| | This journal provides immediate access to some articles. Commentaries Photosynthate allocations in rice plants: Food production or atmospheric methane? Ronald L. Sass and Ralph J. Cicerone PMCID: PMC129384 The genomics of symbiosis: Hosts keep the baby and the bath water Brian Palenik PMCID: PMC129385 Type IA DNA topoisomerases: Strictly one step at a time James J. Champoux PMCID: PMC129386 Physical Sciences Applied Physical Sciences Trojan particles: Large porous carriers of nanoparticles for drug delivery N. Tsapis, D. Bennett, B. Jackson, D. A. Weitz, and D. A. Edwards PMCID: PMC129387 Friction traced to the single atom Franz J. Giessibl, Markus Herz, and Jochen Mannhart PMCID: PMC129388 Geology Rapid atmospheric CO2 changes associated with the 8,200-years-B.P. cooling event Friederike Wagner, Bent Aaby, and Henk Visscher PMCID: PMC129389 Physics Physical constraints and functional characteristics of transcription factor–DNA interaction Ulrich Gerland, J. David Moroz, and Terence Hwa PMCID: PMC129390 Biological Sciences Agricultural Sciences From the Cover:
Optimizing grain yields reduces CH4 emissions from rice paddy fields H. A. C. Denier van der Gon, M. J. Kropff, N. van Breemen, R. Wassmann, R. S. Lantin, E. Aduna, T. M. Corton, and H. H. van Laar PMCID: PMC129391 From the Cover:
The mechanism of type IA topoisomerases N. H. Dekker, V. V. Rybenkov, M. Duguet, N. J. Crisona, N. R. Cozzarelli, D. Bensimon, and V. Croquette PMCID: PMC129409 Applied Biological Sciences Engineering growing tissues Eben Alsberg, Kenneth W. Anderson, Amru Albeiruti, Jon A. Rowley, and David J. Mooney PMCID: PMC129392 Biochemistry The ribosome filter hypothesis Vincent P. Mauro and Gerald M. Edelman PMCID: PMC129393 Crystal structure of calcineurin–cyclophilin–cyclosporin shows common but distinct recognition of immunophilin–drug complexes Qing Huai, Hwa-Young Kim, Yudong Liu, Yingdong Zhao, Angelo Mondragon, Jun O. Liu, and Hengming Ke PMCID: PMC129394 Crosslinking of membrane-embedded cysteines reveals contact points in the EmrE oligomer Misha Soskine, Sonia Steiner-Mordoch, and Shimon Schuldiner PMCID: PMC129395 Gβγ-independent constitutive association of Gαs with SHP-1 and angiotensin II receptor AT2 is essential in AT2-mediated ITIM-independent activation of SHP-1 Ying-Hong Feng, Yan Sun, and Janice G. Douglas PMCID: PMC129396 The binding protein of corticotropin-releasing factor: Ligand-binding site and subunit structure Olaf Jahn, Klaus Eckart, Olaf Brauns, Hossein Tezval, and Joachim Spiess PMCID: PMC129397 Inhibition of hypochlorous acid-induced cellular toxicity by nitrite Matthew Whiteman, D. Craig Hooper, Gwen S. Scott, Hilary Koprowski, and Barry Halliwell PMCID: PMC129398 Convergent evolution sheds light on the anti-β-elimination mechanism common to family 1 and 10 polysaccharide lyases Simon J. Charnock, Ian E. Brown, Johan P. Turkenburg, Gary W. Black, and Gideon J. Davies PMCID: PMC129399 Molecular cloning and functional expression of the first insect FMRFamide receptor Giuseppe Cazzamali and Cornelis J. P. Grimmelikhuijzen PMCID: PMC129400 Cytoplasmic poly(A) polymerases mediate cellular responses to S phase arrest Rebecca L. Read, Rui G. Martinho, Shao-Win Wang, Antony M. Carr, and Chris J. Norbury PMCID: PMC129401 The semaphorin receptor plexin-B1 signals through a direct interaction with the Rho-specific nucleotide exchange factor, LARG Jennifer Aurandt, Haris G. Vikis, J. Silvio Gutkind, Natalie Ahn, and Kun-Liang Guan PMCID: PMC129402 RecX protein abrogates ATP hydrolysis and strand exchange promoted by RecA: Insights into negative regulation of homologous recombination R. Venkatesh, N. Ganesh, N. Guhan, M. Sreedhar Reddy, T. Chandrasekhar, and K. Muniyappa PMCID: PMC129403 Revisiting the kinetics of nitric oxide (NO) binding to soluble guanylate cyclase: The simple NO-binding model is incorrect David P. Ballou, Yunde Zhao, Philip E. Brandish, and Michael A. Marletta PMCID: PMC129404 8-Oxoguanine rearranges the active site of human topoisomerase I Diem-Thu Thieu Lesher, Yves Pommier, Lance Stewart, and Matthew R. Redinbo PMCID: PMC129405 Biosynthesis of terpenes: Studies on 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase Petra Adam, Stefan Hecht, Wolfgang Eisenreich, Johannes Kaiser, Tobias Gräwert, Duilio Arigoni, Adelbert Bacher, and Felix Rohdich PMCID: PMC129406 Dual localization of human DNA topoisomerase IIIα to mitochondria and nucleus Yong Wang, Yi Lisa Lyu, and James C. Wang PMCID: PMC129407 Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases Jürgen J. May, Nadine Kessler, Mohamed A. Marahiel, and Milton T. Stubbs PMCID: PMC129408 Biophysics Physical constraints and functional characteristics of transcription factor–DNA interaction Ulrich Gerland, J. David Moroz, and Terence Hwa PMCID: PMC129390 From the Cover:
The mechanism of type IA topoisomerases N. H. Dekker, V. V. Rybenkov, M. Duguet, N. J. Crisona, N. R. Cozzarelli, D. Bensimon, and V. Croquette PMCID: PMC129409 Application of charge density methods to a protein model compound: Calculation of Coulombic intermolecular interaction energies from the experimental charge density Xue Li, Guang Wu, Yuriy A. Abramov, Anatoliy V. Volkov, and Philip Coppens PMCID: PMC129410 The structural basis for the transition from Ras-GTP to Ras-GDP Brian E. Hall, Dafna Bar-Sagi, and Nicolas Nassar PMCID: PMC129411 A simple method for probing the mechanical unfolding pathway of proteins in detail Robert B. Best, Susan B. Fowler, José L. Toca-Herrera, and Jane Clarke PMCID: PMC129412 Protein assembly and heat stability in developing thylakoid membranes during greening Zoltán Kóta, László I. Horváth, Magdolna Droppa, Gábor Horváth, Tibor Farkas, and Tibor Páli PMCID: PMC129413 The skeletal muscle Ca2+ release channel has an oxidoreductase-like domain Matthew L. Baker, Irina I. Serysheva, Serap Sencer, Yili Wu, Steven J. Ludtke, Wen Jiang, Susan L. Hamilton, and Wah Chiu PMCID: PMC129414 A protease assay for two-photon crosscorrelation and FRET analysis based solely on fluorescent proteins Tobias Kohl, Katrin G. Heinze, Rene Kuhlemann, Andre Koltermann, and Petra Schwille PMCID: PMC129415 M-FISH analysis shows that complex chromosome aberrations induced by α-particle tracks are cumulative products of localized rearrangements Rhona M. Anderson, David L. Stevens, and Dudley T. Goodhead PMCID: PMC129416 Cytochrome c folding pathway: Kinetic native-state hydrogen exchange Linh Hoang, Sabrina Bédard, Mallela M. G. Krishna, Yan Lin, and S. Walter Englander PMCID: PMC129417 Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study Danilo Roccatano, Giorgio Colombo, Marco Fioroni, and Alan E. Mark PMCID: PMC129418 Cell Biology Singularity in budding: A role for the evolutionarily conserved small GTPase Cdc42p Juliane P. Caviston, Serguei E. Tcheperegine, and Erfei Bi PMCID: PMC129419 Cbl-directed monoubiquitination of CIN85 is involved in regulation of ligand-induced degradation of EGF receptors Kaisa Haglund, Noriaki Shimokawa, Iwona Szymkiewicz, and Ivan Dikic PMCID: PMC129420 Inhibition of amyloid-β aggregation and caspase-3 activation by the Ginkgo biloba extract EGb761 Yuan Luo, Julie V. Smith, Vijaykumar Paramasivam, Adam Burdick, Kenneth J. Curry, Justin P. Buford, Ikhlas Khan, William J. Netzer, Huaxi Xu, and Peter Butko PMCID: PMC129421 Purification and electron microscopic visualization of functional human spliceosomes Zhaolan Zhou, Jeonggu Sim, Jack Griffith, and Robin Reed PMCID: PMC129422 A conserved mechanism for extracellular signaling in eukaryotes and prokaryotes Marco Gallio, Gwen Sturgill, Philip Rather, and Per Kylsten PMCID: PMC129423 Nitrogen monoxide-mediated control of ferritin synthesis: Implications for macrophage iron homeostasis Sangwon Kim and Prem Ponka PMCID: PMC129424 Mutagenesis and repair by low doses of α radiation in mammalian cells Theodore T. Puck, Robert Johnson, Patricia Webb, Helen Cui, Joseph G. Valdez, and Harry Crissman PMCID: PMC129425 The antiangiogenic activity of cleaved high molecular weight kininogen is mediated through binding to endothelial cell tropomyosin Jing-Chuan Zhang, Fernando Doñate, Xiaoping Qi, Nicholas P. Ziats, Jose C. Juarez, Andrew P. Mazar, Yuan-Ping Pang, and Keith R. McCrae PMCID: PMC129426 Developmental Biology Multiple thyroid hormone-induced muscle growth and death programs during metamorphosis in Xenopus laevis Biswajit Das, Alexander M. Schreiber, Haochu Huang, and Donald D. Brown PMCID: PMC129427 Experimental control of pancreatic development and maintenance Andrew M. Holland, Michael A. Hale, Hideaki Kagami, Robert E. Hammer, and Raymond J. MacDonald PMCID: PMC129428 Evolution Directional selection is the primary cause of phenotypic diversification Loren H. Rieseberg, Alex Widmer, A. Michele Arntz, and John M. Burke PMCID: PMC129429 From the Cover:
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus William Martin, Tamas Rujan, Erik Richly, Andrea Hansen, Sabine Cornelsen, Thomas Lins, Dario Leister, Bettina Stoebe, Masami Hasegawa, and David Penny PMCID: PMC129430 From the Cover:
Evidence for van der Waals adhesion in gecko setae Kellar Autumn, Metin Sitti, Yiching A. Liang, Anne M. Peattie, Wendy R. Hansen, Simon Sponberg, Thomas W. Kenny, Ronald Fearing, Jacob N. Israelachvili, and Robert J. Full PMCID: PMC129431 Type III secretion systems and the evolution of mutualistic endosymbiosis Colin Dale, Gordon R. Plague, Ben Wang, Howard Ochman, and Nancy A. Moran PMCID: PMC129456 Genetics Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags Jianjun Chen, Miao Sun, Sanggyu Lee, Guolin Zhou, Janet D. Rowley, and San Ming Wang PMCID: PMC129432 A functional polymorphism in the promoter of the progesterone receptor gene associated with endometrial cancer risk Immaculata De Vivo, Gordon S. Huggins, Susan E. Hankinson, Pamela J. Lescault, Marike Boezen, Graham A. Colditz, and David J. Hunter PMCID: PMC129433 MYO18B, a candidate tumor suppressor gene at chromosome 22q12.1, deleted, mutated, and methylated in human lung cancer Michiho Nishioka, Takashi Kohno, Masachika Tani, Nozomu Yanaihara, Yoshio Tomizawa, Ayaka Otsuka, Shigeru Sasaki, Keiko Kobayashi, Toshiro Niki, Arafumi Maeshima, Yoshitaka Sekido, John D. Minna, Saburo Sone, and Jun Yokota PMCID: PMC129434 Immunology Identification of a human telomerase reverse transcriptase peptide of low affinity for HLA A2.1 that induces cytotoxic T lymphocytes and mediates lysis of tumor cells Javier Hernández, Francisco García-Pons, Yu Chun Lone, Huseyin Firat, Joseph D. Schmidt, Pierre Langlade-Demoyen, and Maurizio Zanetti PMCID: PMC129435 STAT4 serine phosphorylation is critical for IL-12-induced IFN-γ production but not for cell proliferation Akio Morinobu, Massimo Gadina, Warren Strober, Roberta Visconti, Albert Fornace, Cristina Montagna, Gerald M. Feldman, Ryuta Nishikomori, and John J. O'Shea PMCID: PMC129436 Tumor necrosis factor-α regulation of CD4+C25+ T cell levels in NOD mice Ava J. Wu, Hong Hua, Sibyl H. Munson, and Hugh O. McDevitt PMCID: PMC129437 Involvement of PD-L1 on tumor cells in the escape from host immune system and tumor immunotherapy by PD-L1 blockade Yoshiko Iwai, Masayoshi Ishida, Yoshimasa Tanaka, Taku Okazaki, Tasuku Honjo, and Nagahiro Minato PMCID: PMC129438 Role of the C-terminal propeptide in the activity and maturation of γ-interferon-inducible lysosomal thiol reductase (GILT) Uyen T. Phan, Rebecca L. Lackman, and Peter Cresswell PMCID: PMC129439 Somatic hypermutation of the AID transgene in B and non-B cells Alberto Martin and Matthew D. Scharff PMCID: PMC129440 Regulation of V(D)J recombination: A dominant role for promoter positioning in gene segment accessibility Michael L. Sikes, Amber Meade, Rajkamal Tripathi, Michael S. Krangel, and Eugene M. Oltz PMCID: PMC129441 Medical Sciences Ubiquitination of inducible nitric oxide synthase is required for its degradation Pawel J. Kolodziejski, Aleksandra Musial, Ja-Seok Koo, and N. Tony Eissa PMCID: PMC129442 Inhibition of Fe-S cluster biosynthesis decreases mitochondrial iron export: Evidence that Yfh1p affects Fe-S cluster synthesis Opal S. Chen, Shawn Hemenway, and Jerry Kaplan PMCID: PMC129443 Induction of cyclooxygenase-2 in a mouse model of Peutz–Jeghers polyposis Derrick J. Rossi, Antti Ylikorkala, Nina Korsisaari, Reijo Salovaara, Keijo Luukko, Virpi Launonen, Mark Henkemeyer, Ari Ristimäki, Lauri A. Aaltonen, and Tomi P. Mäkelä PMCID: PMC129444 Akt induces enhanced myocardial contractility and cell size in vivo in transgenic mice Gianluigi Condorelli, Alessandra Drusco, Giorgio Stassi, Alfonso Bellacosa, Roberta Roncarati, Guido Iaccarino, Matteo A. Russo, Yusu Gu, Nancy Dalton, Clarence Chung, Michael V. G. Latronico, Claudio Napoli, Junichi Sadoshima, Carlo M. Croce, and John Ross, Jr. PMCID: PMC129445 Bcrp1 gene expression is required for normal numbers of side population stem cells in mice, and confers relative protection to mitoxantrone in hematopoietic cells in vivo Sheng Zhou, John J. Morris, Yuxiao Barnes, Lubin Lan, John D. Schuetz, and Brian P. Sorrentino PMCID: PMC129446 Previously uncharacterized isoforms of divalent metal transporter (DMT)-1: Implications for regulation and cellular function Nadia Hubert and Matthias W. Hentze PMCID: PMC129447 Ethyl pyruvate prevents lethality in mice with established lethal sepsis and systemic inflammation Luis Ulloa, Mahendar Ochani, Huan Yang, Mahira Tanovic, Daniel Halperin, Runkuan Yang, Christopher J. Czura, Mitchell P. Fink, and Kevin J. Tracey PMCID: PMC129448 Integrated classification of lung tumors and cell lines by expression profiling Carl Virtanen, Yuichi Ishikawa, Daisuke Honjoh, Mami Kimura, Miyuki Shimane, Tatsu Miyoshi, Hitoshi Nomura, and Michael H. Jones PMCID: PMC129449 A role for glutathione peroxidase in protecting pancreatic β cells against oxidative stress in a model of glucose toxicity Yoshito Tanaka, Phuong Oanh T. Tran, Jamie Harmon, and R. Paul Robertson PMCID: PMC129450 Microbiology A global pH sensor: Agrobacterium sensor protein ChvG regulates acid-inducible genes on its two chromosomes and Ti plasmid Luoping Li, Yonghui Jia, Qingming Hou, Trevor C. Charles, Eugene W. Nester, and Shen Q. Pan PMCID: PMC129451 The two-component system BvrR/BvrS essential for Brucella abortus virulence regulates the expression of outer membrane proteins with counterparts in members of the Rhizobiaceae C. Guzmán-Verri, L. Manterola, A. Sola-Landa, A. Parra, A. Cloeckaert, J. Garin, J.-P. Gorvel, I. Moriyón, E. Moreno, and I. López-Goñi PMCID: PMC129452 A p5 integration efficiency element mediates Rep-dependent integration into AAVS1 at chromosome 19 Nicola J. Philpott, Janette Gomos, Kenneth I. Berns, and Erik Falck-Pedersen PMCID: PMC129453 Mouse transferrin receptor 1 is the cell entry receptor for mouse mammary tumor virus Susan R. Ross, Jason J. Schofield, Christine J. Farr, and Maja Bucan PMCID: PMC129454 Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae Hervé Tettelin, Vega Masignani, Michael J. Cieslewicz, Jonathan A. Eisen, Scott Peterson, Michael R. Wessels, Ian T. Paulsen, Karen E. Nelson, Immaculada Margarit, Timothy D. Read, Lawrence C. Madoff, Alex M. Wolf, Maureen J. Beanan, Lauren M. Brinkac, Sean C. Daugherty, Robert T. DeBoy, A. Scott Durkin, James F. Kolonay, Ramana Madupu, Matthew R. Lewis, Diana Radune, Nadezhda B. Fedorova, David Scanlan, Hoda Khouri, Stephanie Mulligan, Heather A. Carty, Robin T. Cline, Susan E. Van Aken, John Gill, Maria Scarselli, Marirosa Mora, Emilia T. Iacobini, Cecilia Brettoni, Giuliano Galli, Massimo Mariani, Filippo Vegni, Domenico Maione, Daniela Rinaudo, Rino Rappuoli, John L. Telford, Dennis L. Kasper, Guido Grandi, and Claire M. Fraser PMCID: PMC129455 Type III secretion systems and the evolution of mutualistic endosymbiosis Colin Dale, Gordon R. Plague, Ben Wang, Howard Ochman, and Nancy A. Moran PMCID: PMC129456 Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains Anamitra Bhattacharyya, Stephanie Stilwagen, Natalia Ivanova, Mark D'Souza, Axel Bernal, Athanasios Lykidis, Vinayak Kapatral, Iain Anderson, Niels Larsen, Tamara Los, Gary Reznik, Eugene Selkov, Jr., Theresa L. Walunas, Helene Feil, William S. Feil, Alexander Purcell, Jean-Louis Lassez, Trevor L. Hawkins, Robert Haselkorn, Ross Overbeek, Paul F. Predki, and Nikos C. Kyrpides PMCID: PMC129457 Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera-endemic areas of Bangladesh Young-Gun Zo, Irma N. G. Rivera, Estelle Russek-Cohen, M. Sirajul Islam, A. K. Siddique, M. Yunus, R. Bradley Sack, Anwar Huq, and Rita R. Colwell PMCID: PMC129458 Cloning the vaccinia virus genome as a bacterial artificial chromosome in Escherichia coli and recovery of infectious virus in mammalian cells Arban Domi and Bernard Moss PMCID: PMC129459 Neuroscience Act locally and think globally: Intracerebral testosterone implants induce seasonal-like growth of adult avian song control circuits Eliot A. Brenowitz and Karin Lent PMCID: PMC129460 Nerve growth factor controls GAP-43 mRNA stability via the phosphoprotein ARPP-19 Nina Irwin, Steven Chao, Luda Goritchenko, Atsuko Horiuchi, Paul Greengard, Angus C. Nairn, and Larry I. Benowitz PMCID: PMC129461 Nerve growth factor and galantamine ameliorate early signs of neurodegeneration in anti-nerve growth factor mice Simona Capsoni, Sabina Giannotta, and Antonino Cattaneo PMCID: PMC129462 Electrical and chemical synapses among parvalbumin fast-spiking GABAergic interneurons in adult mouse neocortex Mario Galarreta and Shaul Hestrin PMCID: PMC129463 Cortical representation of first and second pain sensation in humans Markus Ploner, Joachim Gross, Lars Timmermann, and Alfons Schnitzler PMCID: PMC129464 Serotonin mediates food-odor associative learning in the nematode Caenorhabditis elegans William M. Nuttley, Karen P. Atkinson-Leadbeater, and Derek van der Kooy PMCID: PMC129465 Pharmacology Topical applications of caffeine or (−)-epigallocatechin gallate (EGCG) inhibit carcinogenesis and selectively increase apoptosis in UVB-induced skin tumors in mice Yao-Ping Lu, You-Rong Lou, Jian-Guo Xie, Qing-Yun Peng, Jie Liao, Chung S. Yang, Mou-Tuan Huang, and Allan H. Conney PMCID: PMC129466 Position of aromatic residues in the S6 domain, not inactivation, dictates cisapride sensitivity of HERG and eag potassium channels Jun Chen, Guiscard Seebohm, and Michael C. Sanguinetti PMCID: PMC129467 Chronic treatment with nitric oxide-releasing aspirin reduces plasma low-density lipoprotein oxidation and oxidative stress, arterial oxidation-specific epitopes, and atherogenesis in hypercholesterolemic mice Claudio Napoli, Eric Ackah, Filomena de Nigris, Piero Del Soldato, Francesco P. D'Armiento, Ettore Crimi, Mario Condorelli, and William C. Sessa PMCID: PMC129468 Heterozygous α2A-adrenergic receptor mice unveil unique therapeutic benefits of partial agonists Christopher M. Tan, Matthew H. Wilson, Leigh B. MacMillan, Brian K. Kobilka, and Lee E. Limbird PMCID: PMC129469 Physiology CFTR chloride channels are regulated by a SNAP-23/syntaxin 1A complex Estelle Cormet-Boyaka, Anke Di, Steven Y. Chang, Anjaparavanda P. Naren, Albert Tousson, Deborah J. Nelson, and Kevin L. Kirk PMCID: PMC129470 Transgenic cyclooxygenase-2 overexpression sensitizes mouse skin for carcinogenesis Karin Müller-Decker, Gitta Neufang, Irina Berger, Melanie Neumann, Friedrich Marks, and Gerhard Fürstenberger PMCID: PMC129471 Plant Biology Folate synthesis in plants: The first step of the pterin branch is mediated by a unique bimodular GTP cyclohydrolase I Gilles Basset, Eoin P. Quinlivan, Michael J. Ziemak, Rocío Díaz de la Garza, Markus Fischer, Susi Schiffmann, Adelbert Bacher, Jesse F. Gregory, III, and Andrew D. Hanson PMCID: PMC129472 Isolation of an Arabidopsis mutant lacking vitamin E and identification of a cyclase essential for all tocopherol biosynthesis Svetlana Porfirova, Eveline Bergmüller, Susanne Tropf, Rainer Lemke, and Peter Dörmann PMCID: PMC129473 Corrections Proc Natl Acad Sci U S A. 2002 September 17; 99(19): 12501. Published online 2002 September 11. doi: 10.1073/pnas.192453899.PMCID: PMC129382 Corrects: Sanaz Memarzadeh, et al. Urokinase plasminogen activator receptor: Prognostic biomarker for endometrial cancer. Proc Natl Acad Sci U S A. 2002 August 6; 99(16): 10647–10652. Proc Natl Acad Sci U S A. 2002 September 17; 99(19): 12501. Published online 2002 September 11. doi: 10.1073/pnas.192372099.PMCID: PMC129383 Corrects: Kathleen M. I. Caron, et al. A genetically clamped renin transgene for the induction of hypertension. Proc Natl Acad Sci U S A. 2002 June 11; 99(12): 8248–8252. |
