| | This journal provides immediate access to some articles. Letters Predicting the unpredictable real-world impact of ARV-based microbicides Lori Heise and Sean Philpott PMCID: PMC2597148 Reply to Heise and Philpott: The paradoxical effects of using antiretroviral-based microbicides to control HIV epidemics Sally Blower, D. P. Wilson, P. M. Coplan, and M. A. Wainberg PMCID: PMC2579403 Do equilibrium clusters exist in concentrated lysozyme solutions? A. Stradner, F. Cardinaux, S. U. Egelhaaf, and P. Schurtenberger PMCID: PMC2597149 Reply to Stradner et al.: Equilibrium clusters are absent in concentrated lysozyme solutions Anuj Shukla, Efstratios Mylonas, Emanuela Di Cola, Stephanie Finet, Peter Timmins, Theyencheri Narayanan, and Dmitri I. Svergun PMCID: PMC2579404 Why elliptical stability diagrams are not related to protein conformational disorder Wolfgang Doster PMCID: PMC2579405 This Week in PNAS Proc Natl Acad Sci U S A. 2008 November 4; 105(44): 16823–16824. doi: 10.1073/iti4408105.PMCID: PMC2579335 Commentaries Protein denaturation by urea: Slash and bond Peter J. Rossky PMCID: PMC2579336 A new SPIN on horizontal transfer Damon Lisch PMCID: PMC2579337 Undoing cocaine's consequences on behavior and brain Barry Setlow PMCID: PMC2579338 Physical Sciences Chemistry From the Cover:
In vivo supramolecular templating enhances the activity of multivalent ligands: A potential therapeutic against the Escherichia coli O157 AB5 toxins Pavel I. Kitov, George L. Mulvey, Thomas P. Griener, Tomasz Lipinski, Dmitry Solomon, Eugenia Paszkiewicz, Jared M. Jacobson, Joanna M. Sadowska, Missao Suzuki, Ken-ichi Yamamura, Glen D. Armstrong, and David R. Bundle PMCID: PMC2573949 The chemistrode: A droplet-based microfluidic device for stimulation and recording with high temporal, spatial, and chemical resolution Delai Chen, Wenbin Du, Ying Liu, Weishan Liu, Andrey Kuznetsov, Felipe E. Mendez, Louis H. Philipson, and Rustem F. Ismagilov PMCID: PMC2579341 Structural selection of graphene supramolecular assembly oriented by molecular conformation and alkyl chain Qing Chen, Ting Chen, Ge-Bo Pan, Hui-Juan Yan, Wei-Guo Song, Li-Jun Wan, Zhong-Tao Li, Zhao-Hui Wang, Bo Shang, Lan-Feng Yuan, and Jin-Long Yang PMCID: PMC2579342 Direct transformation from amorphous to crystalline calcium phosphate facilitated by motif-programmed artificial proteins Toru Tsuji, Kazuo Onuma, Akira Yamamoto, Mayumi Iijima, and Kiyotaka Shiba PMCID: PMC2575226 From the Cover:
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding Lan Hua, Ruhong Zhou, D. Thirumalai, and B. J. Berne PMCID: PMC2579355 Environmental Sciences The effects of 3 environmental risks on mortality disparities across Mexican communities Gretchen A. Stevens, Rodrigo H. Dias, and Majid Ezzati PMCID: PMC2579343 Geology A framework for predicting global silicate weathering and CO2 drawdown rates over geologic time-scales George E. Hilley and Stephen Porder PMCID: PMC2572559 Biological Sciences Biochemistry Direct transformation from amorphous to crystalline calcium phosphate facilitated by motif-programmed artificial proteins Toru Tsuji, Kazuo Onuma, Akira Yamamoto, Mayumi Iijima, and Kiyotaka Shiba PMCID: PMC2575226 Differential effects of central fructose and glucose on hypothalamic malonyl–CoA and food intake Seung Hun Cha, Michael Wolfgang, Yuka Tokutake, Shigeru Chohnan, and M. Daniel Lane PMCID: PMC2579345 Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization Frédéric Kerff, Ana Amoroso, Raphaël Herman, Eric Sauvage, Stéphanie Petrella, Patrice Filée, Paulette Charlier, Bernard Joris, Akira Tabuchi, Nikolas Nikolaidis, and Daniel J. Cosgrove PMCID: PMC2579346 Visualizing myosin–actin interaction with a genetically-encoded fluorescent strain sensor Sosuke Iwai and Taro Q. P. Uyeda PMCID: PMC2579347 Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering María José Marcaida, Jesús Prieto, Pilar Redondo, Alejandro D. Nadra, Andreu Alibés, Luis Serrano, Sylvestre Grizot, Philippe Duchateau, Frédéric Pâques, Francisco J. Blanco, and Guillermo Montoya PMCID: PMC2579348 Protein kinase PKR mutants resistant to the poxvirus pseudosubstrate K3L protein Eun Joo Seo, Furong Liu, Makiko Kawagishi-Kobayashi, Tekly L. Ung, Chune Cao, Arvin C. Dar, Frank Sicheri, and Thomas E. Dever PMCID: PMC2579349 Crystal structure of poxvirus thymidylate kinase: An unexpected dimerization has implications for antiviral therapy Christophe Caillat, Dimitri Topalis, Luigi A. Agrofoglio, Sylvie Pochet, Jan Balzarini, Dominique Deville-Bonne, and Philippe Meyer PMCID: PMC2579350 Human exonuclease 1 and BLM helicase interact to resect DNA and initiate DNA repair Amitabh V. Nimonkar, A. Zeynep Özsoy, Jochen Genschel, Paul Modrich, and Stephen C. Kowalczykowski PMCID: PMC2579351 Ozone production by amino acids contributes to killing of bacteria Kouhei Yamashita, Takashi Miyoshi, Toshiyuki Arai, Nobuyuki Endo, Hiroshi Itoh, Keisuke Makino, Kiyomi Mizugishi, Takashi Uchiyama, and Masataka Sasada PMCID: PMC2579352 Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases Qin Wang, Jiarong Xia, Victor Guallar, Goran Krilov, and Evan R. Kantrowitz PMCID: PMC2579353 Structure of ratcheted ribosomes with tRNAs in hybrid states Patricia Julián, Andrey L. Konevega, Sjors H. W. Scheres, Melisa Lázaro, David Gil, Wolfgang Wintermeyer, Marina V. Rodnina, and Mikel Valle PMCID: PMC2579354 Biophysics From the Cover:
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding Lan Hua, Ruhong Zhou, D. Thirumalai, and B. J. Berne PMCID: PMC2579355 Cell Biology HCO3−/Cl− anion exchanger SLC4A2 is required for proper osteoclast differentiation and function Jing Wu, Laurie H. Glimcher, and Antonios O. Aliprantis PMCID: PMC2579356 Distinct populations of tumor-initiating cells derived from a tumor generated by rat mammary cancer stem cells I. Zucchi, S. Astigiano, G. Bertalot, S. Sanzone, C. Cocola, P. Pelucchi, G. Bertoli, M. Stehling, O. Barbieri, A. Albertini, H. R. Schöler, B. G. Neel, R. A. Reinbold, and R. Dulbecco PMCID: PMC2575224 COPI coat assembly occurs on liquid-disordered domains and the associated membrane deformations are limited by membrane tension Jean-Baptiste Manneville, Jean-François Casella, Ernesto Ambroggio, Pierre Gounon, Julien Bertherat, Patricia Bassereau, Jean Cartaud, Bruno Antonny, and Bruno Goud PMCID: PMC2579358 Membrane proteomics of phagosomes suggests a connection to autophagy Wenqing Shui, Leslie Sheu, Jun Liu, Brian Smart, Christopher J. Petzold, Tsung-yen Hsieh, Austin Pitcher, Jay D. Keasling, and Carolyn R. Bertozzi PMCID: PMC2579359 Inhibition of Thr-55 phosphorylation restores p53 nuclear localization and sensitizes cancer cells to DNA damage Xin Cai and Xuan Liu PMCID: PMC2579360 Staged assembly of histone gene expression machinery at subnuclear foci in the abbreviated cell cycle of human embryonic stem cells Prachi N. Ghule, Zbigniew Dominski, Xiao-cui Yang, William F. Marzluff, Klaus A. Becker, J. Wade Harper, Jane B. Lian, Janet L. Stein, Andre J. van Wijnen, and Gary S. Stein PMCID: PMC2579361 Wnt-mediated self-renewal of neural stem/progenitor cells M. Yashar S. Kalani, Samuel H. Cheshier, Branden J. Cord, Simon R. Bababeygy, Hannes Vogel, Irving L. Weissman, Theo D. Palmer, and Roel Nusse PMCID: PMC2575225 Developmental Biology Osteoblastic regulation of B lymphopoiesis is mediated by Gsα-dependent signaling pathways Joy Y. Wu, Louise E. Purton, Stephen J. Rodda, Min Chen, Lee S. Weinstein, Andrew P. McMahon, David T. Scadden, and Henry M. Kronenberg PMCID: PMC2579363 A second wave of Sonic hedgehog expression during the development of the bat limb Dorit Hockman, Chris J. Cretekos, Mandy K. Mason, Richard R. Behringer, David S. Jacobs, and Nicola Illing PMCID: PMC2579364 Ecology Climatic change and wetland desiccation cause amphibian decline in Yellowstone National Park Sarah K. McMenamin, Elizabeth A. Hadly, and Christopher K. Wright PMCID: PMC2579365 Mean mass-specific metabolic rates are strikingly similar across life's major domains: Evidence for life's metabolic optimum Anastassia M. Makarieva, Victor G. Gorshkov, Bai-Lian Li, Steven L. Chown, Peter B. Reich, and Valery M. Gavrilov PMCID: PMC2572558 Thermal conditions during juvenile development affect adult dispersal in a spider Dries Bonte, Justin M. J. Travis, Nele De Clercq, Ingrid Zwertvaegher, and Luc Lens PMCID: PMC2579367 Connections between climate, food limitation, and carbon cycling in abyssal sediment communities Henry A. Ruhl, Jacob A. Ellena, and Kenneth L. Smith, Jr. PMCID: PMC2579368 Evolutionary history and the effect of biodiversity on plant productivity Marc W. Cadotte, Bradley J. Cardinale, and Todd H. Oakley PMCID: PMC2579369 Predicting and understanding forest dynamics using a simple tractable model Drew W. Purves, Jeremy W. Lichstein, Nikolay Strigul, and Stephen W. Pacala PMCID: PMC2579370 Evolution From the Cover:
Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods John K. Pace, II, Clément Gilbert, Marlena S. Clark, and Cédric Feschotte PMCID: PMC2579371 Phylogenetic patterns of species loss in Thoreau's woods are driven by climate change Charles G. Willis, Brad Ruhfel, Richard B. Primack, Abraham J. Miller-Rushing, and Charles C. Davis PMCID: PMC2573948 Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis Erica Bree Rosenblum, Jason E. Stajich, Nicole Maddox, and Michael B. Eisen PMCID: PMC2566996 Evolution of MDA-5/RIG-I-dependent innate immunity: Independent evolution by domain grafting Devanand Sarkar, Rob DeSalle, and Paul B. Fisher PMCID: PMC2579374 Genetics Persistent epigenetic differences associated with prenatal exposure to famine in humans Bastiaan T. Heijmans, Elmar W. Tobi, Aryeh D. Stein, Hein Putter, Gerard J. Blauw, Ezra S. Susser, P. Eline Slagboom, and L. H. Lumey PMCID: PMC2579375 Variable breakpoints target PAX5 in patients with dicentric chromosomes: A model for the basis of unbalanced translocations in cancer Qian An, Sarah L. Wright, Zoë J. Konn, Elizabeth Matheson, Lynne Minto, Anthony V. Moorman, Helen Parker, Mike Griffiths, Fiona M. Ross, Teresa Davies, Andy G. Hall, Christine J. Harrison, Julie A. Irving, and Jon C. Strefford PMCID: PMC2579376 Escape from X chromosome inactivation is an intrinsic property of the Jarid1c locus Nan Li and Laura Carrel PMCID: PMC2579377 Prediction of human miRNAs using tissue-selective motifs in 3′ UTRs Yao-Ming Chang, Hsueh-Fen Juan, Tzu-Ying Lee, Ya-Ya Chang, Yao-Ming Yeh, Wen-Hsiung Li, and Arthur Chun-Chieh Shih PMCID: PMC2579378 Immunology A p38 MAPK-MEF2C pathway regulates B-cell proliferation Dustin Khiem, Jason G. Cyster, John J. Schwarz, and Brian L. Black PMCID: PMC2579379 Chronic inflammation that facilitates tumor progression creates local immune suppression by inducing indoleamine 2,3 dioxygenase Alexander J. Muller, Madhav D. Sharma, Phillip R. Chandler, James B. DuHadaway, Mary E. Everhart, Burles A. Johnson, III, David J. Kahler, Jeanene Pihkala, Alejandro Peralta Soler, David H. Munn, George C. Prendergast, and Andrew L. Mellor PMCID: PMC2579380 Medical Sciences High sensitivity of BRCA1-deficient mammary tumors to the PARP inhibitor AZD2281 alone and in combination with platinum drugs Sven Rottenberg, Janneke E. Jaspers, Ariena Kersbergen, Eline van der Burg, Anders O. H. Nygren, Serge A. L. Zander, Patrick W. B. Derksen, Michiel de Bruin, John Zevenhoven, Alan Lau, Robert Boulter, Aaron Cranston, Mark J. O'Connor, Niall M. B. Martin, Piet Borst, and Jos Jonkers PMCID: PMC2579381 β-Arrestin 2 is required for lysophosphatidic acid-induced NF-κB activation Jiyuan Sun and Xin Lin PMCID: PMC2579382 The tumor suppressor activity of IKKα in stratified epithelia is exerted in part via the TGF-β antiproliferative pathway Barbara Marinari, Francesca Moretti, Elisabetta Botti, Maria Laura Giustizieri, Pascal Descargues, Alessandro Giunta, Carmine Stolfi, Costanza Ballaro, Marina Papoutsaki, Stefano Alemà, Giovanni Monteleone, Sergio Chimenti, Michael Karin, and Antonio Costanzo PMCID: PMC2579383 Angiopoietin-2 is associated with decreased endothelial nitric oxide and poor clinical outcome in severe falciparum malaria Tsin W. Yeo, Daniel A. Lampah, Retno Gitawati, Emiliana Tjitra, Enny Kenangalem, Kim Piera, Ric N. Price, Stephen B. Duffull, David S. Celermajer, and Nicholas M. Anstey PMCID: PMC2575222 Disruption of the NHR4 domain structure in AML1-ETO abrogates SON binding and promotes leukemogenesis Eun-Young Ahn, Ming Yan, Oxana A. Malakhova, Miao-Chia Lo, Anita Boyapati, Hans Beier Ommen, Robert Hines, Peter Hokland, and Dong-Er Zhang PMCID: PMC2579385 Plasminogen mediates the atherogenic effects of macrophage-expressed urokinase and accelerates atherosclerosis in apoE-knockout mice Michal Kremen, Ranjini Krishnan, Isaac Emery, Jie Hong Hu, Katherine I. Slezicki, Alyssa Wu, Kun Qian, Liang Du, Abigail Plawman, April Stempien-Otero, and David A. Dichek PMCID: PMC2579386 Mouse and human phenotypes indicate a critical conserved role for ERK2 signaling in neural crest development Jason Newbern, Jian Zhong, Rasika S. Wickramasinghe, Xiaoyan Li, Yaohong Wu, Ivy Samuels, Natalie Cherosky, J. Colleen Karlo, Brianne O'Loughlin, Jamie Wikenheiser, Madhusudhana Gargesha, Yong Qiu Doughman, Jean Charron, David D. Ginty, Michiko Watanabe, Sulagna C. Saitta, William D. Snider, and Gary E. Landreth PMCID: PMC2579387 Human domain antibodies to conserved sterically restricted regions on gp120 as exceptionally potent cross-reactive HIV-1 neutralizers Weizao Chen, Zhongyu Zhu, Yang Feng, and Dimiter S. Dimitrov PMCID: PMC2579388 Microbiology From the Cover:
In vivo supramolecular templating enhances the activity of multivalent ligands: A potential therapeutic against the Escherichia coli O157 AB5 toxins Pavel I. Kitov, George L. Mulvey, Thomas P. Griener, Tomasz Lipinski, Dmitry Solomon, Eugenia Paszkiewicz, Jared M. Jacobson, Joanna M. Sadowska, Missao Suzuki, Ken-ichi Yamamura, Glen D. Armstrong, and David R. Bundle PMCID: PMC2573949 From the Cover:
Predataxis behavior in Myxococcus xanthus James E. Berleman, Jodie Scott, Tatiana Chumley, and John R. Kirby PMCID: PMC2579389 Structural and functional analysis of AsbF: Origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis Brian F. Pfleger, Youngchang Kim, Tyler D. Nusca, Natalia Maltseva, Jung Yeop Lee, Christopher M. Rath, Jamie B. Scaglione, Brian K. Janes, Erica C. Anderson, Nicholas H. Bergman, Philip C. Hanna, Andrzej Joachimiak, and David H. Sherman PMCID: PMC2579390 Neuroscience Brain vasopressin is an important regulator of maternal behavior independent of dams' trait anxiety Oliver J. Bosch and Inga D. Neumann PMCID: PMC2579391 From the Cover:
Reversal of cocaine addiction by environmental enrichment Marcello Solinas, Claudia Chauvet, Nathalie Thiriet, Rana El Rawas, and Mohamed Jaber PMCID: PMC2579392 Microglial activation and TNFα production mediate altered CNS excitability following peripheral inflammation Kiarash Riazi, Michael A. Galic, J. Brent Kuzmiski, Winnie Ho, Keith A. Sharkey, and Quentin J. Pittman PMCID: PMC2579393 Dynamical relaying can yield zero time lag neuronal synchrony despite long conduction delays Raul Vicente, Leonardo L. Gollo, Claudio R. Mirasso, Ingo Fischer, and Gordon Pipa PMCID: PMC2575223 A double dissociation revealing bidirectional competition between striatum and hippocampus during learning Anni S. Lee, Ronald S. Duman, and Christopher Pittenger PMCID: PMC2579395 Regulation of neuronal connexin-36 channels by pH Daniel González-Nieto, Juan M. Gómez-Hernández, Belén Larrosa, Cristina Gutiérrez, María D. Muñoz, Ilaria Fasciani, John O'Brien, Agata Zappalà, Federico Cicirata, and Luis C. Barrio PMCID: PMC2579396 Importin-mediated retrograde transport of CREB2 from distal processes to the nucleus in neurons Kwok-On Lai, Yali Zhao, Toh Hean Ch'ng, and Kelsey C. Martin PMCID: PMC2579397 TrkB-mediated activation of geranylgeranyltransferase I promotes dendritic morphogenesis Xiu-Ping Zhou, Kong-Yan Wu, Bin Liang, Xiu-Qing Fu, and Zhen-Ge Luo PMCID: PMC2579398 Physiology The genetic ablation of SRC-3 protects against obesity and improves insulin sensitivity by reducing the acetylation of PGC-1α Agnès Coste, Jean-Francois Louet, Marie Lagouge, Carles Lerin, Maria Cristina Antal, Hamid Meziane, Kristina Schoonjans, Pere Puigserver, Bert W. O'Malley, and Johan Auwerx PMCID: PMC2579399 Plant Biology INAUGURAL ARTICLE by a Recently Elected Academy Member: A PHD-Polycomb Repressive Complex 2 triggers the epigenetic silencing of FLC during vernalization Filomena De Lucia, Pedro Crevillen, Alexandra M. E. Jones, Thomas Greb, and Caroline Dean PMCID: PMC2579339 A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana Olivier Loudet, Todd P. Michael, Brian T. Burger, Claire Le Metté, Todd C. Mockler, Detlef Weigel, and Joanne Chory PMCID: PMC2579400 The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants Marion Eisenhut, Wolfgang Ruth, Maya Haimovich, Hermann Bauwe, Aaron Kaplan, and Martin Hagemann PMCID: PMC2579401 Social Sciences Sustainability Science The effects of 3 environmental risks on mortality disparities across Mexican communities Gretchen A. Stevens, Rodrigo H. Dias, and Majid Ezzati PMCID: PMC2579343 Corrections Correction for Horne et al., Interplay among side chain sequence, backbone composition, and residue rigidification in polypeptide folding and assembly PMCID: PMC2579402 Corrects: W. Seth Horne, et al. Interplay among side chain sequence, backbone composition, and residue rigidification in polypeptide folding and assembly. Proc Natl Acad Sci U S A. 2008 July 8; 105(27): 9151–9156. Correction for Chang et al., Expression of Globo H and SSEA3 in breast cancer stem cells and the involvement of fucosyl transferases 1 and 2 in Globo H synthesis PMCID: PMC2604320 Corrects: Wen-Wei Chang, et al. Expression of Globo H and SSEA3 in breast cancer stem cells and the involvement of fucosyl transferases 1 and 2 in Globo H synthesis. Proc Natl Acad Sci U S A. 2008 August 19; 105(33): 11667–11672. Correction for Begall et al., Magnetic alignment in grazing and resting cattle and deer PMCID: PMC2604321 Corrects: Sabine Begall, et al. Magnetic alignment in grazing and resting cattle and deer. Proc Natl Acad Sci U S A. 2008 September 9; 105(36): 13451–13455. Correction for Martini et al., Uncovering G protein-coupled receptor kinase-5 as a histone deacetylase kinase in the nucleus of cardiomyocytes PMCID: PMC2604322 Corrects: Jeffrey S. Martini, et al. Uncovering G protein-coupled receptor kinase-5 as a histone deacetylase kinase in the nucleus of cardiomyocytes. Proc Natl Acad Sci U S A. 2008 August 26; 105(34): 12457–12462. Correction for Martel and Young, Purported nanobacteria in human blood as calcium carbonate nanoparticles PMCID: PMC2604323 Corrects: Jan Martel, et al. From the Cover:
Purported nanobacteria in human blood as calcium carbonate nanoparticles. Proc Natl Acad Sci U S A. 2008 April 8; 105(14): 5549–5554. Correction for Reynolds et al., Enhanced photoprotection pathways in symbiotic dinoflagellates of shallow-water corals and other cnidarians PMCID: PMC2604324 Corrects: Jennifer McCabe Reynolds, et al. Enhanced photoprotection pathways in symbiotic dinoflagellates of shallow-water corals and other cnidarians. Proc Natl Acad Sci U S A. 2008 September 9; 105(36): 13674–13678. |
