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Table of Contents

January 2009

Cover

Artist's rendition of the cross-section of a seed (image composed of individual tomato seeds).
Issue Image

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.

Image Credit: Cintia Hotta Orsi (Cornell University)

Perspectives

Converging on the Origins of Axonal Ion Channel Clustering

Matthew N. Rasband

PLOS Genetics: published January 16, 2009 | https://doi.org/10.1371/journal.pgen.1000340

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Order and Disorder during Escherichia coli Divergence

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PLOS Genetics: published January 23, 2009 | https://doi.org/10.1371/journal.pgen.1000335

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PLOS Genetics: published January 30, 2009 | https://doi.org/10.1371/journal.pgen.1000359

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Review

A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation

P. J. Hastings, Grzegorz Ira, James R. Lupski

PLOS Genetics: published January 30, 2009 | https://doi.org/10.1371/journal.pgen.1000327

Research Articles

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

PLOS Genetics: published January 2, 2009 | https://doi.org/10.1371/journal.pgen.1000318

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

PLOS Genetics: published January 2, 2009 | https://doi.org/10.1371/journal.pgen.1000320

Non-Coding RNA Prediction and Verification in Saccharomyces cerevisiae

Laura A. Kavanaugh, Fred S. Dietrich

PLOS Genetics: published January 2, 2009 | https://doi.org/10.1371/journal.pgen.1000321

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, The International Multiple Sclerosis Genetics Consortium, Philip L. De Jager, Linda S. Wicker, John A. Todd, David A. Hafler

PLOS Genetics: published January 2, 2009 | https://doi.org/10.1371/journal.pgen.1000322

Instability of Plastid DNA in the Nuclear Genome

Anna E. Sheppard, Jeremy N. Timmis

PLOS Genetics: published January 2, 2009 | https://doi.org/10.1371/journal.pgen.1000323

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

PLOS Genetics: published January 2, 2009 | https://doi.org/10.1371/journal.pgen.1000324

Adaptive Evolution in Zinc Finger Transcription Factors

Ryan O. Emerson, James H. Thomas

PLOS Genetics: published January 2, 2009 | https://doi.org/10.1371/journal.pgen.1000325

A Novel Role for Mc1r in the Parallel Evolution of Depigmentation in Independent Populations of the Cavefish Astyanax mexicanus

Joshua B. Gross, Richard Borowsky, Clifford J. Tabin

PLOS Genetics: published January 2, 2009 | https://doi.org/10.1371/journal.pgen.1000326

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

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PLOS Genetics: published January 9, 2009 | https://doi.org/10.1371/journal.pgen.1000319

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

PLOS Genetics: published January 9, 2009 | https://doi.org/10.1371/journal.pgen.1000328

Why Is the Correlation between Gene Importance and Gene Evolutionary Rate So Weak?

Zhi Wang, Jianzhi Zhang

PLOS Genetics: published January 9, 2009 | https://doi.org/10.1371/journal.pgen.1000329

Evolution of Regulatory Sequences in 12 Drosophila Species

Jaebum Kim, Xin He, Saurabh Sinha

PLOS Genetics: published January 9, 2009 | https://doi.org/10.1371/journal.pgen.1000330

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

PLOS Genetics: published January 9, 2009 | https://doi.org/10.1371/journal.pgen.1000331

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

PLOS Genetics: published January 9, 2009 | https://doi.org/10.1371/journal.pgen.1000332

Gγ1, a Downstream Target for the hmgcr-Isoprenoid Biosynthetic Pathway, Is Required for Releasing the Hedgehog Ligand and Directing Germ Cell Migration

Girish Deshpande, Anuradha Godishala, Paul Schedl

PLOS Genetics: published January 9, 2009 | https://doi.org/10.1371/journal.pgen.1000333

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

PLOS Genetics: published January 16, 2009 | https://doi.org/10.1371/journal.pgen.1000334

Pervasive Hitchhiking at Coding and Regulatory Sites in Humans

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

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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

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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

PLOS Genetics: published January 16, 2009 | https://doi.org/10.1371/journal.pgen.1000339

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

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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

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PLOS Genetics: published January 16, 2009 | https://doi.org/10.1371/journal.pgen.1000345

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

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PLOS Genetics: published January 23, 2009 | https://doi.org/10.1371/journal.pgen.1000344

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Natural Variation in an ABC Transporter Gene Associated with Seed Size Evolution in Tomato Species

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PLOS Genetics: published January 23, 2009 | https://doi.org/10.1371/journal.pgen.1000347

Heterochromatic Threads Connect Oscillating Chromosomes during Prometaphase I in Drosophila Oocytes

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

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