FOCUS ISSUE ON PLANT DATABASES:

EDITORIALS:

Seung Yon Rhee and Bill Crosby

Biological Databases for Plant Research
Plant Physiol. 2005 138: 1-3. [Full Text] [PDF]  

BIOINFORMATICS-PLANT DATABASES:

Mark Wilkinson, Heiko Schoof, Rebecca Ernst, and Dirk Haase

BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case
Plant Physiol. 2005 138: 5-17. [Abstract] [Full Text] [PDF]  

Qiaoping Yuan, Shu Ouyang, Aihui Wang, Wei Zhu, Rama Maiti, Haining Lin, John Hamilton, Brian Haas, Razvan Sultana, Foo Cheung, Jennifer Wortman, and C. Robin Buell

The Institute for Genomic Research Osa1 Rice Genome Annotation Database
Plant Physiol. 2005 138: 18-26. [Abstract] [Full Text] [PDF]  

Peifen Zhang, Hartmut Foerster, Christophe P. Tissier, Lukas Mueller, Suzanne Paley, Peter D. Karp, and Seung Y. Rhee

MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research
Plant Physiol. 2005 138: 27-37. [Abstract] [Full Text] [PDF] [Supplemental Data]  

Steven B. Cannon, John A. Crow, Michael L. Heuer, Xiaohong Wang, Ethalinda K.S. Cannon, Christopher Dwan, Anne-Francoise Lamblin, Jayprakash Vasdewani, Joann Mudge, Andrew Cook, John Gish, Foo Cheung, Steve Kenton, Timothy M. Kunau, Douglas Brown, Gregory D. May, Dongjin Kim, Douglas R. Cook, Bruce A. Roe, Chris D. Town, Nevin D. Young, and Ernest F. Retzel

Databases and Information Integration for the Medicago truncatula Genome and Transcriptome
Plant Physiol. 2005 138: 38-46. [Abstract] [Full Text] [PDF]  

Kevin Horan, Josh Lauricha, Julia Bailey-Serres, Natasha Raikhel, and Thomas Girke

Genome Cluster Database. A Sequence Family Analysis Platform for Arabidopsis and Rice
Plant Physiol. 2005 138: 47-54. [Abstract] [Full Text] [PDF]  

Carolyn J. Lawrence, Trent E. Seigfried, and Volker Brendel

The Maize Genetics and Genomics Database. The Community Resource for Access to Diverse Maize Data
Plant Physiol. 2005 138: 55-58. [Abstract] [Full Text] [PDF]  

Michel Schneider, Amos Bairoch, Cathy H. Wu, and Rolf Apweiler

Plant Protein Annotation in the UniProt Knowledgebase
Plant Physiol. 2005 138: 59-66. [Abstract] [Full Text] [PDF]  

Helen Jenkins, Helen Johnson, Baldeep Kular, Trevor Wang, and Nigel Hardy

Toward Supportive Data Collection Tools for Plant Metabolomics
Plant Physiol. 2005 138: 67-77. [Abstract] [Full Text] [PDF] [Supplemental Data]  

REGULAR ISSUE:

ON THE INSIDE:

Peter V. Minorsky

On the Inside
Plant Physiol. 2005 138: 78-79. [Full Text] [PDF]  

BIOINFORMATICS:

Vishal Pampanwar, Friedrich Engler, James Hatfield, Steve Blundy, Gaurav Gupta, and Carol Soderlund

FPC Web Tools for Rice, Maize, and Distribution
Plant Physiol. 2005 138: 116-126. [Abstract] [Full Text] [PDF]  

MEETING REPORTS:

Anna Amtmann, Hans J. Bohnert, and Ray A. Bressan

Abiotic Stress and Plant Genome Evolution. Search for New Models
Plant Physiol. 2005 138: 127-130. [Full Text] [PDF]  

GENOME ANALYSIS:

Ligeng Ma, Ning Sun, Xigang Liu, Yuling Jiao, Hongyu Zhao, and Xing Wang Deng

Organ-Specific Expression of Arabidopsis Genome during Development
Plant Physiol. 2005 138: 80-91. [Abstract] [Full Text] [PDF] [Supplemental Data]  

Nathan M. Springer and Shawn M. Kaeppler

Evolutionary Divergence of Monocot and Dicot Methyl-CpG-Binding Domain Proteins
Plant Physiol. 2005 138: 92-104. [Abstract] [Full Text] [PDF] [Supplemental Data]  

Chatchawan Jantasuriyarat, Malali Gowda, Karl Haller, Jamie Hatfield, Guodong Lu, Eric Stahlberg, Bo Zhou, Huameng Li, HyRan Kim, Yeisoo Yu, Ralph A. Dean, Rod A. Wing, Carol Soderlund, and Guo-Liang Wang

Large-Scale Identification of Expressed Sequence Tags Involved in Rice and Rice Blast Fungus Interaction
Plant Physiol. 2005 138: 105-115. [Abstract] [Full Text] [PDF]  

BIOCHEMICAL PROCESSES AND MACROMOLECULAR STRUCTURES:

Qisen Zhang, Neil Shirley, Jelle Lahnstein, and Geoffrey B. Fincher

Characterization and Expression Patterns of UDP-D-Glucuronate Decarboxylase Genes in Barley
Plant Physiol. 2005 138: 131-141. First Published on April 22, 2005; 10.1104/pp.104.057869 [Abstract] [Full Text] [PDF] [Supplemental Data]  

Konstantinos A. Paschalidis and Kalliopi A. Roubelakis-Angelakis

Spatial and Temporal Distribution of Polyamine Levels and Polyamine Anabolism in Different Organs/Tissues of the Tobacco Plant. Correlations with Age, Cell Division/Expansion, and Differentiation
Plant Physiol. 2005 138: 142-152. First Published on April 22, 2005; 10.1104/pp.104.055483 [Abstract] [Full Text] [PDF]  

Tamara Verhoeven, Richard Feron, Mieke Wolters-Arts, Johan Edqvist, Tom Gerats, Jan Derksen, and Celestina Mariani

STIG1 Controls Exudate Secretion in the Pistil of Petunia and Tobacco
Plant Physiol. 2005 138: 153-160. First Published on April 8, 2005; 10.1104/pp.104.054809 [Abstract] [Full Text] [PDF] [Supplemental Data]  

Salah E. Abdel-Ghany, Hong Ye, Gulnara F. Garifullina, Lihong Zhang, Elizabeth A.H. Pilon-Smits, and Marinus Pilon

Iron-Sulfur Cluster Biogenesis in Chloroplasts. Involvement of the Scaffold Protein CpIscA
Plant Physiol. 2005 138: 161-172. [Abstract] [Full Text] [PDF]  

Joenel Alcantara, David A. Bird, Vincent R. Franceschi, and Peter J. Facchini

Sanguinarine Biosynthesis Is Associated with the Endoplasmic Reticulum in Cultured Opium Poppy Cells after Elicitor Treatment
Plant Physiol. 2005 138: 173-183. First Published on April 22, 2005; 10.1104/pp.105.059287 [Abstract] [Full Text] [PDF]  

Fabrice Wattebled, Ying Dong, Sylvain Dumez, David Delvallé, Véronique Planchot, Pierre Berbezy, Darshna Vyas, Paul Colonna, Manash Chatterjee, Steven Ball, and Christophe D'Hulst

Mutants of Arabidopsis Lacking a Chloroplastic Isoamylase Accumulate Phytoglycogen and an Abnormal Form of Amylopectin
Plant Physiol. 2005 138: 184-195. First Published on April 22, 2005; 10.1104/pp.105.059295 [Abstract] [Full Text] [PDF] [Supplemental Data]  

Naoya Hirose, Nobue Makita, Tomoyuki Yamaya, and Hitoshi Sakakibara

Functional Characterization and Expression Analysis of a Gene, OsENT2, Encoding an Equilibrative Nucleoside Transporter in Rice Suggest a Function in Cytokinin Transport
Plant Physiol. 2005 138: 196-206. First Published on April 22, 2005; 10.1104/pp.105.060137 [Abstract] [Full Text] [PDF]  

Thierry Tonon, Renwei Qing, David Harvey, Yi Li, Tony Robert Larson, and Ian Alexander Graham

Identification of a Long-Chain Polyunsaturated Fatty Acid Acyl-Coenzyme A Synthetase from the Diatom Thalassiosira pseudonana
Plant Physiol. 2005 138: 402-408. First Published on April 8, 2005; 10.1104/pp.104.054528 [Abstract] [Full Text] [PDF]  

Sangbom M. Lyi, Laurence I. Heller, Michael Rutzke, Ross M. Welch, Leon V. Kochian, and Li Li

Molecular and Biochemical Characterization of the Selenocysteine Se-Methyltransferase Gene and Se-Methylselenocysteine Synthesis in Broccoli
Plant Physiol. 2005 138: 409-420. First Published on April 29, 2005; 10.1104/pp.104.056549 [Abstract] [Full Text] [PDF]  

Fernando Gandía-Herrero, Josefa Escribano, and Francisco García-Carmona

Betaxanthins as Substrates for Tyrosinase. An Approach to the Role of Tyrosinase in the Biosynthetic Pathway of Betalains
Plant Physiol. 2005 138: 421-432. First Published on April 1, 2005; 10.1104/pp.104.057992 [Abstract] [Full Text] [PDF]  

Laura Hopkins, Saroj Parmar, Anna Blaszczyk, Holger Hesse, Rainer Hoefgen, and Malcolm J. Hawkesford

O-Acetylserine and the Regulation of Expression of Genes Encoding Components for Sulfate Uptake and Assimilation in Potato
Plant Physiol. 2005 138: 433-440. First Published on April 1, 2005; 10.1104/pp.104.057521 [Abstract] [Full Text] [PDF]  

Patrick Schaub, Salim Al-Babili, Rachel Drake, and Peter Beyer

Why Is Golden Rice Golden (Yellow) Instead of Red?
Plant Physiol. 2005 138: 441-450. First Published on April 8, 2005; 10.1104/pp.104.057927 [Abstract] [Full Text] [PDF] [Supplemental Data]  

BIOENERGETICS AND PHOTOSYNTHESIS:

Yuji Tanaka, Daisuke Nakatsuma, Hisashi Harada, Maki Ishida, and Yusuke Matsuda

Localization of Soluble -Carbonic Anhydrase in the Marine Diatom Phaeodactylum tricornutum. Sorting to the Chloroplast and Cluster Formation on the Girdle Lamellae
Plant Physiol. 2005 138: 207-217. First Published on April 22, 2005; 10.1104/pp.104.058982 [Abstract] [Full Text] [PDF] [Supplemental Data]  

Stephane Lefebvre, Tracy Lawson, Mike Fryer, Oksana V. Zakhleniuk, Julie C. Lloyd, and Christine A. Raines

Increased Sedoheptulose-1,7-Bisphosphatase Activity in Transgenic Tobacco Plants Stimulates Photosynthesis and Growth from an Early Stage in Development
Plant Physiol. 2005 138: 451-460. First Published on April 29, 2005; 10.1104/pp.104.055046 [Abstract] [Full Text] [PDF]  

CELL BIOLOGY AND SIGNAL TRANSDUCTION:

Mariana E. Kirst, David J. Meyer, Bryan C. Gibbon, Rudolf Jung, and Rebecca S. Boston

Identification and Characterization of Endoplasmic Reticulum-Associated Degradation Proteins Differentially Affected by Endoplasmic Reticulum Stress
Plant Physiol. 2005 138: 218-231. First Published on April 22, 2005; 10.1104/pp.105.060087 [Abstract] [Full Text] [PDF]  

DEVELOPMENT AND HORMONE ACTION:

Huawu Jiang, Shaomin Wang, Lei Dang, Shoufeng Wang, Hanmin Chen, Yunrong Wu, Xinhang Jiang, and Ping Wu

A Novel Short-Root Gene Encodes a Glucosamine-6-Phosphate Acetyltransferase Required for Maintaining Normal Root Cell Shape in Rice
Plant Physiol. 2005 138: 232-242. First Published on April 22, 2005; 10.1104/pp.104.058248 [Abstract] [Full Text] [PDF]  

Dong Ju Lee and Jan A.D. Zeevaart

Molecular Cloning of GA 2-Oxidase3 from Spinach and Its Ectopic Expression in Nicotiana sylvestris
Plant Physiol. 2005 138: 243-254. First Published on April 8, 2005; 10.1104/pp.104.056499 [Abstract] [Full Text] [PDF]  

Beverly A. Underwood, Denise M. Tieman, Kenichi Shibuya, Richard J. Dexter, Holly M. Loucas, Andrew J. Simkin, Charles A. Sims, Eric A. Schmelz, Harry J. Klee, and David G. Clark

Ethylene-Regulated Floral Volatile Synthesis in Petunia Corollas
Plant Physiol. 2005 138: 255-266. First Published on April 22, 2005; 10.1104/pp.104.051144 [Abstract] [Full Text] [PDF] [Supplemental Data]  

Cornelius S. Barry, Ryan P. McQuinn, Andrew J. Thompson, Graham B. Seymour, Donald Grierson, and James J. Giovannoni

Ethylene Insensitivity Conferred by the Green-ripe and Never-ripe 2 Ripening Mutants of Tomato
Plant Physiol. 2005 138: 267-275. First Published on April 15, 2005; 10.1104/pp.104.057745 [Abstract] [Full Text] [PDF]  

ENVIRONMENTAL STRESS AND ADAPTATION:

Wen-Wei Hu, Haibiao Gong, and Eng Chong Pua

The Pivotal Roles of the Plant S-Adenosylmethionine Decarboxylase 5' Untranslated Leader Sequence in Regulation of Gene Expression at the Transcriptional and Posttranscriptional Levels
Plant Physiol. 2005 138: 276-286. First Published on April 8, 2005; 10.1104/pp.104.056770 [Abstract] [Full Text] [PDF]  

Hong Shen, Long Fei He, Takayuki Sasaki, Yoko Yamamoto, Shao Jian Zheng, Ayalew Ligaba, Xiao Long Yan, Sung Ju Ahn, Mineo Yamaguchi, Hideo Sasakawa, and Hideaki Matsumoto

Citrate Secretion Coupled with the Modulation of Soybean Root Tip under Aluminum Stress. Up-Regulation of Transcription, Translation, and Threonine-Oriented Phosphorylation of Plasma Membrane H⁺-ATPase
Plant Physiol. 2005 138: 287-296. First Published on April 15, 2005; 10.1104/pp.104.058065 [Abstract] [Full Text] [PDF]  

Shao Jian Zheng, Jian Li Yang, Yun Feng He, Xue Hui Yu, Lei Zhang, Jiang Feng You, Ren Fang Shen, and Hideaki Matsumoto

Immobilization of Aluminum with Phosphorus in Roots Is Associated with High Aluminum Resistance in Buckwheat
Plant Physiol. 2005 138: 297-303. First Published on April 29, 2005; 10.1104/pp.105.059667 [Abstract] [Full Text] [PDF]  

Victoria J. Nikiforova, Joachim Kopka, Vladimir Tolstikov, Oliver Fiehn, Laura Hopkins, Malcolm J. Hawkesford, Holger Hesse, and Rainer Hoefgen

Systems Rebalancing of Metabolism in Response to Sulfur Deprivation, as Revealed by Metabolome Analysis of Arabidopsis Plants
Plant Physiol. 2005 138: 304-318. First Published on April 15, 2005; 10.1104/pp.104.053793 [Abstract] [Full Text] [PDF] [Supplemental Data]  

Chiung-Wen Chang, Jeffrey L. Moseley, Dennis Wykoff, and Arthur R. Grossman

The LPB1 Gene Is Important for Acclimation of Chlamydomonas reinhardtii to Phosphorus and Sulfur Deprivation
Plant Physiol. 2005 138: 319-329. First Published on April 22, 2005; 10.1104/pp.105.059550 [Abstract] [Full Text] [PDF] [Supplemental Data]  

Marilyn Griffith, Chelsey Lumb, Steven B. Wiseman, Michael Wisniewski, Robert W. Johnson, and Alejandro G. Marangoni

Antifreeze Proteins Modify the Freezing Process In Planta
Plant Physiol. 2005 138: 330-340. First Published on April 1, 2005; 10.1104/pp.104.058628 [Abstract] [Full Text] [PDF]  

Se-Jun Oh, Sang Ik Song, Youn Shic Kim, Hyun-Jun Jang, Soo Young Kim, Minjeong Kim, Yeon-Ki Kim, Baek Hie Nahm, and Ju-Kon Kim

Arabidopsis CBF3/DREB1A and ABF3 in Transgenic Rice Increased Tolerance to Abiotic Stress without Stunting Growth
Plant Physiol. 2005 138: 341-351. First Published on April 15, 2005; 10.1104/pp.104.059147 [Abstract] [Full Text] [PDF] [Supplemental Data]  

Gui-Lan Duan, Yong-Guan Zhu, Yi-Ping Tong, Chao Cai, and Ralf Kneer

Characterization of Arsenate Reductase in the Extract of Roots and Fronds of Chinese Brake Fern, an Arsenic Hyperaccumulator
Plant Physiol. 2005 138: 461-469. First Published on April 15, 2005; 10.1104/pp.104.057422 [Abstract] [Full Text] [PDF]  

Roland Schröder, Manfred Forstreuter, and Monika Hilker

A Plant Notices Insect Egg Deposition and Changes Its Rate of Photosynthesis
Plant Physiol. 2005 138: 470-477. First Published on April 8, 2005; 10.1104/pp.105.059915 [Abstract] [Full Text] [PDF]  

GENETICS, GENOMICS, AND MOLECULAR EVOLUTION:

Ron A. Salzman, Jeff A. Brady, Scott A. Finlayson, Christina D. Buchanan, Elizabeth J. Summer, Feng Sun, Patricia E. Klein, Robert R. Klein, Lee H. Pratt, Marie-Michèle Cordonnier-Pratt, and John E. Mullet

Transcriptional Profiling of Sorghum Induced by Methyl Jasmonate, Salicylic Acid, and Aminocyclopropane Carboxylic Acid Reveals Cooperative Regulation and Novel Gene Responses
Plant Physiol. 2005 138: 352-368. First Published on April 29, 2005; 10.1104/pp.104.058206 [Abstract] [Full Text] [PDF] [Supplemental Data][Supplemental Data]  

Yukihiro Kabeya and Naoki Sato

Unique Translation Initiation at the Second AUG Codon Determines Mitochondrial Localization of the Phage-Type RNA Polymerases in the Moss Physcomitrella patens
Plant Physiol. 2005 138: 369-382. First Published on April 15, 2005; 10.1104/pp.105.059501 [Abstract] [Full Text] [PDF]  

Stefan Hoth, Alexander Schneidereit, Christian Lauterbach, Joachim Scholz-Starke, and Norbert Sauer

Nematode Infection Triggers the de Novo Formation of Unloading Phloem That Allows Macromolecular Trafficking of Green Fluorescent Protein into Syncytia
Plant Physiol. 2005 138: 383-392. First Published on April 22, 2005; 10.1104/pp.104.058800 [Abstract] [Full Text] [PDF]  

Monica Sturaro, Hans Hartings, Elmon Schmelzer, Riccardo Velasco, Francesco Salamini, and Mario Motto

Cloning and Characterization of GLOSSY1, a Maize Gene Involved in Cuticle Membrane and Wax Production
Plant Physiol. 2005 138: 478-489. First Published on April 22, 2005; 10.1104/pp.104.058164 [Abstract] [Full Text] [PDF] [Supplemental Data]  

Martin Lohr, Chung-Soon Im, and Arthur R. Grossman

Genome-Based Examination of Chlorophyll and Carotenoid Biosynthesis in Chlamydomonas reinhardtii
Plant Physiol. 2005 138: 490-515. First Published on April 22, 2005; 10.1104/pp.104.056069 [Abstract] [Full Text] [PDF] [Supplemental Data]  

PLANTS INTERACTING WITH OTHER ORGANISMS:

Christine K.Y. Yu, Karin Springob, Jürgen Schmidt, Ralph L. Nicholson, Ivan K. Chu, Wing Kin Yip, and Clive Lo

A Stilbene Synthase Gene (SbSTS1) Is Involved in Host and Nonhost Defense Responses in Sorghum
Plant Physiol. 2005 138: 393-401. First Published on April 8, 2005; 10.1104/pp.105.059337 [Abstract] [Full Text] [PDF]  

Belinda J. Townsend, Andrew Poole, Christopher J. Blake, and Danny J. Llewellyn

Antisense Suppression of a (+)--Cadinene Synthase Gene in Cotton Prevents the Induction of This Defense Response Gene during Bacterial Blight Infection But Not Its Constitutive Expression
Plant Physiol. 2005 138: 516-528. First Published on April 22, 2005; 10.1104/pp.104.056010 [Abstract] [Full Text] [PDF] [Supplemental Data]  

Frederic Aparicio, Carole L. Thomas, Carsten Lederer, Yan Niu, Daowen Wang, and Andrew J. Maule

Virus Induction of Heat Shock Protein 70 Reflects a General Response to Protein Accumulation in the Plant Cytosol
Plant Physiol. 2005 138: 529-536. First Published on April 1, 2005; 10.1104/pp.104.058958 [Abstract] [Full Text] [PDF]  

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