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Table of Contents: June 2009

COVER

Necrotic protein uptake in garland cells.

Image Credit: Picture taken by Dr. Sandra Soukup in the laboratory of Dr. David Gubb (CICbioGUNE Institute, Derio, Spain).
Issue Image

The garland cells are one of two groups of athrocytes in Drosophila in which extracellular serpin-family inhibitors involved in the innate immune response are taken up and degraded (see Soukup et al., 10.1371/journal.pgen.1000532). The image shows a broken ring of garland cells encircling the oesophagus above the proventriculus (Z-series reconstruction). Endocytosis has been frozen using a Dynamints mutation, allowing Necrotic (red) to be detected within the cortical labyrinthine channels of the garland cells. In a normal fly, Necrotic is endocytosed via the LpR1 trafficking receptor, processed through multi-vesicular bodies, and delivered to the lysosome for degradation.

Perspectives

Review

Pervasive Natural Selection in the Drosophila Genome?

Guy Sella, Dmitri A. Petrov, Molly Przeworski, Peter Andolfatto

Research Articles

Genome-Wide Association Scan Meta-Analysis Identifies Three Loci Influencing Adiposity and Fat Distribution

Cecilia M. Lindgren, Iris M. Heid, Joshua C. Randall, Claudia Lamina, Valgerdur Steinthorsdottir, Lu Qi, Elizabeth K. Speliotes, Gudmar Thorleifsson, Cristen J. Willer, Blanca M. Herrera, Anne U. Jackson, Noha Lim, Paul Scheet, Nicole Soranzo, Najaf Amin, Yurii S. Aulchenko, John C. Chambers, Alexander Drong, Jian'an Luan, Helen N. Lyon, Fernando Rivadeneira, Serena Sanna, Nicholas J. Timpson, M. Carola Zillikens, Jing Hua Zhao, Peter Almgren, Stefania Bandinelli, Amanda J. Bennett, Richard N. Bergman, Lori L. Bonnycastle, Suzannah J. Bumpstead, Stephen J. Chanock, Lynn Cherkas, Peter Chines, Lachlan Coin, Cyrus Cooper, Gabriel Crawford, Angela Doering, Anna Dominiczak, Alex S. F. Doney, Shah Ebrahim, Paul Elliott, Michael R. Erdos, Karol Estrada, Luigi Ferrucci, Guido Fischer, Nita G. Forouhi, Christian Gieger, Harald Grallert, Christopher J. Groves, Scott Grundy, Candace Guiducci, David Hadley, Anders Hamsten, Aki S. Havulinna, Albert Hofman, Rolf Holle, John W. Holloway, Thomas Illig, Bo Isomaa, Leonie C. Jacobs, Karen Jameson, Pekka Jousilahti, Fredrik Karpe, Johanna Kuusisto, Jaana Laitinen, G. Mark Lathrop, Debbie A. Lawlor, Massimo Mangino, Wendy L. McArdle, Thomas Meitinger, Mario A. Morken, Andrew P. Morris, Patricia Munroe, Narisu Narisu, Anna Nordström, Peter Nordström, Ben A. Oostra, Colin N. A. Palmer, Felicity Payne, John F. Peden, Inga Prokopenko, Frida Renström, Aimo Ruokonen, Veikko Salomaa, Manjinder S. Sandhu, Laura J. Scott, Angelo Scuteri, Kaisa Silander, Kijoung Song, Xin Yuan, Heather M. Stringham, Amy J. Swift, Tiinamaija Tuomi, Manuela Uda, Peter Vollenweider, Gerard Waeber, Chris Wallace, G. Bragi Walters, Michael N. Weedon, Jacqueline C. M. Witteman, Cuilin Zhang, Weihua Zhang, Mark J. Caulfield, Francis S. Collins, George Davey Smith, Ian N. M. Day, Paul W. Franks, Andrew T. Hattersley, Frank B. Hu, Marjo-Riitta Jarvelin, Augustine Kong, Jaspal S. Kooner, Markku Laakso, Edward Lakatta, Vincent Mooser, Andrew D. Morris, Leena Peltonen, Nilesh J. Samani, Timothy D. Spector, David P. Strachan, Toshiko Tanaka, Jaakko Tuomilehto, André G. Uitterlinden, Cornelia M. van Duijn, Nicholas J. Wareham, Hugh Watkins for the PROCARDIS consortia, Dawn M. Waterworth, Michael Boehnke, Panos Deloukas, Leif Groop, David J. Hunter, Unnur Thorsteinsdottir, David Schlessinger, H.-Erich Wichmann, Timothy M. Frayling, Gonçalo R. Abecasis, Joel N. Hirschhorn, Ruth J. F. Loos, Kari Stefansson, Karen L. Mohlke, Inês Barroso, Mark I. McCarthy for the GIANT consortium , The Wellcome Trust Case Control Consortium

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

Frank Johannes, Emmanuelle Porcher, Felipe K. Teixeira, Vera Saliba-Colombani, Matthieu Simon, Nicolas Agier, Agnès Bulski, Juliette Albuisson, Fabiana Heredia, Pascal Audigier, David Bouchez, Christine Dillmann, Philippe Guerche, Frédéric Hospital, Vincent Colot

Forging Links between Human Mental Retardation–Associated CNVs and Mouse Gene Knockout Models

Caleb Webber, Jayne Y. Hehir-Kwa, Duc-Quang Nguyen, Bert B. A. de Vries, Joris A. Veltman, Chris P. Ponting

Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions

Soumya Raychaudhuri, Robert M. Plenge, Elizabeth J. Rossin, Aylwin C. Y. Ng, Shaun M. Purcell, Pamela Sklar, Edward M. Scolnick, Ramnik J. Xavier, David Altshuler, Mark J. Daly , International Schizophrenia Consortium

Genome-Wide Analyses of Exonic Copy Number Variants in a Family-Based Study Point to Novel Autism Susceptibility Genes

Maja Bucan, Brett S. Abrahams, Kai Wang, Joseph T. Glessner, Edward I. Herman, Lisa I. Sonnenblick, Ana I. Alvarez Retuerto, Marcin Imielinski, Dexter Hadley, Jonathan P. Bradfield, Cecilia Kim, Nicole B. Gidaya, Ingrid Lindquist, Ted Hutman, Marian Sigman, Vlad Kustanovich, Clara M. Lajonchere, Andrew Singleton, Junhyong Kim, Thomas H. Wassink, William M. McMahon, Thomas Owley, John A. Sweeney, Hilary Coon, John I. Nurnberger Jr, Mingyao Li, Rita M. Cantor, Nancy J. Minshew, James S. Sutcliffe, Edwin H. Cook, Geraldine Dawson, Joseph D. Buxbaum, Struan F. A. Grant, Gerard D. Schellenberg, Daniel H. Geschwind, Hakon Hakonarson

An Integrated Strategy to Study Muscle Development and Myofilament Structure in Caenorhabditis elegans

Barbara Meissner, Adam Warner, Kim Wong, Nicholas Dube, Adam Lorch, Sheldon J. McKay, Jaswinder Khattra, Teresa Rogalski, Aruna Somasiri, Iasha Chaudhry, Rebecca M. Fox, David M. Miller III, David L. Baillie, Robert A. Holt, Steven J. M. Jones, Marco A. Marra, Donald G. Moerman

Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution

Lucia Carbone, R. Alan Harris, Gery M. Vessere, Alan R. Mootnick, Sean Humphray, Jane Rogers, Sung K. Kim, Jeffrey D. Wall, David Martin, Jerzy Jurka, Aleksandar Milosavljevic, Pieter J. de Jong

NRXN3 Is a Novel Locus for Waist Circumference: A Genome-Wide Association Study from the CHARGE Consortium

Nancy L. Heard-Costa, M. Carola Zillikens, Keri L. Monda, Åsa Johansson, Tamara B. Harris, Mao Fu, Talin Haritunians, Mary F. Feitosa, Thor Aspelund, Gudny Eiriksdottir, Melissa Garcia, Lenore J. Launer, Albert V. Smith, Braxton D. Mitchell, Patrick F. McArdle, Alan R. Shuldiner, Suzette J. Bielinski, Eric Boerwinkle, Fred Brancati, Ellen W. Demerath, James S. Pankow, Alice M. Arnold, Yii-Der Ida Chen, Nicole L. Glazer, Barbara McKnight, Bruce M. Psaty, Jerome I. Rotter, Najaf Amin, Harry Campbell, Ulf Gyllensten, Cristian Pattaro, Peter P. Pramstaller, Igor Rudan, Maksim Struchalin, Veronique Vitart, Xiaoyi Gao, Aldi Kraja, Michael A. Province, Qunyuan Zhang, Larry D. Atwood, Josée Dupuis, Joel N. Hirschhorn, Cashell E. Jaquish, Christopher J. O'Donnell, Ramachandran S. Vasan, Charles C. White, Yurii S. Aulchenko, Karol Estrada, Albert Hofman, Fernando Rivadeneira, André G. Uitterlinden, Jacqueline C. M. Witteman, Ben A. Oostra, Robert C. Kaplan, Vilmundur Gudnason, Jeffrey R. O'Connell, Ingrid B. Borecki, Cornelia M. van Duijn, L. Adrienne Cupples, Caroline S. Fox, Kari E. North

The Maternal-Effect Gene cellular island Encodes Aurora B Kinase and Is Essential for Furrow Formation in the Early Zebrafish Embryo

Taijiro Yabe, Xiaoyan Ge, Robin Lindeman, Sreelaja Nair, Greg Runke, Mary C. Mullins, Francisco Pelegri

Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations

Alkes L. Price, Arti Tandon, Nick Patterson, Kathleen C. Barnes, Nicholas Rafaels, Ingo Ruczinski, Terri H. Beaty, Rasika Mathias, David Reich, Simon Myers

Disease-Causing 7.4 kb Cis-Regulatory Deletion Disrupting Conserved Non-Coding Sequences and Their Interaction with the FOXL2 Promotor: Implications for Mutation Screening

Barbara D'haene, Catia Attanasio, Diane Beysen, Josée Dostie, Edmond Lemire, Philippe Bouchard, Michael Field, Kristie Jones, Birgit Lorenz, Björn Menten, Karen Buysse, Filip Pattyn, Marc Friedli, Catherine Ucla, Colette Rossier, Carine Wyss, Frank Speleman, Anne De Paepe, Job Dekker, Stylianos E. Antonarakis, Elfride De Baere

Genetic Variation of Promoter Sequence Modulates XBP1 Expression and Genetic Risk for Vitiligo

Yunqing Ren, Sen Yang, Shengxin Xu, Min Gao, Wei Huang, Tianwen Gao, Qiaoyun Fang, Cheng Quan, Chi Zhang, Liangdan Sun, Yanhua Liang, Jianwen Han, Zhimin Wang, Fengyu Zhang, Youwen Zhou, Jianjun Liu, Xuejun Zhang

Peroxiredoxin Tsa1 Is the Key Peroxidase Suppressing Genome Instability and Protecting against Cell Death in Saccharomyces cerevisiae

Ismail Iraqui, Guy Kienda, Jérémie Soeur, Gérard Faye, Giuseppe Baldacci, Richard D. Kolodner, Meng-Er Huang

Genome-Wide Identification of Alternative Splice Forms Down-Regulated by Nonsense-Mediated mRNA Decay in Drosophila

Kasper Daniel Hansen, Liana F. Lareau, Marco Blanchette, Richard E. Green, Qi Meng, Jan Rehwinkel, Fabian L. Gallusser, Elisa Izaurralde, Donald C. Rio, Sandrine Dudoit, Steven E. Brenner

A Network of Conserved Damage Survival Pathways Revealed by a Genomic RNAi Screen

Dashnamoorthy Ravi, Amy M. Wiles, Selvaraj Bhavani, Jianhua Ruan, Philip Leder, Alexander J. R. Bishop

Comprehensive Linkage and Association Analyses Identify Haplotype, Near to the TNFSF15 Gene, Significantly Associated with Spondyloarthritis

Elena Zinovieva, Catherine Bourgain, Amir Kadi, Franck Letourneur, Brigitte Izac, Roula Said-Nahal, Nicolas Lebrun, Nicolas Cagnard, Agathe Vigier, Sébastien Jacques, Corinne Miceli-Richard, Henri-Jean Garchon, Simon Heath, Céline Charon, Delphine Bacq, Anne Boland, Diana Zelenika, Gilles Chiocchia, Maxime Breban

The Level of the Transcription Factor Pax6 Is Essential for Controlling the Balance between Neural Stem Cell Self-Renewal and Neurogenesis

Stephen N. Sansom, Dean S. Griffiths, Andrea Faedo, Dirk-Jan Kleinjan, Youlin Ruan, James Smith, Veronica van Heyningen, John L. Rubenstein, Frederick J. Livesey

Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens

Dominic Wright, Henrik Boije, Jennifer R. S. Meadows, Bertrand Bed'hom, David Gourichon, Agathe Vieaud, Michèle Tixier-Boichard, Carl-Johan Rubin, Freyja Imsland, Finn Hallböök, Leif Andersson

Differential Regulation of Horizontally Acquired and Core Genome Genes by the Bacterial Modulator H-NS

Rosa C. Baños, Aitziber Vivero, Sonia Aznar, Jesús García, Miquel Pons, Cristina Madrid, Antonio Juárez

Caenorhabditis elegans Protein Arginine Methyltransferase PRMT-5 Negatively Regulates DNA Damage-Induced Apoptosis

Mei Yang, Jianwei Sun, Xiaojuan Sun, Qinfang Shen, Zhiyang Gao, Chonglin Yang

The Role of Geography in Human Adaptation

Graham Coop, Joseph K. Pickrell, John Novembre, Sridhar Kudaravalli, Jun Li, Devin Absher, Richard M. Myers, Luigi Luca Cavalli-Sforza, Marcus W. Feldman, Jonathan K. Pritchard

Systematic Identification of Balanced Transposition Polymorphisms in Saccharomyces cerevisiae

Dina A. Faddah, Eric W. Ganko, Caroline McCoach, Joseph K. Pickrell, Sean E. Hanlon, Frederick G. Mann, Joanna O. Mieczkowska, Corbin D. Jones, Jason D. Lieb, Todd J. Vision

Caenorhabditis elegans Genomic Response to Soil Bacteria Predicts Environment-Specific Genetic Effects on Life History Traits

Joseph D. Coolon, Kenneth L. Jones, Timothy C. Todd, Bryanua C. Carr, Michael A. Herman

Meta-Analysis of 28,141 Individuals Identifies Common Variants within Five New Loci That Influence Uric Acid Concentrations

Melanie Kolz, Toby Johnson, Serena Sanna, Alexander Teumer, Veronique Vitart, Markus Perola, Massimo Mangino, Eva Albrecht, Chris Wallace, Martin Farrall, Åsa Johansson, Dale R. Nyholt, Yurii Aulchenko, Jacques S. Beckmann, Sven Bergmann, Murielle Bochud, Morris Brown, Harry Campbell, John Connell, Anna Dominiczak, Georg Homuth, Claudia Lamina, Mark I. McCarthy, Thomas Meitinger, Vincent Mooser, Patricia Munroe, Matthias Nauck, John Peden, Holger Prokisch, Perttu Salo, Veikko Salomaa, Nilesh J. Samani, David Schlessinger, Manuela Uda, Uwe Völker, Gérard Waeber, Dawn Waterworth, Rui Wang-Sattler, Alan F. Wright, Jerzy Adamski, John B. Whitfield, Ulf Gyllensten, James F. Wilson, Igor Rudan, Peter Pramstaller, Hugh Watkins, Angela Doering, H.-Erich Wichmann, Tim D. Spector, Leena Peltonen, Henry Völzke, Ramaiah Nagaraja, Peter Vollenweider, Mark Caulfield, Thomas Illig, Christian Gieger , for the EUROSPAN Consortium, for the ENGAGE Consortium, for the PROCARDIS Consortium, for the KORA Study, for the WTCCC

The Impact of Divergence Time on the Nature of Population Structure: An Example from Iceland

Alkes L. Price, Agnar Helgason, Snaebjorn Palsson, Hreinn Stefansson, David St. Clair, Ole A. Andreassen, David Reich, Augustine Kong, Kari Stefansson

Genome-Wide uH2A Localization Analysis Highlights Bmi1-Dependent Deposition of the Mark at Repressed Genes

Eric M. Kallin, Ru Cao, Raja Jothi, Kai Xia, Kairong Cui, Keji Zhao, Yi Zhang

In Vivo Generation of Neurotoxic Prion Protein: Role for Hsp70 in Accumulation of Misfolded Isoforms

Pedro Fernandez-Funez, Sergio Casas-Tinto, Yan Zhang, Melisa Gómez-Velazquez, Marco A. Morales-Garza, Ana C. Cepeda-Nieto, Joaquín Castilla, Claudio Soto, Diego E. Rincon-Limas