November 2008

The genomic legacy of the lion, Panthera leo—one of the world's most charismatic carnivores—was studied using a large multigenic dataset. Population genomics of 357 individuals from most of the major lion populations in Africa and Asia refuted the hypothesis that African lions consist of a single, randomly breeding (panmictic) population and provided insight into the lion's natural history (see Antunes et al., doi:10.1371/journal.pgen.1000251). The high population structure observed highlights the importance of preserving lion populations in decline as opposed to prioritizing larger-scale conservation efforts.

Image Credit: Photo of lion cubs from Laikipia District, central Kenya, by James Warwick (http://www.jameswarwick.co.uk).

Perspectives

Spindle Positioning, Meiotic Nonreduction, and Polyploidy in Plants

Sebastien Andreuzza, Imran Siddiqi

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000272

A Closer Look at the eve Stripe 2 Enhancers of Drosophila and Themira

Justin Crocker, Albert Erives

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000276

A Careful Look at Binding Site Reorganization in the even-skipped Enhancers of Drosophila and Sepsids

Emily E. Hare, Brant K. Peterson, Michael B. Eisen

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000268

Research Articles

Physcomitrella patens DCL3 Is Required for 22–24 nt siRNA Accumulation, Suppression of Retrotransposon-Derived Transcripts, and Normal Development

Sung Hyun Cho, Charles Addo-Quaye, Ceyda Coruh, M. Asif Arif, Zhaorong Ma, Wolfgang Frank, Michael J. Axtell

PLOS Genetics: published December 19, 2008 | https://doi.org/10.1371/journal.pgen.1000314

Mutations in AtPS1 (Arabidopsis thaliana Parallel Spindle 1) Lead to the Production of Diploid Pollen Grains

Isabelle d'Erfurth, Sylvie Jolivet, Nicole Froger, Olivier Catrice, Maria Novatchkova, Mathieu Simon, Eric Jenczewski, Raphaël Mercier

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000274

AML1/ETO Oncoprotein Is Directed to AML1 Binding Regions and Co-Localizes with AML1 and HEB on Its Targets

Alessandro Gardini, Matteo Cesaroni, Lucilla Luzi, Akiko J. Okumura, Joseph R. Biggs, Simone P. Minardi, Elisa Venturini, Dong-Er Zhang, Pier Giuseppe Pelicci, Myriam Alcalay

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000275

A PI3-Kinase–Mediated Negative Feedback Regulates Neuronal Excitability

Eric Howlett, Curtis Chun-Jen Lin, William Lavery, Michael Stern

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000277

An Ancient Duplication of Exon 5 in the Snap25 Gene Is Required for Complex Neuronal Development/Function

Jenny U. Johansson, Jesper Ericsson, Juliette Janson, Simret Beraki, Davor Stanić, Slavena A. Mandic, Martin A. Wikström, Tomas Hökfelt, Sven Ove Ögren, Björn Rozell, Per-Olof Berggren, Christina Bark

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000278

SRA-Domain Proteins Required for DRM2-Mediated De Novo DNA Methylation

Lianna M. Johnson, Julie A. Law, Anuj Khattar, Ian R. Henderson, Steven E. Jacobsen

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000280

Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection

Steffen Schmidt, Anna Gerasimova, Fyodor A. Kondrashov, Ivan A. Adzuhbei, Alexey S. Kondrashov, Shamil Sunyaev

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000281

Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum

Christian Gieger, Ludwig Geistlinger, Elisabeth Altmaier, Martin Hrabé de Angelis, Florian Kronenberg, Thomas Meitinger, Hans-Werner Mewes, H.-Erich Wichmann, Klaus M. Weinberger, Jerzy Adamski, Thomas Illig, Karsten Suhre

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000282

Profiling Synaptic Proteins Identifies Regulators of Insulin Secretion and Lifespan

QueeLim Ch'ng, Derek Sieburth, Joshua M. Kaplan

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000283

Chemical–Genetic Profiling of Imidazo[1,2-a]pyridines and -Pyrimidines Reveals Target Pathways Conserved between Yeast and Human Cells

Lisa Yu, Andres Lopez, Abderrahmane Anaflous, Brahim El Bali, Abdellah Hamal, Elke Ericson, Lawrence E. Heisler, Angus McQuibban, Guri Giaever, Corey Nislow, Charles Boone, Grant W. Brown, Mohammed Bellaoui

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000284

Field-Caught Permethrin-Resistant Anopheles gambiae Overexpress CYP6P3, a P450 That Metabolises Pyrethroids

Pie Müller, Emma Warr, Bradley J. Stevenson, Patricia M. Pignatelli, John C. Morgan, Andrew Steven, Alexander E. Yawson, Sara N. Mitchell, Hilary Ranson, Janet Hemingway, Mark J. I. Paine, Martin J. Donnelly

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000286

Genetic Analysis of Human Traits In Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines

Edwin Choy, Roman Yelensky, Sasha Bonakdar, Robert M. Plenge, Richa Saxena, Philip L. De Jager, Stanley Y. Shaw, Cara S. Wolfish, Jacqueline M. Slavik, Chris Cotsapas, Manuel Rivas, Emmanouil T. Dermitzakis, Ellen Cahir-McFarland, Elliott Kieff, David Hafler, Mark J. Daly, David Altshuler

PLOS Genetics: published November 28, 2008 | https://doi.org/10.1371/journal.pgen.1000287

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

Susan M. Huse, Les Dethlefsen, Julie A. Huber, David Mark Welch, David A. Relman, Mitchell L. Sogin

PLOS Genetics: published November 21, 2008 | https://doi.org/10.1371/journal.pgen.1000255

The Coordination of Centromere Replication, Spindle Formation, and Kinetochore–Microtubule Interaction in Budding Yeast

Hong Liu, Fengshan Liang, Fengzhi Jin, Yanchang Wang

PLOS Genetics: published November 21, 2008 | https://doi.org/10.1371/journal.pgen.1000262

Hypermutability of Damaged Single-Strand DNA Formed at Double-Strand Breaks and Uncapped Telomeres in Yeast Saccharomyces cerevisiae

Yong Yang, Joan Sterling, Francesca Storici, Michael A. Resnick, Dmitry A. Gordenin

PLOS Genetics: published November 21, 2008 | https://doi.org/10.1371/journal.pgen.1000264

A Motor Function for the DEAD-Box RNA Helicase, Gemin3, in Drosophila

Ruben J. Cauchi, Kay E. Davies, Ji-Long Liu

PLOS Genetics: published November 21, 2008 | https://doi.org/10.1371/journal.pgen.1000265

A Role for Oxidized DNA Precursors in Huntington's Disease–Like Striatal Neurodegeneration

Gabriele De Luca, Maria Teresa Russo, Paolo Degan, Cecilia Tiveron, Andrea Zijno, Ettore Meccia, Ilenia Ventura, Elisabetta Mattei, Yusaku Nakabeppu, Marco Crescenzi, Rita Pepponi, Antonella Pèzzola, Patrizia Popoli, Margherita Bignami

PLOS Genetics: published November 21, 2008 | https://doi.org/10.1371/journal.pgen.1000266

Indistinguishable Landscapes of Meiotic DNA Breaks in rad50⁺ and rad50S Strains of Fission Yeast Revealed by a Novel rad50⁺ Recombination Intermediate

Randy W. Hyppa, Gareth A. Cromie, Gerald R. Smith

PLOS Genetics: published November 21, 2008 | https://doi.org/10.1371/journal.pgen.1000267

A RAC/CDC-42–Independent GIT/PIX/PAK Signaling Pathway Mediates Cell Migration in C. elegans

Mark Lucanic, Hwai-Jong Cheng

PLOS Genetics: published November 21, 2008 | https://doi.org/10.1371/journal.pgen.1000269

Cell Cycle– and Chaperone-Mediated Regulation of H3K56ac Incorporation in Yeast

Tommy Kaplan, Chih Long Liu, Judith A. Erkmann, John Holik, Michael Grunstein, Paul D. Kaufman, Nir Friedman, Oliver J. Rando

PLOS Genetics: published November 21, 2008 | https://doi.org/10.1371/journal.pgen.1000270

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

Ran Blekhman, Alicia Oshlack, Adrien E. Chabot, Gordon K. Smyth, Yoav Gilad

PLOS Genetics: published November 21, 2008 | https://doi.org/10.1371/journal.pgen.1000271

Gamma-Linolenic and Stearidonic Acids Are Required for Basal Immunity in Caenorhabditis elegans through Their Effects on p38 MAP Kinase Activity

Madhumitha Nandakumar, Man-Wah Tan

PLOS Genetics: published November 21, 2008 | https://doi.org/10.1371/journal.pgen.1000273

p8/TTDA Overexpression Enhances UV-Irradiation Resistance and Suppresses TFIIH Mutations in a Drosophila Trichothiodystrophy Model

Javier Aguilar-Fuentes, Mariana Fregoso, Mariana Herrera, Enrique Reynaud, Cathy Braun, Jean Marc Egly, Mario Zurita

PLOS Genetics: published November 14, 2008 | https://doi.org/10.1371/journal.pgen.1000253

Genetic Control of Variegated KIR Gene Expression: Polymorphisms of the Bi-Directional KIR3DL1 Promoter Are Associated with Distinct Frequencies of Gene Expression

Hongchuan Li, Véronique Pascal, Maureen P. Martin, Mary Carrington, Stephen K. Anderson

PLOS Genetics: published November 14, 2008 | https://doi.org/10.1371/journal.pgen.1000254

Synonymous Genes Explore Different Evolutionary Landscapes

Guillaume Cambray, Didier Mazel

PLOS Genetics: published November 14, 2008 | https://doi.org/10.1371/journal.pgen.1000256

CTCF cis-Regulates Trinucleotide Repeat Instability in an Epigenetic Manner: A Novel Basis for Mutational Hot Spot Determination

Randell T. Libby, Katharine A. Hagerman, Victor V. Pineda, Rachel Lau, Diane H. Cho, Sandy L. Baccam, Michelle M. Axford, John D. Cleary, James M. Moore, Bryce L. Sopher, Stephen J. Tapscott, Galina N. Filippova, Christopher E. Pearson, Albert R. La Spada

PLOS Genetics: published November 14, 2008 | https://doi.org/10.1371/journal.pgen.1000257

Bidirectional Transcription Directs Both Transcriptional Gene Activation and Suppression in Human Cells

Kevin V. Morris, Sharon Santoso, Anne-Marie Turner, Chiara Pastori, Peter G. Hawkins

PLOS Genetics: published November 14, 2008 | https://doi.org/10.1371/journal.pgen.1000258

Murine Dishevelled 3 Functions in Redundant Pathways with Dishevelled 1 and 2 in Normal Cardiac Outflow Tract, Cochlea, and Neural Tube Development

S. Leah Etheridge, Saugata Ray, Shuangding Li, Natasha S. Hamblet, Nardos Lijam, Michael Tsang, Joy Greer, Natalie Kardos, Jianbo Wang, Daniel J. Sussman, Ping Chen, Anthony Wynshaw-Boris

PLOS Genetics: published November 14, 2008 | https://doi.org/10.1371/journal.pgen.1000259

Dissection of a QTL Hotspot on Mouse Distal Chromosome 1 that Modulates Neurobehavioral Phenotypes and Gene Expression

Khyobeni Mozhui, Daniel C. Ciobanu, Thomas Schikorski, Xusheng Wang, Lu Lu, Robert W. Williams

PLOS Genetics: published November 14, 2008 | https://doi.org/10.1371/journal.pgen.1000260

Zebrafish Mutants calamity and catastrophe Define Critical Pathways of Gene–Nutrient Interactions in Developmental Copper Metabolism

Erik C. Madsen, Jonathan D. Gitlin

PLOS Genetics: published November 14, 2008 | https://doi.org/10.1371/journal.pgen.1000261

Aging Predisposes Oocytes to Meiotic Nondisjunction When the Cohesin Subunit SMC1 Is Reduced

Vijayalakshmi V. Subramanian, Sharon E. Bickel

PLOS Genetics: published November 14, 2008 | https://doi.org/10.1371/journal.pgen.1000263

A Glial Variant of the Vesicular Monoamine Transporter Is Required To Store Histamine in the Drosophila Visual System

Rafael Romero-Calderón, Guido Uhlenbrock, Jolanta Borycz, Anne F. Simon, Anna Grygoruk, Susan K. Yee, Amy Shyer, Larry C. Ackerson, Nigel T. Maidment, Ian A. Meinertzhagen, Bernhard T. Hovemann, David E. Krantz

PLOS Genetics: published November 7, 2008 | https://doi.org/10.1371/journal.pgen.1000245

Mutations in the SLC2A9 Gene Cause Hyperuricosuria and Hyperuricemia in the Dog

Danika Bannasch, Noa Safra, Amy Young, Nili Karmi, R. S. Schaible, G. V. Ling

PLOS Genetics: published November 7, 2008 | https://doi.org/10.1371/journal.pgen.1000246

Silent but Not Static: Accelerated Base-Pair Substitution in Silenced Chromatin of Budding Yeasts

Leonid Teytelman, Michael B. Eisen, Jasper Rine

PLOS Genetics: published November 7, 2008 | https://doi.org/10.1371/journal.pgen.1000247

High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution

Yehudit Hasin, Tsviya Olender, Miriam Khen, Claudia Gonzaga-Jauregui, Philip M. Kim, Alexander Eckehart Urban, Michael Snyder, Mark B. Gerstein, Doron Lancet, Jan O. Korbel

PLOS Genetics: published November 7, 2008 | https://doi.org/10.1371/journal.pgen.1000249

The Impact of the Nucleosome Code on Protein-Coding Sequence Evolution in Yeast

Tobias Warnecke, Nizar N. Batada, Laurence D. Hurst

PLOS Genetics: published November 7, 2008 | https://doi.org/10.1371/journal.pgen.1000250

The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics

Agostinho Antunes, Jennifer L. Troyer, Melody E. Roelke, Jill Pecon-Slattery, Craig Packer, Christiaan Winterbach, Hanlie Winterbach, Graham Hemson, Laurence Frank, Philip Stander, Ludwig Siefert, Margaret Driciru, Paul J. Funston, Kathy A. Alexander, Katherine C. Prager, Gus Mills, David Wildt, Mitch Bush, Stephen J. O'Brien, Warren E. Johnson

PLOS Genetics: published November 7, 2008 | https://doi.org/10.1371/journal.pgen.1000251

Functional Polymorphisms in PRODH Are Associated with Risk and Protection for Schizophrenia and Fronto-Striatal Structure and Function

Lucas Kempf, Kristin K. Nicodemus, Bhaskar Kolachana, Radhakrishna Vakkalanka, Beth A. Verchinski, Michael F. Egan, Richard E. Straub, Venkata A. Mattay, Joseph H. Callicott, Daniel R. Weinberger, Andreas Meyer-Lindenberg

PLOS Genetics: published November 7, 2008 | https://doi.org/10.1371/journal.pgen.1000252

Cover

How genetically structured are lion populations?

Perspectives

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