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Table of Contents | January 2012

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Chromosome fusion occurring within a colony of Vibrio cholerae.

In their study, Val et al. show how reorganizing the genome of bacteria in a deliberate manner can help solve biological issues. In this image, blue sectors within a colony of the pathogen Vibrio cholerae indicate successful fusion of the two chromosomes to form a synthetic mono-chromosomal strain by directed site-specific recombination. This mono-chromosomal strain was further used to demonstrate that Dam, RctB, and ParA2/ParB2 factors are only essential for chrII maintenance.

Image Credit: Thibault Rouxel and Marie-Eve Val (Institut Pasteur)

Interview

A Half-Century of Inspiration: An Interview with Hamilton Smith

Jane Gitschier

Review

Tempo and Mode in Evolution of Transcriptional Regulation

Kacy L. Gordon, Ilya Ruvinsky

Research Articles

Two-Component Elements Mediate Interactions between Cytokinin and Salicylic Acid in Plant Immunity

Cristiana T. Argueso, Fernando J. Ferreira, Petra Epple, Jennifer P. C. To, Claire E. Hutchison, G. Eric Schaller, Jeffery L. Dangl, Joseph J. Kieber

Inference of Population Structure using Dense Haplotype Data

Daniel John Lawson, Garrett Hellenthal, Simon Myers, Daniel Falush

A Genome-Wide Association Study Identified AFF1 as a Susceptibility Locus for Systemic Lupus Eyrthematosus in Japanese

Yukinori Okada, Kenichi Shimane, Yuta Kochi, Tomoko Tahira, Akari Suzuki, Koichiro Higasa, Atsushi Takahashi, Tetsuya Horita, Tatsuya Atsumi, Tomonori Ishii, Akiko Okamoto, Keishi Fujio, Michito Hirakata, Hirofumi Amano, Yuya Kondo, Satoshi Ito, Kazuki Takada, Akio Mimori, Kazuyoshi Saito, Makoto Kamachi, Yasushi Kawaguchi, Katsunori Ikari, Osman Wael Mohammed, Koichi Matsuda, Chikashi Terao, Koichiro Ohmura, Keiko Myouzen, Naoya Hosono, Tatsuhiko Tsunoda, Norihiro Nishimoto, Tsuneyo Mimori, Fumihiko Matsuda, Yoshiya Tanaka, Takayuki Sumida, Hisashi Yamanaka, Yoshinari Takasaki, Takao Koike, Takahiko Horiuchi, Kenshi Hayashi, Michiaki Kubo, Naoyuki Kamatani, Ryo Yamada, Yusuke Nakamura, Kazuhiko Yamamoto

Reduced Lentivirus Susceptibility in Sheep with TMEM154 Mutations

Michael P. Heaton, Michael L. Clawson, Carol G. Chitko-Mckown, Kreg A. Leymaster, Timothy P. L. Smith, Gregory P. Harhay, Stephen N. White, Lynn M. Herrmann-Hoesing, Michelle R. Mousel, Gregory S. Lewis, Theodore S. Kalbfleisch, James E. Keen, William W. Laegreid

USF-1 Is Critical for Maintaining Genome Integrity in Response to UV-Induced DNA Photolesions

Yorann Baron, Sébastien Corre, Nicolas Mouchet, Sophie Vaulont, Sharon Prince, Marie-Dominique Galibert

Heterochromatin Formation Promotes Longevity and Represses Ribosomal RNA Synthesis

Kimberly Larson, Shian-Jang Yan, Amy Tsurumi, Jacqueline Liu, Jun Zhou, Kriti Gaur, Dongdong Guo, Thomas H. Eickbush, Willis X. Li

High-Density SNP Mapping of the HLA Region Identifies Multiple Independent Susceptibility Loci Associated with Selective IgA Deficiency

Ricardo C. Ferreira, Qiang Pan-Hammarström, Robert R. Graham, Gumersindo Fontán, Annette T. Lee, Ward Ortmann, Ning Wang, Elena Urcelay, Miguel Fernández-Arquero, Concepción Núñez, Gudmundur Jorgensen, Björn R. Ludviksson, Sinikka Koskinen, Katri Haimila, Leonid Padyukov, Peter K. Gregersen, Lennart Hammarström, Timothy W. Behrens

A Genome-Wide Association Scan on the Levels of Markers of Inflammation in Sardinians Reveals Associations That Underpin Its Complex Regulation

Silvia Naitza, Eleonora Porcu, Maristella Steri, Dennis D. Taub, Antonella Mulas, Xiang Xiao, James Strait, Mariano Dei, Sandra Lai, Fabio Busonero, Andrea Maschio, Gianluca Usala, Magdalena Zoledziewska, Carlo Sidore, Ilenia Zara, Maristella Pitzalis, Alessia Loi, Francesca Virdis, Roberta Piras, Francesca Deidda, Michael B. Whalen, Laura Crisponi, Antonio Concas, Carlo Podda, Sergio Uzzau, Paul Scheet, Dan L. Longo, Edward Lakatta, Gonçalo R. Abecasis, Antonio Cao, David Schlessinger, Manuela Uda, Serena Sanna, Francesco Cucca

A Flexible Bayesian Model for Studying Gene–Environment Interaction

Kai Yu, Sholom Wacholder, William Wheeler, Zhaoming Wang, Neil Caporaso, Maria Teresa Landi, Faming Liang

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

Robert Kofler, Andrea J. Betancourt, Christian Schlötterer

Sex Pheromone Evolution Is Associated with Differential Regulation of the Same Desaturase Gene in Two Genera of Leafroller Moths

Jérôme Albre, Marjorie A. Liénard, Tamara M. Sirey, Silvia Schmidt, Leah K. Tooman, Colm Carraher, David R. Greenwood, Christer Löfstedt, Richard D. Newcomb

Unraveling the Regulatory Mechanisms Underlying Tissue-Dependent Genetic Variation of Gene Expression

Jingyuan Fu, Marcel G. M. Wolfs, Patrick Deelen, Harm-Jan Westra, Rudolf S. N. Fehrmann, Gerard J. te Meerman, Wim A. Buurman, Sander S. M. Rensen, Harry J. M. Groen, Rinse K. Weersma, Leonard H. van den Berg, Jan Veldink, Roel A. Ophoff, Harold Snieder, David van Heel, Ritsert C. Jansen, Marten H. Hofker, Cisca Wijmenga, Lude Franke

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Olin K. Silander, Nela Nikolic, Alon Zaslaver, Anat Bren, Ilya Kikoin, Uri Alon, Martin Ackermann

DNA Methylation and Gene Expression Changes in Monozygotic Twins Discordant for Psoriasis: Identification of Epigenetically Dysregulated Genes

Kristina Gervin, Magnus D. Vigeland, Morten Mattingsdal, Martin Hammerø, Heidi Nygård, Anne O. Olsen, Ingunn Brandt, Jennifer R. Harris, Dag E. Undlien, Robert Lyle

Adaptation and Preadaptation of Salmonella enterica to Bile

Sara B. Hernández, Ignacio Cota, Adrien Ducret, Laurent Aussel, Josep Casadesús

Cohesin Protects Genes against γH2AX Induced by DNA Double-Strand Breaks

Pierre Caron, Francois Aymard, Jason S. Iacovoni, Sébastien Briois, Yvan Canitrot, Beatrix Bugler, Laurent Massip, Ana Losada, Gaëlle Legube

A Spontaneous Mutation of the Rat Themis Gene Leads to Impaired Function of Regulatory T Cells Linked to Inflammatory Bowel Disease

Marianne Chabod, Christophe Pedros, Lucille Lamouroux, Céline Colacios, Isabelle Bernard, Dominique Lagrange, Daniela Balz-Hara, Jean-Francois Mosnier, Christian Laboisse, Nathalie Vergnolle, Olivier Andreoletti, Marie-Paule Roth, Roland Liblau, Gilbert J. Fournié, Abdelhadi Saoudi, Anne S. Dejean

RIC-7 Promotes Neuropeptide Secretion

Yingsong Hao, Zhitao Hu, Derek Sieburth, Joshua M. Kaplan

Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion

Thierry Cheutin, Giacomo Cavalli

Nucleolar Association and Transcriptional Inhibition through 5S rDNA in Mammals

Andrew M. Fedoriw, Joshua Starmer, Della Yee, Terry Magnuson

Insulin Signaling Regulates Fatty Acid Catabolism at the Level of CoA Activation

Xiaojun Xu, Peddinti Gopalacharyulu, Tuulikki Seppänen-Laakso, Anna-Liisa Ruskeepää, Cho Cho Aye, Brian P. Carson, Silvia Mora, Matej Orešič, Aurelio A. Teleman

Genomic Ancestry of North Africans Supports Back-to-Africa Migrations

Brenna M. Henn, Laura R. Botigué, Simon Gravel, Wei Wang, Abra Brisbin, Jake K. Byrnes, Karima Fadhlaoui-Zid, Pierre A. Zalloua, Andres Moreno-Estrada, Jaume Bertranpetit, Carlos D. Bustamante, David Comas

The Drosophila melanogaster Seminal Fluid Protease “Seminase” Regulates Proteolytic and Post-Mating Reproductive Processes

Brooke A. LaFlamme, K. Ravi Ram, Mariana F. Wolfner

Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli

Selwyn Quan, J. Christian J. Ray, Zakari Kwota, Trang Duong, Gábor Balázsi, Tim F. Cooper, Russell D. Monds

A Gene Regulatory Network for Root Epidermis Cell Differentiation in Arabidopsis

Angela Bruex, Raghunandan M. Kainkaryam, Yana Wieckowski, Yeon Hee Kang, Christine Bernhardt, Yang Xia, Xiaohua Zheng, Jean Y. Wang, Myeong Min Lee, Philip Benfey, Peter J. Woolf, John Schiefelbein

An siRNA Screen in Pancreatic Beta Cells Reveals a Role for Gpr27 in Insulin Production

Gregory M. Ku, Zachary Pappalardo, Chun Chieh Luo, Michael S. German, Michael T. McManus

Cdc5-Dependent Asymmetric Localization of Bfa1 Fine-Tunes Timely Mitotic Exit

Junwon Kim, Guangming Luo, Young Yil Bahk, Kiwon Song

A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies

Molly E. McCue, Danika L. Bannasch, Jessica L. Petersen, Jessica Gurr, Ernie Bailey, Matthew M. Binns, Ottmar Distl, Gérard Guérin, Telhisa Hasegawa, Emmeline W. Hill, Tosso Leeb, Gabriella Lindgren, M. Cecilia T. Penedo, Knut H. Røed, Oliver A. Ryder, June E. Swinburne, Teruaki Tozaki, Stephanie J. Valberg, Mark Vaudin, Kerstin Lindblad-Toh, Claire M. Wade, James R. Mickelson

Genetic Evidence for an Indispensable Role of Somatic Embryogenesis Receptor Kinases in Brassinosteroid Signaling

Xiaoping Gou, Hongju Yin, Kai He, Junbo Du, Jing Yi, Shengbao Xu, Honghui Lin, Steven D. Clouse, Jia Li

Cytoplasmic Polyadenylation Element Binding Protein Deficiency Stimulates PTEN and Stat3 mRNA Translation and Induces Hepatic Insulin Resistance

Ilya M. Alexandrov, Maria Ivshina, Dae Young Jung, Randall Friedline, Hwi Jin Ko, Mei Xu, Bryan O'Sullivan-Murphy, Rita Bortell, Yen-Tsung Huang, Fumihiko Urano, Jason K. Kim, Joel D. Richter

Parallel Mapping and Simultaneous Sequencing Reveals Deletions in BCAN and FAM83H Associated with Discrete Inherited Disorders in a Domestic Dog Breed

Oliver P. Forman, Jacques Penderis, Claudia Hartley, Louisa J. Hayward, Sally L. Ricketts, Cathryn S. Mellersh

Calpains Mediate Integrin Attachment Complex Maintenance of Adult Muscle in Caenorhabditis elegans

Timothy Etheridge, Elizabeth A. Oczypok, Susann Lehmann, Brandon D. Fields, Freya Shephard, Lewis A. Jacobson, Nathaniel J. Szewczyk

Genome Engineering in Vibrio cholerae: A Feasible Approach to Address Biological Issues

Marie-Eve Val, Ole Skovgaard, Magaly Ducos-Galand, Michael J. Bland, Didier Mazel

Functional Specialization of the Plant miR396 Regulatory Network through Distinct MicroRNA–Target Interactions

Juan M. Debernardi, Ramiro E. Rodriguez, Martin A. Mecchia, Javier F. Palatnik

Microenvironmental Regulation by Fibrillin-1

Gerhard Sengle, Ko Tsutsui, Douglas R. Keene, Sara F. Tufa, Eric J. Carlson, Noe L. Charbonneau, Robert N. Ono, Takako Sasaki, Mary K. Wirtz, John R. Samples, Liselotte I. Fessler, John H. Fessler, Kiyotoshi Sekiguchi, Susan J. Hayflick, Lynn Y. Sakai

Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm

Milan Spasic, Caroline C. Friedel, Johanna Schott, Jochen Kreth, Kathrin Leppek, Sarah Hofmann, Sevim Ozgur, Georg Stoecklin

Checkpoints in a Yeast Differentiation Pathway Coordinate Signaling during Hyperosmotic Stress

Michal J. Nagiec, Henrik G. Dohlman

Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks

Hisato Kobayashi, Takayuki Sakurai, Misaki Imai, Nozomi Takahashi, Atsushi Fukuda, Obata Yayoi, Shun Sato, Kazuhiko Nakabayashi, Kenichiro Hata, Yusuke Sotomaru, Yutaka Suzuki, Tomohiro Kono

Poly(ADP-Ribose) Polymerase 1 (PARP-1) Regulates Ribosomal Biogenesis in Drosophila Nucleoli

Ernest K. Boamah, Elena Kotova, Mikael Garabedian, Michael Jarnik, Alexei V. Tulin

The Yeast Complex I Equivalent NADH Dehydrogenase Rescues pink1 Mutants

Sven Vilain, Giovanni Esposito, Dominik Haddad, Onno Schaap, Mariya P. Dobreva, Melissa Vos, Stefanie Van Meensel, Vanessa A. Morais, Bart De Strooper, Patrik Verstreken

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