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Table of Contents: September 2011

COVER

Oil produced by Rhodococcus opacus PD630 drips from a spigot.

Image Credit: Microscopy was performed by Jason Holder. Graphic design was performed by Leslie Gaffney, Lauren Solomon, and Jason Holder.
Issue Image

Inside of the oil drop are R. opacus PD630 colonies stained with a lipophilic dye (yellow) during lipid body formation (see Holder et al., doi:10.1371/journal.pgen.1002219).

Research Articles

Association of eGFR-Related Loci Identified by GWAS with Incident CKD and ESRD

Carsten A. Böger, Mathias Gorski, Man Li, Michael M. Hoffmann, Chunmei Huang, Qiong Yang, Alexander Teumer, Vera Krane, Conall M. O'Seaghdha, Zoltán Kutalik, H.-Erich Wichmann, Thomas Haak, Eva Boes, Stefan Coassin, Josef Coresh, Barbara Kollerits, Margot Haun, Bernhard Paulweber, Anna Köttgen, Guo Li, Michael G. Shlipak, Neil Powe, Shih-Jen Hwang, Abbas Dehghan, Fernando Rivadeneira, André Uitterlinden, Albert Hofman, Jacques S. Beckmann, Bernhard K. Krämer, Jacqueline Witteman, Murielle Bochud, David Siscovick, Rainer Rettig, Florian Kronenberg, Christoph Wanner, Ravi I. Thadhani, Iris M. Heid, Caroline S. Fox, W. H. Kao , The CKDGen Consortium

A Genome-Wide Meta-Analysis of Six Type 1 Diabetes Cohorts Identifies Multiple Associated Loci

Jonathan P. Bradfield, Hui-Qi Qu, Kai Wang, Haitao Zhang, Patrick M. Sleiman, Cecilia E. Kim, Frank D. Mentch, Haijun Qiu, Joseph T. Glessner, Kelly A. Thomas, Edward C. Frackelton, Rosetta M. Chiavacci, Marcin Imielinski, Dimitri S. Monos, Rahul Pandey, Marina Bakay, Struan F. A. Grant, Constantin Polychronakos, Hakon Hakonarson

Genomic Analysis of QTLs and Genes Altering Natural Variation in Stochastic Noise

Jose M. Jimenez-Gomez, Jason A. Corwin, Bindu Joseph, Julin N. Maloof, Daniel J. Kliebenstein

A Conserved PHD Finger Protein and Endogenous RNAi Modulate Insulin Signaling in Caenorhabditis elegans

Andres R. Mansisidor, Germano Cecere, Sebastian Hoersch, Morten B. Jensen, Trupti Kawli, Lisa M. Kennedy, Violeta Chavez, Man-Wah Tan, Jason D. Lieb, Alla Grishok

Identification of Type 1 Diabetes–Associated DNA Methylation Variable Positions That Precede Disease Diagnosis

Vardhman K. Rakyan, Huriya Beyan, Thomas A. Down, Mohammed I. Hawa, Siarhei Maslau, Deeqo Aden, Antoine Daunay, Florence Busato, Charles A. Mein, Burkhard Manfras, Kerith-Rae M. Dias, Christopher G. Bell, Jörg Tost, Bernhard O. Boehm, Stephan Beck, R. David Leslie

Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms

Rita Rebollo, Mohammad M. Karimi, Misha Bilenky, Liane Gagnier, Katharine Miceli-Royer, Ying Zhang, Preeti Goyal, Thomas M. Keane, Steven Jones, Martin Hirst, Matthew C. Lorincz, Dixie L. Mager

Misregulation of Scm3p/HJURP Causes Chromosome Instability in Saccharomyces cerevisiae and Human Cells

Prashant K. Mishra, Wei-Chun Au, John S. Choy, P. Henning Kuich, Richard E. Baker, Daniel R. Foltz, Munira A. Basrai

Genome-Wide Analysis of Heteroduplex DNA in Mismatch Repair–Deficient Yeast Cells Reveals Novel Properties of Meiotic Recombination Pathways

Emmanuelle Martini, Valérie Borde, Matthieu Legendre, Stéphane Audic, Béatrice Regnault, Guillaume Soubigou, Bernard Dujon, Bertrand Llorente

MicroRNA Predictors of Longevity in Caenorhabditis elegans

Zachary Pincus, Thalyana Smith-Vikos, Frank J. Slack

A Noncoding Point Mutation of Zeb1 Causes Multiple Developmental Malformations and Obesity in Twirler Mice

Kiyoto Kurima, Ronna Hertzano, Oksana Gavrilova, Kelly Monahan, Karl B. Shpargel, Garani Nadaraja, Yoshiyuki Kawashima, Kyu Yup Lee, Taku Ito, Yujiro Higashi, David J. Eisenman, Scott E. Strome, Andrew J. Griffith

Cell Type–Specific Transcriptome Analysis Reveals a Major Role for Zeb1 and miR-200b in Mouse Inner Ear Morphogenesis

Ronna Hertzano, Ran Elkon, Kiyoto Kurima, Annie Morrisson, Siaw-Lin Chan, Michelle Sallin, Andrew Biedlingmaier, Douglas S. Darling, Andrew J. Griffith, David J. Eisenman, Scott E. Strome

Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

James Angus Chandler, Jenna Morgan Lang, Srijak Bhatnagar, Jonathan A. Eisen, Artyom Kopp

Inference of Relationships in Population Data Using Identity-by-Descent and Identity-by-State

Eric L. Stevens, Greg Heckenberg, Elisha D. O. Roberson, Joseph D. Baugher, Thomas J. Downey, Jonathan Pevsner

Novel Interactions between Actin and the Proteasome Revealed by Complex Haploinsufficiency

Brian Haarer, Dimitra Aggeli, Susan Viggiano, Daniel J. Burke, David C. Amberg

Essential Roles of BCCIP in Mouse Embryonic Development and Structural Stability of Chromosomes

Huimei Lu, Yi-Yuan Huang, Sonam Mehrotra, Roberto Droz-Rosario, Jingmei Liu, Mantu Bhaumik, Eileen White, Zhiyuan Shen

The Abnormal Phenotypes of Cartilage and Bone in Calcium-Sensing Receptor Deficient Mice Are Dependent on the Actions of Calcium, Phosphorus, and PTH

Jingning Liu, Fangqiao Lv, Wen Sun, Chunxiang Tao, Guoxian Ding, Andrew Karaplis, Edward Brown, David Goltzman, Dengshun Miao

A Negative Feedback Loop That Limits the Ectopic Activation of a Cell Type–Specific Sporulation Sigma Factor of Bacillus subtilis

Mónica Serrano, Gonçalo Real, Joana Santos, Jorge Carneiro, Charles P. Moran Jr., Adriano O. Henriques

Conserved Regulation of p53 Network Dosage by MicroRNA–125b Occurs through Evolving miRNA–Target Gene Pairs

Minh T. N. Le, Ng Shyh-Chang, Swea Ling Khaw, Lingzi Chin, Cathleen Teh, Junliang Tay, Elizabeth O'Day, Vladimir Korzh, Henry Yang, Ashish Lal, Judy Lieberman, Harvey F. Lodish, Bing Lim

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development

Jason A. Watts, Chaolin Zhang, Andres J. Klein-Szanto, Jay D. Kormish, Jian Fu, Michael Q. Zhang, Kenneth S. Zaret

Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence

Frederick E. Dewey, Rong Chen, Sergio P. Cordero, Kelly E. Ormond, Colleen Caleshu, Konrad J. Karczewski, Michelle Whirl-Carrillo, Matthew T. Wheeler, Joel T. Dudley, Jake K. Byrnes, Omar E. Cornejo, Joshua W. Knowles, Mark Woon, Katrin Sangkuhl, Li Gong, Caroline F. Thorn, Joan M. Hebert, Emidio Capriotti, Sean P. David, Aleksandra Pavlovic, Anne West, Joseph V. Thakuria, Madeleine P. Ball, Alexander W. Zaranek, Heidi L. Rehm, George M. Church, John S. West, Carlos D. Bustamante, Michael Snyder, Russ B. Altman, Teri E. Klein, Atul J. Butte, Euan A. Ashley

The Receptor Tyrosine Kinase Alk Controls Neurofibromin Functions in Drosophila Growth and Learning

Jean Y. Gouzi, Anastasios Moressis, James A. Walker, Anthi A. Apostolopoulou, Ruth H. Palmer, André Bernards, Efthimios M. C. Skoulakis

Atypical AT Skew in Firmicute Genomes Results from Selection and Not from Mutation

Catherine A. Charneski, Frank Honti, Josephine M. Bryant, Laurence D. Hurst, Edward J. Feil

Inactivation of Pmel Alters Melanosome Shape But Has Only a Subtle Effect on Visible Pigmentation

Anders R. Hellström, Brenda Watt, Shahrzad Shirazi Fard, Danièle Tenza, Paula Mannström, Kristina Narfström, Björn Ekesten, Shosuke Ito, Kazumasa Wakamatsu, Jimmy Larsson, Mats Ulfendahl, Klas Kullander, Graça Raposo, Susanne Kerje, Finn Hallböök, Michael S. Marks, Leif Andersson

Mutations in or near the Transmembrane Domain Alter PMEL Amyloid Formation from Functional to Pathogenic

Brenda Watt, Danièle Tenza, Mark A. Lemmon, Susanne Kerje, Graça Raposo, Leif Andersson, Michael S. Marks

Genetic Variants at Chromosomes 2q35, 5p12, 6q25.1, 10q26.13, and 16q12.1 Influence the Risk of Breast Cancer in Men

Nick Orr, Rosie Cooke, Michael Jones, Olivia Fletcher, Frank Dudbridge, Sarah Chilcott-Burns, Katarzyna Tomczyk, Peter Broderick, Richard Houlston, Alan Ashworth, Anthony Swerdlow

Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development

Jason W. Holder, Jil C. Ulrich, Anthony C. DeBono, Paul A. Godfrey, Christopher A. Desjardins, Jeremy Zucker, Qiandong Zeng, Alex L. B. Leach, Ion Ghiviriga, Christine Dancel, Thomas Abeel, Dirk Gevers, Chinnappa D. Kodira, Brian Desany, Jason P. Affourtit, Bruce W. Birren, Anthony J. Sinskey

Elevated Proteasome Capacity Extends Replicative Lifespan in Saccharomyces cerevisiae

Undine Kruegel, Brett Robison, Thomas Dange, Günther Kahlert, Joe R. Delaney, Soumya Kotireddy, Mitsuhiro Tsuchiya, Scott Tsuchiyama, Christopher J. Murakami, Jennifer Schleit, George Sutphin, Daniel Carr, Krisztina Tar, Gunnar Dittmar, Matt Kaeberlein, Brian K. Kennedy, Marion Schmidt

Genetic Effects at Pleiotropic Loci Are Context-Dependent with Consequences for the Maintenance of Genetic Variation in Populations

Heather A. Lawson, Janet E. Cady, Charlyn Partridge, Jason B. Wolf, Clay F. Semenkovich, James M. Cheverud

PCNA Ubiquitination Is Important, But Not Essential for Translesion DNA Synthesis in Mammalian Cells

Ayal Hendel, Peter H. L. Krijger, Noam Diamant, Zohar Goren, Petra Langerak, Jungmin Kim, Thomas Reißner, Kyoo-young Lee, Nicholas E. Geacintov, Thomas Carell, Kyungjae Myung, Satoshi Tateishi, Alan D'Andrea, Heinz Jacobs, Zvi Livneh

Genetic Association for Renal Traits among Participants of African Ancestry Reveals New Loci for Renal Function

Ching-Ti Liu, Maija K. Garnaas, Adrienne Tin, Anna Kottgen, Nora Franceschini, Carmen A. Peralta, Ian H. de Boer, Xiaoning Lu, Elizabeth Atkinson, Jingzhong Ding, Michael Nalls, Daniel Shriner, Josef Coresh, Abdullah Kutlar, Kirsten Bibbins-Domingo, David Siscovick, Ermeg Akylbekova, Sharon Wyatt, Brad Astor, Josef Mychaleckjy, Man Li, Muredach P. Reilly, Raymond R. Townsend, Adebowale Adeyemo, Alan B. Zonderman, Mariza de Andrade, Stephen T. Turner, Thomas H. Mosley, Tamara B. Harris, Charles N. Rotimi, Yongmei Liu, Sharon L. R. Kardia, Michele K. Evans, Michael G. Shlipak, Holly Kramer, Michael F. Flessner, Albert W. Dreisbach, Wolfram Goessling, L. Adrienne Cupples, W. Linda Kao, Caroline S. Fox , The CKDGen Consortium

Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria

Jennifer Luciano, Rym Agrebi, Anne Valérie Le Gall, Morgane Wartel, Francesca Fiegna, Adrien Ducret, Céline Brochier-Armanet, Tâm Mignot

A Genome-Wide Metabolic QTL Analysis in Europeans Implicates Two Loci Shaped by Recent Positive Selection

George Nicholson, Mattias Rantalainen, Jia V. Li, Anthony D. Maher, Daniel Malmodin, Kourosh R. Ahmadi, Johan H. Faber, Amy Barrett, Josine L. Min, N. William Rayner, Henrik Toft, Maria Krestyaninova, Juris Viksna, Sudeshna Guha Neogi, Marc-Emmanuel Dumas, Ugis Sarkans, Peter Donnelly, Thomas Illig, Jerzy Adamski, Karsten Suhre, Maxine Allen, Krina T. Zondervan, Tim D. Spector, Jeremy K. Nicholson, John C. Lindon, Dorrit Baunsgaard, Elaine Holmes, Mark I. McCarthy, Chris C. Holmes , The MolPAGE Consortium

Sex Chromosome Mosaicism and Hybrid Speciation among Tiger Swallowtail Butterflies

Krushnamegh Kunte, Cristina Shea, Matthew L. Aardema, J. Mark Scriber, Thomas E. Juenger, Lawrence E. Gilbert, Marcus R. Kronforst

Genome-Wide Association Study Identifies Four Loci Associated with Eruption of Permanent Teeth

Frank Geller, Bjarke Feenstra, Hao Zhang, John R. Shaffer, Thomas Hansen, Ann-Louise Esserlind, Heather A. Boyd, Ellen A. Nohr, Nicholas J. Timpson, Ghazaleh Fatemifar, Lavinia Paternoster, David M. Evans, Robert J. Weyant, Steven M. Levy, Mark Lathrop, George Davey Smith, Jeffrey C. Murray, Jes Olesen, Thomas Werge, Mary L. Marazita, Thorkild I. A. Sørensen, Mads Melbye

Heterozygous Mutations of FREM1 Are Associated with an Increased Risk of Isolated Metopic Craniosynostosis in Humans and Mice

Lisenka E. L. M. Vissers, Timothy C. Cox, A. Murat Maga, Kieran M. Short, Fenny Wiradjaja, Irene M. Janssen, Fernanda Jehee, Debora Bertola, Jia Liu, Garima Yagnik, Kiyotoshi Sekiguchi, Daiji Kiyozumi, Hans van Bokhoven, Carlo Marcelis, Michael L. Cunningham, Peter J. Anderson, Simeon A. Boyadjiev, Maria Rita Passos-Bueno, Joris A. Veltman, Ian Smyth, Michael F. Buckley, Tony Roscioli

Cholesterol Metabolism Is Required for Intracellular Hedgehog Signal Transduction In Vivo

Rolf W. Stottmann, Annick Turbe-Doan, Pamela Tran, Lisa E. Kratz, Jennifer L. Moran, Richard I. Kelley, David R. Beier

The Evolutionarily Conserved Longevity Determinants HCF-1 and SIR-2.1/SIRT1 Collaborate to Regulate DAF-16/FOXO

Gizem Rizki, Terri Naoko Iwata, Ji Li, Christian G. Riedel, Colette Lafontaine Picard, Max Jan, Coleen T. Murphy, Siu Sylvia Lee

Separation of Recombination and SOS Response in Escherichia coli RecA Suggests LexA Interaction Sites

Anbu K. Adikesavan, Panagiotis Katsonis, David C. Marciano, Rhonald Lua, Christophe Herman, Olivier Lichtarge

Tsx Produces a Long Noncoding RNA and Has General Functions in the Germline, Stem Cells, and Brain

Montserrat C. Anguera, Weiyuan Ma, Danielle Clift, Satoshi Namekawa, Raymond J. Kelleher III, Jeannie T. Lee

Age-Dependent Recombination Rates in Human Pedigrees

Julie Hussin, Marie-Hélène Roy-Gagnon, Roxanne Gendron, Gregor Andelfinger, Philip Awadalla

VANG-1 and PRKL-1 Cooperate to Negatively Regulate Neurite Formation in Caenorhabditis elegans

Leticia Sanchez-Alvarez, Jiravat Visanuvimol, Andrea McEwan, Anna Su, Janice H. Imai, Antonio Colavita

Germline Genetic Variants Disturbing the Let-7/LIN28 Double-Negative Feedback Loop Alter Breast Cancer Susceptibility

Ao-Xiang Chen, Ke-Da Yu, Lei Fan, Ji-Yu Li, Chen Yang, A-Ji Huang, Zhi-Ming Shao

Drosophila IAP1-Mediated Ubiquitylation Controls Activation of the Initiator Caspase DRONC Independent of Protein Degradation

Tom V. Lee, Yun Fan, Shiuan Wang, Mayank Srivastava, Meike Broemer, Pascal Meier, Andreas Bergmann