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Table of Contents: July 2010

COVER

Iris transillumination defect of Lyst-mutant mice.

Image Credit: Michael Anderson
Issue Image

LYST is a large cytosolic protein that influences the biogenesis of lysosome-related organelles and is relevant to multiple human diseases. Lyst-mutant mice exhibit a variety of defects, including a unique pattern of concentric transillumination defects in the iris. In this issue of PLoS Genetics, Trantow et al. utilized iris phenotypes in a search for modifier genes that influence Lyst pathways. A priori, the expectation would have been that modifiers of Lyst would logically be related to organelle biogenesis. Instead, the authors show that at the level of the whole-animal, oxidative damage to membranes is a highly relevant event.

Interview

Perspective

Review

The Importance of Imprinting in the Human Placenta

Jennifer M. Frost, Gudrun E. Moore

Research Articles

Quantitative and Molecular Genetic Analyses of Mutations Increasing Drosophila Life Span

Michael M. Magwire, Akihiko Yamamoto, Mary Anna Carbone, Natalia V. Roshina, Alexander V. Symonenko, Elena G. Pasyukova, Tatiana V. Morozova, Trudy F. C. Mackay

Association of Variants at UMOD with Chronic Kidney Disease and Kidney Stones—Role of Age and Comorbid Diseases

Daniel F. Gudbjartsson, Hilma Holm, Olafur S. Indridason, Gudmar Thorleifsson, Vidar Edvardsson, Patrick Sulem, Femmie de Vegt, Frank C. H. d'Ancona, Martin den Heijer, Leifur Franzson, Thorunn Rafnar, Kristleifur Kristjansson, Unnur S. Bjornsdottir, Gudmundur I. Eyjolfsson, Lambertus A. Kiemeney, Augustine Kong, Runolfur Palsson, Unnur Thorsteinsdottir, Kari Stefansson

Calpain 8/nCL-2 and Calpain 9/nCL-4 Constitute an Active Protease Complex, G-Calpain, Involved in Gastric Mucosal Defense

Shoji Hata, Manabu Abe, Hidenori Suzuki, Fujiko Kitamura, Noriko Toyama-Sorimachi, Keiko Abe, Kenji Sakimura, Hiroyuki Sorimachi

The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts

Ryan K. Shultzaberger, Daniel S. Malashock, Jack F. Kirsch, Michael B. Eisen

Breast Cancer DNA Methylation Profiles Are Associated with Tumor Size and Alcohol and Folate Intake

Brock C. Christensen, Karl T. Kelsey, Shichun Zheng, E. Andres Houseman, Carmen J. Marsit, Margaret R. Wrensch, Joseph L. Wiemels, Heather H. Nelson, Margaret R. Karagas, Lawrence H. Kushi, Marilyn L. Kwan, John K. Wiencke

Genome-Wide Analysis Reveals Novel Genes Essential for Heme Homeostasis in Caenorhabditis elegans

Scott Severance, Abbhirami Rajagopal, Anita U. Rao, Gustavo C. Cerqueira, Makedonka Mitreva, Najib M. El-Sayed, Michael Krause, Iqbal Hamza

Reconstruction of the Core and Extended Regulons of Global Transcription Factors

Yann S. Dufour, Patricia J. Kiley, Timothy J. Donohue

Ancestry-Shift Refinement Mapping of the C6orf97-ESR1 Breast Cancer Susceptibility Locus

Simon N. Stacey, Patrick Sulem, Carlo Zanon, Sigurjon A. Gudjonsson, Gudmar Thorleifsson, Agnar Helgason, Aslaug Jonasdottir, Soren Besenbacher, Jelena P. Kostic, James D. Fackenthal, Dezheng Huo, Clement Adebamowo, Temidayo Ogundiran, Janet E. Olson, Zachary S. Fredericksen, Xianshu Wang, Maxime P. Look, Anieta M. Sieuwerts, John W. M. Martens, Isabel Pajares, Maria D. Garcia-Prats, Jose M. Ramon-Cajal, Ana de Juan, Angeles Panadero, Eugenia Ortega, Katja K. H. Aben, Sita H. Vermeulen, Fatemeh Asadzadeh, K. C. Anton van Engelenburg, Sara Margolin, Chen-Yang Shen, Pei-Ei Wu, Asta Försti, Per Lenner, Roger Henriksson, Robert Johansson, Kerstin Enquist, Göran Hallmans, Thorvaldur Jonsson, Helgi Sigurdsson, Kristin Alexiusdottir, Julius Gudmundsson, Asgeir Sigurdsson, Michael L. Frigge, Larus Gudmundsson, Kristleifur Kristjansson, Bjarni V. Halldorsson, Unnur Styrkarsdottir, Jeffrey R. Gulcher, Kari Hemminki, Annika Lindblom, Lambertus A. Kiemeney, Jose I. Mayordomo, John A. Foekens, Fergus J. Couch, Olufunmilayo I. Olopade, Daniel F. Gudbjartsson, Unnur Thorsteinsdottir, Thorunn Rafnar, Oskar T. Johannsson, Kari Stefansson

A Collection of Target Mimics for Comprehensive Analysis of MicroRNA Function in Arabidopsis thaliana

Marco Todesco, Ignacio Rubio-Somoza, Javier Paz-Ares, Detlef Weigel

Rad3ATR Decorates Critical Chromosomal Domains with γH2A to Protect Genome Integrity during S-Phase in Fission Yeast

Sophie Rozenzhak, Eva Mejía-Ramírez, Jessica S. Williams, Lana Schaffer, Jennifer A. Hammond, Steven R. Head, Paul Russell

Inter- and Intra-Individual Variation in Allele-Specific DNA Methylation and Gene Expression in Children Conceived using Assisted Reproductive Technology

Nahid Turan, Sunita Katari, Leigh F. Gerson, Raffi Chalian, Michael W. Foster, John P. Gaughan, Christos Coutifaris, Carmen Sapienza

Sex Reversal in Zebrafish fancl Mutants Is Caused by Tp53-Mediated Germ Cell Apoptosis

Adriana Rodríguez-Marí, Cristian Cañestro, Ruth A. BreMiller, Alexandria Nguyen-Johnson, Kazuhide Asakawa, Koichi Kawakami, John H. Postlethwait

Genome-Wide Meta-Analysis for Serum Calcium Identifies Significantly Associated SNPs near the Calcium-Sensing Receptor (CASR) Gene

Karen Kapur, Toby Johnson, Noam D. Beckmann, Joban Sehmi, Toshiko Tanaka, Zoltán Kutalik, Unnur Styrkarsdottir, Weihua Zhang, Diana Marek, Daniel F. Gudbjartsson, Yuri Milaneschi, Hilma Holm, Angelo DiIorio, Dawn Waterworth, Yun Li, Andrew B. Singleton, Unnur S. Bjornsdottir, Gunnar Sigurdsson, Dena G. Hernandez, Ranil DeSilva, Paul Elliott, Gudmundur I. Eyjolfsson, Jack M. Guralnik, James Scott, Unnur Thorsteinsdottir, Stefania Bandinelli, John Chambers, Kari Stefansson, Gérard Waeber, Luigi Ferrucci, Jaspal S. Kooner, Vincent Mooser, Peter Vollenweider, Jacques S. Beckmann, Murielle Bochud, Sven Bergmann

Microevolution of Helicobacter pylori during Prolonged Infection of Single Hosts and within Families

Giovanna Morelli, Xavier Didelot, Barica Kusecek, Sandra Schwarz, Christelle Bahlawane, Daniel Falush, Sebastian Suerbaum, Mark Achtman

Widespread Presence of Human BOULE Homologs among Animals and Conservation of Their Ancient Reproductive Function

Chirag Shah, Michael J. W. VanGompel, Villian Naeem, Yanmei Chen, Terrance Lee, Nicholas Angeloni, Yin Wang, Eugene Yujun Xu

CHD7 Targets Active Gene Enhancer Elements to Modulate ES Cell-Specific Gene Expression

Michael P. Schnetz, Lusy Handoko, Batool Akhtar-Zaidi, Cynthia F. Bartels, C. Filipe Pereira, Amanda G. Fisher, David J. Adams, Paul Flicek, Gregory E. Crawford, Thomas LaFramboise, Paul Tesar, Chia-Lin Wei, Peter C. Scacheri

Genome-Wide Screen in Saccharomyces cerevisiae Identifies Vacuolar Protein Sorting, Autophagy, Biosynthetic, and tRNA Methylation Genes Involved in Life Span Regulation

Paola Fabrizio, Shawn Hoon, Mehrnaz Shamalnasab, Abdulaye Galbani, Min Wei, Guri Giaever, Corey Nislow, Valter D. Longo

The Caenorhabditis elegans Homolog of Gen1/Yen1 Resolvases Links DNA Damage Signaling to DNA Double-Strand Break Repair

Aymeric P. Bailly, Alasdair Freeman, Julie Hall, Anne-Cécile Déclais, Arno Alpi, David M. J. Lilley, Shawn Ahmed, Anton Gartner

Lysosomal Dysfunction Promotes Cleavage and Neurotoxicity of Tau In Vivo

Vikram Khurana, Ilan Elson-Schwab, Tudor A. Fulga, Katherine A. Sharp, Carin A. Loewen, Erin Mulkearns, Jaana Tyynelä, Clemens R. Scherzer, Mel B. Feany

Evaluation of Candidate Stromal Epithelial Cross-Talk Genes Identifies Association between Risk of Serous Ovarian Cancer and TERT, a Cancer Susceptibility “Hot-Spot”

Sharon E. Johnatty, Jonathan Beesley, Xiaoqing Chen, Stuart Macgregor, David L. Duffy, Amanda B. Spurdle, Anna deFazio, Natalie Gava, Penelope M. Webb, Mary Anne Rossing, Jennifer Anne Doherty, Marc T. Goodman, Galina Lurie, Pamela J. Thompson, Lynne R. Wilkens, Roberta B. Ness, Kirsten B. Moysich, Jenny Chang-Claude, Shan Wang-Gohrke, Daniel W. Cramer, Kathryn L. Terry, Susan E. Hankinson, Shelley S. Tworoger, Montserrat Garcia-Closas, Hannah Yang, Jolanta Lissowska, Stephen J. Chanock, Paul D. Pharoah, Honglin Song, Alice S. Whitemore, Celeste L. Pearce, Daniel O. Stram, Anna H. Wu, Malcolm C. Pike, Simon A. Gayther, Susan J. Ramus, Usha Menon, Aleksandra Gentry-Maharaj, Hoda Anton-Culver, Argyrios Ziogas, Estrid Hogdall, Susanne K. Kjaer, Claus Hogdall, Andrew Berchuck, Joellen M. Schildkraut, Edwin S. Iversen, Patricia G. Moorman, Catherine M. Phelan, Thomas A. Sellers, Julie M. Cunningham, Robert A. Vierkant, David N. Rider, Ellen L. Goode, Izhak Haviv, Georgia Chenevix-Trench , Australian Ovarian Cancer Study Group, Australian Cancer Study (Ovarian Cancer), Ovarian Cancer Association Consortium

A Forward-Genetic Screen and Dynamic Analysis of Lambda Phage Host-Dependencies Reveals an Extensive Interaction Network and a New Anti-Viral Strategy

Nathaniel D. Maynard, Elsa W. Birch, Jayodita C. Sanghvi, Lu Chen, Miriam V. Gutschow, Markus W. Covert

Id4, a New Candidate Gene for Senile Osteoporosis, Acts as a Molecular Switch Promoting Osteoblast Differentiation

Yoshimi Tokuzawa, Ken Yagi, Yzumi Yamashita, Yutaka Nakachi, Itoshi Nikaido, Hidemasa Bono, Yuichi Ninomiya, Yukiko Kanesaki-Yatsuka, Masumi Akita, Hiromi Motegi, Shigeharu Wakana, Tetsuo Noda, Fred Sablitzky, Shigeki Arai, Riki Kurokawa, Toru Fukuda, Takenobu Katagiri, Christian Schönbach, Tatsuo Suda, Yosuke Mizuno, Yasushi Okazaki

Regulator of G Protein Signaling 3 Modulates Wnt5b Calcium Dynamics and Somite Patterning

Christina M. Freisinger, Rory A. Fisher, Diane C. Slusarski

Cohesin Is Limiting for the Suppression of DNA Damage–Induced Recombination between Homologous Chromosomes

Shay Covo, James W. Westmoreland, Dmitry A. Gordenin, Michael A. Resnick

Elevated Oxidative Membrane Damage Associated with Genetic Modifiers of Lyst-Mutant Phenotypes

Colleen M. Trantow, Adam Hedberg-Buenz, Sachiyo Iwashita, Steven A. Moore, Michael G. Anderson

Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture

Eitan Yaffe, Shlomit Farkash-Amar, Andreas Polten, Zohar Yakhini, Amos Tanay, Itamar Simon

Multi-Variant Pathway Association Analysis Reveals the Importance of Genetic Determinants of Estrogen Metabolism in Breast and Endometrial Cancer Susceptibility

Yen Ling Low, Yuqing Li, Keith Humphreys, Anbupalam Thalamuthu, Yi Li, Hatef Darabi, Sara Wedrén, Carine Bonnard, Kamila Czene, Mark M. Iles, Tuomas Heikkinen, Kristiina Aittomäki, Carl Blomqvist, Heli Nevanlinna, Per Hall, Edison T. Liu, Jianjun Liu

Variation, Sex, and Social Cooperation: Molecular Population Genetics of the Social Amoeba Dictyostelium discoideum

Jonathan M. Flowers, Si I. Li, Angela Stathos, Gerda Saxer, Elizabeth A. Ostrowski, David C. Queller, Joan E. Strassmann, Michael D. Purugganan

Combinatorial Binding Leads to Diverse Regulatory Responses: Lmd Is a Tissue-Specific Modulator of Mef2 Activity

Paulo M. F. Cunha, Thomas Sandmann, E. Hilary Gustafson, Lucia Ciglar, Michael P. Eichenlaub, Eileen E. M. Furlong