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Table of Contents

February 2005

Cover

The genome sequences of indica and japonica rice.
Issue Image

Comparative genome sequencing of indica and japonica rice reveals that duplication of genes and genomic regions has played a major part in the evolution of grass genomes (See Yu et al.). Like the paper that describes this work, the extensive genomic datasets that were produced are publicly available, for sharing and reuse. The cover shows a child dressed in traditional Han suit, wanting to share his very large bowl of rice.

Image Credit: Photo by Lei Xu and Fang Chen, Beijing Institute of Genomics. Child model: Wensen Cai

Essay

Facts from Text—Is Text Mining Ready to Deliver?

Dietrich Rebholz-Schuhmann, Harald Kirsch, Francisco Couto

PLOS Biology: published February 15, 2005 | https://doi.org/10.1371/journal.pbio.0030065

Feature

Ancient DNA Comes of Age

Henry Nicholls

PLOS Biology: published February 15, 2005 | https://doi.org/10.1371/journal.pbio.0030056

Primers

A New Paradigm in Eukaryotic Biology: HIV Tat and the Control of Transcriptional Elongation

Matjaz Barboric, B. Matija Peterlin

PLOS Biology: published February 15, 2005 | https://doi.org/10.1371/journal.pbio.0030076

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  2. An HIV Protein Plays a Surprising Role in Gene Activation
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  4. HIV-1 Tat Stimulates Transcription Complex Assembly through Recruitment of TBP in the Absence of TAFs

Timing the Brain: Mental Chronometry as a Tool in Neuroscience

Michael I Posner

PLOS Biology: published February 15, 2005 | https://doi.org/10.1371/journal.pbio.0030051

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  1. Parsing a Cognitive Task: A Characterization of the Mind's Bottleneck

Community Page

Discovery-Based Science Education: Functional Genomic Dissection in Drosophila by Undergraduate Researchers

Jiong Chen, Gerald B Call, Elsa Beyer, Chris Bui, Albert Cespedes, Amy Chan, Jenny Chan, Stacy Chan, Akanksha Chhabra, Peter Dang, Artemis Deravanesian, Brenda Hermogeno, James Jen, Eunha Kim, Eric Lee, Gemma Lewis, Jamie Marshall, Kirsten Regalia, Farnaz Shadpour, Aram Shemmassian, Kristin Spivey, Maggie Wells, Joy Wu, Yuki Yamauchi, Amir Yavari, Anna Abrams, Amanda Abramson, Latiffe Amado, Jenny Anderson, Keenan Bashour, Elena Bibikova, Allen Bookatz, Sarah Brewer, Natalie Buu, Stephanie Calvillo, Joseph Cao, Aileen Chang, Daniel Chang, Yuli Chang, Yibing Chen, Joo Choi, Jeyling Chou, Sumit Datta, Ardy Davarifar, Poonam Desai, Jordan Fabrikant, Shahbaz Farnad, Katherine Fu, Eddie Garcia, Nick Garrone, Srpouhi Gasparyan, Phyllis Gayda, Chad Goffstein, Courtney Gonzalez, Mariam Guirguis, Ryan Hassid, Aria Hong, Julie Hong, Lindsay Hovestreydt, Charles Hu, Farid Jamshidian, Katrin Kahen, Linda Kao, Melissa Kelley, Thomas Kho, Sarah Kim, Yein Kim, Brian Kirkpatrick, Emil Kohan, Robert Kwak, Adam Langenbacher, Santino Laxamana, Chris Lee, Janet Lee, So-Youn Lee, To Hang S Lee, Toni Lee, Sheila Lezcano, Henry Lin, Peter Lin, Julie Luu, Thanh Luu, Will Marrs, Erin Marsh, Sarah Min, Tanya Minasian, Amit Misra, Miles Morimoto, Yasaman Moshfegh, Jessica Murray, Cynthia Nguyen, Kha Nguyen, Ernesto Nodado II, Amanda O'Donahue, Ndidi Onugha, Nneka Orjiakor, Bhavin Padhiar, Mara Pavel-Dinu, Alex Pavlenko, Edwin Paz, Sarah Phaklides, Lephong Pham, Preethi Poulose, Russell Powell, Aya Pusic, Divi Ramola, Meghann Ribbens, Bassel Rifai, Desiree Rosselli, Manyak Saakyan, Pamela Saarikoski, Miriam Segura, Ramnik Singh, Vivek Singh, Emily Skinner, Daniel Solomin, Kosha Soneji, Erika Stageberg, Marina Stavchanskiy, Leena Tekchandani, Leo Thai, Jayantha Thiyanaratnam, Maurine Tong, Aneet Toor, Steve Tovar, Kelly Trangsrud, Wah-Yung Tsang, Marc Uemura, Mary Unkovic, Emily Vollmer, Emily Weiss, Damien Wood, Sophia Wu, Winston Wu, Qing Xu, Kevin Yackle, Will Yarosh, Laura Yee, George Yen, Grant Alkin, Sheryllene Go, Devon M Huff, Helena Minye, Eric Paul, Nikki Villarasa, Allison Milchanowski, Utpal Banerjee

PLOS Biology: published February 15, 2005 | https://doi.org/10.1371/journal.pbio.0030059

Research Articles

SIRT1 Regulates HIV Transcription via Tat Deacetylation

Sara Pagans, Angelika Pedal, Brian J North, Katrin Kaehlcke, Brett L Marshall, Alexander Dorr, Claudia Hetzer-Egger, Peter Henklein, Roy Frye, Michael W McBurney, Henning Hruby, Manfred Jung, Eric Verdin, Melanie Ott

PLOS Biology: published February 8, 2005 | https://doi.org/10.1371/journal.pbio.0030041

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HIV-1 Tat Stimulates Transcription Complex Assembly through Recruitment of TBP in the Absence of TAFs

Tamal Raha, S. W. Grace Cheng, Michael R Green

PLOS Biology: published February 8, 2005 | https://doi.org/10.1371/journal.pbio.0030044

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Organized Unidirectional Waves of ATP Hydrolysis within a RecA Filament

Julia M Cox, Oleg V Tsodikov, Michael M Cox

PLOS Biology: published February 8, 2005 | https://doi.org/10.1371/journal.pbio.0030052

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  1. DNA Recombination and Repair—A New Twist to RecA Function

Flux Analysis Uncovers Key Role of Functional Redundancy in Formaldehyde Metabolism

Christopher J Marx, Stephen J Van Dien, Mary E Lidstrom

PLOS Biology: published January 4, 2005 | https://doi.org/10.1371/journal.pbio.0030016

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Cobalamin-Independent Methionine Synthase (MetE): A Face-to-Face Double Barrel That Evolved by Gene Duplication

Robert Pejchal, Martha L Ludwig

PLOS Biology: published December 28, 2004 | https://doi.org/10.1371/journal.pbio.0030031

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The Genomes of Oryza sativa: A History of Duplications

Jun Yu, Jun Wang, Wei Lin, Songgang Li, Heng Li, Jun Zhou, Peixiang Ni, Wei Dong, Songnian Hu, Changqing Zeng, Jianguo Zhang, Yong Zhang, Ruiqiang Li, Zuyuan Xu, Shengting Li, Xianran Li, Hongkun Zheng, Lijuan Cong, Liang Lin, Jianning Yin, Jianing Geng, Guangyuan Li, Jianping Shi, Juan Liu, Hong Lv, Jun Li, Jing Wang, Yajun Deng, Longhua Ran, Xiaoli Shi, Xiyin Wang, Qingfa Wu, Changfeng Li, Xiaoyu Ren, Jingqiang Wang, Xiaoling Wang, Dawei Li, Dongyuan Liu, Xiaowei Zhang, Zhendong Ji, Wenming Zhao, Yongqiao Sun, Zhenpeng Zhang, Jingyue Bao, Yujun Han, Lingli Dong, Jia Ji, Peng Chen, Shuming Wu, Jinsong Liu, Ying Xiao, Dongbo Bu, Jianlong Tan, Li Yang, Chen Ye, Jingfen Zhang, Jingyi Xu, Yan Zhou, Yingpu Yu, Bing Zhang, Shulin Zhuang, Haibin Wei, Bin Liu, Meng Lei, Hong Yu, Yuanzhe Li, Hao Xu, Shulin Wei, Ximiao He, Lijun Fang, Zengjin Zhang, Yunze Zhang, Xiangang Huang, Zhixi Su, Wei Tong, Jinhong Li, Zongzhong Tong, Shuangli Li, Jia Ye, Lishun Wang, Lin Fang, Tingting Lei, Chen Chen, Huan Chen, Zhao Xu, Haihong Li, Haiyan Huang, Feng Zhang, Huayong Xu, Na Li, Caifeng Zhao, Shuting Li, Lijun Dong, Yanqing Huang, Long Li, Yan Xi, Qiuhui Qi, Wenjie Li, Bo Zhang, Wei Hu, Yanling Zhang, Xiangjun Tian, Yongzhi Jiao, Xiaohu Liang, Jiao Jin, Lei Gao, Weimou Zheng, Bailin Hao, Siqi Liu, Wen Wang, Longping Yuan, Mengliang Cao, Jason McDermott, Ram Samudrala, Jian Wang, Gane Ka-Shu Wong, Huanming Yang

PLOS Biology: published February 1, 2005 | https://doi.org/10.1371/journal.pbio.0030038

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Evidence for Widespread Degradation of Gene Control Regions in Hominid Genomes

Peter D Keightley, Martin J Lercher, Adam Eyre-Walker

PLOS Biology: published January 25, 2005 | https://doi.org/10.1371/journal.pbio.0030042

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The Indirect Benefits of Mating with Attractive Males Outweigh the Direct Costs

Megan L Head, John Hunt, Michael D Jennions, Robert Brooks

PLOS Biology: published January 25, 2005 | https://doi.org/10.1371/journal.pbio.0030033

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Aging and Death in an Organism That Reproduces by Morphologically Symmetric Division

Eric J Stewart, Richard Madden, Gregory Paul, François Taddei

PLOS Biology: published February 1, 2005 | https://doi.org/10.1371/journal.pbio.0030045

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Nuclear Hormone Receptor NHR-49 Controls Fat Consumption and Fatty Acid Composition in C. elegans

Marc R. Van Gilst, Haralambos Hadjivassiliou, Amber Jolly, Keith R Yamamoto

PLOS Biology: published February 8, 2005 | https://doi.org/10.1371/journal.pbio.0030053

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Light-Dependent Development of Circadian Gene Expression in Transgenic Zebrafish

Maki Kaneko, Gregory M Cahill

PLOS Biology: published February 1, 2005 | https://doi.org/10.1371/journal.pbio.0030034

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A Functional Neuroimaging Study of Sound Localization: Visual Cortex Activity Predicts Performance in Early-Blind Individuals

Frédéric Gougoux, Robert J Zatorre, Maryse Lassonde, Patrice Voss, Franco Lepore

PLOS Biology: published January 25, 2005 | https://doi.org/10.1371/journal.pbio.0030027

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Parsing a Cognitive Task: A Characterization of the Mind's Bottleneck

Mariano Sigman, Stanislas Dehaene

PLOS Biology: published February 8, 2005 | https://doi.org/10.1371/journal.pbio.0030037

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Corrections

Correction: Components of Coated Vesicles and Nuclear Pore Complexes Share a Common Molecular Architecture

Damien Devos, Svetlana Dokudovskaya, Frank Alber, Rosemary Williams, Brian T Chait, Andrej Sali, Michael P Rout

PLOS Biology: published February 15, 2005 | https://doi.org/10.1371/journal.pbio.0030080

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Correction: Cro-Magnons Conquered Europe, but Left Neanderthals Alone

PLOS Biology: published February 15, 2005 | https://doi.org/10.1371/journal.pbio.0030090

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Book Review%2FScience in the Media

Progress on the Origin of Species

Douglas J Futuyma

PLOS Biology: published February 15, 2005 | https://doi.org/10.1371/journal.pbio.0030062