| | This journal provides immediate access to some articles. In This Issue Proc Natl Acad Sci U S A. 2005 February 15; 102(7): 2261. doi: 10.1073/iti0705102.PMCID: PMC549023 Commentaries Nanoscience enables ultrasensitive detection of Alzheimer's biomarker Christine D. Keating PMCID: PMC549005 Putting the pathway back into protein folding Jeffrey Skolnick PMCID: PMC549015 Animal awareness: The (un)binding of multisensory cues in decision making by animals Ron Hoy PMCID: PMC549007 Tracking down noncoding RNAs Vincent Moulton PMCID: PMC549017 Watching language grow Susan Goldin-Meadow PMCID: PMC549019 Physical Sciences Applied Physical Sciences From the Cover:
Nanoparticle-based detection in cerebral spinal fluid of a soluble pathogenic biomarker for Alzheimer's disease Dimitra G. Georganopoulou, Lei Chang, Jwa-Min Nam, C. Shad Thaxton, Elliott J. Mufson, William L. Klein, and Chad A. Mirkin PMCID: PMC548981 Bacterial swimming and oxygen transport near contact lines Idan Tuval, Luis Cisneros, Christopher Dombrowski, Charles W. Wolgemuth, John O. Kessler, and Raymond E. Goldstein PMCID: PMC548973 From the Cover:
Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem John R. Spear, Jeffrey J. Walker, Thomas M. McCollom, and Norman R. Pace PMCID: PMC548998 Chemistry Kinetics are probe-dependent during downhill folding of an engineered λ6–85 protein Hairong Ma and Martin Gruebele PMCID: PMC548978 Protein recognition of macrocycles: Binding of anti-HIV metallocyclams to lysozyme Tina M. Hunter, Iain W. McNae, Xiangyang Liang, Juraj Bella, Simon Parsons, Malcolm D. Walkinshaw, and Peter J. Sadler PMCID: PMC548988 Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations Michael Samoilov, Sergey Plyasunov, and Adam P. Arkin PMCID: PMC548975 Computer Sciences From the Cover:
Fast and reliable prediction of noncoding RNAs Stefan Washietl, Ivo L. Hofacker, and Peter F. Stadler PMCID: PMC548974 Engineering Speech recognition with amplitude and frequency modulations Fan-Gang Zeng, Kaibao Nie, Ginger S. Stickney, Ying-Yee Kong, Michael Vongphoe, Ashish Bhargave, Chaogang Wei, and Keli Cao PMCID: PMC546014 Physics Experimental measurement of an effective temperature for jammed granular materials Chaoming Song, Ping Wang, and Hernán A. Makse PMCID: PMC549002 Biological Sciences Biochemistry Consolidating critical binding determinants by noncyclic rearrangement of protein secondary structure Ramon K. Tabtiang, Brent O. Cezairliyan, Robert A. Grant, Jesse C. Cochrane, and Robert T. Sauer PMCID: PMC548995 Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations Michael Samoilov, Sergey Plyasunov, and Adam P. Arkin PMCID: PMC548975 A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation Thomas R. Sundermeier, Daniel P. Dulebohn, Hye Jin Cho, and A. Wali Karzai PMCID: PMC549014 Molecular cloning and characterization of murine caspase-12 gene promoter Hammou Oubrahim, Jun Wang, Earl R. Stadtman, and P. Boon Chock PMCID: PMC548331 Suppressor of cytokine signaling (SOCS)-5 is a potential negative regulator of epidermal growth factor signaling Sandra E. Nicholson, Donald Metcalf, Naomi S. Sprigg, Ruth Columbus, Francesca Walker, Anabel Silva, Dale Cary, Tracy A. Willson, Jian-Guo Zhang, Douglas J. Hilton, Warren S. Alexander, and Nicos A. Nicola PMCID: PMC549009 Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, γ-ear-containing, ADP-ribosylation-factor-binding proteins Gali Prag, Sangho Lee, Rafael Mattera, Cecilia N. Arighi, Bridgette M. Beach, Juan S. Bonifacino, and James H. Hurley PMCID: PMC549010 Nitrolinoleic acid: An endogenous peroxisome proliferator-activated receptor γ ligand Francisco J. Schopfer, Yiming Lin, Paul R. S. Baker, Taixing Cui, Minerva Garcia-Barrio, Jifeng Zhang, Kai Chen, Yuqing E. Chen, and Bruce A. Freeman PMCID: PMC548962 Transcriptional activating regions target attached substrates to a cyclin-dependent kinase Aseem Z. Ansari, Anuja Ogirala, and Mark Ptashne PMCID: PMC549008 Phosphorylation at Thr-290 regulates Tpl2 binding to NF-κB1/p105 and Tpl2 activation and degradation by lipopolysaccharide Jeonghee Cho and Philip N. Tsichlis PMCID: PMC548980 A universal plasmid library encoding all permutations of small interfering RNA Meihong Chen, Lishu Zhang, Hong-Yan Zhang, Xiahui Xiong, Bo Wang, Quan Du, Bing Lu, Claes Wahlestedt, and Zicai Liang PMCID: PMC548965 Biophysics Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains Adam Liwo, Mey Khalili, and Harold A. Scheraga PMCID: PMC548970 Stretched exponential decay and correlations in the catalytic activity of fluctuating single lipase molecules Ophir Flomenbom, Kelly Velonia, Davey Loos, Sadahiro Masuo, Mircea Cotlet, Yves Engelborghs, Johan Hofkens, Alan E. Rowan, Roeland J. M. Nolte, Mark Van der Auweraer, Frans C. de Schryver, and Joseph Klafter PMCID: PMC548972 Symmetry and frustration in protein energy landscapes: A near degeneracy resolves the Rop dimer-folding mystery Yaakov Levy, Samuel S. Cho, Tongye Shen, José N. Onuchic, and Peter G. Wolynes PMCID: PMC548997 α-Helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy Jens Bredenbeck, Jan Helbing, Janet R. Kumita, G. Andrew Woolley, and Peter Hamm PMCID: PMC548979 The kinetics of conformational fluctuations in an unfolded protein measured by fluorescence methods Krishnananda Chattopadhyay, Elliot L. Elson, and Carl Frieden PMCID: PMC549012 Force mapping in epithelial cell migration Olivia du Roure, Alexandre Saez, Axel Buguin, Robert H. Austin, Philippe Chavrier, Pascal Siberzan, and Benoit Ladoux PMCID: PMC548966 Cell Biology RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells Ralf Kittler, Laurence Pelletier, Chunling Ma, Ina Poser, Steffi Fischer, Anthony A. Hyman, and Frank Buchholz PMCID: PMC548992 Assembly and regulation of a glycolytic enzyme complex on the human erythrocyte membrane M. Estela Campanella, Haiyan Chu, and Philip S. Low PMCID: PMC549020 Modeling variation in tumors in vivo James R. Stringer, Jon S. Larson, Jared M. Fischer, Mario Medvedovic, Megan N. Hersh, Gregory P. Boivin, and Saundra L. Stringer PMCID: PMC548963 Developmental Biology Transcriptional coactivator PGC-1α regulates chondrogenesis via association with Sox9 Yasuhiko Kawakami, Masanao Tsuda, Shigeru Takahashi, Noboru Taniguchi, Concepción Rodríguez Esteban, Michihisa Zemmyo, Takayuki Furumatsu, Martin Lotz, Juan Carlos Izpisúa Belmonte, and Hiroshi Asahara PMCID: PMC548985 The identification of Hoxc8 target genes Haiyan Lei, Hailong Wang, Aster H. Juan, and Frank H. Ruddle PMCID: PMC549016 Ecology From the Cover:
Cross-modal integration in a dart-poison frog Peter M. Narins, Daniela S. Grabul, Kiran K. Soma, Philippe Gaucher, and Walter Hödl PMCID: PMC548971 Evolution Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human Huai-Dong Song, Chang-Chun Tu, Guo-Wei Zhang, Sheng-Yue Wang, Kui Zheng, Lian-Cheng Lei, Qiu-Xia Chen, Yu-Wei Gao, Hui-Qiong Zhou, Hua Xiang, Hua-Jun Zheng, Shur-Wern Wang Chern, Feng Cheng, Chun-Ming Pan, Hua Xuan, Sai-Juan Chen, Hui-Ming Luo, Duan-Hua Zhou, Yu-Fei Liu, Jian-Feng He, Peng-Zhe Qin, Ling-Hui Li, Yu-Qi Ren, Wen-Jia Liang, Ye-Dong Yu, Larry Anderson, Ming Wang, Rui-Heng Xu, Xin-Wei Wu, Huan-Ying Zheng, Jin-Ding Chen, Guodong Liang, Yang Gao, Ming Liao, Ling Fang, Li-Yun Jiang, Hui Li, Fang Chen, Biao Di, Li-Juan He, Jin-Yan Lin, Suxiang Tong, Xiangang Kong, Lin Du, Pei Hao, Hua Tang, Andrea Bernini, Xiao-Jing Yu, Ottavia Spiga, Zong-Ming Guo, Hai-Yan Pan, Wei-Zhong He, Jean-Claude Manuguerra, Arnaud Fontanet, Antoine Danchin, Neri Niccolai, Yi-Xue Li, Chung-I Wu, and Guo-Ping Zhao PMCID: PMC548959 Characterization of MADS-box genes in charophycean green algae and its implication for the evolution of MADS-box genes Yoichi Tanabe, Mitsuyasu Hasebe, Hiroyuki Sekimoto, Tomoaki Nishiyama, Masakazu Kitani, Katrin Henschel, Thomas Münster, Günter Theissen, Hisayoshi Nozaki, and Motomi Ito PMCID: PMC548990 Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization Peter L. Morrell, Donna M. Toleno, Karen E. Lundy, and Michael T. Clegg PMCID: PMC549024 Genetics Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells Jiang F. Zhong, Yi Zhao, Susan Sutton, Andrew Su, Yuxia Zhan, Lunjian Zhu, Chunli Yan, Tim Gallaher, Patrick B. Johnston, W. French Anderson, and Michael P. Cooke PMCID: PMC548308 From the Cover:
Fast and reliable prediction of noncoding RNAs Stefan Washietl, Ivo L. Hofacker, and Peter F. Stadler PMCID: PMC548974 Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation Jonathan D. Werner, Justin O. Borevitz, Norman Warthmann, Gabriel T. Trainer, Joseph R. Ecker, Joanne Chory, and Detlef Weigel PMCID: PMC548991 Immunology Influence of switch region length on immunoglobulin class switch recombination Ali A. Zarrin, Ming Tian, Jing Wang, Tiffany Borjeson, and Frederick W. Alt PMCID: PMC548964 Artemis-independent functions of DNA-dependent protein kinase in Ig heavy chain class switch recombination and development Sean Rooney, Frederick W. Alt, JoAnn Sekiguchi, and John P. Manis PMCID: PMC548986 Using a baculovirus display library to identify MHC class I mimotopes Yibing Wang, Anatoyla Rubtsov, Ryan Heiser, Janice White, Frances Crawford, Philippa Marrack, and John W. Kappler PMCID: PMC548325 Two distinctive pathways for recruitment of naïve and primed IgM+ B cells to the gut lamina propria Keiichiro Suzuki, Bob Meek, Yasuko Doi, Tasuku Honjo, and Sidonia Fagarasan PMCID: PMC548994 Toll-like receptor 4 polymorphisms are associated with resistance to Legionnaires' disease Thomas R. Hawn, Annelies Verbon, Marta Janer, Lue Ping Zhao, Bruce Beutler, and Alan Aderem PMCID: PMC549026 Medical Sciences Estrogen contributes to the onset, persistence, and malignant progression of cervical cancer in a human papillomavirus-transgenic mouse model Tiffany Brake and Paul F. Lambert PMCID: PMC548999 Resistance to diet-induced obesity in mice globally overexpressing OGH/GPB5 Lynn E. Macdonald, Katherine E. Wortley, Lori C. Gowen, Keith D. Anderson, Jane D. Murray, William T. Poueymirou, Mary V. Simmons, Dianna Barber, David M. Valenzuela, Aris N. Economides, Stanley J. Wiegand, George D. Yancopoulos, Mark W. Sleeman, and Andrew J. Murphy PMCID: PMC548327 A Mendelian locus on chromosome 16 determines susceptibility to doxorubicin nephropathy in the mouse Zongyu Zheng, Kai M. Schmidt-Ott, Streamson Chua, Kirk A. Foster, Rachelle Z. Frankel, Paul Pavlidis, Jonathan Barasch, Vivette D. D'Agati, and Ali G. Gharavi PMCID: PMC549022 Increased efficiency of oligonucleotide-mediated gene repair through slowing replication fork progression Xue-Song Wu, Li Xin, Wen-Xuan Yin, Xi-Ying Shang, Lu Lu, Rory M. Watt, Kathryn S. E. Cheah, Jian-Dong Huang, De-Pei Liu, and Chih-Chuan Liang PMCID: PMC548982 Abnormal GABAA receptors from the human epileptic hippocampal subiculum microtransplanted to Xenopus oocytes Eleonora Palma, Gabriele Spinelli, Gregorio Torchia, A. Martinez-Torres, Davide Ragozzino, Ricardo Miledi, and Fabrizio Eusebi PMCID: PMC549013 Muscle regeneration in the prolonged absence of myostatin Kathryn R. Wagner, Xiaosong Liu, Xiaoli Chang, and Ronald E. Allen PMCID: PMC548322 The R-enantiomer of the nonsteroidal antiinflammatory drug etodolac binds retinoid X receptor and induces tumor-selective apoptosis Siva Kumar Kolluri, Maripat Corr, Sharon Y. James, Michele Bernasconi, Desheng Lu, Wen Liu, Howard B. Cottam, Lorenzo M. Leoni, Dennis A. Carson, and Xiao-kun Zhang PMCID: PMC548323 Impaired vasodilation by red blood cells in sickle cell disease John R. Pawloski, Douglas T. Hess, and Jonathan S. Stamler PMCID: PMC548996 Acute leptin deficiency, leptin resistance, and the physiologic response to leptin withdrawal Jason M. Montez, Alex Soukas, Esra Asilmaz, Gulnorakhon Fayzikhodjaeva, Giamila Fantuzzi, and Jeffrey M. Friedman PMCID: PMC548993 Identification of pathway-selective estrogen receptor ligands that inhibit NF-κB transcriptional activity Christopher C. Chadwick, Susan Chippari, Edward Matelan, Lisa Borges-Marcucci, Amy M. Eckert, James C. Keith, Jr., Leo M. Albert, Yelena Leathurby, Heather A. Harris, Ramesh A. Bhat, Mark Ashwell, Eugene Trybulski, Richard C. Winneker, Steven J. Adelman, Robert J. Steffan, and Douglas C. Harnish PMCID: PMC548967 Microbiology A high-throughput, near-saturating screen for type III effector genes from Pseudomonas syringae Jeff H. Chang, Jonathan M. Urbach, Terry F. Law, Larry W. Arnold, An Hu, Saurabh Gombar, Sarah R. Grant, Frederick M. Ausubel, and Jeffery L. Dangl PMCID: PMC549004 From the Cover:
Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem John R. Spear, Jeffrey J. Walker, Thomas M. McCollom, and Norman R. Pace PMCID: PMC548998 Hepatitis C virus RNA replication is regulated by host geranylgeranylation and fatty acids Sharookh B. Kapadia and Francis V. Chisari PMCID: PMC549027 Genomic insights that advance the species definition for prokaryotes Konstantinos T. Konstantinidis and James M. Tiedje PMCID: PMC549018 Profiling early infection responses: Pseudomonas aeruginosa eludes host defenses by suppressing antimicrobial peptide gene expression Yiorgos Apidianakis, Michael N. Mindrinos, Wenzhong Xiao, Gee W. Lau, Regina L. Baldini, Ronald W. Davis, and Laurence G. Rahme PMCID: PMC549001 An in vitro model of hepatitis C virion production Theo Heller, Satoru Saito, Jonathan Auerbach, Tarice Williams, Tzivia Rachel Moreen, Allison Jazwinski, Brian Cruz, Neha Jeurkar, Ronda Sapp, Guangxiang Luo, and T. Jake Liang PMCID: PMC549006 A baculovirus-encoded protein tyrosine phosphatase gene induces enhanced locomotory activity in a lepidopteran host Shizuo G. Kamita, Koukichi Nagasaka, Josie W. Chua, Toru Shimada, Kazuei Mita, Masahiko Kobayashi, Susumu Maeda, and Bruce D. Hammock PMCID: PMC548987 Neuroscience Speech recognition with amplitude and frequency modulations Fan-Gang Zeng, Kaibao Nie, Ginger S. Stickney, Ying-Yee Kong, Michael Vongphoe, Ashish Bhargave, Chaogang Wei, and Keli Cao PMCID: PMC546014 Effects of familial hemiplegic migraine type 1 mutations on neuronal P/Q-type Ca2+ channel activity and inhibitory synaptic transmission Yu-Qing Cao and Richard W. Tsien PMCID: PMC548328 Analysis of congenital hypomyelinating Egr2Lo/Lo nerves identifies Sox2 as an inhibitor of Schwann cell differentiation and myelination Nam Le, Rakesh Nagarajan, James Y. T. Wang, Toshiyuki Araki, Robert E. Schmidt, and Jeffrey Milbrandt PMCID: PMC548989 Disturbed Ca2+ signaling and apoptosis of medium spiny neurons in Huntington's disease Tie-Shan Tang, Elizabeth Slow, Vitalie Lupu, Irina G. Stavrovskaya, Mutsuyuki Sugimori, Rodolfo Llinás, Bruce S. Kristal, Michael R. Hayden, and Ilya Bezprozvanny PMCID: PMC548984 A noncanonical E-box enhancer drives mouse Period2 circadian oscillations in vivo Seung-Hee Yoo, Caroline H. Ko, Phillip L. Lowrey, Ethan D. Buhr, Eun-joo Song, Suhwan Chang, Ook Joon Yoo, Shin Yamazaki, Choogon Lee, and Joseph S. Takahashi PMCID: PMC548324 Proteolysis of SNARE proteins alters facilitation and depression in a specific way Samuel M. Young, Jr. PMCID: PMC549003 A soluble mouse brain splice variant of type 2α corticotropin-releasing factor (CRF) receptor binds ligands and modulates their activity Alon M. Chen, Marilyn H. Perrin, Michael R. DiGruccio, Joan M. Vaughan, Bhawanjit K. Brar, Carlos M. Arias, Kathy A. Lewis, Jean E. Rivier, Paul E. Sawchenko, and Wylie W. Vale PMCID: PMC549000 Remembering one year later: Role of the amygdala and the medial temporal lobe memory system in retrieving emotional memories Florin Dolcos, Kevin S. LaBar, and Roberto Cabeza PMCID: PMC548968 Pharmacology Rapid nitric oxide-mediated S-nitrosylation of estrogen receptor: Regulation of estrogen-dependent gene transcription Hermes J. Garbán, Diana C. Márquez-Garbán, Richard J. Pietras, and Louis J. Ignarro PMCID: PMC548976 Physiology Pituitary adenylate cyclase-activating polypeptide prevents the effects of ceramides on migration, neurite outgrowth, and cytoskeleton remodeling Anthony Falluel-Morel, David Vaudry, Nicolas Aubert, Ludovic Galas, Magalie Benard, Magali Basille, Marc Fontaine, Alain Fournier, Hubert Vaudry, and Bruno J. Gonzalez PMCID: PMC549011 Convergent signaling by acidosis and receptor activator of NF-κB ligand (RANKL) on the calcium/calcineurin/NFAT pathway in osteoclasts Svetlana V. Komarova, Alexey Pereverzev, Jonathan W. Shum, Stephen M. Sims, and S. Jeffrey Dixon PMCID: PMC548977 Plant Biology A plasma membrane H+-ATPase is required for the formation of proanthocyanidins in the seed coat endothelium of Arabidopsis thaliana Ivan R. Baxter, Jeffery C. Young, Gordon Armstrong, Nathan Foster, Naomi Bogenschutz, Tatiana Cordova, Wendy Ann Peer, Samuel P. Hazen, Angus S. Murphy, and Jeffrey F. Harper PMCID: PMC548969 Lipopolysaccharides as a communication signal for progression of legume endosymbiosis René Mathis, Frédérique Van Gijsegem, Riet De Rycke, Wim D'Haeze, Els Van Maelsaeke, Erin Anthonio, Marc Van Montagu, Marcelle Holsters, and Danny Vereecke PMCID: PMC549025 Social Sciences Anthropology From the Cover:
The emergence of grammar: Systematic structure in a new language Wendy Sandler, Irit Meir, Carol Padden, and Mark Aronoff PMCID: PMC548320 Social Sciences Indirect reciprocity, image scoring, and moral hazard Hannelore Brandt and Karl Sigmund PMCID: PMC548983 Correction Proc Natl Acad Sci U S A. 2005 February 15; 102(7): 2671. Published online 2005 February 1. doi: 10.1073/pnas.0500257102.PMCID: PMC549021 Corrects: Eva Syková, et al. Changes in extracellular space size and geometry in APP23 transgenic mice: A model of Alzheimer's disease. Proc Natl Acad Sci U S A. 2005 January 11; 102(2): 479–484. |
