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Table of Contents: July 2011

COVER

Fell ponies grazing in Ravenstonedale, Cumbria provide an iconic image.

Image Credit: Laura Fox-Clipsham (Animal Health Trust)
Issue Image

Fell ponies have played a pivotal role as working animals in the agricultural and industrial development of northern England, and today are valued as versatile family ponies around the UK and also overseas. However, their survival has been threatened in recent years by a fatal recessive disease that causes immune deficiency and progressive anemia. Using an equine SNP array followed by resequencing of the critical interval, Fox-Clipsham et al. mapped the defect and enabled the development of a diagnostic test for carriers and affected foals.

Perspective

Reviews

Research Articles

Gene-Based Tests of Association

Hailiang Huang, Pritam Chanda, Alvaro Alonso, Joel S. Bader, Dan E. Arking

Pervasive Sign Epistasis between Conjugative Plasmids and Drug-Resistance Chromosomal Mutations

Rui F. Silva, Sílvia C. M. Mendonça, Luís M. Carvalho, Ana M. Reis, Isabel Gordo, Sandra Trindade, Francisco Dionisio

Genetic Anticipation Is Associated with Telomere Shortening in Hereditary Breast Cancer

Beatriz Martinez-Delgado, Kira Yanowsky, Lucia Inglada-Perez, Samuel Domingo, Miguel Urioste, Ana Osorio, Javier Benitez

Recombination and Population Structure in Salmonella enterica

Xavier Didelot, Rory Bowden, Teresa Street, Tanya Golubchik, Chris Spencer, Gil McVean, Vartul Sangal, Muna F. Anjum, Mark Achtman, Daniel Falush, Peter Donnelly

Colon Stem Cell and Crypt Dynamics Exposed by Cell Lineage Reconstruction

Yitzhak Reizel, Noa Chapal-Ilani, Rivka Adar, Shalev Itzkovitz, Judith Elbaz, Yosef E. Maruvka, Elad Segev, Liran I. Shlush, Nava Dekel, Ehud Shapiro

Genetic Loci Associated with Plasma Phospholipid n-3 Fatty Acids: A Meta-Analysis of Genome-Wide Association Studies from the CHARGE Consortium

Rozenn N. Lemaitre, Toshiko Tanaka, Weihong Tang, Ani Manichaikul, Millennia Foy, Edmond K. Kabagambe, Jennifer A. Nettleton, Irena B. King, Lu-Chen Weng, Sayanti Bhattacharya, Stefania Bandinelli, Joshua C. Bis, Stephen S. Rich, David R. Jacobs Jr., Antonio Cherubini, Barbara McKnight, Shuang Liang, Xiangjun Gu, Kenneth Rice, Cathy C. Laurie, Thomas Lumley, Brian L. Browning, Bruce M. Psaty, Yii-Der I. Chen, Yechiel Friedlander, Luc Djousse, Jason H. Y. Wu, David S. Siscovick, André G. Uitterlinden, Donna K. Arnett, Luigi Ferrucci, Myriam Fornage, Michael Y. Tsai, Dariush Mozaffarian, Lyn M. Steffen

LGI2 Truncation Causes a Remitting Focal Epilepsy in Dogs

Eija H. Seppälä, Tarja S. Jokinen, Masaki Fukata, Yuko Fukata, Matthew T. Webster, Elinor K. Karlsson, Sami K. Kilpinen, Frank Steffen, Elisabeth Dietschi, Tosso Leeb, Ranja Eklund, Xiaochu Zhao, Jennifer J. Rilstone, Kerstin Lindblad-Toh, Berge A. Minassian, Hannes Lohi

A Rice Plastidial Nucleotide Sugar Epimerase Is Involved in Galactolipid Biosynthesis and Improves Photosynthetic Efficiency

Chunlai Li, Yiqin Wang, Linchuan Liu, Yingchun Hu, Fengxia Zhang, Sod Mergen, Guodong Wang, Michael R. Schläppi, Chengcai Chu

Fine Mapping of Five Loci Associated with Low-Density Lipoprotein Cholesterol Detects Variants That Double the Explained Heritability

Serena Sanna, Bingshan Li, Antonella Mulas, Carlo Sidore, Hyun M. Kang, Anne U. Jackson, Maria Grazia Piras, Gianluca Usala, Giuseppe Maninchedda, Alessandro Sassu, Fabrizio Serra, Maria Antonietta Palmas, William H. Wood III, Inger Njølstad, Markku Laakso, Kristian Hveem, Jaakko Tuomilehto, Timo A. Lakka, Rainer Rauramaa, Michael Boehnke, Francesco Cucca, Manuela Uda, David Schlessinger, Ramaiah Nagaraja, Gonçalo R. Abecasis

A Role for Phosphatidic Acid in the Formation of “Supersized” Lipid Droplets

Weihua Fei, Guanghou Shui, Yuxi Zhang, Natalie Krahmer, Charles Ferguson, Tamar S. Kapterian, Ruby C. Lin, Ian W. Dawes, Andrew J. Brown, Peng Li, Xun Huang, Robert G. Parton, Markus R. Wenk, Tobias C. Walther, Hongyuan Yang

An Epigenetic Switch Involving Overlapping Fur and DNA Methylation Optimizes Expression of a Type VI Secretion Gene Cluster

Yannick R. Brunet, Christophe S. Bernard, Marthe Gavioli, Roland Lloubès, Eric Cascales

Stress-Induced PARP Activation Mediates Recruitment of Drosophila Mi-2 to Promote Heat Shock Gene Expression

Magdalena Murawska, Markus Hassler, Renate Renkawitz-Pohl, Andreas Ladurner, Alexander Brehm

Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes

Stephen B. Montgomery, Tuuli Lappalainen, Maria Gutierrez-Arcelus, Emmanouil T. Dermitzakis

Expression of Arf Tumor Suppressor in Spermatogonia Facilitates Meiotic Progression in Male Germ Cells

Michelle L. Churchman, Ignasi Roig, Maria Jasin, Scott Keeney, Charles J. Sherr

Nonlinear Fitness Landscape of a Molecular Pathway

Lilia Perfeito, Stéphane Ghozzi, Johannes Berg, Karin Schnetz, Michael Lässig

A Functional Variant at a Prostate Cancer Predisposition Locus at 8q24 Is Associated with PVT1 Expression

Kerstin B. Meyer, Ana-Teresa Maia, Martin O'Reilly, Maya Ghoussaini, Radhika Prathalingam, Patricia Porter-Gill, Stefan Ambs, Ludmila Prokunina-Olsson, Jason Carroll, Bruce A. J. Ponder

CHD1 Remodels Chromatin and Influences Transient DNA Methylation at the Clock Gene frequency

William J. Belden, Zachary A. Lewis, Eric U. Selker, Jennifer J. Loros, Jay C. Dunlap

Genome-Wide Association Study Identifies HLA-DP as a Susceptibility Gene for Pediatric Asthma in Asian Populations

Emiko Noguchi, Hiromi Sakamoto, Tomomitsu Hirota, Kaori Ochiai, Yoshimasa Imoto, Masafumi Sakashita, Fumitake Kurosaka, Akira Akasawa, Shigemi Yoshihara, Noriko Kanno, Yumi Yamada, Naoki Shimojo, Yoichi Kohno, Yoichi Suzuki, Mi-Jin Kang, Ji-Won Kwon, Soo-Jong Hong, Ken Inoue, Yu-ichi Goto, Fumio Yamashita, Takashi Asada, Hiroshi Hirose, Ikuo Saito, Shigeharu Fujieda, Nobuyuki Hizawa, Toru Sakamoto, Hironori Masuko, Yusuke Nakamura, Ichiro Nomura, Mayumi Tamari, Tadao Arinami, Teruhiko Yoshida, Hirohisa Saito, Kenji Matsumoto

DAF-12 Regulates a Connected Network of Genes to Ensure Robust Developmental Decisions

Daniel Hochbaum, Yue Zhang, Carsten Stuckenholz, Paul Labhart, Vassili Alexiadis, René Martin, Hans-Joachim Knölker, Alfred L. Fisher

Replication and Explorations of High-Order Epistasis Using a Large Advanced Intercross Line Pedigree

Mats Pettersson, Francois Besnier, Paul B. Siegel, Örjan Carlborg

Drosophila Araucan and Caupolican Integrate Intrinsic and Signalling Inputs for the Acquisition by Muscle Progenitors of the Lateral Transverse Fate

Marta Carrasco-Rando, Antonio S. Tutor, Silvia Prieto-Sánchez, Esther González-Pérez, Natalia Barrios, Annalisa Letizia, Paloma Martín, Sonsoles Campuzano, Mar Ruiz-Gómez

Adaptations to Endosymbiosis in a Cnidarian-Dinoflagellate Association: Differential Gene Expression and Specific Gene Duplications

Philippe Ganot, Aurélie Moya, Virginie Magnone, Denis Allemand, Paola Furla, Cécile Sabourault

Regulatory Cross-Talk Links Vibrio cholerae Chromosome II Replication and Segregation

Yoshiharu Yamaichi, Matthew A. Gerding, Brigid M. Davis, Matthew K. Waldor

Mechanisms of Chromosome Number Evolution in Yeast

Jonathan L. Gordon, Kevin P. Byrne, Kenneth H. Wolfe

The Epistatic Relationship between BRCA2 and the Other RAD51 Mediators in Homologous Recombination

Yong Qing, Mitsuyoshi Yamazoe, Kouji Hirota, Donniphat Dejsuphong, Wataru Sakai, Kimiyo N. Yamamoto, Douglas K. Bishop, XiaoHua Wu, Shunichi Takeda

Genome-Wide Association Study Identifies Novel Restless Legs Syndrome Susceptibility Loci on 2p14 and 16q12.1

Juliane Winkelmann, Darina Czamara, Barbara Schormair, Franziska Knauf, Eva C. Schulte, Claudia Trenkwalder, Yves Dauvilliers, Olli Polo, Birgit Högl, Klaus Berger, Andrea Fuhs, Nadine Gross, Karin Stiasny-Kolster, Wolfgang Oertel, Cornelius G. Bachmann, Walter Paulus, Lan Xiong, Jacques Montplaisir, Guy A. Rouleau, Ingo Fietze, Jana Vávrová, David Kemlink, Karel Sonka, Sona Nevsimalova, Siong-Chi Lin, Zbigniew Wszolek, Carles Vilariño-Güell, Matthew J. Farrer, Viola Gschliesser, Birgit Frauscher, Tina Falkenstetter, Werner Poewe, Richard P. Allen, Christopher J. Earley, William G. Ondo, Wei-Dong Le, Derek Spieler, Maria Kaffe, Alexander Zimprich, Johannes Kettunen, Markus Perola, Kaisa Silander, Isabelle Cournu-Rebeix, Marcella Francavilla, Claire Fontenille, Bertrand Fontaine, Pavel Vodicka, Holger Prokisch, Peter Lichtner, Paul Peppard, Juliette Faraco, Emmanuel Mignot, Christian Gieger, Thomas Illig, H.-Erich Wichmann, Bertram Müller-Myhsok, Thomas Meitinger

Auxin Response Factor2 (ARF2) and Its Regulated Homeodomain Gene HB33 Mediate Abscisic Acid Response in Arabidopsis

Li Wang, Deping Hua, Junna He, Ying Duan, Zhizhong Chen, Xuhui Hong, Zhizhong Gong

Molecular Mechanisms Generating and Stabilizing Terminal 22q13 Deletions in 44 Subjects with Phelan/McDermid Syndrome

Maria Clara Bonaglia, Roberto Giorda, Silvana Beri, Cristina De Agostini, Francesca Novara, Marco Fichera, Lucia Grillo, Ornella Galesi, Annalisa Vetro, Roberto Ciccone, Maria Teresa Bonati, Sabrina Giglio, Renzo Guerrini, Sara Osimani, Susan Marelli, Claudio Zucca, Rita Grasso, Renato Borgatti, Elisa Mani, Cristina Motta, Massimo Molteni, Corrado Romano, Donatella Greco, Santina Reitano, Anna Baroncini, Elisabetta Lapi, Antonella Cecconi, Giulia Arrigo, Maria Grazia Patricelli, Chiara Pantaleoni, Stefano D'Arrigo, Daria Riva, Francesca Sciacca, Bernardo Dalla Bernardina, Leonardo Zoccante, Francesca Darra, Cristiano Termine, Emanuela Maserati, Stefania Bigoni, Emanuela Priolo, Armand Bottani, Stefania Gimelli, Frederique Bena, Alfredo Brusco, Eleonora di Gregorio, Irene Bagnasco, Ursula Giussani, Lucio Nitsch, Pierluigi Politi, Maria Luisa Martinez-Frias, Maria Luisa Martínez-Fernández, Nieves Martínez Guardia, Anna Bremer, Britt-Marie Anderlid, Orsetta Zuffardi

Caenorhabditis briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility and the Evolution of Recombination

Joseph A. Ross, Daniel C. Koboldt, Julia E. Staisch, Helen M. Chamberlin, Bhagwati P. Gupta, Raymond D. Miller, Scott E. Baird, Eric S. Haag

Identification of Novel Genetic Markers Associated with Clinical Phenotypes of Systemic Sclerosis through a Genome-Wide Association Strategy

Olga Gorlova, Jose-Ezequiel Martin, Blanca Rueda, Bobby P. C. Koeleman, Jun Ying, Maria Teruel, Lina-Marcela Diaz-Gallo, Jasper C. Broen, Madelon C. Vonk, Carmen P. Simeon, Behrooz Z. Alizadeh, Marieke J. H. Coenen, Alexandre E. Voskuyl, Annemie J. Schuerwegh, Piet L. C. M. van Riel, Marie Vanthuyne, Ruben van 't Slot, Annet Italiaander, Roel A. Ophoff, Nicolas Hunzelmann, Vicente Fonollosa, Norberto Ortego-Centeno, Miguel A. González-Gay, Francisco J. García-Hernández, María F. González-Escribano, Paolo Airo, Jacob van Laar, Jane Worthington, Roger Hesselstrand, Vanessa Smith, Filip de Keyser, Fredric Houssiau, Meng May Chee, Rajan Madhok, Paul G. Shiels, Rene Westhovens, Alexander Kreuter, Elfride de Baere, Torsten Witte, Leonid Padyukov, Annika Nordin, Raffaella Scorza, Claudio Lunardi, Benedicte A. Lie, Anna-Maria Hoffmann-Vold, Øyvind Palm, Paloma García de la Peña, Patricia Carreira, John Varga, Monique Hinchcliff, Annette T. Lee, Pravitt Gourh, Christopher I. Amos, Frederick M. Wigley, Laura K. Hummers, J. Hummers, J. Lee Nelson, Gabriella Riemekasten, Ariane Herrick, Lorenzo Beretta, Carmen Fonseca, Christopher P. Denton, Peter K. Gregersen, Sandeep Agarwal, Shervin Assassi, Filemon K. Tan, Frank C. Arnett, Timothy R. D. J. Radstake, Maureen D. Mayes, Javier Martin , Spanish Scleroderma Group

Genome-Wide Scan Identifies TNIP1, PSORS1C1, and RHOB as Novel Risk Loci for Systemic Sclerosis

Yannick Allanore, Mohamad Saad, Philippe Dieudé, Jérôme Avouac, Jorg H. W. Distler, Philippe Amouyel, Marco Matucci-Cerinic, Gabriella Riemekasten, Paolo Airo, Inga Melchers, Eric Hachulla, Daniele Cusi, H.-Erich Wichmann, Julien Wipff, Jean-Charles Lambert, Nicolas Hunzelmann, Kiet Tiev, Paola Caramaschi, Elisabeth Diot, Otylia Kowal-Bielecka, Gabriele Valentini, Luc Mouthon, László Czirják, Nemanja Damjanov, Erika Salvi, Costanza Conti, Martina Müller, Ulf Müller-Ladner, Valeria Riccieri, Barbara Ruiz, Jean-Luc Cracowski, Luc Letenneur, Anne Marie Dupuy, Oliver Meyer, André Kahan, Arnold Munnich, Catherine Boileau, Maria Martinez

Loss of the BMP Antagonist, SMOC-1, Causes Ophthalmo-Acromelic (Waardenburg Anophthalmia) Syndrome in Humans and Mice

Joe Rainger, Ellen van Beusekom, Jacqueline K. Ramsay, Lisa McKie, Lihadh Al-Gazali, Rosanna Pallotta, Anita Saponari, Peter Branney, Malcolm Fisher, Harris Morrison, Louise Bicknell, Philippe Gautier, Paul Perry, Kishan Sokhi, David Sexton, Tanya M. Bardakjian, Adele S. Schneider, Nursel Elcioglu, Ferda Ozkinay, Rainer Koenig, Andre Mégarbané, C. Nur Semerci, Ayesha Khan, Saemah Zafar, Raoul Hennekam, Sérgio B. Sousa, Lina Ramos, Livia Garavelli, Andrea Superti Furga, Anita Wischmeijer, Ian J. Jackson, Gabriele Gillessen-Kaesbach, Han G. Brunner, Dagmar Wieczorek, Hans van Bokhoven, David R. FitzPatrick

Identification of a Mutation Associated with Fatal Foal Immunodeficiency Syndrome in the Fell and Dales Pony

Laura Y. Fox-Clipsham, Stuart D. Carter, Ian Goodhead, Neil Hall, Derek C. Knottenbelt, Paul D. F. May, William E. Ollier, June E. Swinburne

Translation Reinitiation Relies on the Interaction between eIF3a/TIF32 and Progressively Folded cis-Acting mRNA Elements Preceding Short uORFs

Vanda Munzarová, Josef Pánek, Stanislava Gunišová, István Dányi, Béla Szamecz, Leoš Shivaya Valášek

Foxp2 Regulates Gene Networks Implicated in Neurite Outgrowth in the Developing Brain

Sonja C. Vernes, Peter L. Oliver, Elizabeth Spiteri, Helen E. Lockstone, Rathi Puliyadi, Jennifer M. Taylor, Joses Ho, Cedric Mombereau, Ariel Brewer, Ernesto Lowy, Jérôme Nicod, Matthias Groszer, Dilair Baban, Natasha Sahgal, Jean-Baptiste Cazier, Jiannis Ragoussis, Kay E. Davies, Daniel H. Geschwind, Simon E. Fisher

Pathologic and Phenotypic Alterations in a Mouse Expressing a Connexin47 Missense Mutation That Causes Pelizaeus-Merzbacher–Like Disease in Humans

Oliver Tress, Marta Maglione, Armin Zlomuzica, Dennis May, Nikolai Dicke, Joachim Degen, Ekrem Dere, Helmut Kettenmann, Dieter Hartmann, Klaus Willecke

Interactions between Glucocorticoid Treatment and Cis-Regulatory Polymorphisms Contribute to Cellular Response Phenotypes

Joseph C. Maranville, Francesca Luca, Allison L. Richards, Xiaoquan Wen, David B. Witonsky, Shaneen Baxter, Matthew Stephens, Anna Di Rienzo

Adult Circadian Behavior in Drosophila Requires Developmental Expression of cycle, But Not period

Tadahiro Goda, Karolina Mirowska, Jake Currie, Min-Ho Kim, Neethi Varadaraja Rao, Gloribel Bonilla, Herman Wijnen

NatF Contributes to an Evolutionary Shift in Protein N-Terminal Acetylation and Is Important for Normal Chromosome Segregation

Petra Van Damme, Kristine Hole, Ana Pimenta-Marques, Kenny Helsens, Joël Vandekerckhove, Rui G. Martinho, Kris Gevaert, Thomas Arnesen