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Table of Contents: January 2009

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Seed size is a key adaptive trait in plant evolution. Different species produce seeds of different sizes, and these differences can vary by several orders of magnitude among species. An article by Cintia Hotta Orsi and Steven D. Tanksley investigates the cause of seed size differences between the cultivated tomato and wild, related species (see Orsi and Tanksley, doi:10.1371/journal.pgen.1000347). The major cause of the seed size difference can be traced to natural genetic variation in a gene encoding an ABC transporter protein.

Perspectives

CCL3L Copy Number Variation and the Co-Evolution of Primate and Viral Genomes

German Gornalusse, Srinivas Mummidi, Weijing He, Guido Silvestri, Mike Bamshad, Sunil K. Ahuja

Review

Research Articles

LINE Retrotransposon RNA Is an Essential Structural and Functional Epigenetic Component of a Core Neocentromeric Chromatin

Anderly C. Chueh, Emma L. Northrop, Kate H. Brettingham-Moore, K. H. Andy Choo, Lee H. Wong

DETORQUEO, QUIRKY, and ZERZAUST Represent Novel Components Involved in Organ Development Mediated by the Receptor-Like Kinase STRUBBELIG in Arabidopsis thaliana

Lynette Fulton, Martine Batoux, Prasad Vaddepalli, Ram Kishor Yadav, Wolfgang Busch, Stig U. Andersen, Sangho Jeong, Jan U. Lohmann, Kay Schneitz

Genetic Evidence for Single-Strand Lesions Initiating Nbs1-Dependent Homologous Recombination in Diversification of Ig V in Chicken B Lymphocytes

Makoto Nakahara, Eiichiro Sonoda, Kuniharu Nojima, Julian E. Sale, Katsuya Takenaka, Koji Kikuchi, Yoshihito Taniguchi, Kyoko Nakamura, Yoshiki Sumitomo, Ronan T. Bree, Noel F. Lowndes, Shunichi Takeda

Learning a Prior on Regulatory Potential from eQTL Data

Su-In Lee, Aimée M. Dudley, David Drubin, Pamela A. Silver, Nevan J. Krogan, Dana Pe'er, Daphne Koller

Reduced Neutrophil Count in People of African Descent Is Due To a Regulatory Variant in the Duffy Antigen Receptor for Chemokines Gene

David Reich, Michael A. Nalls, W. H. Linda Kao, Ermeg L. Akylbekova, Arti Tandon, Nick Patterson, James Mullikin, Wen-Chi Hsueh, Ching-Yu Cheng, Josef Coresh, Eric Boerwinkle, Man Li, Alicja Waliszewska, Julie Neubauer, Rongling Li, Tennille S. Leak, Lynette Ekunwe, Joe C. Files, Cheryl L. Hardy, Joseph M. Zmuda, Herman A. Taylor, Elad Ziv, Tamara B. Harris, James G. Wilson

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

Marie Touchon, Claire Hoede, Olivier Tenaillon, Valérie Barbe, Simon Baeriswyl, Philippe Bidet, Edouard Bingen, Stéphane Bonacorsi, Christiane Bouchier, Odile Bouvet, Alexandra Calteau, Hélène Chiapello, Olivier Clermont, Stéphane Cruveiller, Antoine Danchin, Médéric Diard, Carole Dossat, Meriem El Karoui, Eric Frapy, Louis Garry, Jean Marc Ghigo, Anne Marie Gilles, James Johnson, Chantal Le Bouguénec, Mathilde Lescat, Sophie Mangenot, Vanessa Martinez-Jéhanne, Ivan Matic, Xavier Nassif, Sophie Oztas, Marie Agnès Petit, Christophe Pichon, Zoé Rouy, Claude Saint Ruf, Dominique Schneider, Jérôme Tourret, Benoit Vacherie, David Vallenet, Claudine Médigue, Eduardo P. C. Rocha, Erick Denamur

Copy Number Variation of CCL3-like Genes Affects Rate of Progression to Simian-AIDS in Rhesus Macaques (Macaca mulatta)

Jeremiah D. Degenhardt, Paola de Candia, Adrien Chabot, Stuart Schwartz, Les Henderson, Binhua Ling, Meredith Hunter, Zhaoshi Jiang, Robert E. Palermo, Michael Katze, Evan E. Eichler, Mario Ventura, Jeffrey Rogers, Preston Marx, Yoav Gilad, Carlos D. Bustamante

Heterochromatic Threads Connect Oscillating Chromosomes during Prometaphase I in Drosophila Oocytes

Stacie E. Hughes, William D. Gilliland, Jeffrey L. Cotitta, Satomi Takeo, Kim A. Collins, R. Scott Hawley

Integrating Computational Biology and Forward Genetics in Drosophila

Stein Aerts, Sven Vilain, Shu Hu, Leon-Charles Tranchevent, Roland Barriot, Jiekun Yan, Yves Moreau, Bassem A. Hassan, Xiao-Jiang Quan

A Systematic Approach to Mapping Recessive Disease Genes in Individuals from Outbred Populations

Friedhelm Hildebrandt, Saskia F. Heeringa, Franz Rüschendorf, Massimo Attanasio, Gudrun Nürnberg, Christian Becker, Dominik Seelow, Norbert Huebner, Gil Chernin, Christopher N. Vlangos, Weibin Zhou, John F. O'Toole, Bethan E. Hoskins, Matthias T. F. Wolf, Bernward G. Hinkes, Hassan Chaib, Shazia Ashraf, Dominik S. Schoeb, Bugsu Ovunc, Susan J. Allen, Virginia Vega-Warner, Eric Wise, Heather M. Harville, Robert H. Lyons, Joseph Washburn, James MacDonald, Peter Nürnberg, Edgar A. Otto

Deletion Hotspots in AMACR Promoter CpG Island Are cis-Regulatory Elements Controlling the Gene Expression in the Colon

Xiang Zhang, Irwin Leav, Monica P. Revelo, Ranjan Deka, Mario Medvedovic, Zhong Jiang, Shuk-Mei Ho

Pervasive Hitchhiking at Coding and Regulatory Sites in Humans

James J. Cai, J. Michael Macpherson, Guy Sella, Dmitri A. Petrov

Genome-Wide Association Study of Plasma Polyunsaturated Fatty Acids in the InCHIANTI Study

Toshiko Tanaka, Jian Shen, Gonçalo R. Abecasis, Aliaksei Kisialiou, Jose M. Ordovas, Jack M. Guralnik, Andrew Singleton, Stefania Bandinelli, Antonio Cherubini, Donna Arnett, Michael Y. Tsai, Luigi Ferrucci

Yeast Genetic Analysis Reveals the Involvement of Chromatin Reassembly Factors in Repressing HIV-1 Basal Transcription

Manuela Vanti, Edurne Gallastegui, Iñaki Respaldiza, Alfonso Rodríguez-Gil, Fernando Gómez-Herreros, Silvia Jimeno-González, Albert Jordan, Sebastián Chávez

Contrasting Mode of Evolution at a Coat Color Locus in Wild and Domestic Pigs

Meiying Fang, Greger Larson, Helena Soares Ribeiro, Ning Li, Leif Andersson

Genetic Differences between the Determinants of Lipid Profile Phenotypes in African and European Americans: The Jackson Heart Study

Rahul C. Deo, David Reich, Arti Tandon, Ermeg Akylbekova, Nick Patterson, Alicja Waliszewska, Sekar Kathiresan, Daniel Sarpong, Herman A. Taylor Jr., James G. Wilson

Sequences From First Settlers Reveal Rapid Evolution in Icelandic mtDNA Pool

Agnar Helgason, Carles Lalueza-Fox, Shyamali Ghosh, Sigrún Sigurðardóttir, Maria Lourdes Sampietro, Elena Gigli, Adam Baker, Jaume Bertranpetit, Lilja Árnadóttir, Unnur Þorsteinsdottir, Kári Stefánsson

TraR, a Homolog of a RNAP Secondary Channel Interactor, Modulates Transcription

Matthew D. Blankschien, Katarzyna Potrykus, Elicia Grace, Abha Choudhary, Daniel Vinella, Michael Cashel, Christophe Herman

A Genome-Wide Association Study Identifies Novel and Functionally Related Susceptibility Loci for Kawasaki Disease

David Burgner, Sonia Davila, Willemijn B. Breunis, Sarah B. Ng, Yi Li, Carine Bonnard, Ling Ling, Victoria J. Wright, Anbupalam Thalamuthu, Miranda Odam, Chisato Shimizu, Jane C. Burns, Michael Levin, Taco W. Kuijpers, Martin L. Hibberd , International Kawasaki Disease Genetics Consortium

Arabidopsis CULLIN3 Genes Regulate Primary Root Growth and Patterning by Ethylene-Dependent and -Independent Mechanisms

Alexis Thomann, Esther Lechner, Maureen Hansen, Eva Dumbliauskas, Yves Parmentier, Joe Kieber, Ben Scheres, Pascal Genschik

Mouse Genome-Wide Association Mapping Needs Linkage Analysis to Avoid False-Positive Loci

Giacomo Manenti, Antonella Galvan, Angela Pettinicchio, Gaia Trincucci, Elena Spada, Anna Zolin, Silvano Milani, Anna Gonzalez-Neira, Tommaso A. Dragani

A cis-Acting Diversification Activator Both Necessary and Sufficient for AID-Mediated Hypermutation

Artem Blagodatski, Vera Batrak, Sabine Schmidl, Ulrike Schoetz, Randolph B. Caldwell, Hiroshi Arakawa, Jean-Marie Buerstedde

Neuropeptide Y Gene Polymorphisms Confer Risk of Early-Onset Atherosclerosis

Svati H. Shah, Neil J. Freedman, Lisheng Zhang, David R. Crosslin, David H. Stone, Carol Haynes, Jessica Johnson, Sarah Nelson, Liyong Wang, Jessica J. Connelly, Michael Muehlbauer, Geoffrey S. Ginsburg, David C. Crossman, Christopher J. H. Jones, Jeffery Vance, Michael H. Sketch Jr, Christopher B. Granger, Christopher B. Newgard, Simon G. Gregory, Pascal J. Goldschmidt-Clermont, William E. Kraus, Elizabeth R. Hauser

Regulation of Small RNA Accumulation in the Maize Shoot Apex

Fabio T. S. Nogueira, Daniel H. Chitwood, Shahinez Madi, Kazuhiro Ohtsu, Patrick S. Schnable, Michael J. Scanlon, Marja C. P. Timmermans

IL2RA Genetic Heterogeneity in Multiple Sclerosis and Type 1 Diabetes Susceptibility and Soluble Interleukin-2 Receptor Production

Lisa M. Maier, Christopher E. Lowe, Jason Cooper, Kate Downes, David E. Anderson, Christopher Severson, Pamela M. Clark, Brian Healy, Neil Walker, Cristin Aubin, Jorge R. Oksenberg, Stephen L. Hauser, Alistair Compston, Stephen Sawcer, Philip L. De Jager, Linda S. Wicker, John A. Todd, David A. Hafler , The International Multiple Sclerosis Genetics Consortium

Instability of Plastid DNA in the Nuclear Genome

Anna E. Sheppard, Jeremy N. Timmis

ATR and Chk1 Suppress a Caspase-3–Dependent Apoptotic Response Following DNA Replication Stress

Katie Myers, Mary E. Gagou, Pedro Zuazua-Villar, Rene Rodriguez, Mark Meuth