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Table of Contents: August 2008

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Neuropsychiatric disorders such as depression and psychosis affect 1/4 of all individuals during their lifetime, and despite efforts to improve the selectivity of psychoactive drugs, all are associated with side effects. Using a genome-wide chemogenomic assay, the authors found that these medications perturbed many evolutionarily conserved genes and cellular pathways (see Ericson et al., doi:10.1371/journal.pgen.1000151).

Interview

Perspectives

Rise of the Machines

David Gresham, Leonid Kruglyak

Research Articles

Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection

Vincent Castric, Jesper Bechsgaard, Mikkel H. Schierup, Xavier Vekemans

The Evolution of Epigenetic Regulators CTCF and BORIS/CTCFL in Amniotes

Timothy A. Hore, Janine E. Deakin, Jennifer A. Marshall Graves

WDR55 Is a Nucleolar Modulator of Ribosomal RNA Synthesis, Cell Cycle Progression, and Teleost Organ Development

Norimasa Iwanami, Tomokazu Higuchi, Yumi Sasano, Toshinobu Fujiwara, Vu Q. Hoa, Minoru Okada, Sadiqur R. Talukder, Sanae Kunimatsu, Jie Li, Fumi Saito, Chitralekha Bhattacharya, Angabin Matin, Takashi Sasaki, Nobuyoshi Shimizu, Hiroshi Mitani, Heinz Himmelbauer, Akihiro Momoi, Hisato Kondoh, Makoto Furutani-Seiki, Yousuke Takahama

The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus

Claudia Steglich, Matthias E. Futschik, Debbie Lindell, Bjoern Voss, Sallie W. Chisholm, Wolfgang R. Hess

A Catalog of Neutral and Deleterious Polymorphism in Yeast

Scott W. Doniger, Hyun Seok Kim, Devjanee Swain, Daniella Corcuera, Morgan Williams, Shiaw-Pyng Yang, Justin C. Fay

An Sp1/Sp3 Binding Polymorphism Confers Methylation Protection

Yanis A. Boumber, Yutaka Kondo, Xuqi Chen, Lanlan Shen, Yi Guo, Carmen Tellez, Marcos R. H. Estécio, Saira Ahmed, Jean-Pierre J. Issa

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq

Alexandra Sittka, Sacha Lucchini, Kai Papenfort, Cynthia M. Sharma, Katarzyna Rolle, Tim T. Binnewies, Jay C. D. Hinton, Jörg Vogel

Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice

Ki-Hong Jung, Jinwon Lee, Chris Dardick, Young-Su Seo, Peijian Cao, Patrick Canlas, Jirapa Phetsom, Xia Xu, Shu Ouyang, Kyungsook An, Yun-Ja Cho, Geun-Cheol Lee, Yoosook Lee, Gynheung An, Pamela C. Ronald

Divergent Evolution of CHD3 Proteins Resulted in MOM1 Refining Epigenetic Control in Vascular Plants

Marian Čaikovski, Chotika Yokthongwattana, Yoshiki Habu, Taisuke Nishimura, Olivier Mathieu, Jerzy Paszkowski

Genome-Wide Scan on Total Serum IgE Levels Identifies FCER1A as Novel Susceptibility Locus

Stephan Weidinger, Christian Gieger, Elke Rodriguez, Hansjörg Baurecht, Martin Mempel, Norman Klopp, Henning Gohlke, Stefan Wagenpfeil, Markus Ollert, Johannes Ring, Heidrun Behrendt, Joachim Heinrich, Natalija Novak, Thomas Bieber, Ursula Krämer, Dietrich Berdel, Andrea von Berg, Carl Peter Bauer, Olf Herbarth, Sibylle Koletzko, Holger Prokisch, Divya Mehta, Thomas Meitinger, Martin Depner, Erika von Mutius, Liming Liang, Miriam Moffatt, William Cookson, Michael Kabesch, H.-Erich Wichmann, Thomas Illig

The Identification of Zebrafish Mutants Showing Alterations in Senescence-Associated Biomarkers

Shuji Kishi, Peter E. Bayliss, Junzo Uchiyama, Eriko Koshimizu, Jie Qi, Purushothama Nanjappa, Shintaro Imamura, Asiful Islam, Donna Neuberg, Adam Amsterdam, Thomas M. Roberts

Mutant Screen Distinguishes between Residues Necessary for Light-Signal Perception and Signal Transfer by Phytochrome B

Yoshito Oka, Tomonao Matsushita, Nobuyoshi Mochizuki, Peter H. Quail, Akira Nagatani

Context Differences Reveal Insulator and Activator Functions of a Su(Hw) Binding Region

Alexey A. Soshnev, Xingguo Li, Misty D. Wehling, Pamela K. Geyer

Genetic Variation in an Individual Human Exome

Pauline C. Ng, Samuel Levy, Jiaqi Huang, Timothy B. Stockwell, Brian P. Walenz, Kelvin Li, Nelson Axelrod, Dana A. Busam, Robert L. Strausberg, J. Craig Venter

Delayed and Accelerated Aging Share Common Longevity Assurance Mechanisms

Björn Schumacher, Ingrid van der Pluijm, Michael J. Moorhouse, Theodore Kosteas, Andria Rasile Robinson, Yousin Suh, Timo M. Breit, Harry van Steeg, Laura J. Niedernhofer, Wilfred van IJcken, Andrzej Bartke, Stephen R. Spindler, Jan H. J. Hoeijmakers, Gijsbertus T. J. van der Horst, George A. Garinis

High-Resolution Mapping of Gene Expression Using Association in an Outbred Mouse Stock

Anatole Ghazalpour, Sudheer Doss, Hyun Kang, Charles Farber, Ping-Zi Wen, Alec Brozell, Ruth Castellanos, Eleazar Eskin, Desmond J. Smith, Thomas A. Drake, Aldons J. Lusis

Off-Target Effects of Psychoactive Drugs Revealed by Genome-Wide Assays in Yeast

Elke Ericson, Marinella Gebbia, Lawrence E. Heisler, Jan Wildenhain, Mike Tyers, Guri Giaever, Corey Nislow

E2F and p53 Induce Apoptosis Independently during Drosophila Development but Intersect in the Context of DNA Damage

Nam-Sung Moon, Luisa Di Stefano, Erick J. Morris, Reena Patel, Kristin White, Nicholas J. Dyson

Genetic Evidence of Serum Phosphate-Independent Functions of FGF-23 on Bone

Despina Sitara, Somi Kim, Mohammed S. Razzaque, Clemens Bergwitz, Takashi Taguchi, Christiane Schüler, Reinhold G. Erben, Beate Lanske

High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies

Anjana Srivatsan, Yi Han, Jianlan Peng, Ashley K. Tehranchi, Richard Gibbs, Jue D. Wang, Rui Chen

Efficient Genetic Method for Establishing Drosophila Cell Lines Unlocks the Potential to Create Lines of Specific Genotypes

Amanda Simcox, Sayan Mitra, Sharon Truesdell, Litty Paul, Ting Chen, Jonathan P. Butchar, Steven Justiniano

FHY1 Mediates Nuclear Import of the Light-Activated Phytochrome A Photoreceptor

Thierry Genoud, Fabian Schweizer, Anke Tscheuschler, Dimitry Debrieux, Jorge J. Casal, Eberhard Schäfer, Andreas Hiltbrunner, Christian Fankhauser

Patterns of Positive Selection in Six Mammalian Genomes

Carolin Kosiol, Tomáš Vinař, Rute R. da Fonseca, Melissa J. Hubisz, Carlos D. Bustamante, Rasmus Nielsen, Adam Siepel

Antagonism between DNA and H3K27 Methylation at the Imprinted Rasgrf1 Locus

Anders M. Lindroth, Yoon Jung Park, Chelsea M. McLean, Gregoriy A. Dokshin, Jenna M. Persson, Herry Herman, Diego Pasini, Xavier Miró, Mary E. Donohoe, Jeannie T. Lee, Kristian Helin, Paul D. Soloway

Unveiling Novel RecO Distant Orthologues Involved in Homologous Recombination

Stéphanie Marsin, Aurélie Mathieu, Thierry Kortulewski, Raphaël Guérois, J. Pablo Radicella