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Table of Contents: September 2010

COVER

A leaf-cutter ant worker carries a leaf fragment back to her colony.

Image Credit: Jarrod J. Scott (University of Wisconsin-Madison)
Issue Image

Leaf-cutter ants cut and harvest fresh leaves, which they use to farm a fungus in specialized subterranean garden chambers. This fungus, which serves as the primary food source for the entire colony, can support the growth of millions of workers. In this issue of PLoS Genetics, Suen et al. reveal that leaf-cutter ant fungus gardens also contain a diverse community of bacteria with a high capacity for plant biomass degradation. The ability of leaf-cutter ants to maintain an external microbial digestive system capable of converting plant biomass into nutrients likely represents a key step in their establishment as one of the most widespread insect herbivores in the Neotropics.

Review

Research Articles

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

Qi Zheng, Paul Ryvkin, Fan Li, Isabelle Dragomir, Otto Valladares, Jamie Yang, Kajia Cao, Li-San Wang, Brian D. Gregory

FliO Regulation of FliP in the Formation of the Salmonella enterica Flagellum

Clive S. Barker, Irina V. Meshcheryakova, Alla S. Kostyukova, Fadel A. Samatey

Gene–Environment Interactions at Nucleotide Resolution

Justin Gerke, Kim Lorenz, Shelina Ramnarine, Barak Cohen

The Genome of a Pathogenic Rhodococcus: Cooptive Virulence Underpinned by Key Gene Acquisitions

Michal Letek, Patricia González, Iain MacArthur, Héctor Rodríguez, Tom C. Freeman, Ana Valero-Rello, Mónica Blanco, Tom Buckley, Inna Cherevach, Ruth Fahey, Alexia Hapeshi, Jolyon Holdstock, Desmond Leadon, Jesús Navas, Alain Ocampo, Michael A. Quail, Mandy Sanders, Mariela M. Scortti, John F. Prescott, Ursula Fogarty, Wim G. Meijer, Julian Parkhill, Stephen D. Bentley, José A. Vázquez-Boland

Genetic Variants and Their Interactions in the Prediction of Increased Pre-Clinical Carotid Atherosclerosis: The Cardiovascular Risk in Young Finns Study

Sebastian Okser, Terho Lehtimäki, Laura L. Elo, Nina Mononen, Nina Peltonen, Mika Kähönen, Markus Juonala, Yue-Mei Fan, Jussi A. Hernesniemi, Tomi Laitinen, Leo-Pekka Lyytikäinen, Riikka Rontu, Carita Eklund, Nina Hutri-Kähönen, Leena Taittonen, Mikko Hurme, Jorma S. A. Viikari, Olli T. Raitakari, Tero Aittokallio

Cdc20 Is Critical for Meiosis I and Fertility of Female Mice

Fang Jin, Masakazu Hamada, Liviu Malureanu, Karthik B. Jeganathan, Wei Zhou, Dean E. Morbeck, Jan M. van Deursen

Widespread Over-Expression of the X Chromosome in Sterile F1 Hybrid Mice

Jeffrey M. Good, Thomas Giger, Matthew D. Dean, Michael W. Nachman

An Insect Herbivore Microbiome with High Plant Biomass-Degrading Capacity

Garret Suen, Jarrod J. Scott, Frank O. Aylward, Sandra M. Adams, Susannah G. Tringe, Adrián A. Pinto-Tomás, Clifton E. Foster, Markus Pauly, Paul J. Weimer, Kerrie W. Barry, Lynne A. Goodwin, Pascal Bouffard, Lewyn Li, Jolene Osterberger, Timothy T. Harkins, Steven C. Slater, Timothy J. Donohue, Cameron R. Currie

Dementia Revealed: Novel Chromosome 6 Locus for Late-Onset Alzheimer Disease Provides Genetic Evidence for Folate-Pathway Abnormalities

Adam C. Naj, Gary W. Beecham, Eden R. Martin, Paul J. Gallins, Eric H. Powell, Ioanna Konidari, Patrice L. Whitehead, Guiqing Cai, Vahram Haroutunian, William K. Scott, Jeffery M. Vance, Michael A. Slifer, Harry E. Gwirtsman, John R. Gilbert, Jonathan L. Haines, Joseph D. Buxbaum, Margaret A. Pericak-Vance

A Novel Statistic for Genome-Wide Interaction Analysis

Xuesen Wu, Hua Dong, Li Luo, Yun Zhu, Gang Peng, John D. Reveille, Momiao Xiong

DCAF26, an Adaptor Protein of Cul4-Based E3, Is Essential for DNA Methylation in Neurospora crassa

Hui Xu, Jiyong Wang, Qiwen Hu, Yun Quan, Huijie Chen, Yingqiong Cao, Chunbo Li, Ying Wang, Qun He

Identification of Early Requirements for Preplacodal Ectoderm and Sensory Organ Development

Hye-Joo Kwon, Neha Bhat, Elly M. Sweet, Robert A. Cornell, Bruce B. Riley

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

Robert S. Illingworth, Ulrike Gruenewald-Schneider, Shaun Webb, Alastair R. W. Kerr, Keith D. James, Daniel J. Turner, Colin Smith, David J. Harrison, Robert Andrews, Adrian P. Bird

Analysis of the Basidiomycete Coprinopsis cinerea Reveals Conservation of the Core Meiotic Expression Program over Half a Billion Years of Evolution

Claire Burns, Jason E. Stajich, Andreas Rechtsteiner, Lorna Casselton, Sean E. Hanlon, Sarah K. Wilke, Oleksandr P. Savytskyy, Allen C. Gathman, Walt W. Lilly, Jason D. Lieb, Miriam E. Zolan, Patricia J. Pukkila

Germline Variation Controls the Architecture of Somatic Alterations in Tumors

Amy M. Dworkin, Katie Ridd, Dianne Bautista, Dawn C. Allain, O. Hans Iwenofu, Ritu Roy, Boris C. Bastian, Amanda Ewart Toland

dMyc Functions Downstream of Yorkie to Promote the Supercompetitive Behavior of Hippo Pathway Mutant Cells

Marcello Ziosi, Luis Alberto Baena-López, Daniela Grifoni, Francesca Froldi, Andrea Pession, Flavio Garoia, Vincenzo Trotta, Paola Bellosta, Sandro Cavicchi, Annalisa Pession

SNPs Associated with Cerebrospinal Fluid Phospho-Tau Levels Influence Rate of Decline in Alzheimer's Disease

Carlos Cruchaga, John S. K. Kauwe, Kevin Mayo, Noah Spiegel, Sarah Bertelsen, Petra Nowotny, Aarti R. Shah, Richard Abraham, Paul Hollingworth, Denise Harold, Michael M. Owen, Julie Williams, Simon Lovestone, Elaine R. Peskind, Ge Li, James B. Leverenz, Douglas Galasko, John C. Morris, Anne M. Fagan, David M. Holtzman, Alison M. Goate , The Alzheimer's Disease Neuroimaging Initiative

Mice Doubly-Deficient in Lysosomal Hexosaminidase A and Neuraminidase 4 Show Epileptic Crises and Rapid Neuronal Loss

Volkan Seyrantepe, Pablo Lema, Aurore Caqueret, Larbi Dridi, Samar Bel Hadj, Stephane Carpentier, Francine Boucher, Thierry Levade, Lionel Carmant, Roy A. Gravel, Edith Hamel, Pascal Vachon, Graziella Di Cristo, Jacques L. Michaud, Carlos R. Morales, Alexey V. Pshezhetsky

Differentiation of Zebrafish Melanophores Depends on Transcription Factors AP2 Alpha and AP2 Epsilon

Eric Van Otterloo, Wei Li, Gregory Bonde, Kristopher M. Day, Mei-Yu Hsu, Robert A. Cornell

Rice Snl6, a Cinnamoyl-CoA Reductase-Like Gene Family Member, Is Required for NH1-Mediated Immunity to Xanthomonas oryzae pv. oryzae

Rebecca S. Bart, Mawsheng Chern, Miguel E. Vega-Sánchez, Patrick Canlas, Pamela C. Ronald

ETS-4 Is a Transcriptional Regulator of Life Span in Caenorhabditis elegans

Bargavi Thyagarajan, Adam G. Blaszczak, Katherine J. Chandler, Jennifer L. Watts, W. Evan Johnson, Barbara J. Graves

Allelic Variation at the 8q23.3 Colorectal Cancer Risk Locus Functions as a Cis-Acting Regulator of EIF3H

Alan M. Pittman, Silvia Naranjo, Sanni E. Jalava, Philip Twiss, Yussanne Ma, Bianca Olver, Amy Lloyd, Jayaram Vijayakrishnan, Mobshra Qureshi, Peter Broderick, Tom van Wezel, Hans Morreau, Sari Tuupanen, Lauri A. Aaltonen, M. Eva Alonso, Miguel Manzanares, Angela Gavilán, Tapio Visakorpi, José Luis Gómez-Skarmeta, Richard S. Houlston

Identification of New Genetic Risk Variants for Type 2 Diabetes

Xiao Ou Shu, Jirong Long, Qiuyin Cai, Lu Qi, Yong-Bing Xiang, Yoon Shin Cho, E. Shyong Tai, Xiangyang Li, Xu Lin, Wong-Ho Chow, Min Jin Go, Mark Seielstad, Wei Bao, Huaixing Li, Marilyn C. Cornelis, Kai Yu, Wanqing Wen, Jiajun Shi, Bok-Ghee Han, Xue Ling Sim, Liegang Liu, Qibin Qi, Hyung-Lae Kim, Daniel P. K. Ng, Jong-Young Lee, Young Jin Kim, Chun Li, Yu-Tang Gao, Wei Zheng, Frank B. Hu

Longitudinal Genome-Wide Association of Cardiovascular Disease Risk Factors in the Bogalusa Heart Study

Erin N. Smith, Wei Chen, Mika Kähönen, Johannes Kettunen, Terho Lehtimäki, Leena Peltonen, Olli T. Raitakari, Rany M. Salem, Nicholas J. Schork, Marian Shaw, Sathanur R. Srinivasan, Eric J. Topol, Jorma S. Viikari, Gerald S. Berenson, Sarah S. Murray

Accurately Assessing the Risk of Schizophrenia Conferred by Rare Copy-Number Variation Affecting Genes with Brain Function

Soumya Raychaudhuri, Joshua M. Korn, Steven A. McCarroll, David Altshuler, Pamela Sklar, Shaun Purcell, Mark J. Daly , The International Schizophrenia Consortium

The APETALA-2-Like Transcription Factor OsAP2-39 Controls Key Interactions between Abscisic Acid and Gibberellin in Rice

Mahmoud W. Yaish, Ashraf El-kereamy, Tong Zhu, Perrin H. Beatty, Allen G. Good, Yong-Mei Bi, Steven J. Rothstein

Long- and Short-Term Selective Forces on Malaria Parasite Genomes

Sanne Nygaard, Alexander Braunstein, Gareth Malsen, Stijn Van Dongen, Paul P. Gardner, Anders Krogh, Thomas D. Otto, Arnab Pain, Matthew Berriman, Jon McAuliffe, Emmanouil T. Dermitzakis, Daniel C. Jeffares

Network Analysis Identifies ELF3 as a QTL for the Shade Avoidance Response in Arabidopsis

José M. Jiménez-Gómez, Andreah D. Wallace, Julin N. Maloof

A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis

Regla Bustos, Gabriel Castrillo, Francisco Linhares, María Isabel Puga, Vicente Rubio, Julian Pérez-Pérez, Roberto Solano, Antonio Leyva, Javier Paz-Ares

A Single cis Element Maintains Repression of the Key Developmental Regulator Gata2

Jonathan W. Snow, Jennifer J. Trowbridge, Tohru Fujiwara, Nikla E. Emambokus, Jeffrey A. Grass, Stuart H. Orkin, Emery H. Bresnick

DNMT3L Modulates Significant and Distinct Flanking Sequence Preference for DNA Methylation by DNMT3A and DNMT3B In Vivo

Bethany L. Wienholz, Michael S. Kareta, Amir H. Moarefi, Catherine A. Gordon, Paul A. Ginno, Frédéric Chédin

Optimal Strategy for Competence Differentiation in Bacteria

C. Scott Wylie, Aaron D. Trout, David A. Kessler, Herbert Levine

The Baker's Yeast Diploid Genome Is Remarkably Stable in Vegetative Growth and Meiosis

K. T. Nishant, Wu Wei, Eugenio Mancera, Juan Lucas Argueso, Andreas Schlattl, Nicolas Delhomme, Xin Ma, Carlos D. Bustamante, Jan O. Korbel, Zhenglong Gu, Lars M. Steinmetz, Eric Alani

The Characterization of Twenty Sequenced Human Genomes

Kimberly Pelak, Kevin V. Shianna, Dongliang Ge, Jessica M. Maia, Mingfu Zhu, Jason P. Smith, Elizabeth T. Cirulli, Jacques Fellay, Samuel P. Dickson, Curtis E. Gumbs, Erin L. Heinzen, Anna C. Need, Elizabeth K. Ruzzo, Abanish Singh, C. Ryan Campbell, Linda K. Hong, Katharina A. Lornsen, Alexander M. McKenzie, Nara L. M. Sobreira, Julie E. Hoover-Fong, Joshua D. Milner, Ruth Ottman, Barton F. Haynes, James J. Goedert, David B. Goldstein

An Immune Response Network Associated with Blood Lipid Levels

Michael Inouye, Kaisa Silander, Eija Hamalainen, Veikko Salomaa, Kennet Harald, Pekka Jousilahti, Satu Männistö, Johan G. Eriksson, Janna Saarela, Samuli Ripatti, Markus Perola, Gert-Jan B. van Ommen, Marja-Riitta Taskinen, Aarno Palotie, Emmanouil T. Dermitzakis, Leena Peltonen

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data

Abigail Bigham, Marc Bauchet, Dalila Pinto, Xianyun Mao, Joshua M. Akey, Rui Mei, Stephen W. Scherer, Colleen G. Julian, Megan J. Wilson, David López Herráez, Tom Brutsaert, Esteban J. Parra, Lorna G. Moore, Mark D. Shriver

Commercially Available Outbred Mice for Genome-Wide Association Studies

Binnaz Yalcin, Jérôme Nicod, Amarjit Bhomra, Stuart Davidson, James Cleak, Laurent Farinelli, Magne Østerås, Adam Whitley, Wei Yuan, Xiangchao Gan, Martin Goodson, Paul Klenerman, Ansu Satpathy, Diane Mathis, Christophe Benoist, David J. Adams, Richard Mott, Jonathan Flint

Allelic Selection of Amplicons in Glioblastoma Revealed by Combining Somatic and Germline Analysis

Thomas LaFramboise, Ninad Dewal, Katherine Wilkins, Itsik Pe'er, Matthew L. Freedman

Inhibition of GSK-3 Ameliorates Aβ Pathology in an Adult-Onset Drosophila Model of Alzheimer's Disease

Oyinkan Sofola, Fiona Kerr, Iain Rogers, Richard Killick, Hrvoje Augustin, Carina Gandy, Marcus J. Allen, John Hardy, Simon Lovestone, Linda Partridge

Response to Mechanical Stress Is Mediated by the TRPA Channel Painless in the Drosophila Heart

Sébastien Sénatore, Vatrapu Rami Reddy, Michel Sémériva, Laurent Perrin, Nathalie Lalevée

A Negative Regulatory Loop between MicroRNA and Hox Gene Controls Posterior Identities in Caenorhabditis elegans

Zhongying Zhao, Thomas J. Boyle, Zongzhi Liu, John I. Murray, William B. Wood, Robert H. Waterston

The Histone H3K36 Methyltransferase MES-4 Acts Epigenetically to Transmit the Memory of Germline Gene Expression to Progeny

Andreas Rechtsteiner, Sevinc Ercan, Teruaki Takasaki, Taryn M. Phippen, Thea A. Egelhofer, Wenchao Wang, Hiroshi Kimura, Jason D. Lieb, Susan Strome

Lactic Acidosis Triggers Starvation Response with Paradoxical Induction of TXNIP through MondoA

Julia Ling-Yu Chen, Daniel Merl, Christopher W. Peterson, Jianli Wu, Patrick Yantyng Liu, Hanwei Yin, Deborah M. Muoio, Don E. Ayer, Mike West, Jen-Tsan Chi

The Potential for Enhancing the Power of Genetic Association Studies in African Americans through the Reuse of Existing Genotype Data

Gary K. Chen, Robert C. Millikan, Esther M. John, Christine B. Ambrosone, Leslie Bernstein, Wei Zheng, Jennifer J. Hu, Stephen J. Chanock, Regina G. Ziegler, Elisa V. Bandera, Brian E. Henderson, Christopher A. Haiman, Daniel O. Stram