| | Other Issues: latest | archiveINAUGURAL ARTICLE by a Recently Elected Academy Member: The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages Yuri I. Wolf, Pavel S. Novichkov, Georgy P. Karev, Eugene V. Koonin, and David J. Lipman PMCID: PMC2666616 From the Cover:
Disruption of NMDAR-dependent burst firing by dopamine neurons provides selective assessment of phasic dopamine-dependent behavior Larry S. Zweifel, Jones G. Parker, Collin J. Lobb, Aundrea Rainwater, Valerie Z. Wall, Jonathan P. Fadok, Martin Darvas, Min J. Kim, Sheri J. Y. Mizumori, Carlos A. Paladini, Paul E. M. Phillips, and Richard D. Palmiter PMCID: PMC2678650 Flexible electrical recording from cells using nanowire transistor arrays Tzahi Cohen-Karni, Brian P. Timko, Lucien E. Weiss, and Charles M. Lieber PMCID: PMC2678623 Fermi surface nesting induced strong pairing in iron-based superconductors K. Terashima, Y. Sekiba, J. H. Bowen, K. Nakayama, T. Kawahara, T. Sato, P. Richard, Y.-M. Xu, L. J. Li, G. H. Cao, Z.-A. Xu, H. Ding, and T. Takahashi PMCID: PMC2667370 Political complexity predicts the spread of ethnolinguistic groups Thomas E. Currie and Ruth Mace PMCID: PMC2670878 Spatial ensemble statistics are efficient codes that can be represented with reduced attention George A. Alvarez and Aude Oliva PMCID: PMC2670879 Electrophysiological characterization of LacY Juan J. Garcia-Celma, Irina N. Smirnova, H. Ronald Kaback, and Klaus Fendler PMCID: PMC2671326 Insights into pilus assembly and secretion from the structure and functional characterization of usher PapC Yihua Huang, Barbara S. Smith, Lucy X. Chen, Richard H. G. Baxter, and Johann Deisenhofer PMCID: PMC2670885 Charting the molecular network of the drug target Bcr-Abl Marc Brehme, Oliver Hantschel, Jacques Colinge, Ines Kaupe, Melanie Planyavsky, Thomas Köcher, Karl Mechtler, Keiryn L. Bennett, and Giulio Superti-Furga PMCID: PMC2670881 ERα as ligand-independent activator of CDH-1 regulates determination and maintenance of epithelial morphology in breast cancer cells Maria Dafne Cardamone, Chiara Bardella, Arantxa Gutierrez, Luciano Di Croce, Michael G. Rosenfeld, Maria Flavia Di Renzo, and Michele De Bortoli PMCID: PMC2671327 Docking for fragment inhibitors of AmpC β-lactamase Denise G. Teotico, Kerim Babaoglu, Gabriel J. Rocklin, Rafaela S. Ferreira, Anthony M. Giannetti, and Brian K. Shoichet PMCID: PMC2671983 Muscle hypertrophy driven by myostatin blockade does not require stem/precursor-cell activity Helge Amthor, Anthony Otto, Adeline Vulin, Anne Rochat, Julie Dumonceaux, Luis Garcia, Etienne Mouisel, Christophe Hourdé, Raymond Macharia, Melanie Friedrichs, Frederic Relaix, Peter S. Zammit, Antonios Matsakas, Ketan Patel, and Terence Partridge PMCID: PMC2671322 Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans Sarah E. Calvo, David J. Pagliarini, and Vamsi K. Mootha PMCID: PMC2669787 Depletion of interfering antibodies in chronic hepatitis C patients and vaccinated chimpanzees reveals broad cross-genotype neutralizing activity Pei Zhang, Lilin Zhong, Evi Budo Struble, Hisayoshi Watanabe, Alla Kachko, Kathleen Mihalik, Maria Luisa Virata-Theimer, Harvey J. Alter, Stephen Feinstone, and Marian Major PMCID: PMC2670884 Cardiomyocyte cyclooxygenase-2 influences cardiac rhythm and function Dairong Wang, Vickas V. Patel, Emanuela Ricciotti, Rong Zhou, Mark D. Levin, Ehre Gao, Zhou Yu, Victor A. Ferrari, Min Min Lu, Junwang Xu, Hualei Zhang, Yiqun Hui, Yan Cheng, Nataliya Petrenko, Ying Yu, and Garret A. FitzGerald PMCID: PMC2670242 Statistical estimation of cell-cycle progression and lineage commitment in Plasmodium falciparum reveals a homogeneous pattern of transcription in ex vivo culture Jacob E. Lemieux, Natalia Gomez-Escobar, Avi Feller, Celine Carret, Alfred Amambua-Ngwa, Robert Pinches, Felix Day, Sue A. Kyes, David J. Conway, Chris C. Holmes, and Chris I. Newbold PMCID: PMC2670243 Minimal molecular constraints for respiratory droplet transmission of an avian–human H9N2 influenza A virus Erin M. Sorrell, Hongquan Wan, Yonas Araya, Haichen Song, and Daniel R. Perez PMCID: PMC2670882 Site-specific integration of adeno-associated virus involves partial duplication of the target locus Els Henckaerts, Nathalie Dutheil, Nadja Zeltner, Steven Kattman, Erik Kohlbrenner, Peter Ward, Nathalie Clément, Patricia Rebollo, Marion Kennedy, Gordon M. Keller, and R. Michael Linden PMCID: PMC2669786 Aberrant cleavage of TDP-43 enhances aggregation and cellular toxicity Yong-Jie Zhang, Ya-Fei Xu, Casey Cook, Tania F. Gendron, Paul Roettges, Christopher D. Link, Wen-Lang Lin, Jimei Tong, Monica Castanedes-Casey, Peter Ash, Jennifer Gass, Vijayaraghavan Rangachari, Emanuele Buratti, Francisco Baralle, Todd E. Golde, Dennis W. Dickson, and Leonard Petrucelli PMCID: PMC2671323 Efficient production of mesencephalic dopamine neurons by Lmx1a expression in embryonic stem cells Stina Friling, Elisabet Andersson, Lachlan H. Thompson, Marie E. Jönsson, Josephine B. Hebsgaard, Evanthia Nanou, Zhanna Alekseenko, Ulrika Marklund, Susanna Kjellander, Nikolaos Volakakis, Outi Hovatta, Abdeljabbar El Manira, Anders Björklund, Thomas Perlmann, and Johan Ericson PMCID: PMC2671325 Molecular dissection of Alzheimer's disease neuropathology by depletion of serum amyloid P component Simon E. Kolstoe, Basil H. Ridha, Vittorio Bellotti, Nan Wang, Carol V. Robinson, Sebastian J. Crutch, Geoffrey Keir, Riitta Kukkastenvehmas, J. Ruth Gallimore, Winston L. Hutchinson, Philip N. Hawkins, Stephen P. Wood, Martin N. Rossor, and Mark B. Pepys PMCID: PMC2669789 Transcriptome transfer produces a predictable cellular phenotype Jai-Yoon Sul, Chia-wen K. Wu, Fanyi Zeng, Jeanine Jochems, Miler T. Lee, Tae Kyung Kim, Tiina Peritz, Peter Buckley, David J. Cappelleri, Margaret Maronski, Minsun Kim, Vijay Kumar, David Meaney, Junhyong Kim, and James Eberwine PMCID: PMC2670883 Hv1 proton channels are required for high-level NADPH oxidase-dependent superoxide production during the phagocyte respiratory burst I. Scott Ramsey, Evelyne Ruchti, J. Stefan Kaczmarek, and David E. Clapham PMCID: PMC2669790 Examining the relative influence of familial, genetic, and environmental covariate information in flexible risk models Héctor Corrada Bravo, Kristine E. Lee, Barbara E. K. Klein, Ronald Klein, Sudha K. Iyengar, and Grace Wahba PMCID: PMC2677979 A possible mechanism for exonuclease 1-independent eukaryotic mismatch repair Farid A. Kadyrov, Jochen Genschel, Yanan Fang, Elisabeth Penland, Winfried Edelmann, and Paul Modrich PMCID: PMC2677980 Sanfilippo syndrome type B, a lysosomal storage disease, is also a tauopathy Kazuhiro Ohmi, Lili C. Kudo, Sergey Ryazantsev, Hui-Zhi Zhao, Stanislav L. Karsten, and Elizabeth F. Neufeld PMCID: PMC2677546 Top marine predators track Lagrangian coherent structures Emilie Tew Kai, Vincent Rossi, Joel Sudre, Henri Weimerskirch, Cristobal Lopez, Emilio Hernandez-Garcia, Francis Marsac, and Veronique Garçon PMCID: PMC2677090 The tumor suppressor WTX shuttles to the nucleus and modulates WT1 activity Miguel N. Rivera, Woo Jae Kim, Julie Wells, Amanda Stone, Alexa Burger, Erik J. Coffman, Jianmin Zhang, and Daniel A. Haber PMCID: PMC2677091 Historical invasions of the intertidal zone of Atlantic North America associated with distinctive patterns of trade and emigration Susan H. Brawley, James A. Coyer, April M. H. Blakeslee, Galice Hoarau, Ladd E. Johnson, James E. Byers, Wytze T. Stam, and Jeanine L. Olsen PMCID: PMC2677092 Vernalization-induced flowering in cereals is associated with changes in histone methylation at the VERNALIZATION1 gene Sandra N. Oliver, E. Jean Finnegan, Elizabeth S. Dennis, W. James Peacock, and Ben Trevaskis PMCID: PMC2677093 Identification of ARIA regulating endothelial apoptosis and angiogenesis by modulating proteasomal degradation of cIAP-1 and cIAP-2 Koji Ikeda, Ritsuko Nakano, Maki Uraoka, Yusuke Nakagawa, Masahiro Koide, Asako Katsume, Keizo Minamino, Eri Yamada, Haruhiko Yamada, Thomas Quertermous, and Hiroaki Matsubara PMCID: PMC2676168 Sustained activation of XBP1 splicing leads to endothelial apoptosis and atherosclerosis development in response to disturbed flow Lingfang Zeng, Anna Zampetaki, Andriana Margariti, Anna Elena Pepe, Saydul Alam, Daniel Martin, Qingzhong Xiao, Wen Wang, Zheng-Gen Jin, Gillian Cockerill, Kazutoshi Mori, Yi-shuan Julie Li, Yanhua Hu, Shu Chien, and Qingbo Xu PMCID: PMC2676169 INAUGURAL ARTICLE by a Recently Elected Academy Member: Magnetic stabilization and vorticity in submillimeter paramagnetic liquid tubes J. Michael D. Coey, Ryoichi Aogaki, Fiona Byrne, and Plamen Stamenov PMCID: PMC2675569 Role of mutant SOD1 disulfide oxidation and aggregation in the pathogenesis of familial ALS Celeste M. Karch, Mercedes Prudencio, Duane D. Winkler, P. John Hart, and David R. Borchelt PMCID: PMC2675570 Squeezing out the entropy of fermions in optical lattices Tin-Lun Ho and Qi Zhou PMCID: PMC2678422 De novo design and in vivo activity of conformationally restrained antimicrobial arylamide foldamers Sungwook Choi, Andre Isaacs, Dylan Clements, Dahui Liu, Hyemin Kim, Richard W. Scott, Jeffrey D. Winkler, and William F. DeGrado PMCID: PMC2667368 Mechanisms of chiral discrimination by topoisomerase IV K. C. Neuman, G. Charvin, D. Bensimon, and V. Croquette PMCID: PMC2667371 The augmin complex plays a critical role in spindle microtubule generation for mitotic progression and cytokinesis in human cells Ryota Uehara, Ryu-suke Nozawa, Akiko Tomioka, Sabine Petry, Ronald D. Vale, Chikashi Obuse, and Gohta Goshima PMCID: PMC2668966 Dissecting genetic requirements of human breast tumorigenesis in a tissue transgenic model of human breast cancer in mice Min Wu, Lina Jung, Adrian B. Cooper, Christina Fleet, Lihao Chen, Lyne Breault, Kimberly Clark, Zuhua Cai, Sylvie Vincent, Steve Bottega, Qiong Shen, Andrea Richardson, Marcus Bosenburg, Stephen P. Naber, Ronald A. DePinho, Charlotte Kuperwasser, and Murray O. Robinson PMCID: PMC2669443 Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development Zhe Ji, Ju Youn Lee, Zhenhua Pan, Bingjun Jiang, and Bin Tian PMCID: PMC2669788 Propagule supply controls grazer community structure and primary production in a benthic marine ecosystem Sarah C. Lee and John F. Bruno PMCID: PMC2667366 Temperature sensitivity of drought-induced tree mortality portends increased regional die-off under global-change-type drought Henry D. Adams, Maite Guardiola-Claramonte, Greg A. Barron-Gafford, Juan Camilo Villegas, David D. Breshears, Chris B. Zou, Peter A. Troch, and Travis E. Huxman PMCID: PMC2678423 Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution Raquel Assis and Alexey S. Kondrashov PMCID: PMC2667148 Experimentally observed phenomena on cardiac energetics in heart failure emerge from simulations of cardiac metabolism Fan Wu, Jianyi Zhang, and Daniel A. Beard PMCID: PMC2667147 Gene encoding erythrocyte binding ligand linked to blood stage multiplication rate phenotype in Plasmodium yoelii yoelii Sittiporn Pattaradilokrat, Richard L. Culleton, Sandra J. Cheesman, and Richard Carter PMCID: PMC2667367 p21-Activated kinase mediates rapid estradiol-negative feedback actions in the reproductive axis Zhen Zhao, Cheryl Park, Melissa A. McDevitt, Christine Glidewell-Kenney, Pierre Chambon, Jeffrey Weiss, J. Larry Jameson, and Jon E. Levine PMCID: PMC2667369 Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination Atsushi Fukushima, Miyako Kusano, Norihito Nakamichi, Makoto Kobayashi, Naomi Hayashi, Hitoshi Sakakibara, Takeshi Mizuno, and Kazuki Saito PMCID: PMC2667372 Dynamic hybrid materials for constitutional self-instructed membranes Adinela Cazacu, Yves-Marie Legrand, Andreea Pasc, Gihane Nasr, Arie Van der Lee, Eugene Mahon, and Mihail Barboiu PMCID: PMC2674937 Endogenous expression of HrasG12V induces developmental defects and neoplasms with copy number imbalances of the oncogene Xu Chen, Norisato Mitsutake, Krista LaPerle, Nagako Akeno, Pat Zanzonico, Valerie A. Longo, Shin Mitsutake, Edna T. Kimura, Hartmut Geiger, Eugenio Santos, Hans G. Wendel, Aime Franco, Jeffrey A. Knauf, and James A. Fagin PMCID: PMC2674938 Characterizing the resistance generated by a molecular bond as it is forcibly separated L. B. Freund PMCID: PMC2674939 Detection of circular polarization in light scattered from photosynthetic microbes William B. Sparks, James Hough, Thomas A. Germer, Feng Chen, Shiladitya DasSarma, Priya DasSarma, Frank T. Robb, Nadine Manset, Ludmilla Kolokolova, Neill Reid, F. Duccio Macchetto, and William Martin PMCID: PMC2674403 Synergy between pathogen release and resource availability in plant invasion Dana Blumenthal, Charles E. Mitchell, Petr Pyšek, and Vojtěch Jarošík PMCID: PMC2674393 A chemical screen for biological small molecule–RNA conjugates reveals CoA-linked RNA Walter E. Kowtoniuk, Yinghua Shen, Jennifer M. Heemstra, Isha Agarwal, and David R. Liu PMCID: PMC2674394 An age-related homeostasis mechanism is essential for spontaneous amelioration of hemophilia B Leyden Sumiko Kurachi, Jeffrey S. Huo, Afshin Ameri, Kezhong Zhang, Akiyasu C. Yoshizawa, and Kotoku Kurachi PMCID: PMC2674395 Design of anti- and pro-aggregation variants to assess the effects of methionine oxidation in human prion protein Christina Wolschner, Armin Giese, Hans A. Kretzschmar, Robert Huber, Luis Moroder, and Nediljko Budisa PMCID: PMC2674404 Many different Vβ CDR3s can reveal the inherent MHC reactivity of germline-encoded TCR V regions Kira Rubtsova, James P. Scott-Browne, Frances Crawford, Shaodong Dai, Philippa Marrack, and John W. Kappler PMCID: PMC2674405 Fast rise of broadly cross-reactive antibodies after boosting long-lived human memory B cells primed by an MF59 adjuvanted prepandemic vaccine Grazia Galli, Kathy Hancock, Katja Hoschler, Joshua DeVos, Michaela Praus, Monia Bardelli, Carmine Malzone, Flora Castellino, Chiara Gentile, Teresa McNally, Giuseppe Del Giudice, Angelika Banzhoff, Volker Brauer, Emanuele Montomoli, Maria Zambon, Jacqueline Katz, Karl Nicholson, and Iain Stephenson PMCID: PMC2674105 Prostaglandin F2α elevates blood pressure and promotes atherosclerosis Ying Yu, Margaret B. Lucitt, Jane Stubbe, Yan Cheng, Ulla G. Friis, Pernille B. Hansen, Boye L. Jensen, Emer M. Smyth, and Garret A. FitzGerald PMCID: PMC2673134 Host–pathogen time series data in wildlife support a transmission function between density and frequency dependence Matthew J. Smith, Sandra Telfer, Eva R. Kallio, Sarah Burthe, Alex R. Cook, Xavier Lambin, and Michael Begon PMCID: PMC2672915 A randomized trial of the effect of estrogen and testosterone on economic behavior Niklas Zethraeus, Ljiljana Kocoska-Maras, Tore Ellingsen, Bo von Schoultz, Angelica Lindén Hirschberg, and Magnus Johannesson PMCID: PMC2666090 Childhood poverty, chronic stress, and adult working memory Gary W. Evans and Michelle A. Schamberg PMCID: PMC2662958 Examining the conspicuousness and prominence of two required warnings on OTC pain relievers Laura Bix, Nora M. Bello, Rafael Auras, Jon Ranger, and Maria K. Lapinski PMCID: PMC2662957 From the Cover:
Initial formation of an indigenous crop complex in eastern North America at 3800 B.P Bruce D. Smith and Richard A. Yarnell PMCID: PMC2666091 Plastid production of protein antibiotics against pneumonia via a new strategy for high-level expression of antimicrobial proteins Melanie Oey, Marc Lohse, Lars B. Scharff, Bernd Kreikemeyer, and Ralph Bock PMCID: PMC2662961 Electromechanical coupling in the membranes of Shaker-transfected HEK cells Arthur Beyder and Frederick Sachs PMCID: PMC2666089 β-Arrestin-dependent signaling and trafficking of 7-transmembrane receptors is reciprocally regulated by the deubiquitinase USP33 and the E3 ligase Mdm2 Sudha K. Shenoy, Aalok S. Modi, Arun K. Shukla, Kunhong Xiao, Magali Berthouze, Seungkirl Ahn, Keith D. Wilkinson, William E. Miller, and Robert J. Lefkowitz PMCID: PMC2667797 From the Cover:
The emergence of lineage-specific chromosomal topologies from coordinate gene regulation Indika Rajapakse, Michael D. Perlman, David Scalzo, Charles Kooperberg, Mark Groudine, and Steven T. Kosak PMCID: PMC2654024 A point mutation in TRPC3 causes abnormal Purkinje cell development and cerebellar ataxia in moonwalker mice Esther B. E. Becker, Peter L. Oliver, Maike D. Glitsch, Gareth T. Banks, Francesca Achilli, Andrea Hardy, Patrick M. Nolan, Elizabeth M. C. Fisher, and Kay E. Davies PMCID: PMC2666615 High-throughput, high-accuracy array-based resequencing Jianbiao Zheng, Martin Moorhead, Li Weng, Farooq Siddiqui, Victoria E. H. Carlton, James S. Ireland, Liana Lee, Joseph Peterson, Jennifer Wilkins, Sean Lin, Zhengyan Kan, Somasekar Seshagiri, Ronald W. Davis, and Malek Faham PMCID: PMC2672536 Microbial translocation, the innate cytokine response, and HIV-1 disease progression in Africa Andrew D. Redd, Djeneba Dabitao, Jay H. Bream, Blake Charvat, Oliver Laeyendecker, Noah Kiwanuka, Tom Lutalo, Godfrey Kigozi, Aaron A. R. Tobian, Jordyn Gamiel, Jessica D. Neal, Amy E. Oliver, Joseph B. Margolick, Nelson Sewankambo, Steven J. Reynolds, Maria J. Wawer, David Serwadda, Ronald H. Gray, and Thomas C. Quinn PMCID: PMC2667149 G-CSF-initiated myeloid cell mobilization and angiogenesis mediate tumor refractoriness to anti-VEGF therapy in mouse models Farbod Shojaei, Xiumin Wu, Xueping Qu, Marcin Kowanetz, Lanlan Yu, Martha Tan, Y. Gloria Meng, and Napoleone Ferrara PMCID: PMC2665197 Daily rhythms of food-anticipatory behavioral activity do not require the known circadian clock Kai-Florian Storch and Charles J. Weitz PMCID: PMC2666092 Fibrillar amyloid-β burden in cognitively normal people at 3 levels of genetic risk for Alzheimer's disease Eric M. Reiman, Kewei Chen, Xiaofen Liu, Daniel Bandy, Meixiang Yu, Wendy Lee, Napatkamon Ayutyanont, Jennifer Keppler, Stephanie A. Reeder, Jessica B. S. Langbaum, Gene E. Alexander, William E. Klunk, Chester A. Mathis, Julie C. Price, Howard J. Aizenstein, Steven T. DeKosky, and Richard J. Caselli PMCID: PMC2665196 Structure-based discovery of β2-adrenergic receptor ligands Peter Kolb, Daniel M. Rosenbaum, John J. Irwin, Juan José Fung, Brian K. Kobilka, and Brian K. Shoichet PMCID: PMC2672528 Quantitative genome-scale analysis of protein localization in an asymmetric bacterium John N. Werner, Eric Y. Chen, Jonathan M. Guberman, Angela R. Zippilli, Joseph J. Irgon, and Zemer Gitai PMCID: PMC2671984 Fine mapping and functional analysis of a common variant in MSMB on chromosome 10q11.2 associated with prostate cancer susceptibility Hong Lou, Meredith Yeager, Hongchuan Li, Jesus Gonzalez Bosquet, Richard B. Hayes, Nick Orr, Kai Yu, Amy Hutchinson, Kevin B. Jacobs, Peter Kraft, Sholom Wacholder, Nilanjan Chatterjee, Heather Spencer Feigelson, Michael J. Thun, W. Ryan Diver, Demetrius Albanes, Jarmo Virtamo, Stephanie Weinstein, Jing Ma, J. Michael Gaziano, Meir Stampfer, Fredrick R. Schumacher, Edward Giovannucci, Geraldine Cancel-Tassin, Olivier Cussenot, Antoine Valeri, Gerald L. Andriole, E. David Crawford, Stephen K. Anderson, Margaret Tucker, Robert N. Hoover, Joseph F. Fraumeni, Jr., Gilles Thomas, David J. Hunter, Michael Dean, and Stephen J. Chanock PMCID: PMC2671324 Neural correlates of admiration and compassion Mary Helen Immordino-Yang, Andrea McColl, Hanna Damasio, and Antonio Damasio PMCID: PMC2670880 From the Cover: Inaugural Article:
Translesion DNA polymerases remodel the replisome and alter the speed of the replicative helicase Chiara Indiani, Lance D. Langston, Olga Yurieva, Myron F. Goodman, and Mike O'Donnell PMCID: PMC2654394 The grinding tip of the sea urchin tooth exhibits exquisite control over calcite crystal orientation and Mg distribution Yurong Ma, Barbara Aichmayer, Oskar Paris, Peter Fratzl, Anders Meibom, Rebecca A. Metzler, Yael Politi, Lia Addadi, P. U. P. A. Gilbert, and Steve Weiner PMCID: PMC2662956 From the Cover:
An information-bearing seed for nucleating algorithmic self-assembly Robert D. Barish, Rebecca Schulman, Paul W. K. Rothemund, and Erik Winfree PMCID: PMC2660060 Synthesis and characterization of a new structure of gas hydrate L. Yang, C. A. Tulk, D. D. Klug, I. L. Moudrakovski, C. I. Ratcliffe, J. A. Ripmeester, B. C. Chakoumakos, L. Ehm, C. D. Martin, and J. B. Parise PMCID: PMC2662955 From the Cover:
Scaleable manufacture of HIV-1 entry inhibitor griffithsin and validation of its safety and efficacy as a topical microbicide component Barry R. O'Keefe, Fakhrieh Vojdani, Viviana Buffa, Robin J. Shattock, David C. Montefiori, James Bakke, Jon Mirsalis, Anna-Lisa d'Andrea, Steven D. Hume, Barry Bratcher, Carrie J. Saucedo, James B. McMahon, Gregory P. Pogue, and Kenneth E. Palmer PMCID: PMC2662964 Mammalian cell penetration, siRNA transfection, and DNA transfection by supercharged proteins Brian R. McNaughton, James J. Cronican, David B. Thompson, and David R. Liu PMCID: PMC2659711 FRET-based mapping of calmodulin bound to the RyR1 Ca2+ release channel Razvan L. Cornea, Florentin Nitu, Simon Gruber, Katherine Kohler, Michael Satzer, David D. Thomas, and Bradley R. Fruen PMCID: PMC2662960 Mechanistic role of movement and strain sensitivity in muscle contraction Julien S. Davis and Neal D. Epstein PMCID: PMC2661314 MRAP and MRAP2 are bidirectional regulators of the melanocortin receptor family Li F. Chan, Tom R. Webb, Teng-Teng Chung, Eirini Meimaridou, Sadani N. Cooray, Leonardo Guasti, J. Paul Chapple, Michaela Egertová, Maurice R. Elphick, Michael E. Cheetham, Louise A. Metherell, and Adrian J. L. Clark PMCID: PMC2661846 Interaction of phosphodiesterase 3A with brefeldin A-inhibited guanine nucleotide-exchange proteins BIG1 and BIG2 and effect on ARF1 activity Ermanno Puxeddu, Marina Uhart, Chun-Chun Li, Faiyaz Ahmad, Gustavo Pacheco-Rodriguez, Vincent C. Manganiello, Joel Moss, and Martha Vaughan PMCID: PMC2662965 Neuropilin 1 signaling guides neural crest cells to coordinate pathway choice with cell specification Quenten Schwarz, Charlotte Henrietta Maden, Joaquim M. Vieira, and Christiana Ruhrberg PMCID: PMC2661313 An integrative framework for stochastic, size-structured community assembly J. P. O'Dwyer, J. K. Lake, A. Ostling, V. M. Savage, and J. L. Green PMCID: PMC2663776 Elevated CO2 stimulates marsh elevation gain, counterbalancing sea-level rise J. Adam Langley, Karen L. McKee, Donald R. Cahoon, Julia A. Cherry, and J. Patrick Megonigal PMCID: PMC2661312 Dynamic remodeling of in-group bias during the 2008 presidential election David G. Rand, Thomas Pfeiffer, Anna Dreber, Rachel W. Sheketoff, Nils C. Wernerfelt, and Yochai Benkler PMCID: PMC2664153 A UV-sensitive syndrome patient with a specific CSA mutation reveals separable roles for CSA in response to UV and oxidative DNA damage Tiziana Nardo, Roberta Oneda, Graciela Spivak, Bruno Vaz, Laurent Mortier, Pierre Thomas, Donata Orioli, Vincent Laugel, Anne Stary, Philip C. Hanawalt, Alain Sarasin, and Miria Stefanini PMCID: PMC2667150 Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriers Patricia Arashiro, Iris Eisenberg, Alvin T. Kho, Antonia M. P. Cerqueira, Marta Canovas, Helga C. A. Silva, Rita C. M. Pavanello, Sergio Verjovski-Almeida, Louis M. Kunkel, and Mayana Zatz PMCID: PMC2664154 Activation of antibacterial autophagy by NADPH oxidases Ju Huang, Veronica Canadien, Grace Y. Lam, Benjamin E. Steinberg, Mary C. Dinauer, Marco A. O. Magalhaes, Michael Glogauer, Sergio Grinstein, and John H. Brumell PMCID: PMC2664152 Endocytic sequestration of the B cell antigen receptor and toll-like receptor 9 in anergic cells Shannon K. O'Neill, Margaret L. Veselits, Miao Zhang, Christine Labno, Yanxia Cao, Alison Finnegan, Melissa Uccellini, Maria-Luisa Alegre, John C. Cambier, and Marcus R. Clark PMCID: PMC2662959 A multi-marker assay to distinguish malignant melanomas from benign nevi Mohammed Kashani-Sabet, Javier Rangel, Sima Torabian, Mehdi Nosrati, Jeff Simko, David M. Jablons, Dan H. Moore, Chris Haqq, James R. Miller, III, and Richard W. Sagebiel PMCID: PMC2662963 Transient expression of the Arf tumor suppressor during male germ cell and eye development in Arf-Cre reporter mice Adam Gromley, Michelle L. Churchman, Frederique Zindy, and Charles J. Sherr PMCID: PMC2664155 Notch and Wnt signals cooperatively control cell proliferation and tumorigenesis in the intestine Silvia Fre, S. K. Pallavi, Mathilde Huyghe, Marick Laé, Klaus-Peter Janssen, Sylvie Robine, Spyros Artavanis-Tsakonas, and Daniel Louvard PMCID: PMC2649205 Isolation of a cellular factor that can reactivate latent HIV-1 without T cell activation Hung-Chih Yang, Lin Shen, Robert F. Siliciano, and Joel L. Pomerantz PMCID: PMC2663775 Drosophila IKK-related kinase Ik2 and Katanin p60-like 1 regulate dendrite pruning of sensory neuron during metamorphosis Hsiu-Hsiang Lee, Lily Yeh Jan, and Yuh-Nung Jan PMCID: PMC2661847 Neuronal M3 muscarinic acetylcholine receptors are essential for somatotroph proliferation and normal somatic growth Dinesh Gautam, Jongrye Jeon, Matthew F. Starost, Sung-Jun Han, Fadi F. Hamdan, Yinghong Cui, Albert F. Parlow, Oksana Gavrilova, Ildiko Szalayova, Eva Mezey, and Jürgen Wess PMCID: PMC2662962 Mathematical test models for superparametrization in anisotropic turbulence Andrew J. Majda and Marcus J. Grote PMCID: PMC2657592 Probing the role of the proximal heme ligand in cytochrome P450cam by recombinant incorporation of selenocysteine Caroline Aldag, Igor A. Gromov, Inés García-Rubio, Konstanze von Koenig, Ilme Schlichting, Bernhard Jaun, and Donald Hilvert PMCID: PMC2657087 From the Cover:
Generation of hyperpolarized substrates by secondary labeling with [1,1-13C] acetic anhydride David M. Wilson, Ralph E. Hurd, Kayvan Keshari, Mark Van Criekinge, Albert P. Chen, Sarah J. Nelson, Daniel B. Vigneron, and John Kurhanewicz PMCID: PMC2654026 Structural arrangement of the transmission interface in the antigen ABC transport complex TAP Giani Oancea, Megan L. O'Mara, W. F. Drew Bennett, D. Peter Tieleman, Rupert Abele, and Robert Tampé PMCID: PMC2657591 Structural plasticity of an acid-activated chaperone allows promiscuous substrate binding Timothy L. Tapley, Jan L. Körner, Madhuri T. Barge, Julia Hupfeld, Joseph A. Schauerte, Ari Gafni, Ursula Jakob, and James C. A. Bardwell PMCID: PMC2660062 Interference of mismatch and base excision repair during the processing of adjacent U/G mispairs may play a key role in somatic hypermutation Silvia Schanz, Dennis Castor, Franziska Fischer, and Josef Jiricny PMCID: PMC2659717 A dedicated thioesterase of the Hotdog-fold family is required for the biosynthesis of the naphthoquinone ring of vitamin K1 Joshua R. Widhalm, Chloë van Oostende, Fabienne Furt, and Gilles J. C. Basset PMCID: PMC2660889 The Epstein–Barr virus Bcl-2 homolog, BHRF1, blocks apoptosis by binding to a limited amount of Bim Anthony L. Desbien, John W. Kappler, and Philippa Marrack PMCID: PMC2657086 Regulation of the processivity and intracellular localization of Saccharomyces cerevisiae dynein by dynactin Julia R. Kardon, Samara L. Reck-Peterson, and Ronald D. Vale PMCID: PMC2657088 Larval dispersal connects fish populations in a network of marine protected areas Serge Planes, Geoffrey P. Jones, and Simon R. Thorrold PMCID: PMC2659712 The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans Lisa Klasson, Joakim Westberg, Panagiotis Sapountzis, Kristina Näslund, Ylva Lutnaes, Alistair C. Darby, Zoe Veneti, Lanming Chen, Henk R. Braig, Roger Garrett, Kostas Bourtzis, and Siv G. E. Andersson PMCID: PMC2659715 Transcriptional neoteny in the human brain Mehmet Somel, Henriette Franz, Zheng Yan, Anna Lorenc, Song Guo, Thomas Giger, Janet Kelso, Birgit Nickel, Michael Dannemann, Sabine Bahn, Maree J. Webster, Cynthia S. Weickert, Michael Lachmann, Svante Pääbo, and Philipp Khaitovich PMCID: PMC2659716 The cost of gene expression underlies a fitness trade-off in yeast Gregory I. Lang, Andrew W. Murray, and David Botstein PMCID: PMC2658138 Posttranscriptional regulation of interleukin-10 expression by hsa-miR-106a Amit Sharma, Manish Kumar, Jyotirmoi Aich, Manoj Hariharan, Samir K. Brahmachari, Anurag Agrawal, and Balaram Ghosh PMCID: PMC2659714 Malaria primes the innate immune response due to interferon-γ induced enhancement of toll-like receptor expression and function Bernardo S. Franklin, Peggy Parroche, Marco Antǒnio Ataíde, Fanny Lauw, Catherine Ropert, Rosane B. de Oliveira, Dhelio Pereira, Mauro Shugiro Tada, Paulo Nogueira, Luiz Hildebrando Pereira da Silva, Harry Bjorkbacka, Douglas T. Golenbock, and Ricardo T. Gazzinelli PMCID: PMC2657593 miR-375 maintains normal pancreatic α- and β-cell mass Matthew N. Poy, Jean Hausser, Mirko Trajkovski, Matthias Braun, Stephan Collins, Patrik Rorsman, Mihaela Zavolan, and Markus Stoffel PMCID: PMC2656556 From the Cover:
MUC1-induced alterations in a lipid metabolic gene network predict response of human breast cancers to tamoxifen treatment Sean P. Pitroda, Nikolai N. Khodarev, Michael A. Beckett, Donald W. Kufe, and Ralph R. Weichselbaum PMCID: PMC2656554 Seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance (SeSAME syndrome) caused by mutations in KCNJ10 Ute I. Scholl, Murim Choi, Tiewen Liu, Vincent T. Ramaekers, Martin G. Häusler, Joanne Grimmer, Sheldon W. Tobe, Anita Farhi, Carol Nelson-Williams, and Richard P. Lifton PMCID: PMC2656559 Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla Michael A. Mahowald, Federico E. Rey, Henning Seedorf, Peter J. Turnbaugh, Robert S. Fulton, Aye Wollam, Neha Shah, Chunyan Wang, Vincent Magrini, Richard K. Wilson, Brandi L. Cantarel, Pedro M. Coutinho, Bernard Henrissat, Lara W. Crock, Alison Russell, Nathan C. Verberkmoes, Robert L. Hettich, and Jeffrey I. Gordon PMCID: PMC2660063 Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites Sandrine Belouzard, Victor C. Chu, and Gary R. Whittaker PMCID: PMC2660061 Synaptic transmission block by presynaptic injection of oligomeric amyloid beta Herman Moreno, Eunah Yu, Gustavo Pigino, Alejandro I. Hernandez, Natalia Kim, Jorge E. Moreira, Mutsuyuki Sugimori, and Rodolfo R. Llinás PMCID: PMC2659170 Ruling out and ruling in neural codes Adam L. Jacobs, Gene Fridman, Robert M. Douglas, Nazia M. Alam, Peter. E. Latham, Glen T. Prusky, and Sheila Nirenberg PMCID: PMC2657589 Thyroid hormone modulates glucose production via a sympathetic pathway from the hypothalamic paraventricular nucleus to the liver Lars P. Klieverik, Sarah F. Janssen, Annelieke van Riel, Ewout Foppen, Peter H. Bisschop, Mireille J. Serlie, Anita Boelen, Mariëtte T. Ackermans, Hans P. Sauerwein, Eric Fliers, and Andries Kalsbeek PMCID: PMC2660059 Ethylene is an endogenous stimulator of cell division in the cambial meristem of Populus Jonathan Love, Simon Björklund, Jorma Vahala, Magnus Hertzberg, Jaakko Kangasjärvi, and Björn Sundberg PMCID: PMC2657089 Manipulability of comparative tests Wojciech Olszewski and Alvaro Sandroni PMCID: PMC2656560 Thinking like a trader selectively reduces individuals' loss aversion Peter Sokol-Hessner, Ming Hsu, Nina G. Curley, Mauricio R. Delgado, Colin F. Camerer, and Elizabeth A. Phelps PMCID: PMC2656558 Imprecise probability assessment of tipping points in the climate system Elmar Kriegler, Jim W. Hall, Hermann Held, Richard Dawson, and Hans Joachim Schellnhuber PMCID: PMC2657590 Synthesis of programmable integrases Russell M. Gordley, Charles A. Gersbach, and Carlos F. Barbas, III PMCID: PMC2654808 An inducible system for highly efficient production of recombinant adeno-associated virus (rAAV) vectors in insect Sf9 cells George Aslanidi, Kenneth Lamb, and Sergei Zolotukhin PMCID: PMC2654393 Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells Pierre-Olivier Estève, Hang Gyeong Chin, Jack Benner, George R. Feehery, Mala Samaranayake, Gregory A. Horwitz, Steven E. Jacobsen, and Sriharsa Pradhan PMCID: PMC2654809 Antibodies specifically targeting a locally misfolded region of tumor associated EGFR Thomas P. J. Garrett, Antony W. Burgess, Hui K. Gan, Rod B. Luwor, Glenn Cartwright, Francesca Walker, Suzanne G. Orchard, Andrew H. A. Clayton, Edouard C. Nice, Julie Rothacker, Bruno Catimel, Webster K. Cavenee, Lloyd J. Old, Elisabeth Stockert, Gerd Ritter, Timothy E. Adams, Peter A. Hoyne, Dane Wittrup, Ginger Chao, Jennifer R. Cochran, Cindy Luo, Mezhen Lou, Trevor Huyton, Yibin Xu, W. Douglas Fairlie, Shenggen Yao, Andrew M. Scott, and Terrance G. Johns PMCID: PMC2656555 Energy transduction in protein transport and the ATP hydrolytic cycle of SecA Alice Robson, Vicki A. M. Gold, Skye Hodson, Anthony R. Clarke, and Ian Collinson PMCID: PMC2653558 Negative autoregulation linearizes the dose–response and suppresses the heterogeneity of gene expression Dmitry Nevozhay, Rhys M. Adams, Kevin F. Murphy, Krešimir Josić, and Gábor Balázsi PMCID: PMC2654390 A unified model of protein dynamics Hans Frauenfelder, Guo Chen, Joel Berendzen, Paul W. Fenimore, Helén Jansson, Benjamin H. McMahon, Izabela R. Stroe, Jan Swenson, and Robert D. Young PMCID: PMC2649210 Crystal structure of dimeric cardiac L-type calcium channel regulatory domains bridged by Ca2+·calmodulins Jennifer L. Fallon, Mariah R. Baker, Liangwen Xiong, Ryan E. Loy, Guojun Yang, Robert T. Dirksen, Susan L. Hamilton, and Florante A. Quiocho PMCID: PMC2654391 FOXO3a-dependent regulation of Pink1 (Park6) mediates survival signaling in response to cytokine deprivation Yang Mei, Yiru Zhang, Kazuo Yamamoto, Wei Xie, Tak W. Mak, and Han You PMCID: PMC2654023 An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency Lena Ho, Jehnna L. Ronan, Jiang Wu, Brett T. Staahl, Lei Chen, Ann Kuo, Julie Lessard, Alexey I. Nesvizhskii, Jeff Ranish, and Gerald R. Crabtree PMCID: PMC2654396 An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network Lena Ho, Raja Jothi, Jehnna L. Ronan, Kairong Cui, Keji Zhao, and Gerald R. Crabtree PMCID: PMC2654397 Dynamic changes in paternal X-chromosome activity during imprinted X-chromosome inactivation in mice Catherine Patrat, Ikuhiro Okamoto, Patricia Diabangouaya, Vivian Vialon, Patricia Le Baccon, Jennifer Chow, and Edith Heard PMCID: PMC2653561 Skull and brain of a 300-million-year-old chimaeroid fish revealed by synchrotron holotomography Alan Pradel, Max Langer, John G. Maisey, Didier Geffard-Kuriyama, Peter Cloetens, Philippe Janvier, and Paul Tafforeau PMCID: PMC2653559 Reconstructing web evolution and spider diversification in the molecular era Todd A. Blackledge, Nikolaj Scharff, Jonathan A. Coddington, Tamas Szüts, John W. Wenzel, Cheryl Y. Hayashi, and Ingi Agnarsson PMCID: PMC2656561 Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals Hidenori Nishihara, Shigenori Maruyama, and Norihiro Okada PMCID: PMC2655268 Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck Ya-Long Guo, Jesper S. Bechsgaard, Tanja Slotte, Barbara Neuffer, Martin Lascoux, Detlef Weigel, and Mikkel H. Schierup PMCID: PMC2659713 H3 trimethyl K9 and H3 acetyl K9 chromatin modifications are associated with class switch recombination Fei Li Kuang, Zhonghui Luo, and Matthew D. Scharff PMCID: PMC2654022 IFNα kinoid vaccine-induced neutralizing antibodies prevent clinical manifestations in a lupus flare murine model Daniel Zagury, Hélène Le Buanec, Alexis Mathian, Patrick Larcier, Roger Burnett, Zahir Amoura, Dominique Emilie, Gabriel Peltre, Armand Bensussan, Bernard Bizzini, Robert C. Gallo, and Sophie Koutouzov PMCID: PMC2654395 EZH2 is a mediator of EWS/FLI1 driven tumor growth and metastasis blocking endothelial and neuro-ectodermal differentiation Günther H. S. Richter, Stephanie Plehm, Annette Fasan, Sabine Rössler, Rebekka Unland, Idriss M. Bennani-Baiti, Marc Hotfilder, Diana Löwel, Irene von Luettichau, Ilona Mossbrugger, Leticia Quintanilla-Martinez, Heinrich Kovar, Martin S. Staege, Carsten Müller-Tidow, and Stefan Burdach PMCID: PMC2656557 The ratio of NR2A/B NMDA receptor subunits determines the qualities of ocular dominance plasticity in visual cortex Kathleen K. A. Cho, Lena Khibnik, Benjamin D. Philpot, and Mark F. Bear PMCID: PMC2654025 Small-molecule screen identifies inhibitors of the neuronal K-Cl cotransporter KCC2 Eric Delpire, Emily Days, L. Michelle Lewis, Dehui Mi, Kwangho Kim, Craig W. Lindsley, and C. David Weaver PMCID: PMC2654392 A new model for studying tissue-specific mdr1a gene expression in vivo by live imaging Long Gu, Walter M. Tsark, Donna A. Brown, Suzette Blanchard, Timothy W. Synold, and Susan E. Kane PMCID: PMC2654810 INAUGURAL ARTICLE by a Recently Elected Academy Member: Identification of the phosphorylation sites on the E3 ubiquitin ligase Pellino that are critical for activation by IRAK1 and IRAK4 Hilary Smith, Mark Peggie, David G. Campbell, Franck Vandermoere, Emma Carrick, and Philip Cohen PMCID: PMC2651833 From the Cover:
Toxicity of atmospheric aerosols on marine phytoplankton Adina Paytan, Katherine R. M. Mackey, Ying Chen, Ivan D. Lima, Scott C. Doney, Natalie Mahowald, Rochelle Labiosa, and Anton F. Post PMCID: PMC2653564 Label-free biosensing with functionalized nanopipette probes Senkei Umehara, Miloslav Karhanek, Ronald W. Davis, and Nader Pourmand PMCID: PMC2651834 Identifying the proteins to which small-molecule probes and drugs bind in cells Shao-En Ong, Monica Schenone, Adam A. Margolin, Xiaoyu Li, Kathy Do, Mary K. Doud, D. R. Mani, Letian Kuai, Xiang Wang, John L. Wood, Nicola J. Tolliday, Angela N. Koehler, Lisa A. Marcaurelle, Todd R. Golub, Robert J. Gould, Stuart L. Schreiber, and Steven A. Carr PMCID: PMC2649954 Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy Timothy K. Lu and James J. Collins PMCID: PMC2649960 Membrane-associated farnesylated UCH-L1 promotes α-synuclein neurotoxicity and is a therapeutic target for Parkinson's disease Zhihua Liu, Robin K. Meray, Tom N. Grammatopoulos, Ross A. Fredenburg, Mark R. Cookson, Yichin Liu, Todd Logan, and Peter T. Lansbury, Jr. PMCID: PMC2651203 A P-type ATPase importer that discriminates between essential and toxic transition metals Oded Lewinson, Allen T. Lee, and Douglas C. Rees PMCID: PMC2651836 Identification of two distinct inactive conformations of the β2-adrenergic receptor reconciles structural and biochemical observations Ron O. Dror, Daniel H. Arlow, David W. Borhani, Morten Ø. Jensen, Stefano Piana, and David E. Shaw PMCID: PMC2650503 MLL5, a trithorax homolog, indirectly regulates H3K4 methylation, represses cyclin A2 expression, and promotes myogenic differentiation Soji Sebastian, Prethish Sreenivas, Ramkumar Sambasivan, Sirisha Cheedipudi, Prashanth Kandalla, Grace K. Pavlath, and Jyotsna Dhawan PMCID: PMC2651835 Noonan syndrome cardiac defects are caused by PTPN11 acting in endocardium to enhance endocardial-mesenchymal transformation Toshiyuki Araki, Gordon Chan, Susan Newbigging, Lily Morikawa, Roderick T. Bronson, and Benjamin G. Neel PMCID: PMC2649209 Revising the nitrogen cycle in the Peruvian oxygen minimum zone Phyllis Lam, Gaute Lavik, Marlene M. Jensen, Jack van de Vossenberg, Markus Schmid, Dagmar Woebken, Dimitri Gutiérrez, Rudolf Amann, Mike S. M. Jetten, and Marcel M. M. Kuypers PMCID: PMC2649953 The impact of human-made ecological changes on the genetic architecture of Daphnia species Nora Brede, Christoph Sandrock, Dietmar Straile, Piet Spaak, Thomas Jankowski, Bruno Streit, and Klaus Schwenk PMCID: PMC2653563 Identification of IL-17-producing FOXP3+ regulatory T cells in humans Kui Shin Voo, Yui-Hsi Wang, Fabio R. Santori, Cesar Boggiano, Yi-Hong Wang, Kazuhiko Arima, Laura Bover, Shino Hanabuchi, Jahan Khalili, Ekaterina Marinova, Biao Zheng, Dan R. Littman, and Yong-Jun Liu PMCID: PMC2653560 Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers Kimberly D. Siegmund, Paul Marjoram, Yen-Jung Woo, Simon Tavaré, and Darryl Shibata PMCID: PMC2651202 A family of Salmonella virulence factors functions as a distinct class of autoregulated E3 ubiquitin ligases Cindy M. Quezada, Stuart W. Hicks, Jorge E. Galán, and C. Erec Stebbins PMCID: PMC2653562 The role of the dioxin-responsive element cluster between the Cyp1a1 and Cyp1a2 loci in aryl hydrocarbon receptor biology Manabu Nukaya, Susan Moran, and Christopher A. Bradfield PMCID: PMC2651201 Large-scale impacts of herbivores on the structural diversity of African savannas Gregory P. Asner, Shaun R. Levick, Ty Kennedy-Bowdoin, David E. Knapp, Ruth Emerson, James Jacobson, Matthew S. Colgan, and Roberta E. Martin PMCID: PMC2650504 INAUGURAL ARTICLE by a Recently Elected Academy Member: Inhibition of HIV-1 replication by eIF3f Susana T. Valente, Greg M. Gilmartin, Christina Mott, Brie Falkard, and Stephen P. Goff PMCID: PMC2646627 Site-specific C-functionalization of free-(NH) peptides and glycine derivatives via direct C–H bond functionalization Liang Zhao, Oliver Baslé, and Chao-Jun Li PMCID: PMC2649206 A designed protein as experimental model of primordial folding Mourad Sadqi, Eva de Alba, Raúl Pérez-Jiménez, Jose M. Sanchez-Ruiz, and Victor Muñoz PMCID: PMC2647338 From the Cover:
Assessing dangerous climate change through an update of the Intergovernmental Panel on Climate Change (IPCC) “reasons for concern” Joel B. Smith, Stephen H. Schneider, Michael Oppenheimer, Gary W. Yohe, William Hare, Michael D. Mastrandrea, Anand Patwardhan, Ian Burton, Jan Corfee-Morlot, Chris H. D. Magadza, Hans-Martin Füssel, A. Barrie Pittock, Atiq Rahman, Avelino Suarez, and Jean-Pascal van Ypersele PMCID: PMC2648893 A FERM domain autoregulates Drosophila myosin 7a activity Yi Yang, Thomas G. Baboolal, Verl Siththanandan, Michael Chen, Matthew L. Walker, Peter J. Knight, Michelle Peckham, and James R. Sellers PMCID: PMC2649957 Identification and structural analysis of type I collagen sites in complex with fibronectin fragments Michèle C. Erat, David A. Slatter, Edward D. Lowe, Christopher J. Millard, Richard W. Farndale, Iain D. Campbell, and Ioannis Vakonakis PMCID: PMC2649207 Three-dimensional structure of the human copper transporter hCTR1 Christopher J. De Feo, Stephen G. Aller, Gnana S. Siluvai, Ninian J. Blackburn, and Vinzenz M. Unger PMCID: PMC2647337 Hedgehog signaling is restricted to the stromal compartment during pancreatic carcinogenesis Hua Tian, Christopher A. Callahan, Kelly J. DuPree, Walter C. Darbonne, Christina P. Ahn, Suzie J. Scales, and Frederic J. de Sauvage PMCID: PMC2647977 EGF receptor signaling blocks aryl hydrocarbon receptor-mediated transcription and cell differentiation in human epidermal keratinocytes Carrie Hayes Sutter, Hong Yin, Yunbo Li, Jennifer S. Mammen, Sridevi Bodreddigari, Gaylene Stevens, Judith A. Cole, and Thomas R. Sutter PMCID: PMC2649958 From the Cover:
Wnt/β-Catenin and noncanonical Wnt signaling interact in tissue evagination in the simple eumetazoan Hydra Isabelle Philipp, Roland Aufschnaiter, Suat Özbek, Stefanie Pontasch, Marcell Jenewein, Hiroshi Watanabe, Fabian Rentzsch, Thomas W. Holstein, and Bert Hobmayer PMCID: PMC2646623 Nitrous oxide emission by aquatic macrofauna Peter Stief, Morten Poulsen, Lars Peter Nielsen, Hans Brix, and Andreas Schramm PMCID: PMC2651200 A Bayesian approach for evaluating the impact of historical events on rates of diversification Brian R. Moore and Michael J. Donoghue PMCID: PMC2648891 Transcription factor function and promoter architecture govern the evolution of bacterial regulons J. Christian Perez and Eduardo A. Groisman PMCID: PMC2649204 Dendritic cell targeting of Bacillus anthracis protective antigen expressed by Lactobacillus acidophilus protects mice from lethal challenge M. Mohamadzadeh, T. Duong, S. J. Sandwick, T. Hoover, and T. R. Klaenhammer PMCID: PMC2647975 Glatiramer acetate increases IL-1 receptor antagonist but decreases T cell-induced IL-1β in human monocytes and multiple sclerosis Danielle Burger, Nicolas Molnarfi, Martin S. Weber, Karim J. Brandt, Mahdia Benkhoucha, Lyssia Gruaz, Michel Chofflon, Scott S. Zamvil, and Patrice H. Lalive PMCID: PMC2649955 From the Cover:
Instant immunity through chemically programmable vaccination and covalent self-assembly Mikhail Popkov, Beatriz Gonzalez, Subhash C. Sinha, and Carlos F. Barbas, III PMCID: PMC2649956 Angiotensin II signaling increases activity of the renal Na-Cl cotransporter through a WNK4-SPAK-dependent pathway Pedro San-Cristobal, Diana Pacheco-Alvarez, Ciaran Richardson, Aaron M. Ring, Norma Vazquez, Fatema H. Rafiqi, Divya Chari, Kristopher T. Kahle, Qiang Leng, Norma A. Bobadilla, Steven C. Hebert, Dario R. Alessi, Richard P. Lifton, and Gerardo Gamba PMCID: PMC2647339 Pulmonary autoimmunity as a feature of autoimmune polyendocrine syndrome type 1 and identification of KCNRG as a bronchial autoantigen Mohammad Alimohammadi, Noémie Dubois, Filip Sköldberg, Åsa Hallgren, Isabelle Tardivel, Håkan Hedstrand, Jan Haavik, Eystein S. Husebye, Jan Gustafsson, Fredrik Rorsman, Antonella Meloni, Christer Janson, Bernard Vialettes, Merja Kajosaari, William Egner, Ravishankar Sargur, Fredrik Pontén, Zahir Amoura, Alain Grimfeld, Filippo De Luca, Corrado Betterle, Jaakko Perheentupa, Olle Kämpe, and Jean-Claude Carel PMCID: PMC2648890 RE-1–silencing transcription factor shows tumor-suppressor functions and negatively regulates the oncogenic TAC1 in breast cancer cells Bobby Y. Reddy, Steven J. Greco, Prem S. Patel, Katarzyna A. Trzaska, and Pranela Rameshwar PMCID: PMC2647978 Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis Kristina A. Fox, Arati Ramesh, Jennifer E. Stearns, Agathe Bourgogne, Angelica Reyes-Jara, Wade C. Winkler, and Danielle A. Garsin PMCID: PMC2647976 Broad spectrum O-linked protein glycosylation in the human pathogen Neisseria gonorrhoeae Åshild Vik, Finn Erik Aas, Jan Haug Anonsen, Shaun Bilsborough, Andrea Schneider, Wolfgang Egge-Jacobsen, and Michael Koomey PMCID: PMC2648892 Intracerebroventricular amyloid-β antibodies reduce cerebral amyloid angiopathy and associated micro-hemorrhages in aged Tg2576 mice Deepak R. Thakker, Marcy R. Weatherspoon, Jonathan Harrison, Thomas E. Keene, Deanna S. Lane, William F. Kaemmerer, Gregory R. Stewart, and Lisa L. Shafer PMCID: PMC2647980 V600EBRAF is associated with disabled feedback inhibition of RAF–MEK signaling and elevated transcriptional output of the pathway Christine A. Pratilas, Barry S. Taylor, Qing Ye, Agnes Viale, Chris Sander, David B. Solit, and Neal Rosen PMCID: PMC2649208 The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis Tara J. Holman, Peter D. Jones, Laurel Russell, Anne Medhurst, Susana Úbeda Tomás, Prabhavathi Talloji, Julietta Marquez, Heike Schmuths, Swee-Ang Tung, Ian Taylor, Steven Footitt, Andreas Bachmair, Frederica L. Theodoulou, and Michael J. Holdsworth PMCID: PMC2649959 Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice Yasuyuki Takahashi, Kosuke M. Teshima, Shuji Yokoi, Hideki Innan, and Ko Shimamoto PMCID: PMC2647979 Normal forms for reduced stochastic climate models Andrew J. Majda, Christian Franzke, and Daan Crommelin PMCID: PMC2645348 From the Cover:
The outbreak of cooperation among success-driven individuals under noisy conditions Dirk Helbing and Wenjian Yu PMCID: PMC2646628 Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2g2 Wei Li, Daqi Tu, Lianyun Li, Thomas Wollert, Rodolfo Ghirlando, Axel T. Brunger, and Yihong Ye PMCID: PMC2644258 Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform R. J. Taylor, D. Falconnet, A. Niemistö, S. A. Ramsey, S. Prinz, I. Shmulevich, T. Galitski, and C. L. Hansen PMCID: PMC2644260 Computational structure-based redesign of enzyme activity Cheng-Yu Chen, Ivelin Georgiev, Amy C. Anderson, and Bruce R. Donald PMCID: PMC2645347 Sequence context-specific profiles for homology searching A. Biegert and J. Söding PMCID: PMC2645910 Rosid radiation and the rapid rise of angiosperm-dominated forests Hengchang Wang, Michael J. Moore, Pamela S. Soltis, Charles D. Bell, Samuel F. Brockington, Roolse Alexandre, Charles C. Davis, Maribeth Latvis, Steven R. Manchester, and Douglas E. Soltis PMCID: PMC2644257 Directed evolution of adeno-associated virus to an infectious respiratory virus Katherine J. D. A. Excoffon, James T. Koerber, David D. Dickey, Matthew Murtha, Shaf Keshavjee, Brian K. Kaspar, Joseph Zabner, and David V. Schaffer PMCID: PMC2646629 From the Cover:
Adjuvanted H5N1 vaccine induces early CD4+ T cell response that predicts long-term persistence of protective antibody levels Grazia Galli, Duccio Medini, Erica Borgogni, Luisanna Zedda, Monia Bardelli, Carmine Malzone, Sandra Nuti, Simona Tavarini, Chiara Sammicheli, Anne K. Hilbert, Volker Brauer, Angelika Banzhoff, Rino Rappuoli, Giuseppe Del Giudice, and Flora Castellino PMCID: PMC2646626 Glycogen synthase kinase 3β missplicing contributes to leukemia stem cell generation Annelie E. Abrahamsson, Ifat Geron, Jason Gotlib, Kim-Hien T. Dao, Charlene F. Barroga, Isabel G. Newton, Francis J. Giles, Jeffrey Durocher, Remi S. Creusot, Mobin Karimi, Carol Jones, James L. Zehnder, Armand Keating, Robert S. Negrin, Irving L. Weissman, and Catriona H. M. Jamieson PMCID: PMC2646624 Discordant memory B cell and circulating anti-Env antibody responses in HIV-1 infection Yongjun Guan, Mohammad M. Sajadi, Roberta Kamin-Lewis, Timothy R. Fouts, Anthony Dimitrov, Zhixin Zhang, Robert R. Redfield, Anthony L. DeVico, Robert C. Gallo, and George K. Lewis PMCID: PMC2644653 Abnormal lymphangiogenesis in idiopathic pulmonary fibrosis with insights into cellular and molecular mechanisms Souheil El-Chemaly, Daniela Malide, Enrique Zudaire, Yoshihiko Ikeda, Benjamin A. Weinberg, Gustavo Pacheco-Rodriguez, Ivan O. Rosas, Marta Aparicio, Ping Ren, Sandra D. MacDonald, Hai-Ping Wu, Steven D. Nathan, Frank Cuttitta, J. Philip McCoy, Bernadette R. Gochuico, and Joel Moss PMCID: PMC2646625 Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device AmirAli H. Talasaz, Ashley A. Powell, David E. Huber, James G. Berbee, Kyung-Ho Roh, Wong Yu, Wenzhong Xiao, Mark M. Davis, R. Fabian Pease, Michael N. Mindrinos, Stefanie S. Jeffrey, and Ronald W. Davis PMCID: PMC2645911 Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing D. R. Yoder-Himes, P. S. G. Chain, Y. Zhu, O. Wurtzel, E. M. Rubin, James M. Tiedje, and R. Sorek PMCID: PMC2645912 Pathogenic adaptation of intracellular bacteria by rewiring a cis-regulatory input function Suzanne E. Osborne, Don Walthers, Ana M. Tomljenovic, David T. Mulder, Uma Silphaduang, Nancy Duong, Michael J. Lowden, Mark E. Wickham, Ross F. Waller, Linda J. Kenney, and Brian K. Coombes PMCID: PMC2645909 Multimodal neuroimaging provides a highly consistent picture of energy metabolism, validating 31P MRS for measuring brain ATP synthesis Myriam M. Chaumeil, Julien Valette, Martine Guillermier, Emmanuel Brouillet, Fawzi Boumezbeur, Anne-Sophie Herard, Gilles Bloch, Philippe Hantraye, and Vincent Lebon PMCID: PMC2645913 Fos and Jun potentiate individual release sites and mobilize the reserve synaptic-vesicle pool at the Drosophila larval motor synapse Susy M. Kim, Vimlesh Kumar, Yong-Qi Lin, Shanker Karunanithi, and Mani Ramaswami PMCID: PMC2645346 K+-dependent paradoxical membrane depolarization and Na+ overload, major and reversible contributors to weakness by ion channel leaks Karin Jurkat-Rott, Marc-André Weber, Michael Fauler, Xiu-Hai Guo, Boris D. Holzherr, Agathe Paczulla, Nikolai Nordsborg, Wolfgang Joechle, and Frank Lehmann-Horn PMCID: PMC2644652 Positive regulation of minichromosome maintenance gene expression, DNA replication, and cell transformation by a plant retinoblastoma gene Paolo A. Sabelli, George Hoerster, Lucina E. Lizarraga, Sara W. Brown, William J. Gordon-Kamm, and Brian A. Larkins PMCID: PMC2645908 Micromagnetic selection of aptamers in microfluidic channels Xinhui Lou, Jiangrong Qian, Yi Xiao, Lisan Viel, Aren E. Gerdon, Eric T. Lagally, Paul Atzberger, Theodore M. Tarasow, Alan J. Heeger, and H. Tom Soh PMCID: PMC2637280 Oceanic acidification affects marine carbon pump and triggers extended marine oxygen holes Matthias Hofmann and Hans-Joachim Schellnhuber PMCID: PMC2642667 From the Cover:
Sensitive dependence of the motion of a legged robot on granular media Chen Li, Paul B. Umbanhowar, Haldun Komsuoglu, Daniel E. Koditschek, and Daniel I. Goldman PMCID: PMC2637910 From the Cover:
Reducing environmental risk by improving N management in intensive Chinese agricultural systems Xiao-Tang Ju, Guang-Xi Xing, Xin-Ping Chen, Shao-Lin Zhang, Li-Juan Zhang, Xue-Jun Liu, Zhen-Ling Cui, Bin Yin, Peter Christie, Zhao-Liang Zhu, and Fu-Suo Zhang PMCID: PMC2644255 Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes Douglas H. Sieglaff, W. Augustine Dunn, Xiaohui S. Xie, Karyn Megy, Osvaldo Marinotti, and Anthony A. James PMCID: PMC2640218 Identification of mRNA splicing factors as the endothelial receptor for carbohydrate-dependent lung colonization of cancer cells Shingo Hatakeyama, Kazuhiro Sugihara, Jun Nakayama, Tomoya O. Akama, Shuk-Man Annie Wong, Hiroto Kawashima, Jianing Zhang, David F. Smith, Chikara Ohyama, Minoru Fukuda, and Michiko N. Fukuda PMCID: PMC2642669 Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure Gleb Shtengel, James A. Galbraith, Catherine G. Galbraith, Jennifer Lippincott-Schwartz, Jennifer M. Gillette, Suliana Manley, Rachid Sougrat, Clare M. Waterman, Pakorn Kanchanawong, Michael W. Davidson, Richard D. Fetter, and Harald F. Hess PMCID: PMC2637278 Rubisco in complex with Rubisco large subunit methyltransferase Stefan Raunser, Roberta Magnani, Zhong Huang, Robert L. Houtz, Raymond C. Trievel, Pawel A. Penczek, and Thomas Walz PMCID: PMC2638739 Live cell microscopy analysis of radiation-induced DNA double-strand break motion B. Jakob, J. Splinter, M. Durante, and G. Taucher-Scholz PMCID: PMC2642473 Hedgehog signal transduction by Smoothened: Pharmacologic evidence for a 2-step activation process Rajat Rohatgi, Ljiljana Milenkovic, Ryan B. Corcoran, and Matthew P. Scott PMCID: PMC2642660 Dramatic declines in neotropical salamander populations are an important part of the global amphibian crisis Sean M. Rovito, Gabriela Parra-Olea, Carlos R. Vásquez-Almazán, Theodore J. Papenfuss, and David B. Wake PMCID: PMC2637906 Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing Moran Yassour, Tommy Kaplan, Hunter B. Fraser, Joshua Z. Levin, Jenna Pfiffner, Xian Adiconis, Gary Schroth, Shujun Luo, Irina Khrebtukova, Andreas Gnirke, Chad Nusbaum, Dawn-Anne Thompson, Nir Friedman, and Aviv Regev PMCID: PMC2638735 Purified hematopoietic stem cell allografts reconstitute immunity superior to bone marrow Gabriel J. Tsao, Jessica A. Allen, Kathryn A. Logronio, Laura C. Lazzeroni, and Judith A. Shizuru PMCID: PMC2644259 Enhanced selection of FoxP3+ T-regulatory cells protects CTLA-4-deficient mice from CNS autoimmune disease Johan Verhagen, Leona Gabryšová, Sophie Minaee, Catherine A. Sabatos, Graham Anderson, Arlene H. Sharpe, and David C. Wraith PMCID: PMC2642665 Receptor-mediated phagocytosis elicits cross-presentation in nonprofessional antigen-presenting cells Alessandra Giodini, Christoph Rahner, and Peter Cresswell PMCID: PMC2642664 From the Cover:
Small molecule blockers of the Alzheimer Aβ calcium channel potently protect neurons from Aβ cytotoxicity Juan Carlos Diaz, Olga Simakova, Kenneth A. Jacobson, Nelson Arispe, and Harvey B. Pollard PMCID: PMC2637905 Role of COX-2 in epithelial–stromal cell interactions and progression of ductal carcinoma in situ of the breast Min Hu, Guillermo Peluffo, Haiyan Chen, Rebecca Gelman, Stuart Schnitt, and Kornelia Polyak PMCID: PMC2642666 Dysregulated gene expression networks in human acute myelogenous leukemia stem cells Ravindra Majeti, Michael W. Becker, Qiang Tian, Tsung-Lu Michael Lee, Xiaowei Yan, Rui Liu, Jung-Hsien Chiang, Leroy Hood, Michael F. Clarke, and Irving L. Weissman PMCID: PMC2642659 Activated TNF-α/NF-κB signaling via down-regulation of Fas-associated factor 1 in asbestos-induced mesotheliomas from Arf knockout mice Deborah A. Altomare, Craig W. Menges, Jianming Pei, Lili Zhang, Kristine L. Skele-Stump, Michele Carbone, Agnes B. Kane, and Joseph R. Testa PMCID: PMC2644256 Early and sustained innate immune response defines pathology and death in nonhuman primates infected by highly pathogenic influenza virus Carole R. Baskin, Helle Bielefeldt-Ohmann, Terrence M. Tumpey, Patrick J. Sabourin, James P. Long, Adolfo García-Sastre, Airn-E. Tolnay, Randy Albrecht, John A. Pyles, Pam H. Olson, Lauri D. Aicher, Elizabeth R. Rosenzweig, Kaja Murali-Krishna, Edward A. Clark, Mark S. Kotur, Jamie L. Fornek, Sean Proll, Robert E. Palermo, Carol L. Sabourin, and Michael G. Katze PMCID: PMC2642661 Sigma factor mimicry involved in regulation of general stress response Anne Francez-Charlot, Julia Frunzke, Christian Reichen, Judith Zingg Ebneter, Benjamin Gourion, and Julia A. Vorholt PMCID: PMC2642658 Highly sensitive, quantitative cell-based assay for prions adsorbed to solid surfaces Julie Ann Edgeworth, Graham S. Jackson, Anthony R. Clarke, Charles Weissmann, and John Collinge PMCID: PMC2637901 Rescuing Z+ agrin splicing in Nova null mice restores synapse formation and unmasks a physiologic defect in motor neuron firing Matteo Ruggiu, Ruth Herbst, Natalie Kim, Marko Jevsek, John J. Fak, Mary Anne Mann, Gerald Fischbach, Steven J. Burden, and Robert B. Darnell PMCID: PMC2642475 Dual involvement of G-substrate in motor learning revealed by gene deletion Shogo Endo, Fumihiro Shutoh, Tung Le Dinh, Takehito Okamoto, Toshio Ikeda, Michiyuki Suzuki, Shigenori Kawahara, Dai Yanagihara, Yamato Sato, Kazuyuki Yamada, Toshiro Sakamoto, Yutaka Kirino, Nicholas A. Hartell, Kazuhiko Yamaguchi, Shigeyoshi Itohara, Angus C. Nairn, Paul Greengard, Soichi Nagao, and Masao Ito PMCID: PMC2642668 Odorant receptors at the growth cone are coupled to localized cAMP and Ca2+ increases Micol Maritan, Giovanni Monaco, Ilaria Zamparo, Manuela Zaccolo, Tullio Pozzan, and Claudia Lodovichi PMCID: PMC2642662 Dynamic regulation of mitochondrial function by glucocorticoids Jing Du, Yun Wang, Richard Hunter, Yanling Wei, Rayah Blumenthal, Cynthia Falke, Rushaniya Khairova, Rulun Zhou, Peixiong Yuan, Rodrigo Machado-Vieira, Bruce S. McEwen, and Husseini K. Manji PMCID: PMC2637276 AMPA receptor and GEF-H1/Lfc complex regulates dendritic spine development through RhoA signaling cascade Myoung-Goo Kang, Yurong Guo, and Richard L. Huganir PMCID: PMC2638734 Hippocampal theta rhythm and its coupling with gamma oscillations require fast inhibition onto parvalbumin-positive interneurons Peer Wulff, Alexey A. Ponomarenko, Marlene Bartos, Tatiana M. Korotkova, Elke C. Fuchs, Florian Bähner, Martin Both, Adriano B. L. Tort, Nancy J. Kopell, William Wisden, and Hannah Monyer PMCID: PMC2637907 Oxidant regulated inter-subunit disulfide bond formation between ASIC1a subunits Xiang-ming Zha, Runping Wang, Dan M. Collier, Peter M. Snyder, John A. Wemmie, and Michael J. Welsh PMCID: PMC2642663 Mechanism of PTC124 activity in cell-based luciferase assays of nonsense codon suppression Douglas S. Auld, Natasha Thorne, William F. Maguire, and James Inglese PMCID: PMC2638738 Acute regulation of tight junction ion selectivity in human airway epithelia Andrea N. Flynn, Omar A. Itani, Thomas O. Moninger, and Michael J. Welsh PMCID: PMC2638737 Genomic basis for stimulated respiration by plants growing under elevated carbon dioxide Andrew D. B. Leakey, Fangxiu Xu, Kelly M. Gillespie, Justin M. McGrath, Elizabeth A. Ainsworth, and Donald R. Ort PMCID: PMC2637909 Maize AMEIOTIC1 is essential for multiple early meiotic processes and likely required for the initiation of meiosis Wojciech P. Pawlowski, Chung-Ju Rachel Wang, Inna N. Golubovskaya, Jessica M. Szymaniak, Liang Shi, Olivier Hamant, Tong Zhu, Lisa Harper, William F. Sheridan, and W. Zacheus Cande PMCID: PMC2637902 From the Cover:
Cytokinins modulate auxin-induced organogenesis in plants via regulation of the auxin efflux Markéta Pernisová, Petr Klíma, Jakub Horák, Martina Válková, Jiří Malbeck, Přemysl Souček, Pavel Reichman, Klára Hoyerová, Jaroslava Dubová, Jiří Friml, Eva Za;žímalová, and Jan Hejátko PMCID: PMC2640219 Diatom plastids depend on nucleotide import from the cytosol Michelle Ast, Ansgar Gruber, Stephan Schmitz-Esser, Horst Ekkehard Neuhaus, Peter G. Kroth, Matthias Horn, and Ilka Haferkamp PMCID: PMC2642474 Identification of cis-regulatory sequences that activate transcription in the suspensor of plant embryos Tomokazu Kawashima, Xingjun Wang, Kelli F. Henry, Yuping Bi, Koen Weterings, and Robert B. Goldberg PMCID: PMC2638740 Aligned carbon nanotubes as polarization-sensitive, molecular near-field detectors Ertugrul Cubukcu, Fatih Degirmenci, Coskun Kocabas, Mariano A. Zimmler, John A. Rogers, and Federico Capasso PMCID: PMC2636739 From the Cover:
Dislocation theory of chirality-controlled nanotube growth Feng Ding, Avetik R. Harutyunyan, and Boris I. Yakobson PMCID: PMC2637275 Interference in acetylene intersystem crossing acts as the molecular analog of Young's double-slit experiment Mattijs de Groot, Robert W. Field, and Wybren J. Buma PMCID: PMC2632712 From the Cover:
Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase Sheena McGowan, Corrine J. Porter, Jonathan Lowther, Colin M. Stack, Sarah J. Golding, Tina S. Skinner-Adams, Katharine R. Trenholme, Franka Teuscher, Sheila M. Donnelly, Jolanta Grembecka, Artur Mucha, Pawel Kafarski, Ross DeGori, Ashley M. Buckle, Donald L. Gardiner, James C. Whisstock, and John P. Dalton PMCID: PMC2636733 Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays Yifat Merbl and Marc W. Kirschner PMCID: PMC2633216 Crystal structure of human prion protein bound to a therapeutic antibody S. V. Antonyuk, C. R. Trevitt, R. W. Strange, G. S. Jackson, D. Sangar, M. Batchelor, S. Cooper, C. Fraser, S. Jones, T. Georgiou, A. Khalili-Shirazi, A. R. Clarke, S. S. Hasnain, and J. Collinge PMCID: PMC2637903 Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron Sumit Borah, Anthony C. Wong, and Joan A. Steitz PMCID: PMC2636732 Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter Yan Gu, Indira H. Shrivastava, Susan G. Amara, and Ivet Bahar PMCID: PMC2637273 Identifying essential genes in Escherichia coli from a metabolic optimization principle Carlotta Martelli, Andrea De Martino, Enzo Marinari, Matteo Marsili, and Isaac Pérez Castillo PMCID: PMC2636734 Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin Ayana Tomita, Tokushi Sato, Kouhei Ichiyanagi, Shunsuke Nozawa, Hirohiko Ichikawa, Matthieu Chollet, Fumihiro Kawai, Sam-Yong Park, Takayuki Tsuduki, Takahisa Yamato, Shin-ya Koshihara, and Shin-ichi Adachi PMCID: PMC2637904 Estrogen promotes the survival and pulmonary metastasis of tuberin-null cells Jane J. Yu, Victoria A. Robb, Tasha A. Morrison, Eric A. Ariazi, Magdalena Karbowniczek, Aristotelis Astrinidis, Chunrong Wang, Lisa Hernandez-Cuebas, Laura F. Seeholzer, Emmanuelle Nicolas, Harvey Hensley, V. Craig Jordan, Cheryl L. Walker, and Elizabeth P. Henske PMCID: PMC2637277 Distinct functions for the catalytic and hemopexin domains of a Drosophila matrix metalloproteinase Bernadette M. Glasheen, Aashish T. Kabra, and Andrea Page-McCaw PMCID: PMC2636737 Culling experiments demonstrate size-class specific biomass increases with mortality A. Schröder, L. Persson, and A. M. de Roos PMCID: PMC2635838 Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions Gregory E. Sims, Se-Ran Jun, Guohong A. Wu, and Sung-Hou Kim PMCID: PMC2634796 Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata Silvia Poláková, Christian Blume, Julián Álvarez Zárate, Marek Mentel, Dorte Jørck-Ramberg, Jørgen Stenderup, and Jure Piškur PMCID: PMC2637908 B7-H1 (PD-L1) on T cells is required for T-cell-mediated conditioning of dendritic cell maturation Oezcan Talay, Ching-Hung Shen, Lieping Chen, and Jianzhu Chen PMCID: PMC2637274 Prevention of autoimmune disease by induction of tolerance to Toll-like receptor 7 Tomoko Hayashi, Christine S. Gray, Michael Chan, Rommel I. Tawatao, Lisa Ronacher, Maureen A. McGargill, Sandip K. Datta, Dennis A. Carson, and Maripat Corr PMCID: PMC2634806 Genome-wide association analysis reveals a SOD1 mutation in canine degenerative myelopathy that resembles amyotrophic lateral sclerosis Tomoyuki Awano, Gary S. Johnson, Claire M. Wade, Martin L. Katz, Gayle C. Johnson, Jeremy F. Taylor, Michele Perloski, Tara Biagi, Izabella Baranowska, Sam Long, Philip A. March, Natasha J. Olby, G. Diane Shelton, Shahnawaz Khan, Dennis P. O'Brien, Kerstin Lindblad-Toh, and Joan R. Coates PMCID: PMC2634802 The miR-17~92 cluster collaborates with the Sonic Hedgehog pathway in medulloblastoma Tamar Uziel, Fedor V. Karginov, Suqing Xie, Joel S. Parker, Yong-Dong Wang, Amar Gajjar, Lin He, David Ellison, Richard J. Gilbertson, Gregory Hannon, and Martine F. Roussel PMCID: PMC2636735 Prognostic gene signatures for non-small-cell lung cancer Paul C. Boutros, Suzanne K. Lau, Melania Pintilie, Ni Liu, Frances A. Shepherd, Sandy D. Der, Ming-Sound Tsao, Linda Z. Penn, and Igor Jurisica PMCID: PMC2636731 Potassium softens vascular endothelium and increases nitric oxide release H. Oberleithner, C. Callies, K. Kusche-Vihrog, H. Schillers, V. Shahin, C. Riethmüller, G. A. MacGregor, and H. E. de Wardener PMCID: PMC2637279 Knockin of mutant PIK3CA activates multiple oncogenic pathways John P. Gustin, Bedri Karakas, Michele B. Weiss, Abde M. Abukhdeir, Josh Lauring, Joseph P. Garay, David Cosgrove, Akina Tamaki, Hiroyuki Konishi, Yuko Konishi, Morassa Mohseni, Grace Wang, D. Marc Rosen, Samuel R. Denmeade, Michaela J. Higgins, Michele I. Vitolo, Kurtis E. Bachman, and Ben Ho Park PMCID: PMC2636736 Loss of cryptochrome reduces cancer risk in p53 mutant mice Nuri Ozturk, Jin Hyup Lee, Shobhan Gaddameedhi, and Aziz Sancar PMCID: PMC2634797 Noninvasive prediction of tumor responses to gemcitabine using positron emission tomography Rachel E. Laing, Martin A. Walter, Dean O. Campbell, Harvey R. Herschman, Nagichettiar Satyamurthy, Michael E. Phelps, Johannes Czernin, Owen N. Witte, and Caius G. Radu PMCID: PMC2636738 From the Cover:
Circadian oscillation of nucleotide excision repair in mammalian brain Tae-Hong Kang, Joyce T. Reardon, Michael Kemp, and Aziz Sancar PMCID: PMC2629438 Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization Grigory E. Pinchuk, Dmitry A. Rodionov, Chen Yang, Xiaoqing Li, Andrei L. Osterman, Etienne Dervyn, Oleg V. Geydebrekht, Samantha B. Reed, Margaret F. Romine, Frank R. Collart, James H. Scott, Jim K. Fredrickson, and Alexander S. Beliaev PMCID: PMC2636740 Discovery of a functional protein complex of netrin-4, laminin γ1 chain, and integrin α6β1 in mouse neural stem cells Fernanda I. Staquicini, Emmanuel Dias-Neto, Jianxue Li, Evan Y. Snyder, Richard L. Sidman, Renata Pasqualini, and Wadih Arap PMCID: PMC2635839 Glutamatergic regulation of serine racemase via reversal of PIP2 inhibition Asif K. Mustafa, Damian B. van Rossum, Randen L. Patterson, David Maag, Jeffrey T. Ehmsen, Sadia K. Gazi, Anutosh Chakraborty, Roxanne K. Barrow, L. Mario Amzel, and Solomon H. Snyder PMCID: PMC2635840 Calcium-activated nonspecific cation current and synaptic depression promote network-dependent burst oscillations Jonathan E. Rubin, John A. Hayes, Jeffrey L. Mendenhall, and Christopher A. Del Negro PMCID: PMC2636730 Early childhood stress is associated with elevated antibody levels to herpes simplex virus type 1 Elizabeth A. Shirtcliff, Christopher L. Coe, and Seth D. Pollak PMCID: PMC2634803 Stoichiometry of molecular complexes at adhesions in living cells Michelle A. Digman, Paul W. Wiseman, Colin Choi, Alan R. Horwitz, and Enrico Gratton PMCID: PMC2630200 An unrecognized extracellular function for an intracellular adapter protein released from the cytoplasm into the tumor microenvironment Paul J. Mintz, Marina Cardó-Vila, Michael G. Ozawa, Amin Hajitou, Roberto Rangel, Liliana Guzman-Rojas, Dawn R. Christianson, Marco A. Arap, Ricardo J. Giordano, Glauco R. Souza, Jeffrey Easley, Ahmad Salameh, Salvatore Oliviero, Ricardo R. Brentani, Erkki Koivunen, Wadih Arap, and Renata Pasqualini PMCID: PMC2630201 PGC-1α is coupled to HIF-1α-dependent gene expression by increasing mitochondrial oxygen consumption in skeletal muscle cells Kathleen A. O'Hagan, Sinead Cocchiglia, Alexander V. Zhdanov, Murtaza M. Tambuwala, Eoin P. Cummins, Mona Monfared, Terence A. Agbor, John F. Garvey, Dmitri B. Papkovsky, Cormac T. Taylor, and Bernard B. Allan PMCID: PMC2632715 ERAD inhibitors integrate ER stress with an epigenetic mechanism to activate BH3-only protein NOXA in cancer cells Qiuyan Wang, Helena Mora-Jensen, Marc A. Weniger, Patricia Perez-Galan, Chris Wolford, Tsonwin Hai, David Ron, Weiping Chen, William Trenkle, Adrian Wiestner, and Yihong Ye PMCID: PMC2629785 Na,K-ATPase signal transduction triggers CREB activation and dendritic growth Luc Desfrere, Marie Karlsson, Hiromi Hiyoshi, Seth Malmersjö, Evanthia Nanou, Manuel Estrada, Ayako Miyakawa, Hugo Lagercrantz, Abdeljabbar El Manira, Mark Lal, and Per Uhlén PMCID: PMC2629786 Nodal points and complexity of Notch-Ras signal integration Gregory D. Hurlbut, Mark W. Kankel, and Spyros Artavanis-Tsakonas PMCID: PMC2631081 Multiple transcription factor codes activate epidermal wound–response genes in Drosophila Joseph C. Pearson, Michelle T. Juarez, Myungjin Kim, and William McGinnis PMCID: PMC2630199 Long-lived Indy induces reduced mitochondrial reactive oxygen species production and oxidative damage Nicola Neretti, Pei-Yu Wang, Alexander S. Brodsky, Hieu H. Nyguyen, Kevin P. White, Blanka Rogina, and Stephen L. Helfand PMCID: PMC2629441 Design of 240,000 orthogonal 25mer DNA barcode probes Qikai Xu, Michael R. Schlabach, Gregory J. Hannon, and Stephen J. Elledge PMCID: PMC2631075 Human gut microbiota in obesity and after gastric bypass Husen Zhang, John K. DiBaise, Andrea Zuccolo, Dave Kudrna, Michele Braidotti, Yeisoo Yu, Prathap Parameswaran, Michael D. Crowell, Rod Wing, Bruce E. Rittmann, and Rosa Krajmalnik-Brown PMCID: PMC2629490 Quantitative peptidomics reveal brain peptide signatures of behavior Axel Brockmann, Suresh P. Annangudi, Timothy A. Richmond, Seth A. Ament, Fang Xie, Bruce R. Southey, Sandra R. Rodriguez-Zas, Gene E. Robinson, and Jonathan V. Sweedler PMCID: PMC2632711 Identification of compounds that potentiate CREB signaling as possible enhancers of long-term memory Menghang Xia, Ruili Huang, Vicky Guo, Noel Southall, Ming-Hsuang Cho, James Inglese, Christopher P. Austin, and Marshall Nirenberg PMCID: PMC2638736 Risk assessment in man and mouse Fuat Balci, David Freestone, and Charles R. Gallistel PMCID: PMC2634808 Disentangling prenatal and inherited influences in humans with an experimental design Frances Rice, Gordon T. Harold, Jacky Boivin, Dale F. Hay, Marianne van den Bree, and Anita Thapar PMCID: PMC2634805 Newborn infants detect the beat in music István Winkler, Gábor P. Háden, Olivia Ladinig, István Sziller, and Henkjan Honing PMCID: PMC2631079 Metamaterials and the Landau–Lifshitz permeability argument: Large permittivity begets high-frequency magnetism Roberto Merlin PMCID: PMC2634807 A hybrid nanomemristor/transistor logic circuit capable of self-programming Julien Borghetti, Zhiyong Li, Joseph Straznicky, Xuema Li, Douglas A. A. Ohlberg, Wei Wu, Duncan R. Stewart, and R. Stanley Williams PMCID: PMC2631082 Irreversible climate change due to carbon dioxide emissions Susan Solomon, Gian-Kasper Plattner, Reto Knutti, and Pierre Friedlingstein PMCID: PMC2632717 From the Cover:
Strong profiling is not mathematically optimal for discovering rare malfeasors William H. Press PMCID: PMC2634801 Direct quantification of polo-like kinase 1 activity in cells and tissues using a highly sensitive and specific ELISA assay Jung-Eun Park, Luowei Li, Joobae Park, Rainald Knecht, Klaus Strebhardt, Stuart H. Yuspa, and Kyung S. Lee PMCID: PMC2633213 Type III restriction enzymes communicate in 1D without looping between their target sites Subramanian P. Ramanathan, Kara van Aelst, Alice Sears, Luke J. Peakman, Fiona M. Diffin, Mark D. Szczelkun, and Ralf Seidel PMCID: PMC2633214 Aberrant miR-182 expression promotes melanoma metastasis by repressing FOXO3 and microphthalmia-associated transcription factor Miguel F. Segura, Douglas Hanniford, Silvia Menendez, Linsey Reavie, Xuanyi Zou, Silvia Alvarez-Diaz, Jan Zakrzewski, Elen Blochin, Amy Rose, Dusan Bogunovic, David Polsky, Jianjun Wei, Peng Lee, Ilana Belitskaya-Levy, Nina Bhardwaj, Iman Osman, and Eva Hernando PMCID: PMC2634798 Transient ciliogenesis involving Bardet-Biedl syndrome proteins is a fundamental characteristic of adipogenic differentiation Vincent Marion, Corinne Stoetzel, Dominique Schlicht, Nadia Messaddeq, Michael Koch, Elisabeth Flori, Jean Marc Danse, Jean-Louis Mandel, and Hélène Dollfus PMCID: PMC2635307 Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning Thouis R. Jones, Anne E. Carpenter, Michael R. Lamprecht, Jason Moffat, Serena J. Silver, Jennifer K. Grenier, Adam B. Castoreno, Ulrike S. Eggert, David E. Root, Polina Golland, and David M. Sabatini PMCID: PMC2634799 Regulation of Cyclin A protein in meiosis and early embryogenesis Leah Vardy, Jillian A. Pesin, and Terry L. Orr-Weaver PMCID: PMC2633217 Biosynthesis of the Caenorhabditis elegans dauer pheromone Rebecca A. Butcher, Justin R. Ragains, Weiqing Li, Gary Ruvkun, Jon Clardy, and Ho Yi Mak PMCID: PMC2631283 Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line Qi Zhao, Otavia L. Caballero, Samuel Levy, Brian J. Stevenson, Christian Iseli, Sandro J. de Souza, Pedro A. Galante, Dana Busam, Margaret A. Leversha, Kalyani Chadalavada, Yu-Hui Rogers, J. Craig Venter, Andrew J. G. Simpson, and Robert L. Strausberg PMCID: PMC2633215 The default mode network and self-referential processes in depression Yvette I. Sheline, Deanna M. Barch, Joseph L. Price, Melissa M. Rundle, S. Neil Vaishnavi, Abraham Z. Snyder, Mark A. Mintun, Suzhi Wang, Rebecca S. Coalson, and Marcus E. Raichle PMCID: PMC2631078 Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases Jennifer M. Brulc, Dionysios A. Antonopoulos, Margret E. Berg Miller, Melissa K. Wilson, Anthony C. Yannarell, Elizabeth A. Dinsdale, Robert E. Edwards, Edward D. Frank, Joanne B. Emerson, Pirjo Wacklin, Pedro M. Coutinho, Bernard Henrissat, Karen E. Nelson, and Bryan A. White PMCID: PMC2633212 From the Cover:
Protection of synapses against Alzheimer's-linked toxins: Insulin signaling prevents the pathogenic binding of Aβ oligomers Fernanda G. De Felice, Marcelo N. N. Vieira, Theresa R. Bomfim, Helena Decker, Pauline T. Velasco, Mary P. Lambert, Kirsten L. Viola, Wei-Qin Zhao, Sergio T. Ferreira, and William L. Klein PMCID: PMC2634809 An anterior temporal face patch in human cortex, predicted by macaque maps Reza Rajimehr, Jeremy C. Young, and Roger B. H. Tootell PMCID: PMC2632713 The carboxy-terminal domain of complexin I stimulates liposome fusion Jörg Malsam, Florian Seiler, Yvette Schollmeier, Patricia Rusu, Jean Michel Krause, and Thomas H. Söllner PMCID: PMC2632952 Tbx2b is required for ultraviolet photoreceptor cell specification during zebrafish retinal development Karen Alvarez-Delfin, Ann C. Morris, Corey D. Snelson, Joshua T. Gamse, Tripti Gupta, Florence L. Marlow, Mary C. Mullins, Harold A. Burgess, Michael Granato, and James M. Fadool PMCID: PMC2632714 Predicting human resting-state functional connectivity from structural connectivity C. J. Honey, O. Sporns, L. Cammoun, X. Gigandet, J. P. Thiran, R. Meuli, and P. Hagmann PMCID: PMC2634800 Functional coding variation in recombinant inbred mouse lines reveals multiple serotonin transporter-associated phenotypes Ana M. D. Carneiro, David C. Airey, Brent Thompson, Chong-Bin Zhu, Lu Lu, Elissa J. Chesler, Keith M. Erikson, and Randy D. Blakely PMCID: PMC2632716 Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes Fei Lu, Jetty S. S. Ammiraju, Abhijit Sanyal, Shengli Zhang, Rentao Song, Jinfeng Chen, Guisheng Li, Yi Sui, Xiang Song, Zhukuan Cheng, Antonio Costa de Oliveira, Jeffrey L. Bennetzen, Scott A. Jackson, Rod A. Wing, and Mingsheng Chen PMCID: PMC2629783 Climate change and health costs of air emissions from biofuels and gasoline Jason Hill, Stephen Polasky, Erik Nelson, David Tilman, Hong Huo, Lindsay Ludwig, James Neumann, Haochi Zheng, and Diego Bonta PMCID: PMC2634804 From the Cover:
Nanoscale magnetic resonance imaging C. L. Degen, M. Poggio, H. J. Mamin, C. T. Rettner, and D. Rugar PMCID: PMC2628306 Phase separation in hydrogen–helium mixtures at Mbar pressures Miguel A. Morales, Eric Schwegler, David Ceperley, Carlo Pierleoni, Sebastien Hamel, and Kyle Caspersen PMCID: PMC2631077 Behavioral experiments on biased voting in networks Michael Kearns, Stephen Judd, Jinsong Tan, and Jennifer Wortman PMCID: PMC2630202 Anthropogenic enhancement of Egypt's Mediterranean fishery Autumn J. Oczkowski, Scott W. Nixon, Stephen L. Granger, Abdel-Fattah M. El-Sayed, and Richard A. McKinney PMCID: PMC2629448 Quantifying environmental adaptation of metabolic pathways in metagenomics Tara A. Gianoulis, Jeroen Raes, Prianka V. Patel, Robert Bjornson, Jan O. Korbel, Ivica Letunic, Takuji Yamada, Alberto Paccanaro, Lars J. Jensen, Michael Snyder, Peer Bork, and Mark B. Gerstein PMCID: PMC2629784 Libraries against libraries for combinatorial selection of replicating antigen–antibody pairs Diana R. Bowley, Teresa M. Jones, Dennis R. Burton, and Richard A. Lerner PMCID: PMC2621251 Progressive aggregation despite chaperone associations of a mutant SOD1-YFP in transgenic mice that develop ALS Jiou Wang, George W. Farr, Caroline J. Zeiss, Diego J. Rodriguez-Gil, Jean H. Wilson, Krystyna Furtak, D. Thomas Rutkowski, Randal J. Kaufman, Cristian I. Ruse, John R. Yates, III, Steve Perrin, Mel B. Feany, and Arthur L. Horwich PMCID: PMC2631083 A signal-anchor sequence stimulates signal recognition particle binding to ribosomes from inside the exit tunnel Uta Berndt, Stefan Oellerer, Ying Zhang, Arthur E. Johnson, and Sabine Rospert PMCID: PMC2629443 Generalized ensemble methods for de novo structure prediction Alena Shmygelska and Michael Levitt PMCID: PMC2631076 Chloroplast protein targeting involves localized translation in Chlamydomonas James Uniacke and William Zerges PMCID: PMC2629442 Negative regulation of Caenorhabditis elegans epidermal damage responses by death-associated protein kinase Amy Tong, Grace Lynn, Vy Ngo, Daniel Wong, Sarah L. Moseley, Jonathan J. Ewbank, Alexandr Goncharov, Yi-Chun Wu, Nathalie Pujol, and Andrew D. Chisholm PMCID: PMC2629440 Expression profiling during ocular development identifies 2 Nlz genes with a critical role in optic fissure closure Jacob D. Brown, Sunit Dutta, Kapil Bharti, Robert F. Bonner, Peter J. Munson, Igor B. Dawid, Amana L. Akhtar, Ighovie F. Onojafe, Ramakrishna P. Alur, Jeffrey M. Gross, J. Fielding Hejtmancik, Xiaodong Jiao, Wai-Yee Chan, and Brian P. Brooks PMCID: PMC2631080 The influence of oceanographic fronts and early-life-history traits on connectivity among littoral fish species Juan A. Galarza, Josep Carreras-Carbonell, Enrique Macpherson, Marta Pascual, Severine Roques, George F. Turner, and Ciro Rico PMCID: PMC2629446 A calpain unique to alveolates is essential in Plasmodium falciparum and its knockdown reveals an involvement in pre-S-phase development Ilaria Russo, Anna Oksman, Barbara Vaupel, and Daniel E. Goldberg PMCID: PMC2629787 Integrin αvβ1 promotes infection by human metapneumovirus Gabriella Cseke, Melissa S. Maginnis, Reagan G. Cox, Sharon J. Tollefson, Amy B. Podsiad, David W. Wright, Terence S. Dermody, and John V. Williams PMCID: PMC2629439 Polymicrobial interactions stimulate resistance to host innate immunity through metabolite perception Matthew M. Ramsey and Marvin Whiteley PMCID: PMC2629492 Erythropoietin modulation of astrocyte water permeability as a component of neuroprotection Eli Gunnarson, Yutong Song, Jacob M. Kowalewski, Hjalmar Brismar, Michael Brines, Anthony Cerami, Ulf Andersson, Marina Zelenina, and Anita Aperia PMCID: PMC2629445 Adipokinetic hormone signaling through the gonadotropin-releasing hormone receptor modulates egg-laying in Caenorhabditis elegans Marleen Lindemans, Feng Liu, Tom Janssen, Steven J. Husson, Inge Mertens, Gerd Gäde, and Liliane Schoofs PMCID: PMC2629444 RNA-directed DNA methylation induces transcriptional activation in plants Kenichi Shibuya, Setsuko Fukushima, and Hiroshi Takatsuji PMCID: PMC2629447 Recordkeeping alters economic history by promoting reciprocity Sudipta Basu, John Dickhaut, Gary Hecht, Kristy Towry, and Gregory Waymire PMCID: PMC2627807 Structure of the human RECQ1 helicase reveals a putative strand-separation pin Ashley C. W. Pike, Binesh Shrestha, Venkateswarlu Popuri, Nicola Burgess-Brown, Laura Muzzolini, Silvia Costantini, Alessandro Vindigni, and Opher Gileadi PMCID: PMC2628305 Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis Elizabeth Villa, Jayati Sengupta, Leonardo G. Trabuco, Jamie LeBarron, William T. Baxter, Tanvir R. Shaikh, Robert A. Grassucci, Poul Nissen, Måns Ehrenberg, Klaus Schulten, and Joachim Frank PMCID: PMC2613361 Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus Ekta Khurana, Matteo Dal Peraro, Russell DeVane, Satyavani Vemparala, William F. DeGrado, and Michael L. Klein PMCID: PMC2626606 DJ-1/PARK7 is an important mediator of hypoxia-induced cellular responses Sophie Vasseur, Samia Afzal, Joël Tardivel-Lacombe, David S. Park, Juan Lucio Iovanna, and Tak Wah Mak PMCID: PMC2626605 A network biology approach to aging in yeast David R. Lorenz, Charles R. Cantor, and James J. Collins PMCID: PMC2629491 Constitutional hypomorphic telomerase mutations in patients with acute myeloid leukemia Rodrigo T. Calado, Joshua A. Regal, Mark Hills, William T. Yewdell, Leandro F. Dalmazzo, Marco A. Zago, Peter M. Lansdorp, Donna Hogge, Stephen J. Chanock, Elihu H. Estey, Roberto P. Falcão, and Neal S. Young PMCID: PMC2627806 Activated Wnt/ß-catenin signaling in melanoma is associated with decreased proliferation in patient tumors and a murine melanoma model Andy J. Chien, Erin C. Moore, Anke S. Lonsdorf, Rima M. Kulikauskas, Bonnie Gould Rothberg, Aaron J. Berger, Michael B. Major, Sam T. Hwang, David L. Rimm, and Randall T. Moon PMCID: PMC2626610 Intermittent hypoxia degrades HIF-2α via calpains resulting in oxidative stress: Implications for recurrent apnea-induced morbidities Jayasri Nanduri, Ning Wang, Guoxiang Yuan, Shakil A. Khan, Dangjai Souvannakitti, Ying-Jie Peng, Ganesh K. Kumar, Joseph A. Garcia, and Nanduri R. Prabhakar PMCID: PMC2626608 INAUGURAL ARTICLE by a Recently Elected Academy Member: A human B cell methylome at 100−base pair resolution Tibor A. Rauch, Xiwei Wu, Xueyan Zhong, Arthur D. Riggs, and Gerd P. Pfeifer PMCID: PMC2621253 Small-molecule inhibitors of integrin α2β1 that prevent pathological thrombus formation via an allosteric mechanism Meredith W. Miller, Sandeep Basra, Daniel W. Kulp, Paul C. Billings, Sungwook Choi, Mary Pat Beavers, Owen J. T. McCarty, Zhiying Zou, Mark L. Kahn, Joel S. Bennett, and William F. DeGrado PMCID: PMC2625282 Dual biosynthetic pathways to phytosterol via cycloartenol and lanosterol in Arabidopsis Kiyoshi Ohyama, Masashi Suzuki, Jun Kikuchi, Kazuki Saito, and Toshiya Muranaka PMCID: PMC2621255 The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3′ mRNA processing factors Orit Rozenblatt-Rosen, Takashi Nagaike, Joshua M. Francis, Syuzo Kaneko, Karen A. Glatt, Christina M. Hughes, Thomas LaFramboise, James L. Manley, and Matthew Meyerson PMCID: PMC2615665 TAp73 regulates the spindle assembly checkpoint by modulating BubR1 activity Richard Tomasini, Katsuya Tsuchihara, Chiharu Tsuda, Suzanne K. Lau, Margareta Wilhelm, Alessandro Ruffini, Ming-sound Tsao, Juan L. Iovanna, Andrea Jurisicova, Gerry Melino, and Tak W. Mak PMCID: PMC2621249 Tetrapyrrole signal as a cell-cycle coordinator from organelle to nuclear DNA replication in plant cells Yuki Kobayashi, Yu Kanesaki, Ayumi Tanaka, Haruko Kuroiwa, Tsuneyoshi Kuroiwa, and Kan Tanaka PMCID: PMC2625283 Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: A systems biological analysis Ruoyu Luo, Haibin Wei, Lin Ye, Kankan Wang, Fan Chen, Lijun Luo, Lei Liu, Yuanyuan Li, M. James C. Crabbe, Li Jin, Yixue Li, and Yang Zhong PMCID: PMC2615022 Regulation of ribonuclease E activity by the L4 ribosomal protein of Escherichia coli Dharam Singh, Ssu-Jean Chang, Pei-Hsun Lin, Olga V. Averina, Vladimir R. Kaberdin, and Sue Lin-Chao PMCID: PMC2626609 Aag-initiated base excision repair drives alkylation-induced retinal degeneration in mice Lisiane B. Meira, Catherine A. Moroski-Erkul, Stephanie L. Green, Jennifer A. Calvo, Roderick T. Bronson, Dharini Shah, and Leona D. Samson PMCID: PMC2621254 Psychosocial stress reversibly disrupts prefrontal processing and attentional control C. Liston, B. S. McEwen, and B. J. Casey PMCID: PMC2621252 Subdivisions of primary motor cortex based on cortico-motoneuronal cells Jean-Alban Rathelot and Peter L. Strick PMCID: PMC2621250 Prediction of a Rift Valley fever outbreak Assaf Anyamba, Jean-Paul Chretien, Jennifer Small, Compton J. Tucker, Pierre B. Formenty, Jason H. Richardson, Seth C. Britch, David C. Schnabel, Ralph L. Erickson, and Kenneth J. Linthicum PMCID: PMC2626607 INAUGURAL ARTICLE by a Recently Elected Academy Member: Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules Jovencio Hilario, Ichiro Amitani, Ronald J. Baskin, and Stephen C. Kowalczykowski PMCID: PMC2613362 From the Cover:
Nonequilibrium scale selection mechanism for columnar jointing Lucas Goehring, L. Mahadevan, and Stephen W. Morris PMCID: PMC2615021 From the Cover:
Forecasting United States mortality using cohort smoking histories Haidong Wang and Samuel H. Preston PMCID: PMC2613940 The specificity of T cell regulation that enables self-nonself discrimination in the periphery Yilun Wu, Zongyu Zheng, Yihua Jiang, Leonard Chess, and Hong Jiang PMCID: PMC2613037 O6-methylguanine-induced cell death involves exonuclease 1 as well as DNA mismatch recognition in vivo Joanna Klapacz, Lisiane B. Meira, David G. Luchetti, Jennifer A. Calvo, Roderick T. Bronson, Winfried Edelmann, and Leona D. Samson PMCID: PMC2613938 Cryo-electron tomography of mouse hepatitis virus: Insights into the structure of the coronavirion Montserrat Bárcena, Gert T. Oostergetel, Willem Bartelink, Frank G. A. Faas, Arie Verkleij, Peter J. M. Rottier, Abraham J. Koster, and Berend Jan Bosch PMCID: PMC2613939 Neuronal activity regulates phosphorylation-dependent surface delivery of G protein-activated inwardly rectifying potassium channels Hee Jung Chung, Xiang Qian, Melissa Ehlers, Yuh Nung Jan, and Lily Yeh Jan PMCID: PMC2613039 G protein-activated inwardly rectifying potassium channels mediate depotentiation of long-term potentiation Hee Jung Chung, Woo-Ping Ge, Xiang Qian, Ofer Wiser, Yuh Nung Jan, and Lily Yeh Jan PMCID: PMC2613041 Tyrosine phosphorylation of the BRI1 receptor kinase emerges as a component of brassinosteroid signaling in Arabidopsis Man-Ho Oh, Xiaofeng Wang, Uma Kota, Michael B. Goshe, Steven D. Clouse, and Steven C. Huber PMCID: PMC2613937 Glyconanoparticles allow pre-symptomatic in vivo imaging of brain disease Sander I. van Kasteren, Sandra J. Campbell, Sébastien Serres, Daniel C. Anthony, Nicola R. Sibson, and Benjamin G. Davis PMCID: PMC2607245 Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity Jonathan L. Payne, Alison G. Boyer, James H. Brown, Seth Finnegan, Michał Kowalewski, Richard A. Krause, Jr., S. Kathleen Lyons, Craig R. McClain, Daniel W. McShea, Philip M. Novack-Gottshall, Felisa A. Smith, Jennifer A. Stempien, and Steve C. Wang PMCID: PMC2607246 Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis Chin-Yu Chen, Chia-Chi Chang, Chi-Fu Yen, Michael T.-K. Chiu, and Wei-Hau Chang PMCID: PMC2610012 A conserved protonation-dependent switch controls drug binding in the Abl kinase Yibing Shan, Markus A. Seeliger, Michael P. Eastwood, Filipp Frank, Huafeng Xu, Morten Ø Jensen, Ron O. Dror, John Kuriyan, and David E. Shaw PMCID: PMC2610013 Trophic cascades promote threshold-like shifts in pelagic marine ecosystems Michele Casini, Joakim Hjelm, Juan-Carlos Molinero, Johan Lövgren, Massimiliano Cardinale, Valerio Bartolino, Andrea Belgrano, and Georgs Kornilovs PMCID: PMC2629246 On the fate of anthropogenic nitrogen William H. Schlesinger PMCID: PMC2613040 A regulatory interplay between miR-27a and Runx1 during megakaryopoiesis Oren Ben-Ami, Niv Pencovich, Joseph Lotem, Ditsa Levanon, and Yoram Groner PMCID: PMC2612036 ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes Adam A. Margolin, Teresa Palomero, Pavel Sumazin, Andrea Califano, Adolfo A. Ferrando, and Gustavo Stolovitzky PMCID: PMC2613038 From the Cover:
An empirical explanation of aperture effects Kyongje Sung, William T. Wojtach, and Dale Purves PMCID: PMC2612037 The Drosophila cell adhesion molecule Klingon is required for long-term memory formation and is regulated by Notch Motomi Matsuno, Junjiro Horiuchi, Tim Tully, and Minoru Saitoe PMCID: PMC2606903 Dividing glial cells maintain differentiated properties including complex morphology and functional synapses Woo-Ping Ge, Wei Zhou, Qingming Luo, Lily Yeh Jan, and Yuh Nung Jan PMCID: PMC2610014 INAUGURAL ARTICLE by a Recently Elected Academy Member: Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes Peter Kijun Kim, Dale Warren Hailey, Robert Thomas Mullen, and Jennifer Lippincott-Schwartz PMCID: PMC2602605 Multiplex protein assays based on real-time magnetic nanotag sensing Sebastian J. Osterfeld, Heng Yu, Richard S. Gaster, Stefano Caramuta, Liang Xu, Shu-Jen Han, Drew A. Hall, Robert J. Wilson, Shouheng Sun, Robert L. White, Ronald W. Davis, Nader Pourmand, and Shan X. Wang PMCID: PMC2602607 Structural basis for cross-resistance to ribosomal PTC antibiotics Chen Davidovich, Anat Bashan, and Ada Yonath PMCID: PMC2605634 Single virus detection from the reactive shift of a whispering-gallery mode F. Vollmer, S. Arnold, and D. Keng PMCID: PMC2603258 Determination of cell fate selection during phage lambda infection François St-Pierre and Drew Endy PMCID: PMC2605630 Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation Daichi Okuno, Ryo Fujisawa, Ryota Iino, Yoko Hirono-Hara, Hiromi Imamura, and Hiroyuki Noji PMCID: PMC2603257 Antagonism of E2F-1 regulated Bnip3 transcription by NF-κB is essential for basal cell survival James Shaw, Natalia Yurkova, Tong Zhang, Hongying Gang, Floribeth Aguilar, Danielle Weidman, Carly Scramstad, Harvey Weisman, and Lorrie A. Kirshenbaum PMCID: PMC2603431 A chemical biology approach reveals period shortening of the mammalian circadian clock by specific inhibition of GSK-3β Tsuyoshi Hirota, Warren G. Lewis, Andrew C. Liu, Jae Wook Lee, Peter G. Schultz, and Steve A. Kay PMCID: PMC2606900 White spot syndrome virus protein ICP11: A histone-binding DNA mimic that disrupts nucleosome assembly Hao-Ching Wang, Han-Ching Wang, Tzu-Ping Ko, Yu-May Lee, Jiann-Horng Leu, Chun-Han Ho, Wei-Pang Huang, Chu-Fang Lo, and Andrew H.-J. Wang PMCID: PMC2605418 Regulation of bone formation by osteoclasts involves Wnt/BMP signaling and the chemokine sphingosine-1-phosphate Larry Pederson, Ming Ruan, Jennifer J. Westendorf, Sundeep Khosla, and Merry Jo Oursler PMCID: PMC2603259 Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas Marco Minoia, Muriel Gaillard, Friedrich Reinhard, Milos Stojanov, Vladimir Sentchilo, and Jan Roelof van der Meer PMCID: PMC2605633 Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface Shipra Vaishnava, Cassie L. Behrendt, Anisa S. Ismail, Lars Eckmann, and Lora V. Hooper PMCID: PMC2603261 A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes Kasper Lage, Niclas Tue Hansen, E. Olof Karlberg, Aron C. Eklund, Francisco S. Roque, Patricia K. Donahoe, Zoltan Szallasi, Thomas Skøt Jensen, and Søren Brunak PMCID: PMC2606902 E3 ligase activity of BRCA1 is not essential for mammalian cell viability or homology-directed repair of double-strand DNA breaks Latarsha J. Reid, Reena Shakya, Ami P. Modi, Maria Lokshin, Jiin-Tsuey Cheng, Maria Jasin, Richard Baer, and Thomas Ludwig PMCID: PMC2603436 Trop2 identifies a subpopulation of murine and human prostate basal cells with stem cell characteristics Andrew S. Goldstein, Devon A. Lawson, Donghui Cheng, Wenyi Sun, Isla P. Garraway, and Owen N. Witte PMCID: PMC2603432 The co-chaperone BAG3 regulates Herpes Simplex Virus replication Christos A. Kyratsous and Saul J. Silverstein PMCID: PMC2603433 Molecular mechanism for the umami taste synergism Feng Zhang, Boris Klebansky, Richard M. Fine, Hong Xu, Alexey Pronin, Haitian Liu, Catherine Tachdjian, and Xiaodong Li PMCID: PMC2606899 Circuitry-based gene expression profiles in GABA cells of the trisynaptic pathway in schizophrenics versus bipolars Francine M. Benes, Benjamin Lim, David Matzilevich, Sivan Subburaju, and John P. Walsh PMCID: PMC2606901 The neuronal connexin36 interacts with and is phosphorylated by CaMKII in a way similar to CaMKII interaction with glutamate receptors Cantas Alev, Stephanie Urschel, Stephan Sonntag, Georg Zoidl, Alfredo G. Fort, Thorsten Höher, Mamoru Matsubara, Klaus Willecke, David C. Spray, and Rolf Dermietzel PMCID: PMC2605416 Neurogenesis and widespread forebrain migration of distinct GABAergic neurons from the postnatal subventricular zone Dragos Inta, Julieta Alfonso, Jakob von Engelhardt, Maria M. Kreuzberg, Axel H. Meyer, Johannes A. van Hooft, and Hannah Monyer PMCID: PMC2605417 Palmitoylation gates phosphorylation-dependent regulation of BK potassium channels Lijun Tian, Owen Jeffries, Heather McClafferty, Adam Molyvdas, Iain C. M. Rowe, Fozia Saleem, Lie Chen, Jennifer Greaves, Luke H. Chamberlain, Hans-Guenther Knaus, Peter Ruth, and Michael J. Shipston PMCID: PMC2605631 Association of the circadian rhythmic expression of GmCRY1a with a latitudinal cline in photoperiodic flowering of soybean Qingzhu Zhang, Hongyu Li, Rui Li, Ruibo Hu, Chengming Fan, Fulu Chen, Zonghua Wang, Xu Liu, Yongfu Fu, and Chentao Lin PMCID: PMC2607247 Discovery and revision of Arabidopsis genes by proteogenomics Natalie E. Castellana, Samuel H. Payne, Zhouxin Shen, Mario Stanke, Vineet Bafna, and Steven P. Briggs PMCID: PMC2605632 INAUGURAL ARTICLE by a Recently Elected Academy Member: AGO1-miR173 complex initiates phased siRNA formation in plants Taiowa A. Montgomery, Seong Jeon Yoo, Noah Fahlgren, Sunny D. Gilbert, Miya D. Howell, Christopher M. Sullivan, Amanda Alexander, Goretti Nguyen, Edwards Allen, Ji Hoon Ahn, and James C. Carrington PMCID: PMC2598728 Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model Hairi Li, Michael T. Lovci, Young-Soo Kwon, Michael G. Rosenfeld, Xiang-Dong Fu, and Gene W. Yeo PMCID: PMC2603435 Modeling the temporal evolution of the spindle assembly checkpoint and role of Aurora B kinase Hitesh B. Mistry, David E. MacCallum, Robert C. Jackson, Mark A. J. Chaplain, and Fordyce A. Davidson PMCID: PMC2629297 Multilayer three-dimensional super resolution imaging of thick biological samples Alipasha Vaziri, Jianyong Tang, Hari Shroff, and Charles V. Shank PMCID: PMC2603430 Solvent dramatically affects protein structure refinement Gaurav Chopra, Christopher M. Summa, and Michael Levitt PMCID: PMC2600579 A cytokine-neutralizing antibody as a structural mimetic of 2 receptor interactions Christian Grütter, Trevor Wilkinson, Richard Turner, Sadhana Podichetty, Donna Finch, Matthew McCourt, Scott Loning, Lutz Jermutus, and Markus G. Grütter PMCID: PMC2600578 Computation of mutual fitness by competing bacteria Juan E. Keymer, Peter Galajda, Guillaume Lambert, David Liao, and Robert H. Austin PMCID: PMC2600899 Rationalizing translation attenuation in the network architecture of the unfolded protein response Ala Trusina, Feroz R. Papa, and Chao Tang PMCID: PMC2603256 The Nore1B/Mst1 complex restrains antigen receptor-induced proliferation of naïve T cells Dawang Zhou, Benjamin D. Medoff, Lanfen Chen, Lequn Li, Xian-feng Zhang, Maria Praskova, Matthew Liu, Aimee Landry, Richard S. Blumberg, Vassiliki A. Boussiotis, Ramnik Xavier, and Joseph Avruch PMCID: PMC2600581 The role of nutricline depth in regulating the ocean carbon cycle Pedro Cermeño, Stephanie Dutkiewicz, Roger P. Harris, Mick Follows, Oscar Schofield, and Paul G. Falkowski PMCID: PMC2603260 From the Cover:
A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution Robert J. Gifford, Aris Katzourakis, Michael Tristem, Oliver G. Pybus, Mark Winters, and Robert W. Shafer PMCID: PMC2603253 Highly parallel identification of essential genes in cancer cells Biao Luo, Hiu Wing Cheung, Aravind Subramanian, Tanaz Sharifnia, Michael Okamoto, Xiaoping Yang, Greg Hinkle, Jesse S. Boehm, Rameen Beroukhim, Barbara A. Weir, Craig Mermel, David A. Barbie, Tarif Awad, Xiaochuan Zhou, Tuyen Nguyen, Bruno Piqani, Cheng Li, Todd R. Golub, Matthew Meyerson, Nir Hacohen, William C. Hahn, Eric S. Lander, David M. Sabatini, and David E. Root PMCID: PMC2629277 One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome Daniel G. Gibson, Gwynedd A. Benders, Kevin C. Axelrod, Jayshree Zaveri, Mikkel A. Algire, Monzia Moodie, Michael G. Montague, J. Craig Venter, Hamilton O. Smith, and Clyde A. Hutchison, III PMCID: PMC2600582 Genome-wide analysis of cancer/testis gene expression Oliver Hofmann, Otavia L. Caballero, Brian J. Stevenson, Yao-Tseng Chen, Tzeela Cohen, Ramon Chua, Christopher A. Maher, Sumir Panji, Ulf Schaefer, Adele Kruger, Minna Lehvaslaiho, Piero Carninci, Yoshihide Hayashizaki, C. Victor Jongeneel, Andrew J. G. Simpson, Lloyd J. Old, and Winston Hide PMCID: PMC2603434 Growth hormone-releasing hormone as an agonist of the ghrelin receptor GHS-R1a Felipe F. Casanueva, Jesus P. Camiña, Marcos C. Carreira, Yolanda Pazos, Jozsef L. Varga, and Andrew V. Schally PMCID: PMC2603429 Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma Rossa W. K. Chiu, K. C. Allen Chan, Yuan Gao, Virginia Y. M. Lau, Wenli Zheng, Tak Y. Leung, Chris H. F. Foo, Bin Xie, Nancy B. Y. Tsui, Fiona M. F. Lun, Benny C. Y. Zee, Tze K. Lau, Charles R. Cantor, and Y. M. Dennis Lo PMCID: PMC2600580 Early visual brain areas reflect the percept of an ambiguous scene Lauri Parkkonen, Jesper Andersson, Matti Hämäläinen, and Riitta Hari PMCID: PMC2602606 A selective Gβγ-linked intracellular mechanism for modulation of a ligand-gated ion channel by ethanol Gonzalo E. Yevenes, Gustavo Moraga-Cid, Robert W. Peoples, Günther Schmalzing, and Luis G. Aguayo PMCID: PMC2602604 Small-interfering RNAs from natural antisense transcripts derived from a cellulose synthase gene modulate cell wall biosynthesis in barley Michael A. Held, Bryan Penning, Amanda S. Brandt, Sarah A. Kessans, Weidong Yong, Steven R. Scofield, and Nicholas C. Carpita PMCID: PMC2603254 Increasing corn for biofuel production reduces biocontrol services in agricultural landscapes Douglas A. Landis, Mary M. Gardiner, Wopke van der Werf, and Scott M. Swinton PMCID: PMC2603255 From the Cover: Feature Article:
Light-arousal and circadian photoreception circuits intersect at the large PDF cells of the Drosophila brain Yuhua Shang, Leslie C. Griffith, and Michael Rosbash PMCID: PMC2596742 Nanodomain fragmentation and local rearrangements in CdSe under pressure Stefano Leoni, Reiner Ramlau, Katrin Meier, Marcus Schmidt, and Ulrich Schwarz PMCID: PMC2593618 Quantifying errors in trace species transport modeling Michael J. Prather, Xin Zhu, Susan E. Strahan, Stephen D. Steenrod, and Jose M. Rodriguez PMCID: PMC2598731 MicroRNA regulation of a cancer network: Consequences of the feedback loops involving miR-17-92, E2F, and Myc Baltazar D. Aguda, Yangjin Kim, Melissa G. Piper-Hunter, Avner Friedman, and Clay B. Marsh PMCID: PMC2598727 Overlapping functions of the four class XI myosins in Arabidopsis growth, root hair elongation, and organelle motility Alexey I. Prokhnevsky, Valera V. Peremyslov, and Valerian V. Dolja PMCID: PMC2596744 Bivalent domains enforce transcriptional memory of DNA methylated genes in cancer cells Jairo Rodriguez, Mar Muñoz, Laura Vives, Costas G. Frangou, Mark Groudine, and Miguel A. Peinado PMCID: PMC2596747 HIV infection-associated immune activation occurs by two distinct pathways that differentially affect CD4 and CD8 T cells Marta Catalfamo, Michele Di Mascio, Zonghui Hu, Sharat Srinivasula, Vishakha Thaker, Joseph Adelsberger, Adam Rupert, Michael Baseler, Yutaka Tagaya, Gregg Roby, Catherine Rehm, Dean Follmann, and H. Clifford Lane PMCID: PMC2596741 ERK-mediated regulation of leukotriene biosynthesis by androgens: A molecular basis for gender differences in inflammation and asthma Carlo Pergola, Gabriele Dodt, Antonietta Rossi, Eva Neunhoeffer, Barbara Lawrenz, Hinnak Northoff, Bengt Samuelsson, Olof Rådmark, Lidia Sautebin, and Oliver Werz PMCID: PMC2597692 A DNA transposon-based approach to validate oncogenic mutations in the mouse Qin Su, Haydn M. Prosser, Lia S. Campos, Mariaestela Ortiz, Takuro Nakamura, Madhuri Warren, Adam J. Dupuy, Nancy A. Jenkins, Neal G. Copeland, Allan Bradley, and Pentao Liu PMCID: PMC2597691 Noninvasive prenatal diagnosis of monogenic diseases by digital size selection and relative mutation dosage on DNA in maternal plasma Fiona M. F. Lun, Nancy B. Y. Tsui, K. C. Allen Chan, Tak Y. Leung, Tze K. Lau, Pimlak Charoenkwan, Katherine C. K. Chow, Wyatt Y. W. Lo, Chanane Wanapirak, Torpong Sanguansermsri, Charles R. Cantor, Rossa W. K. Chiu, and Y. M. Dennis Lo PMCID: PMC2596743 Paradoxical effects of increased expression of PGC-1α on muscle mitochondrial function and insulin-stimulated muscle glucose metabolism Cheol Soo Choi, Douglas E. Befroy, Roberto Codella, Sheene Kim, Richard M. Reznick, Yu-Jin Hwang, Zhen-Xiang Liu, Hui-Young Lee, Alberto Distefano, Varman T. Samuel, Dongyan Zhang, Gary W. Cline, Christoph Handschin, Jiandie Lin, Kitt F. Petersen, Bruce M. Spiegelman, and Gerald I. Shulman PMCID: PMC2598730 Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice Michelle M. Becker, Rachel L. Graham, Eric F. Donaldson, Barry Rockx, Amy C. Sims, Timothy Sheahan, Raymond J. Pickles, Davide Corti, Robert E. Johnston, Ralph S. Baric, and Mark R. Denison PMCID: PMC2588415 Role of prostaglandin D2 receptor DP as a suppressor of tumor hyperpermeability and angiogenesis in vivo Takahisa Murata, Michelle I. Lin, Kosuke Aritake, Shigeko Matsumoto, Shu Narumiya, Hiroshi Ozaki, Yoshihiro Urade, Masatoshi Hori, and William C. Sessa PMCID: PMC2596745 SMRT repression of nuclear receptors controls the adipogenic set point and metabolic homeostasis Russell R. Nofsinger, Pingping Li, Suk-Hyun Hong, Johan W. Jonker, Grant D. Barish, Hao Ying, Sheue-yann Cheng, Mathias LeBlanc, Wei Xu, Liming Pei, Yeon-Joo Kang, Michael Nelson, Michael Downes, Ruth T. Yu, Jerrold M. Olefsky, Chih-Hao Lee, and Ronald M. Evans PMCID: PMC2598729 INAUGURAL ARTICLE by a Recently Elected Academy Member: Phage ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) 29 protein p56 prevents viral DNA replication impairment caused by uracil excision activity of uracil-DNA glycosylase Gemma Serrano-Heras, Alicia Bravo, and Margarita Salas PMCID: PMC2565649 Global temperature responses to current emissions from the transport sectors Terje Berntsen and Jan Fuglestvedt PMCID: PMC2592361 Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules Qidong Hu, Young-Soo Kwon, Esperanza Nunez, Maria Dafne Cardamone, Kasey R. Hutt, Kenneth A. Ohgi, Ivan Garcia-Bassets, David W. Rose, Christopher K. Glass, Michael G. Rosenfeld, and Xiang-Dong Fu PMCID: PMC2593616 Requirement for binding multiple ATPs to convert a GroEL ring to the folding-active state Eli Chapman, George W. Farr, Wayne A. Fenton, Steven M. Johnson, and Arthur L. Horwich PMCID: PMC2592988 Identification of Barkor as a mammalian autophagy-specific factor for Beclin 1 and class III phosphatidylinositol 3-kinase Qiming Sun, Weiliang Fan, Keling Chen, Xiaojun Ding, She Chen, and Qing Zhong PMCID: PMC2592986 Kinesin's cover-neck bundle folds forward to generate force Ahmad S. Khalil, David C. Appleyard, Anna K. Labno, Adrien Georges, Martin Karplus, Angela M. Belcher, Wonmuk Hwang, and Matthew J. Lang PMCID: PMC2592363 Cell shape and cell-wall organization in Gram-negative bacteria Kerwyn Casey Huang, Ranjan Mukhopadhyay, Bingni Wen, Zemer Gitai, and Ned S. Wingreen PMCID: PMC2592989 Generation of a functional and durable vascular niche by the adenoviral E4ORF1 gene Marco Seandel, Jason M. Butler, Hideki Kobayashi, Andrea T. Hooper, Ian A. White, Fan Zhang, Eva L. Vertes, Mariko Kobayashi, Yan Zhang, Sergey V. Shmelkov, Neil R. Hackett, Sina Rabbany, Julie L. Boyer, and Shahin Rafii PMCID: PMC2588414 MicroRNA-184 antagonizes microRNA-205 to maintain SHIP2 levels in epithelia Jia Yu, David G. Ryan, Spiro Getsios, Michelle Oliveira-Fernandes, Anees Fatima, and Robert M. Lavker PMCID: PMC2587229 Forkhead Box m1 transcription factor is required for perinatal lung function Tanya V. Kalin, I-Ching Wang, Lucille Meliton, Yufang Zhang, Susan E. Wert, Xiaomeng Ren, Jonathan Snyder, Sheila M. Bell, Lloyd Graf, Jr., Jeffrey A. Whitsett, and Vladimir V. Kalinichenko PMCID: PMC2587228 Canopy nitrogen, carbon assimilation, and albedo in temperate and boreal forests: Functional relations and potential climate feedbacks S. V. Ollinger, A. D. Richardson, M. E. Martin, D. Y. Hollinger, S. E. Frolking, P. B. Reich, L. C. Plourde, G. G. Katul, J. W. Munger, R. Oren, M.-L. Smith, K. T. Paw U, P. V. Bolstad, B. D. Cook, M. C. Day, T. A. Martin, R. K. Monson, and H. P. Schmid PMCID: PMC2593617 mTORC1-dependent and -independent regulation of stem cell renewal, differentiation, and mobilization Boyi Gan, Ergün Sahin, Shan Jiang, Abel Sanchez-Aguilera, Kenneth L. Scott, Lynda Chin, David A. Williams, David J. Kwiatkowski, and Ronald A. DePinho PMCID: PMC2593615 Memory-like CD8+ and CD4+ T cells cooperate to break peripheral tolerance under lymphopenic conditions Cecile Le Saout, Sandie Mennechet, Naomi Taylor, and Javier Hernandez PMCID: PMC2587230 A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities Katherine S. Garman, Chaitanya R. Acharya, Elena Edelman, Marian Grade, Jochen Gaedcke, Shivani Sud, William Barry, Anna Mae Diehl, Dawn Provenzale, Geoffrey S. Ginsburg, B. Michael Ghadimi, Thomas Ried, Joseph R. Nevins, Sayan Mukherjee, David Hsu, and Anil Potti PMCID: PMC2592987 A zinc-dependent adhesion module is responsible for intercellular adhesion in staphylococcal biofilms Deborah G. Conrady, Cristin C. Brescia, Katsunori Horii, Alison A. Weiss, Daniel J. Hassett, and Andrew B. Herr PMCID: PMC2592360 S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions Sergey R. Konstantinov, Hauke Smidt, Willem M. de Vos, Sven C. M. Bruijns, Satwinder Kaur Singh, Florence Valence, Daniel Molle, Sylvie Lortal, Eric Altermann, Todd R. Klaenhammer, and Yvette van Kooyk PMCID: PMC2592362 Left-right asymmetry of the hippocampal synapses with differential subunit allocation of glutamate receptors Yoshiaki Shinohara, Hajime Hirase, Masahiko Watanabe, Makoto Itakura, Masami Takahashi, and Ryuichi Shigemoto PMCID: PMC2593619 Endogenous methyl palmitate modulates nicotinic receptor-mediated transmission in the superior cervical ganglion Hung Wen Lin, Chao-Zong Liu, Deshou Cao, Po-Yi Chen, Mei-Fang Chen, Shinn-Zong Lin, Mansoor Mozayan, Alex F. Chen, Louis S. Premkumar, Donald S. Torry, and Tony J.-F. Lee PMCID: PMC2596137 Rods-cones and melanopsin detect light and dark to modulate sleep independent of image formation C. M. Altimus, A. D. Güler, K. L. Villa, D. S. McNeill, T. A. LeGates, and S. Hattar PMCID: PMC2596746 From the Cover: Feature Article:
Initiation and elongation in fibrillation of ALS-linked superoxide dismutase Madhuri Chattopadhyay, Armando Durazo, Se Hui Sohn, Cynthia D. Strong, Edith B. Gralla, Julian P. Whitelegge, and Joan Selverstone Valentine PMCID: PMC2585484 From the Cover:
Materials and noncoplanar mesh designs for integrated circuits with linear elastic responses to extreme mechanical deformations Dae-Hyeong Kim, Jizhou Song, Won Mook Choi, Hoon-Sik Kim, Rak-Hwan Kim, Zhuangjian Liu, Yonggang Y. Huang, Keh-Chih Hwang, Yong-wei Zhang, and John A. Rogers PMCID: PMC2584145 A general framework for multiple testing dependence Jeffrey T. Leek and John D. Storey PMCID: PMC2586646 Restoration of electron transport without proton pumping in mammalian mitochondria Ester Perales-Clemente, Maria Pilar Bayona-Bafaluy, Acisclo Pérez-Martos, Antoni Barrientos, Patricio Fernández-Silva, and Jose Antonio Enriquez PMCID: PMC2585044 Cell packing influences planar cell polarity signaling Dali Ma, Keith Amonlirdviman, Robin L. Raffard, Alessandro Abate, Claire J. Tomlin, and Jeffrey D. Axelrod PMCID: PMC2585485 Wnt signaling promotes AChR aggregation at the neuromuscular synapse in collaboration with agrin Juan P. Henriquez, Anna Webb, Matthew Bence, Heidi Bildsoe, Macarena Sahores, Simon M. Hughes, and Patricia C. Salinas PMCID: PMC2585041 Network analysis identifies weak and strong links in a metapopulation system Alejandro F. Rozenfeld, Sophie Arnaud-Haond, Emilio Hernández-García, Víctor M. Eguíluz, Ester A. Serrão, and Carlos M. Duarte PMCID: PMC2585483 Evolutionary and functional divergence between the cystic fibrosis transmembrane conductance regulator and related ATP-binding cassette transporters I. King Jordan, Karthik C. Kota, Guiying Cui, Christopher H. Thompson, and Nael A. McCarty PMCID: PMC2585040 Notch and Kras reprogram pancreatic acinar cells to ductal intraepithelial neoplasia Jean-Paul De La O, Lyska L. Emerson, Jessica L. Goodman, Scott C. Froebe, Benjamin E. Illum, Andrew B. Curtis, and L. Charles Murtaugh PMCID: PMC2585942 Live-cell imaging of dendritic spines by STED microscopy U. Valentin Nägerl, Katrin I. Willig, Birka Hein, Stefan W. Hell, and Tobias Bonhoeffer PMCID: PMC2585941 Transmitter-receptor mismatch in GABAergic synapses in the absence of activity Roberta Cesa, Laura Morando, and Piergiorgio Strata PMCID: PMC2585043 Leptin-enhanced neointimal hyperplasia is reduced by mTOR and PI3K inhibitors Jian Shan, Thomas B. Nguyen, Hana Totary-Jain, Hayes Dansky, Steven O. Marx, and Andrew R. Marks PMCID: PMC2585045 INAUGURAL ARTICLE by a Recently Elected Academy Member: Apoptosis is triggered when prosurvival Bcl-2 proteins cannot restrain Bax Jamie I. Fletcher, Sarina Meusburger, Christine J. Hawkins, David T. Riglar, Erinna F. Lee, W. Douglas Fairlie, David C. S. Huang, and Jerry M. Adams PMCID: PMC2577705 Micrometeorites from the Transantarctic Mountains P. Rochette, L. Folco, C. Suavet, M. van Ginneken, J. Gattacceca, N. Perchiazzi, R. Braucher, and R. P. Harvey PMCID: PMC2583132 Water conservation in irrigation can increase water use Frank A. Ward and Manuel Pulido-Velazquez PMCID: PMC2584147 A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway Christian D. Schlieker, Annemarthe G. Van der Veen, Jadyn R. Damon, Eric Spooner, and Hidde L. Ploegh PMCID: PMC2584574 DNA energy landscapes via calorimetric detection of microstate ensembles of metastable macrostates and triplet repeat diseases Jens Völker, Horst H. Klump, and Kenneth J. Breslauer PMCID: PMC2584148 Impaired bone development and increased mesenchymal progenitor cells in calvaria of RB1−/− mice Gabriel M. Gutierrez, Elizabeth Kong, Yves Sabbagh, Nelson E. Brown, Jong-Seo Lee, Marie B. Demay, David M. Thomas, and Philip W. Hinds PMCID: PMC2585042 Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa Rebecca L. Vega Thurber, Katie L. Barott, Dana Hall, Hong Liu, Beltran Rodriguez-Mueller, Christelle Desnues, Robert A. Edwards, Matthew Haynes, Florent E. Angly, Linda Wegley, and Forest L. Rohwer PMCID: PMC2584576 Mitomycin C-treated dendritic cells inactivate autoreactive T cells: Toward the development of a tolerogenic vaccine in autoimmune diseases Peter Terness, Thilo Oelert, Sandra Ehser, Jing Jing Chuang, Imad Lahdou, Christian Kleist, Florian Velten, Günter J. Hämmerling, Bernd Arnold, and Gerhard Opelz PMCID: PMC2584573 Medial temporal lobe BOLD activity at rest predicts individual differences in memory ability in healthy young adults Gagan S. Wig, Scott T. Grafton, Kathryn E. Demos, George L. Wolford, Steven E. Petersen, and William M. Kelley PMCID: PMC2582045 Altered surface trafficking of presynaptic cannabinoid type 1 receptor in and out synaptic terminals parallels receptor desensitization Lenka Mikasova, Laurent Groc, Daniel Choquet, and Olivier J. Manzoni PMCID: PMC2584146 Functional assessment of allelic variants in the SLC26A4 gene involved in Pendred syndrome and nonsyndromic EVA Alejandra Pera, Silvia Dossena, Simona Rodighiero, Marta Gandía, Guido Bottà, Giuliano Meyer, Felipe Moreno, Charity Nofziger, Concepción Hernández-Chico, and Markus Paulmichl PMCID: PMC2584577 High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries Luca Mannocci, Yixin Zhang, Jörg Scheuermann, Markus Leimbacher, Gianluca De Bellis, Ermanno Rizzi, Christoph Dumelin, Samu Melkko, and Dario Neri PMCID: PMC2584757 Computing the stability diagram of the Trp-cage miniprotein Dietmar Paschek, Sascha Hempel, and Angel E. García PMCID: PMC2582582 The mechanism of transport by mitochondrial carriers based on analysis of symmetry Alan J. Robinson, Catherine Overy, and Edmund R. S. Kunji PMCID: PMC2582046 Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor Tanja Mittag, Stephen Orlicky, Wing-Yiu Choy, Xiaojing Tang, Hong Lin, Frank Sicheri, Lewis E. Kay, Mike Tyers, and Julie D. Forman-Kay PMCID: PMC2582940 microRNA-138 modulates cardiac patterning during embryonic development Sarah U. Morton, Paul J. Scherz, Kimberly R. Cordes, Kathryn N. Ivey, Didier Y. R. Stainier, and Deepak Srivastava PMCID: PMC2582580 Sustaining biodiversity in ancient tropical countryside Jai Ranganathan, R. J. Ranjit Daniels, M. D. Subash Chandran, Paul R. Ehrlich, and Gretchen C. Daily PMCID: PMC2577706 From the Cover:
Carbon and nitrogen stable isotopes in fast food: Signatures of corn and confinement A. Hope Jahren and Rebecca A. Kraft PMCID: PMC2582047 A single-cell view on the ecophysiology of anaerobic phototrophic bacteria Niculina Musat, Hannah Halm, Bärbel Winterholler, Peter Hoppe, Sandro Peduzzi, Francois Hillion, Francois Horreard, Rudolf Amann, Bo B. Jørgensen, and Marcel M. M. Kuypers PMCID: PMC2582579 Frequency-dependent selection maintains clonal diversity in an asexual organism Andrew R. Weeks and Ary A. Hoffmann PMCID: PMC2582578 Intralymphatic allergen administration renders specific immunotherapy faster and safer: A randomized controlled trial Gabriela Senti, Bettina M. Prinz Vavricka, Iris Erdmann, Mella I. Diaz, Richard Markus, Stephen J. McCormack, John J. Simard, Brunello Wüthrich, Reto Crameri, Nicole Graf, Pål Johansen, and Thomas M. Kündig PMCID: PMC2582048 T lymphocytes potentiate endogenous neuroprotective inflammation in a mouse model of ALS Isaac M. Chiu, Adam Chen, Yi Zheng, Bela Kosaras, Stefanos A. Tsiftsoglou, Timothy K. Vartanian, Robert H. Brown, Jr, and Michael C. Carroll PMCID: PMC2581614 Dynamic NMR effects in breast cancer dynamic-contrast-enhanced MRI Xin Li, Wei Huang, Elizabeth A. Morris, Luminita A. Tudorica, Venkatraman E. Seshan, William D. Rooney, Ian Tagge, Ya Wang, Jingang Xu, and Charles S. Springer, Jr PMCID: PMC2582941 The magnetic resonance shutter speed discriminates vascular properties of malignant and benign breast tumors in vivo Wei Huang, Xin Li, Elizabeth A. Morris, Luminita A. Tudorica, Venkatraman E. Seshan, William D. Rooney, Ian Tagge, Ya Wang, Jingang Xu, and Charles S. Springer PMCID: PMC2582583 Deletion of the chloride transporter Slc26a9 causes loss of tubulovesicles in parietal cells and impairs acid secretion in the stomach Jie Xu, Penghong Song, Marian L. Miller, Frank Borgese, Sharon Barone, Brigitte Riederer, Zhaohui Wang, Seth L. Alper, John G. Forte, Gary E. Shull, Jordi Ehrenfeld, Ursula Seidler, and Manoocher Soleimani PMCID: PMC2582584 In vivo efficacy of the Bcl-2 antagonist ABT-737 against aggressive Myc-driven lymphomas Kylie D. Mason, Cassandra J. Vandenberg, Clare L. Scott, Andrew H. Wei, Suzanne Cory, David C. S. Huang, and Andrew W. Roberts PMCID: PMC2582212 BCR-ABL-transformed GMP as myeloid leukemic stem cells Yosuke Minami, Scott A. Stuart, Tomokatsu Ikawa, Yong Jiang, Asoka Banno, Irina C. Hunton, Dennis J. Young, Tomoki Naoe, Cornelis Murre, Catriona H. M. Jamieson, and Jean Y. J. Wang PMCID: PMC2582213 F-pili dynamics by live-cell imaging Margaret Clarke, Lucinda Maddera, Robin L. Harris, and Philip M. Silverman PMCID: PMC2582581 Stimulation of Ebola virus production from persistent infection through activation of the Ras/MAPK pathway James E. Strong, Gary Wong, Shane E. Jones, Allen Grolla, Steven Theriault, Gary P. Kobinger, and Heinz Feldmann PMCID: PMC2577702 Ocean methane hydrates as a slow tipping point in the global carbon cycle David Archer, Bruce Buffett, and Victor Brovkin PMCID: PMC2584575 |
