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Table of Contents

March 2007

Cover

The yacht Sorcerer II during the Global Ocean Sampling expedition.
Issue Image

Aboard the Sorcerer II, the Global Ocean Sampling expedition made it way from Canada, through the Panama Canal, into the South Pacific, collecting genomic sequences from marine microorganisms. The resulting data are explored in three papers in this issue of PLoS Biology (see Rusch et al., e77; Yooseph et al., e16; and Kannan et al., e17).

Editorial

Global Ocean Sampling Collection

Hemai Parthasarathy, Emma Hill, Catriona MacCallum

PLOS Biology: published March 13, 2007 | https://doi.org/10.1371/journal.pbio.0050083

Synopses

Protein–RNA Interaction Links Fragile X Syndrome and Alzheimer Disease

Richard Robinson

PLOS Biology: published February 13, 2007 | https://doi.org/10.1371/journal.pbio.0050084

Untapped Bounty: Sampling the Seas to Survey Microbial Biodiversity

Liza Gross

PLOS Biology: published March 13, 2007 | https://doi.org/10.1371/journal.pbio.0050085

Does Bacteriophage φ29 Pack Its DNA with a Twist?

Mary Hoff

PLOS Biology: published February 20, 2007 | https://doi.org/10.1371/journal.pbio.0050091

Related Articles

  1. Experimental Test of Connector Rotation during DNA Packaging into Bacteriophage φ29 Capsids
  2. Correction: Does Bacteriophage ϕ29 Pack Its DNA with a Twist?

A Single Gene Coordinates the Social Life of Honeybees

Liza Gross

PLOS Biology: published March 6, 2007 | https://doi.org/10.1371/journal.pbio.0050086

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  1. The Gene vitellogenin Has Multiple Coordinating Effects on Social Organization

Essays

Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes

Jonathan A Eisen

PLOS Biology: published March 13, 2007 | https://doi.org/10.1371/journal.pbio.0050082

Synthetic Biology: Caught between Property Rights, the Public Domain, and the Commons

Arti Rai, James Boyle

PLOS Biology: published March 13, 2007 | https://doi.org/10.1371/journal.pbio.0050058

Feature

Sorcerer II: The Search for Microbial Diversity Roils the Waters

Henry Nicholls

PLOS Biology: published March 13, 2007 | https://doi.org/10.1371/journal.pbio.0050074

Community Page

CAMERA: A Community Resource for Metagenomics

Rekha Seshadri, Saul A Kravitz, Larry Smarr, Paul Gilna, Marvin Frazier

PLOS Biology: published March 13, 2007 | https://doi.org/10.1371/journal.pbio.0050075

Research Articles

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

Douglas B Rusch, Aaron L Halpern, Granger Sutton, Karla B Heidelberg, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A Eisen, Jeff M Hoffman, Karin Remington, Karen Beeson, Bao Tran, Hamilton Smith, Holly Baden-Tillson, Clare Stewart, Joyce Thorpe, Jason Freeman, Cynthia Andrews-Pfannkoch, Joseph E Venter, Kelvin Li, Saul Kravitz, John F Heidelberg, Terry Utterback, Yu-Hui Rogers, Luisa I Falcón, Valeria Souza, Germán Bonilla-Rosso, Luis E Eguiarte, David M Karl, Shubha Sathyendranath, Trevor Platt, Eldredge Bermingham, Victor Gallardo, Giselle Tamayo-Castillo, Michael R Ferrari, Robert L Strausberg, Kenneth Nealson, Robert Friedman, Marvin Frazier, J. Craig Venter

PLOS Biology: published March 13, 2007 | https://doi.org/10.1371/journal.pbio.0050077

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

Shibu Yooseph, Granger Sutton, Douglas B Rusch, Aaron L Halpern, Shannon J Williamson, Karin Remington, Jonathan A Eisen, Karla B Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S Miller, Huiying Li, Susan T Mashiyama, Marcin P Joachimiak, Christopher van Belle, John-Marc Chandonia, David A Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benjamin J Raphael, Vineet Bafna, Robert Friedman, Steven E Brenner, Adam Godzik, David Eisenberg, Jack E Dixon, Susan S Taylor, Robert L Strausberg, Marvin Frazier, J. Craig Venter

PLOS Biology: published March 13, 2007 | https://doi.org/10.1371/journal.pbio.0050016

Structural and Functional Diversity of the Microbial Kinome

Natarajan Kannan, Susan S Taylor, Yufeng Zhai, J. Craig Venter, Gerard Manning

PLOS Biology: published March 13, 2007 | https://doi.org/10.1371/journal.pbio.0050017

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Kristin D Kasschau, Noah Fahlgren, Elisabeth J Chapman, Christopher M Sullivan, Jason S Cumbie, Scott A Givan, James C Carrington

PLOS Biology: published February 13, 2007 | https://doi.org/10.1371/journal.pbio.0050057

LACHESIS Restricts Gametic Cell Fate in the Female Gametophyte of Arabidopsis

Rita Groß-Hardt, Christina Kägi, Nadine Baumann, James M Moore, Ramamurthy Baskar, Wendy B Gagliano, Gerd Jürgens, Ueli Grossniklaus

PLOS Biology: published February 27, 2007 | https://doi.org/10.1371/journal.pbio.0050047

A Novel Role for the TIR Domain in Association with Pathogen-Derived Elicitors

Tessa M Burch-Smith, Michael Schiff, Jeffrey L Caplan, Jeffrey Tsao, Kirk Czymmek, Savithramma P Dinesh-Kumar

PLOS Biology: published February 13, 2007 | https://doi.org/10.1371/journal.pbio.0050068

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  1. Correction: A Novel Role for the TIR Domain in Association with Pathogen-Derived Elicitors

In Vivo Reinsertion of Excised Episomes by the V(D)J Recombinase: A Potential Threat to Genomic Stability

Katrina Vanura, Bertrand Montpellier, Trang Le, Salvatore Spicuglia, Jean-Marc Navarro, Olivier Cabaud, Sandrine Roulland, Elodie Vachez, Immo Prinz, Pierre Ferrier, Rodrig Marculescu, Ulrich Jäger, Bertrand Nadel

PLOS Biology: published February 13, 2007 | https://doi.org/10.1371/journal.pbio.0050043

Revisiting the Basic Reproductive Number for Malaria and Its Implications for Malaria Control

David L Smith, F. Ellis McKenzie, Robert W Snow, Simon I Hay

PLOS Biology: published February 20, 2007 | https://doi.org/10.1371/journal.pbio.0050042

Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells

Quynh T Phan, Carter L Myers, Yue Fu, Donald C Sheppard, Michael R Yeaman, William H Welch, Ashraf S Ibrahim, John E Edwards Jr., Scott G Filler

PLOS Biology: published February 20, 2007 | https://doi.org/10.1371/journal.pbio.0050064

Experimental Test of Connector Rotation during DNA Packaging into Bacteriophage φ29 Capsids

Thorsten Hugel, Jens Michaelis, Craig L Hetherington, Paul J Jardine, Shelley Grimes, Jessica M Walter, Wayne Falk, Dwight L Anderson, Carlos Bustamante

PLOS Biology: published February 20, 2007 | https://doi.org/10.1371/journal.pbio.0050059

Related Articles

  1. Does Bacteriophage φ29 Pack Its DNA with a Twist?

Surviving Endoplasmic Reticulum Stress Is Coupled to Altered Chondrocyte Differentiation and Function

Kwok Yeung Tsang, Danny Chan, Deborah Cheslett, Wilson C. W Chan, Chi Leong So, Ian G Melhado, Tori W. Y Chan, Kin Ming Kwan, Ernst B Hunziker, Yoshihiko Yamada, John F Bateman, Kenneth M. C Cheung, Kathryn S. E Cheah

PLOS Biology: published February 13, 2007 | https://doi.org/10.1371/journal.pbio.0050044

Arkadia Enhances Nodal/TGF-β Signaling by Coupling Phospho-Smad2/3 Activity and Turnover

Konstantinos J Mavrakis, Rebecca L Andrew, Kian Leong Lee, Chariklia Petropoulou, James E Dixon, Naveenan Navaratnam, Dominic P Norris, Vasso Episkopou

PLOS Biology: published March 6, 2007 | https://doi.org/10.1371/journal.pbio.0050067

Functional Modulation of Cardiac Form through Regionally Confined Cell Shape Changes

Heidi J Auman, Hope Coleman, Heather E Riley, Felix Olale, Huai-Jen Tsai, Deborah Yelon

PLOS Biology: published February 20, 2007 | https://doi.org/10.1371/journal.pbio.0050053

Absence of Ret Signaling in Mice Causes Progressive and Late Degeneration of the Nigrostriatal System

Edgar R Kramer, Liviu Aron, Geert M. J Ramakers, Sabine Seitz, Xiaoxi Zhuang, Klaus Beyer, Marten P Smidt, Rüdiger Klein

PLOS Biology: published February 13, 2007 | https://doi.org/10.1371/journal.pbio.0050039

FMRP Mediates mGluR5-Dependent Translation of Amyloid Precursor Protein

Cara J Westmark, James S Malter

PLOS Biology: published February 13, 2007 | https://doi.org/10.1371/journal.pbio.0050052

Retinal Ganglion Cells Can Rapidly Change Polarity from Off to On

Maria Neimark Geffen, Saskia E. J de Vries, Markus Meister

PLOS Biology: published March 6, 2007 | https://doi.org/10.1371/journal.pbio.0050065

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  1. Correction: Retinal Ganglion Cells Can Rapidly Change Polarity from Off to On
  2. Correction: Retinal Ganglion Cells Can Rapidly Change Polarity from Off to On

A Burst-Based “Hebbian” Learning Rule at Retinogeniculate Synapses Links Retinal Waves to Activity-Dependent Refinement

Daniel A Butts, Patrick O Kanold, Carla J Shatz

PLOS Biology: published March 6, 2007 | https://doi.org/10.1371/journal.pbio.0050061

Auditory Short-Term Memory Behaves Like Visual Short-Term Memory

Kristina M Visscher, Elina Kaplan, Michael J Kahana, Robert Sekuler

PLOS Biology: published February 20, 2007 | https://doi.org/10.1371/journal.pbio.0050056

The Gene vitellogenin Has Multiple Coordinating Effects on Social Organization

C. Mindy Nelson, Kate E Ihle, M. Kim Fondrk, Robert E Page Jr., Gro V Amdam

PLOS Biology: published March 6, 2007 | https://doi.org/10.1371/journal.pbio.0050062

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