-Strand Breaks Leads to De Novo Telomere Formation and Enhances Gene Targeting

Woo-Hyun Chung, Zhu Zhu, Alma Papusha, Anna Malkova, Grzegorz Ira

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000948

Related Articles

  1. Sgs1 and Exo1 Redundantly Inhibit Break-Induced Replication and De Novo Telomere Addition at Broken Chromosome Ends
  2. Extensive DNA End Processing by Exo1 and Sgs1 Inhibits Break-Induced Replication

Transposed Genes in Arabidopsis Are Often Associated with Flanking Repeats

Margaret R. Woodhouse, Brent Pedersen, Michael Freeling

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000949

Age- and Temperature-Dependent Somatic Mutation Accumulation in Drosophila melanogaster

Ana Maria Garcia, R. Brent Calder, Martijn E. T. Dollé, Martha Lundell, Pankaj Kapahi, Jan Vijg

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000950

Characterization of Oxidative Guanine Damage and Repair in Mammalian Telomeres

Zhilong Wang, David B. Rhee, Jian Lu, Christina T. Bohr, Fang Zhou, Haritha Vallabhaneni, Nadja C. de Souza-Pinto, Yie Liu

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000951

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

J. Raphael Gibbs, Marcel P. van der Brug, Dena G. Hernandez, Bryan J. Traynor, Michael A. Nalls, Shiao-Lin Lai, Sampath Arepalli, Allissa Dillman, Ian P. Rafferty, Juan Troncoso, Robert Johnson, H. Ronald Zielke, Luigi Ferrucci, Dan L. Longo, Mark R. Cookson, Andrew B. Singleton

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000952

Transcription Factors Mat2 and Znf2 Operate Cellular Circuits Orchestrating Opposite- and Same-Sex Mating in Cryptococcus neoformans

Xiaorong Lin, Jennifer C. Jackson, Marianna Feretzaki, Chaoyang Xue, Joseph Heitman

PLOS Genetics: published May 13, 2010 | https://doi.org/10.1371/journal.pgen.1000953

A MATE-Family Efflux Pump Rescues the Escherichia coli 8-Oxoguanine-Repair-Deficient Mutator Phenotype and Protects Against H2O2 Killing

Javier R. Guelfo, Alexandro Rodríguez-Rojas, Ivan Matic, Jesús Blázquez

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000931

Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes

Hua Zhong, John Beaulaurier, Pek Yee Lum, Cliona Molony, Xia Yang, Douglas J. MacNeil, Drew T. Weingarth, Bin Zhang, Danielle Greenawalt, Radu Dobrin, Ke Hao, Sangsoon Woo, Christine Fabre-Suver, Su Qian, Michael R. Tota, Mark P. Keller, Christina M. Kendziorski, Brian S. Yandell, Victor Castro, Alan D. Attie, Lee M. Kaplan, Eric E. Schadt

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000932

Post-Replication Repair Suppresses Duplication-Mediated Genome Instability

Christopher D. Putnam, Tikvah K. Hayes, Richard D. Kolodner

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000933

Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci

Fan Liu, Andreas Wollstein, Pirro G. Hysi, Georgina A. Ankra-Badu, Timothy D. Spector, Daniel Park, Gu Zhu, Mats Larsson, David L. Duffy, Grant W. Montgomery, David A. Mackey, Susan Walsh, Oscar Lao, Albert Hofman, Fernando Rivadeneira, Johannes R. Vingerling, André G. Uitterlinden, Nicholas G. Martin, Christopher J. Hammond, Manfred Kayser

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000934

B-Cyclin/CDKs Regulate Mitotic Spindle Assembly by Phosphorylating Kinesins-5 in Budding Yeast

Mark K. Chee, Steven B. Haase

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000935

B1 SOX Coordinate Cell Specification with Patterning and Morphogenesis in the Early Zebrafish Embryo

Yuichi Okuda, Eri Ogura, Hisato Kondoh, Yusuke Kamachi

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000936

The Nuclear Receptor DHR3 Modulates dS6 Kinase–Dependent Growth in Drosophila

Jacques Montagne, Caroline Lecerf, Jean-Philippe Parvy, Janis M. Bennion, Thomas Radimerski, Marie-Laure Ruhf, Frederic Zilbermann, Nicole Vouilloz, Hugo Stocker, Ernst Hafen, Sara C. Kozma, George Thomas

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000937

Myeloid Cell-Restricted Insulin Receptor Deficiency Protects Against Obesity-Induced Inflammation and Systemic Insulin Resistance

Jan Mauer, Bhagirath Chaurasia, Leona Plum, Thomas Quast, Brigitte Hampel, Matthias Blüher, Waldemar Kolanus, C. Ronald Kahn, Jens C. Brüning

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000938

DNA Adenine Methylation Is Required to Replicate Both Vibrio cholerae Chromosomes Once per Cell Cycle

Gaëlle Demarre, Dhruba K. Chattoraj

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000939

Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature

Benjamin Brachi, Nathalie Faure, Matt Horton, Emilie Flahauw, Adeline Vazquez, Magnus Nordborg, Joy Bergelson, Joel Cuguen, Fabrice Roux

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000940

Involvement of Global Genome Repair, Transcription Coupled Repair, and Chromatin Remodeling in UV DNA Damage Response Changes during Development

Hannes Lans, Jurgen A. Marteijn, Björn Schumacher, Jan H. J. Hoeijmakers, Gert Jansen, Wim Vermeulen

PLOS Genetics: published May 6, 2010 | https://doi.org/10.1371/journal.pgen.1000941