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Table of Contents: April 2011

COVER

Rural Scenes from Togo, West Africa.

Image Credit: Shannon Heuklom
Issue Image

Infectious diseases like malaria are major causes of morbidity and mortality in Sub-Saharan Africa. These microbes are able to rapidly evolve resistance to the drug treatments we develop, threatening our ability to treat these diseases, and placing millions at great risk (see Van Tyne et al.).

Perspective

Review

The Liberation of Embryonic Stem Cells

Kathryn Blair, Jason Wray, Austin Smith

Research Articles

Genomic Instability, Defective Spermatogenesis, Immunodeficiency, and Cancer in a Mouse Model of the RIDDLE Syndrome

Toshiyuki Bohgaki, Miyuki Bohgaki, Renato Cardoso, Stephanie Panier, Dimphy Zeegers, Li Li, Grant S. Stewart, Otto Sanchez, M. Prakash Hande, Daniel Durocher, Anne Hakem, Razqallah Hakem

ESR1 Is Co-Expressed with Closely Adjacent Uncharacterised Genes Spanning a Breast Cancer Susceptibility Locus at 6q25.1

Anita K. Dunbier, Helen Anderson, Zara Ghazoui, Elena Lopez-Knowles, Sunil Pancholi, Ricardo Ribas, Suzanne Drury, Kally Sidhu, Alexandra Leary, Lesley-Ann Martin, Mitch Dowsett

The Phylogenetic Origin of oskar Coincided with the Origin of Maternally Provisioned Germ Plasm and Pole Cells at the Base of the Holometabola

Jeremy A. Lynch, Orhan Özüak, Abderrahman Khila, Ehab Abouheif, Claude Desplan, Siegfried Roth

PTG Depletion Removes Lafora Bodies and Rescues the Fatal Epilepsy of Lafora Disease

Julie Turnbull, Anna A. DePaoli-Roach, Xiaochu Zhao, Miguel A. Cortez, Nela Pencea, Erica Tiberia, Mark Piliguian, Peter J. Roach, Peixiang Wang, Cameron A. Ackerley, Berge A. Minassian

Phosphorylation-Dependent Differential Regulation of Plant Growth, Cell Death, and Innate Immunity by the Regulatory Receptor-Like Kinase BAK1

Benjamin Schwessinger, Milena Roux, Yasuhiro Kadota, Vardis Ntoukakis, Jan Sklenar, Alexandra Jones, Cyril Zipfel

Beyond Missing Heritability: Prediction of Complex Traits

Robert Makowsky, Nicholas M. Pajewski, Yann C. Klimentidis, Ana I. Vazquez, Christine W. Duarte, David B. Allison, Gustavo de los Campos

Deficiency of Huntingtin Has Pleiotropic Effects in the Social Amoeba Dictyostelium discoideum

Michael A. Myre, Amanda L. Lumsden, Morgan N. Thompson, Wilma Wasco, Marcy E. MacDonald, James F. Gusella

Arabidopsis HDA6 Regulates Locus-Directed Heterochromatin Silencing in Cooperation with MET1

Taiko Kim To, Jong-Myong Kim, Akihiro Matsui, Yukio Kurihara, Taeko Morosawa, Junko Ishida, Maho Tanaka, Takaho Endo, Tetsuji Kakutani, Tetsuro Toyoda, Hiroshi Kimura, Shigeyuki Yokoyama, Kazuo Shinozaki, Motoaki Seki

The Complete Spectrum of Yeast Chromosome Instability Genes Identifies Candidate CIN Cancer Genes and Functional Roles for ASTRA Complex Components

Peter C. Stirling, Michelle S. Bloom, Tejomayee Solanki-Patil, Stephanie Smith, Payal Sipahimalani, Zhijian Li, Megan Kofoed, Shay Ben-Aroya, Kyungjae Myung, Philip Hieter

A Large-Scale Complex Haploinsufficiency-Based Genetic Interaction Screen in Candida albicans: Analysis of the RAM Network during Morphogenesis

Nike Bharucha, Yeissa Chabrier-Roselló, Tao Xu, Cole Johnson, Sarah Sobczynski, Qingxuan Song, Craig J. Dobry, Matthew J. Eckwahl, Christopher P. Anderson, Andrew J. Benjamin, Anuj Kumar, Damian J. Krysan

Epigenetic Regulation of Cell Type–Specific Expression Patterns in the Human Mammary Epithelium

Reo Maruyama, Sibgat Choudhury, Adam Kowalczyk, Marina Bessarabova, Bryan Beresford-Smith, Thomas Conway, Antony Kaspi, Zhenhua Wu, Tatiana Nikolskaya, Vanessa F. Merino, Pang-Kuo Lo, X. Shirley Liu, Yuri Nikolsky, Saraswati Sukumar, Izhak Haviv, Kornelia Polyak

Enhanced Statistical Tests for GWAS in Admixed Populations: Assessment using African Americans from CARe and a Breast Cancer Consortium

Bogdan Pasaniuc, Noah Zaitlen, Guillaume Lettre, Gary K. Chen, Arti Tandon, W. H. Linda Kao, Ingo Ruczinski, Myriam Fornage, David S. Siscovick, Xiaofeng Zhu, Emma Larkin, Leslie A. Lange, L. Adrienne Cupples, Qiong Yang, Ermeg L. Akylbekova, Solomon K. Musani, Jasmin Divers, Joe Mychaleckyj, Mingyao Li, George J. Papanicolaou, Robert C. Millikan, Christine B. Ambrosone, Esther M. John, Leslie Bernstein, Wei Zheng, Jennifer J. Hu, Regina G. Ziegler, Sarah J. Nyante, Elisa V. Bandera, Sue A. Ingles, Michael F. Press, Stephen J. Chanock, Sandra L. Deming, Jorge L. Rodriguez-Gil, Cameron D. Palmer, Sarah Buxbaum, Lynette Ekunwe, Joel N. Hirschhorn, Brian E. Henderson, Simon Myers, Christopher A. Haiman, David Reich, Nick Patterson, James G. Wilson, Alkes L. Price

Genome-Wide Association Study Using Extreme Truncate Selection Identifies Novel Genes Affecting Bone Mineral Density and Fracture Risk

Emma L. Duncan, Patrick Danoy, John P. Kemp, Paul J. Leo, Eugene McCloskey, Geoffrey C. Nicholson, Richard Eastell, Richard L. Prince, John A. Eisman, Graeme Jones, Philip N. Sambrook, Ian R. Reid, Elaine M. Dennison, John Wark, J. Brent Richards, Andre G. Uitterlinden, Tim D. Spector, Chris Esapa, Roger D. Cox, Steve D. M. Brown, Rajesh V. Thakker, Kathryn A. Addison, Linda A. Bradbury, Jacqueline R. Center, Cyrus Cooper, Catherine Cremin, Karol Estrada, Dieter Felsenberg, Claus-C. Glüer, Johanna Hadler, Margaret J. Henry, Albert Hofman, Mark A. Kotowicz, Joanna Makovey, Sing C. Nguyen, Tuan V. Nguyen, Julie A. Pasco, Karena Pryce, David M. Reid, Fernando Rivadeneira, Christian Roux, Kari Stefansson, Unnur Styrkarsdottir, Gudmar Thorleifsson, Rumbidzai Tichawangana, David M. Evans, Matthew A. Brown

The History of African Gene Flow into Southern Europeans, Levantines, and Jews

Priya Moorjani, Nick Patterson, Joel N. Hirschhorn, Alon Keinan, Li Hao, Gil Atzmon, Edward Burns, Harry Ostrer, Alkes L. Price, David Reich

Genome-Wide Association Analysis of Soluble ICAM-1 Concentration Reveals Novel Associations at the NFKBIK, PNPLA3, RELA, and SH2B3 Loci

Guillaume Paré, Paul M. Ridker, Lynda Rose, Maja Barbalic, Josée Dupuis, Abbas Dehghan, Joshua C. Bis, Emelia J. Benjamin, Dov Shiffman, Alexander N. Parker, Daniel I. Chasman

Adaptations to Climate-Mediated Selective Pressures in Humans

Angela M. Hancock, David B. Witonsky, Gorka Alkorta-Aranburu, Cynthia M. Beall, Amha Gebremedhin, Rem Sukernik, Gerd Utermann, Jonathan K. Pritchard, Graham Coop, Anna Di Rienzo

Ribosomal DNA Deletions Modulate Genome-Wide Gene Expression: “rDNA–Sensitive” Genes and Natural Variation

Silvana Paredes, Alan T. Branco, Daniel L. Hartl, Keith A. Maggert, Bernardo Lemos

PDP-1 Links the TGF-β and IIS Pathways to Regulate Longevity, Development, and Metabolism

Sri Devi Narasimhan, Kelvin Yen, Ankita Bansal, Eun-Soo Kwon, Srivatsan Padmanabhan, Heidi A. Tissenbaum

GWAS of Follicular Lymphoma Reveals Allelic Heterogeneity at 6p21.32 and Suggests Shared Genetic Susceptibility with Diffuse Large B-cell Lymphoma

Karin E. Smedby, Jia Nee Foo, Christine F. Skibola, Hatef Darabi, Lucia Conde, Henrik Hjalgrim, Vikrant Kumar, Ellen T. Chang, Nathaniel Rothman, James R. Cerhan, Angela R. Brooks-Wilson, Emil Rehnberg, Ishak D. Irwan, Lars P. Ryder, Peter N. Brown, Paige M. Bracci, Luz Agana, Jacques Riby, Wendy Cozen, Scott Davis, Patricia Hartge, Lindsay M. Morton, Richard K. Severson, Sophia S. Wang, Susan L. Slager, Zachary S. Fredericksen, Anne J. Novak, Neil E. Kay, Thomas M. Habermann, Bruce Armstrong, Anne Kricker, Sam Milliken, Mark P. Purdue, Claire M. Vajdic, Peter Boyle, Qing Lan, Shelia H. Zahm, Yawei Zhang, Tongzhang Zheng, Stephen Leach, John J. Spinelli, Martyn T. Smith, Stephen J. Chanock, Leonid Padyukov, Lars Alfredsson, Lars Klareskog, Bengt Glimelius, Mads Melbye, Edison T. Liu, Hans-Olov Adami, Keith Humphreys, Jianjun Liu

Evolution Meets Disease: Penetrance and Functional Epistasis of Mitochondrial tRNA Mutations

Raquel Moreno-Loshuertos, Gustavo Ferrín, Rebeca Acín-Pérez, M. Esther Gallardo, Carlo Viscomi, Acisclo Pérez-Martos, Massimo Zeviani, Patricio Fernández-Silva, José Antonio Enríquez

A Sustained Dietary Change Increases Epigenetic Variation in Isogenic Mice

Cheryl C. Y. Li, Jennifer E. Cropley, Mark J. Cowley, Thomas Preiss, David I. K. Martin, Catherine M. Suter

Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum

Daria Van Tyne, Daniel J. Park, Stephen F. Schaffner, Daniel E. Neafsey, Elaine Angelino, Joseph F. Cortese, Kayla G. Barnes, David M. Rosen, Amanda K. Lukens, Rachel F. Daniels, Danny A. Milner Jr., Charles A. Johnson, Ilya Shlyakhter, Sharon R. Grossman, Justin S. Becker, Daniel Yamins, Elinor K. Karlsson, Daouda Ndiaye, Ousmane Sarr, Souleymane Mboup, Christian Happi, Nicholas A. Furlotte, Eleazar Eskin, Hyun Min Kang, Daniel L. Hartl, Bruce W. Birren, Roger C. Wiegand, Eric S. Lander, Dyann F. Wirth, Sarah K. Volkman, Pardis C. Sabeti

Tissue-Autonomous Function of Drosophila Seipin in Preventing Ectopic Lipid Droplet Formation

Yuan Tian, Junfeng Bi, Guanghou Shui, Zhonghua Liu, Yanhui Xiang, Yuan Liu, Markus R. Wenk, Hongyuan Yang, Xun Huang

An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing

Jevon Plunkett, Scott Doniger, Guilherme Orabona, Thomas Morgan, Ritva Haataja, Mikko Hallman, Hilkka Puttonen, Ramkumar Menon, Edward Kuczynski, Errol Norwitz, Victoria Snegovskikh, Aarno Palotie, Leena Peltonen, Vineta Fellman, Emily A. DeFranco, Bimal P. Chaudhari, Tracy L. McGregor, Jude J. McElroy, Matthew T. Oetjens, Kari Teramo, Ingrid Borecki, Justin Fay, Louis Muglia

Genome Analysis Reveals Interplay between 5′UTR Introns and Nuclear mRNA Export for Secretory and Mitochondrial Genes

Can Cenik, Hon Nian Chua, Hui Zhang, Stefan P. Tarnawsky, Abdalla Akef, Adnan Derti, Murat Tasan, Melissa J. Moore, Alexander F. Palazzo, Frederick P. Roth

14-3-3 Proteins Regulate Exonuclease 1–Dependent Processing of Stalled Replication Forks

Kim Engels, Michele Giannattasio, Marco Muzi-Falconi, Massimo Lopes, Stefano Ferrari

Towards Establishment of a Rice Stress Response Interactome

Young-Su Seo, Mawsheng Chern, Laura E. Bartley, Muho Han, Ki-Hong Jung, Insuk Lee, Harkamal Walia, Todd Richter, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E. Canlas, Randy Ruan, Chang-Jin Park, Xuewei Chen, Sohyun Hwang, Jong-Seong Jeon, Pamela C. Ronald

Eight Common Genetic Variants Associated with Serum DHEAS Levels Suggest a Key Role in Ageing Mechanisms

Guangju Zhai, Alexander Teumer, Lisette Stolk, John R. B. Perry, Liesbeth Vandenput, Andrea D. Coviello, Annemarie Koster, Jordana T. Bell, Shalender Bhasin, Joel Eriksson, Anna Eriksson, Florian Ernst, Luigi Ferrucci, Timothy M. Frayling, Daniel Glass, Elin Grundberg, Robin Haring, Åsa K. Hedman, Albert Hofman, Douglas P. Kiel, Heyo K. Kroemer, Yongmei Liu, Kathryn L. Lunetta, Marcello Maggio, Mattias Lorentzon, Massimo Mangino, David Melzer, Iva Miljkovic, Alexandra Nica, Brenda W. J. H. Penninx, Ramachandran S. Vasan, Fernando Rivadeneira, Kerrin S. Small, Nicole Soranzo, André G. Uitterlinden, Henry Völzke, Scott G. Wilson, Li Xi, Wei Vivian Zhuang, Tamara B. Harris, Joanne M. Murabito, Claes Ohlsson, Anna Murray, Frank H. de Jong, Tim D. Spector, Henri Wallaschofski , MuTHER Consortium

DNA Damage, Somatic Aneuploidy, and Malignant Sarcoma Susceptibility in Muscular Dystrophies

Wolfgang M. Schmidt, Mohammed H. Uddin, Sandra Dysek, Karin Moser-Thier, Christine Pirker, Harald Höger, Inge M. Ambros, Peter F. Ambros, Walter Berger, Reginald E. Bittner

Highly Precise and Developmentally Programmed Genome Assembly in Paramecium Requires Ligase IV–Dependent End Joining

Aurélie Kapusta, Atsushi Matsuda, Antoine Marmignon, Michael Ku, Aude Silve, Eric Meyer, James D. Forney, Sophie Malinsky, Mireille Bétermier

Loss-of-Function Mutations in PTPN11 Cause Metachondromatosis, but Not Ollier Disease or Maffucci Syndrome

Margot E. Bowen, Eric D. Boyden, Ingrid A. Holm, Belinda Campos-Xavier, Luisa Bonafé, Andrea Superti-Furga, Shiro Ikegawa, Valerie Cormier-Daire, Judith V. Bovée, Twinkal C. Pansuriya, Sérgio B. de Sousa, Ravi Savarirayan, Elena Andreucci, Miikka Vikkula, Livia Garavelli, Caroline Pottinger, Toshihiko Ogino, Akinori Sakai, Bianca M. Regazzoni, Wim Wuyts, Luca Sangiorgi, Elena Pedrini, Mei Zhu, Harry P. Kozakewich, James R. Kasser, Jon G. Seidman, Kyle C. Kurek, Matthew L. Warman

The Exocyst Protein Sec10 Interacts with Polycystin-2 and Knockdown Causes PKD-Phenotypes

Ben Fogelgren, Shin-Yi Lin, Xiaofeng Zuo, Kimberly M. Jaffe, Kwon Moo Park, Ryan J. Reichert, P. Darwin Bell, Rebecca D. Burdine, Joshua H. Lipschutz

Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects

Stephen Gregory Addinall, Eva-Maria Holstein, Conor Lawless, Min Yu, Kaye Chapman, A. Peter Banks, Hien-Ping Ngo, Laura Maringele, Morgan Taschuk, Alexander Young, Adam Ciesiolka, Allyson Lurena Lister, Anil Wipat, Darren James Wilkinson, David Lydall

Transferability of Type 2 Diabetes Implicated Loci in Multi-Ethnic Cohorts from Southeast Asia

Xueling Sim, Rick Twee-Hee Ong, Chen Suo, Wan-Ting Tay, Jianjun Liu, Daniel Peng-Keat Ng, Michael Boehnke, Kee-Seng Chia, Tien-Yin Wong, Mark Seielstad, Yik-Ying Teo, E-Shyong Tai

Genome-Wide Meta-Analysis Identifies Regions on 7p21 (AHR) and 15q24 (CYP1A2) As Determinants of Habitual Caffeine Consumption

Marilyn C. Cornelis, Keri L. Monda, Kai Yu, Nina Paynter, Elizabeth M. Azzato, Siiri N. Bennett, Sonja I. Berndt, Eric Boerwinkle, Stephen Chanock, Nilanjan Chatterjee, David Couper, Gary Curhan, Gerardo Heiss, Frank B. Hu, David J. Hunter, Kevin Jacobs, Majken K. Jensen, Peter Kraft, Maria Teresa Landi, Jennifer A. Nettleton, Mark P. Purdue, Preetha Rajaraman, Eric B. Rimm, Lynda M. Rose, Nathaniel Rothman, Debra Silverman, Rachael Stolzenberg-Solomon, Amy Subar, Meredith Yeager, Daniel I. Chasman, Rob M. van Dam, Neil E. Caporaso

Mouse Genome-Wide Association and Systems Genetics Identify Asxl2 As a Regulator of Bone Mineral Density and Osteoclastogenesis

Charles R. Farber, Brian J. Bennett, Luz Orozco, Wei Zou, Ana Lira, Emrah Kostem, Hyun Min Kang, Nicholas Furlotte, Ani Berberyan, Anatole Ghazalpour, Jaijam Suwanwela, Thomas A. Drake, Eleazar Eskin, Q. Tian Wang, Steven L. Teitelbaum, Aldons J. Lusis

Dynamic Regulation of H3K27 Trimethylation during Arabidopsis Differentiation

Marcel Lafos, Phillip Kroll, Mareike L. Hohenstatt, Frazer L. Thorpe, Oliver Clarenz, Daniel Schubert