September 6, 2011 u vol. 108 u no. 36 u 14707–15010

Cover image: Pictured are gastric epithelial cells infected with the gut bacteria, Helicobacter pylori, which are associated with an increased risk of gastric cancers. Isabella M. Toller et al. found that H. pylori infection damages the genome of host cells, causing breaks in both complementary strands of DNA. The damage triggered DNA repair responses, but pro- longed infection resulted in unrepaired DNA breaks and harmed host cell viability. The findings suggest a possible mechanism for the bacteria’s carcinogenic properties. See the article by Toller et al. on pages 14944–14949. Image courtesy of Martin Oeggerli (Micronaut and School of Applied Sciences Northwestern Switzerland, Muttenz, Switzerland). From the Cover

14944 Helicobacter pylori can cause DNA damage 14723 MicroRNA and olfactory conditioning 14819 Unraveling protein–DNA interactions 14902 Pathogenesis of Epstein-Barr virus 14998 Neuronal basis of delayed gratification

14711 Olfactory habituation: Fresh insights from flies Contents David L. Glanzman See companion articles on pages E646 and 14721 and pages E655 and 14723

THIS WEEK IN PNAS 14713 (Compressed) sensing and sensibility Vijay S. Pande See companion article on page 14819 14707 In This Issue 14715 Transcription factor RBPJ/CSL: A genome-wide look at transcriptional regulation Lucio Miele LETTERS (ONLINE ONLY) See companion articles on pages 14902 and 14908

E625 Social influence benefits the wisdom of individuals in the crowd Simon Farrell PNAS PLUS (AUTHOR SUMMARIES) E626 Reply to Farrell: Improved individual estimation success can imply collective tunnel vision BIOLOGICAL SCIENCES Heiko Rauhut, Jan Lorenz, Frank Schweitzer, and Dirk Helbing BIOCHEMISTRY 14717 Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner COMMENTARIES Hua-Lin Zhou, Melissa N. Hinman, Victoria A. Barron, Cuiyu Geng, Guangjin Zhou, Guangbin Luo, Ruth E. Siegel, and Hua Lou 14709 Himalayan glaciers: The big picture is a montage See full research article on page E627 of www.pnas.org Jeffrey S. Kargel, J. Graham Cogley, Gregory J. Leonard, Umesh Haritashya, and Alton Byers 14719 Human Polymerase-Associated Factor complex (PAFc) See companion article on page 14011 of issue 34 connects the Super Elongation Complex (SEC) to RNA in volume 108 polymerase II on chromatin Nanhai He, Caleb K. Chan, Bijan Sobhian, Seemay Chou, Yuhua Xue, Min Liu, Tom Alber, Monsef Benkirane, and Qiang Zhou Free online through the PNAS open access option. See full research article on page E636 of www.pnas.org

PNAS u September 6, 2011 u vol. 108 u no. 36 u iii–ix Downloaded by guest on September 24, 2021 GENETICS 14757 Photoelectron spectroscopic and computational studies 1− 1−/2− 14721 Plasticity of local GABAergic interneurons drives of the Pt@Pb10 and Pt@Pb12 anions olfactory habituation Andrej Grubisic, Haopeng Wang, Xiang Li, Yeon-Jae Ko, Sudeshna Das, Madhumala K. Sadanandappa, Adrian F. Sanem Kocak, Mark R. Pederson, Kit H. Bowen, Dervan, Aoife Larkin, John Anthony Lee, Indulekha P. and Bryan W. Eichhorn Sudhakaran, Rashi Priya, Raheleh Heidari, Eimear E. 14763 In situ molecular NMR picture of bioavailable calcium Holohan, Angel Pimentel, Avni Gandhi, Kei Ito, Subhabrata stabilized as amorphous CaCO3 biomineral in Sanyal, Jing W. Wang, Veronica Rodrigues, crayfish gastroliths and Mani Ramaswami Anat Akiva-Tal, Shifi Kababya, Yael S. Balazs, Lilah Glazer, See full research article on page E646 of www.pnas.org Amir Berman, Amir Sagi, and Asher Schmidt See Commentary on page 14711 14795 Tracking a defined route for O2 migration in 14723 The Ataxin-2 protein is required for microRNA function a dioxygen-activating diiron enzyme fi and synapse-speci c long-term olfactory habituation Woon Ju Song, Grant Gucinski, Matthew H. Sazinsky, Cathal McCann, Eimear E. Holohan, Sudeshna Das, Adrian and Stephen J. Lippard Dervan, Aoife Larkin, John Anthony Lee, Veronica Rodrigues, Roy Parker, and Mani Ramaswami 14831 Dynamics and mechanism of cyclobutane pyrimidine See full research article on page E655 of www.pnas.org dimer repair by DNA photolyase See Commentary on page 14711 Zheyun Liu, Chuang Tan, Xunmin Guo, Ya-Ting Kao, Jiang Li, Lijuan Wang, Aziz Sancar, and Dongping Zhong

ENVIRONMENTAL SCIENCES INAUGURAL ARTICLES 14769 Permafrost carbon-climate feedbacks accelerate global warming + hi 14725 Expansion of a unique CD57 NKG2C natural killer cell Charles D. Koven, Bruno Ringeval, Pierre Friedlingstein, subset during acute human cytomegalovirus infection Philippe Ciais, Patricia Cadule, Dmitry Khvorostyanov, Sandra Lopez-Vergès, Jeffrey M. Milush, Brian S. Schwartz, Gerhard Krinner, and Charles Tarnocai Marcelo J. Pando, Jessica Jarjoura, Vanessa A. York, Jeffrey P. Houchins, Steve Miller, Sang-Mo Kang, Phillip J. 14775 Energetics of Al13 Keggin cluster compounds Norris, Douglas F. Nixon, and Lewis L. Lanier Christopher R. Armstrong, William H. Casey, and Alexandra Navrotsky 14733 Minimization of the Legionella pneumophila genome reveals chromosomal regions involved in host range expansion PHYSICS Tamara J. O’Connor, Yewande Adepoju, Dana Boyd, 14780 Relationship between topological order and glass and Ralph R. Isberg forming ability in densely packed enstatite and forsterite composition glasses S. Kohara, J. Akola, H. Morita, K. Suzuya, J. K. R. Weber, M. C. Wilding, and C. J. Benmore PHYSICAL SCIENCES

APPLIED PHYSICAL SCIENCES SOCIAL SCIENCES 14741 Three-dimensional structure of a sheet crumpled into a ball Anne Dominique Cambou and Narayanan Menon ECONOMIC SCIENCES 14746 Observation of spatial propagation of amyloid assembly 14786 Nurture affects gender differences in spatial abilities from single nuclei Moshe Hoffman, Uri Gneezy, and John A. List Tuomas P. J. Knowles, Duncan A. White, Adam R. Abate, Jeremy J. Agresti, Samuel I. A. Cohen, Ralph A. Sperling, Erwin J. De Genst, Christopher M. Dobson, and David A. Weitz BIOLOGICAL SCIENCES 14819 Direct inference of protein–DNA interactions using compressed sensing methods APPLIED BIOLOGICAL SCIENCES Mohammed AlQuraishi and Harley H. McAdams 14789 Improved vascular organization enhances functional See Commentary on page 14713 integration of engineered skeletal muscle grafts 14825 Spatiotemporal regulation of chemical reactions by Jacob Koffler, Keren Kaufman-Francis, Shandalov Yulia, active cytoskeletal remodeling Egozi Dana, Amiad Pavlov Daria, Amir Landesberg, Abhishek Chaudhuri, Bhaswati Bhattacharya, Kripa and Shulamit Levenberg Gowrishankar, Satyajit Mayor, and Madan Rao BIOCHEMISTRY CHEMISTRY 14795 Tracking a defined route for O2 migration in 14752 Racemization as a stereochemical measure of dynamics a dioxygen-activating diiron enzyme and robustness in shape-shifting organic molecules Woon Ju Song, Grant Gucinski, Matthew H. Sazinsky, Maggie He and Jeffrey W. Bode and Stephen J. Lippard

iv u www.pnas.org Downloaded by guest on September 24, 2021 14801 Long-range pseudoknot interactions dictate the IMMUNOLOGY regulatory response in the tetrahydrofolate riboswitch 14725 Expansion of a unique CD57+NKG2Chi natural killer cell Lili Huang, Satoko Ishibe-Murakami, Dinshaw J. Patel, subset during acute human cytomegalovirus infection and Alexander Serganov Sandra Lopez-Vergès, Jeffrey M. Milush, Brian S. Schwartz, 14807 Multilevel autoregulation of λ repressor protein CI by Marcelo J. Pando, Jessica Jarjoura, Vanessa A. York, DNA looping in vitro Jeffrey P. Houchins, Steve Miller, Sang-Mo Kang, Phillip J. Dale Lewis, Phuoc Le, Chiara Zurla, Laura Finzi, Norris, Douglas F. Nixon, and Lewis L. Lanier and Sankar Adhya 14867 NLRP3 inflammasome plays a critical role in the 14813 Topology of human apolipoprotein E3 uniquely pathogenesis of hydroxyapatite-associated arthropathy regulates its diverse biological functions Chengcheng Jin, Patrick Frayssinet, Richard Pelker, Diane Jianglei Chen, Qianqian Li, and Jianjun Wang Cwirka, Bo Hu, Agnès Vignery, Stephanie C. Eisenbarth, and Richard A. Flavell

BIOPHYSICS AND COMPUTATIONAL BIOLOGY 14873 Transcription factor AP4 modulates reversible and 14819 Direct inference of protein–DNA interactions using epigenetic silencing of the Cd4 gene compressed sensing methods Takeshi Egawa and Dan R. Littman Mohammed AlQuraishi and Harley H. McAdams See Commentary on page 14713 14879 Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction 14825 Spatiotemporal regulation of chemical reactions by and disease protection active cytoskeletal remodeling Eugene Valkov, Anna Stamp, Frank DiMaio, David Baker, Abhishek Chaudhuri, Bhaswati Bhattacharya, Kripa Brett Verstak, Pietro Roversi, Stuart Kellie, Matthew J. Sweet, Gowrishankar, Satyajit Mayor, and Madan Rao Ashley Mansell, Nicholas J. Gay, Jennifer L. Martin, 14831 Dynamics and mechanism of cyclobutane pyrimidine and Bostjan Kobe dimer repair by DNA photolyase Zheyun Liu, Chuang Tan, Xunmin Guo, Ya-Ting Kao, 14885 Basic leucine zipper transcription factor, ATF-like (BATF) Jiang Li, Lijuan Wang, Aziz Sancar, and Dongping Zhong regulates epigenetically and energetically effector CD8 T-cell differentiation via Sirt1 expression 14837 Three-dimensional structure and function of the Shoko Kuroda, Maya Yamazaki, Manabu Abe, Kenji Paramecium bursaria chlorella virus capsid Sakimura, Hiroshi Takayanagi, and Yoshiko Iwai Xinzheng Zhang, Ye Xiang, David D. Dunigan, Thomas Klose, Paul R. Chipman, James L. Van Etten, 14890 CD4+CD25+Foxp3+ regulatory T cell formation requires and Michael G. Rossmann more specific recognition of a self-peptide than thymocyte deletion Cristina Cozzo Picca, Donald M. Simons, Soyoung Oh, CELL BIOLOGY Malinda Aitken, Olivia A. Perng, Christina Mergenthaler, 14843 Nuclear receptor chicken ovalbumin upstream Elizabeth Kropf, Jan Erikson, and Andrew J. Caton promoter-transcription factor II (COUP-TFII) modulates mesenchymal cell commitment and differentiation 14896 Nucleotide oligomerization domain-containing proteins Xin Xie, Jun Qin, Sue-Hwa Lin, Sophia Y. Tsai, instruct T cell helper type 2 immunity through and Ming-Jer Tsai stromal activation Joao G. Magalhaes, Stephen J. Rubino, Leonardo H. fi 14849 Identi cation and characterization of a functional Travassos, Lionel Le Bourhis, Wei Duan, Gernot Sellge, mitochondrial angiotensin system Karou Geddes, Colin Reardon, Matthias Lechmann, Peter M. Abadir, D. Brian Foster, Michael Crow, Carol A. Leticia A. Carneiro, Thirumahal Selvanantham, Jorg H. Fritz, Cooke, Jasma J. Rucker, Alka Jain, Barbara J. Smith, Betsy C. Taylor, David Artis, Tak Wah Mak, Michael R. Tyesha N. Burks, Ronald D. Cohn, Neal S. Fedarko, Comeau, Michael Croft, Stephen E. Girardin, ’ Robert M. Carey, Brian O Rourke, and Jeremy D. Walston and Dana J. Philpott

DEVELOPMENTAL BIOLOGY MEDICAL SCIENCES 14855 Drosophila Inducer of MEiosis 4 (IME4) is required for Notch signaling during oogenesis 14902 Epstein-Barr virus exploits intrinsic B-lymphocyte Cintia F. Hongay and Terry L. Orr-Weaver transcription programs to achieve immortal cell growth Bo Zhao, James Zou, Hongfang Wang, Eric Johannsen, 14861 Functional melanocytes derived from human pluripotent Chih-wen Peng, John Quackenbush, Jessica C. Mar, Cynthia stem cells engraft into pluristratified epidermis Casson Morton, Matthew L. Freedman, Stephen C. Blacklow, Xavier Nissan, Lionel Larribere, Manoubia Saidani, Ilse Jon C. Aster, Bradley E. Bernstein, and Elliott Kieff Hurbain, Cédric Delevoye, Jessica Feteira, Gilles Lemaitre, See Commentary on page 14715 Marc Peschanski, and Christine Baldeschi 14908 Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine ENVIRONMENTAL SCIENCES T-lymphoblastic leukemia cells 14769 Permafrost carbon-climate feedbacks accelerate Hongfang Wang, James Zou, Bo Zhao, Eric Johannsen, Todd global warming Ashworth, Hoifung Wong, Warren S. Pear, Jonathan Schug, Charles D. Koven, Bruno Ringeval, Pierre Friedlingstein, Stephen C. Blacklow, Kelly L. Arnett, Bradley E. Bernstein, Philippe Ciais, Patricia Cadule, Dmitry Khvorostyanov, Elliott Kieff, and Jon C. Aster Gerhard Krinner, and Charles Tarnocai See Commentary on page 14715

vi u www.pnas.org Downloaded by guest on September 24, 2021 14914 Proteasome assembly defect due to a proteasome 14962 Tsukushi functions as a Wnt signaling inhibitor by subunit beta type 8 (PSMB8) mutation causes the competing with Wnt2b for binding to transmembrane autoinflammatory disorder, Nakajo-Nishimura syndrome protein Frizzled4 Kazuhiko Arima, Akira Kinoshita, Hiroyuki Mishima, Nobuo Kunimasa Ohta, Ayako Ito, Sei Kuriyama, Giuseppe Lupo, Kanazawa, Takeumi Kaneko, Tsunehiro Mizushima, Kunihiro Mitsuko Kosaka, Shin-ichi Ohnuma, Shinichi Nakagawa, Ichinose, Hideki Nakamura, Akira Tsujino, Atsushi and Hideaki Tanaka Kawakami, Masahiro Matsunaka, Shimpei Kasagi, Seiji Kawano, Shunichi Kumagai, Koichiro Ohmura, Tsuneyo 14968 Serotonin signaling is associated with lower amyloid-β Mimori, Makito Hirano, Satoshi Ueno, Keiko Tanaka, levels and plaques in transgenic mice and humans Masami Tanaka, Itaru Toyoshima, Hirotoshi Sugino, Akio John R. Cirrito, Brianne M. Disabato, Jessica L. Restivo, Yamakawa, Keiji Tanaka, Norio Niikawa, Fukumi Furukawa, Deborah K. Verges, Whitney D. Goebel, Anshul Sathyan, Shigeo Murata, Katsumi Eguchi, Hiroaki Ida, Davinder Hayreh, Gina D’Angelo, Tammie Benzinger, and Koh-ichiro Yoshiura Hyejin Yoon, Jungsu Kim, John C. Morris, Mark A. Mintun, and Yvette I. Sheline

MICROBIOLOGY 14974 Homeostatic plasticity drives tinnitus perception in an animal model 14733 Minimization of the Legionella pneumophila genome Sungchil Yang, Benjamin D. Weiner, Li S. Zhang, reveals chromosomal regions involved in host Sung-Jin Cho, and Shaowen Bao range expansion Tamara J. O’Connor, Yewande Adepoju, Dana Boyd, and Ralph R. Isberg PHYSIOLOGY 14920 Structure of the Newcastle disease virus 14980 The central cavity in trimeric glutamate transporters hemagglutinin-neuraminidase (HN) ectodomain reveals restricts ligand diffusion a four-helix bundle stalk Greg P. Leary, David C. Holley, Emily F. Stone, Ping Yuan, Kurt A. Swanson, George P. Leser, Reay G. Brent R. Lyda, Leonid V. Kalachev, Paterson, Robert A. Lamb, and Theodore S. Jardetzky and Michael P. Kavanaugh 14926 Recombinant Rift Valley fever vaccines induce protective 14986 Estrogen receptor α AF-2 mutation results in antagonist levels of antibody in baboons and resistance to lethal reversal and reveals tissue selective function of challenge in mice estrogen receptor modulators James F. Papin, Paulo H. Verardi, Leslie A. Jones, Francisco Yukitomo Arao, Katherine J. Hamilton, Manas K. Ray, Monge-Navarro, Aaron C. Brault, Michael R. Holbrook, Gregory Scott, Yuji Mishina, and Kenneth S. Korach Melissa N. Worthy, Alexander N. Freiberg, and Tilahun D. Yilma 14932 A quorum-sensing molecule acts as a morphogen PLANT BIOLOGY controlling gas vesicle organelle biogenesis and 14992 Cis-regulatory code of stress-responsive transcription in adaptive flotation in an enterobacterium Arabidopsis thaliana Joshua P. Ramsay, Neil R. Williamson, David R. Spring, Cheng Zou, Kelian Sun, Joshua D. Mackaluso, Alexander E. and George P. C. Salmond Seddon, Rong Jin, Michael F. Thomashow, and Shin-Han Shiu 14938 Mammalian Pragmin regulates Src family kinases via the Glu-Pro-Ile-Tyr-Ala (EPIYA) motif that is exploited by bacterial effectors PSYCHOLOGICAL AND COGNITIVE SCIENCES Fatemeh Safari, Naoko Murata-Kamiya, Yasuhiro Saito, and Masanori Hatakeyama 14998 Behavioral and neural correlates of delay of gratification 40 years later 14944 Carcinogenic bacterial pathogen Helicobacter pylori B. J. Casey, Leah H. Somerville, Ian H. Gotlib, Ozlem Ayduk, triggers DNA double-strand breaks and a DNA damage Nicholas T. Franklin, Mary K. Askren, John Jonides, Marc G. response in its host cells Berman, Nicole L. Wilson, Theresa Teslovich, Gary Glover, Isabella M. Toller, Kai J. Neelsen, Martin Steger, Mara L. Vivian Zayas, Walter Mischel, and Yuichi Shoda Hartung, Michael O. Hottiger, Manuel Stucki, Behnam Kalali, Markus Gerhard, Alessandro A. Sartori, Massimo Lopes, and Anne Müller SYSTEMS BIOLOGY 15004 Random partitioning of molecules at cell division NEUROSCIENCE Dann Huh and Johan Paulsson 14950 Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing Albert E. Ayoub, Sunghee Oh, Yanhua Xie, Jing Leng, Justin Cotney, Martin H. Dominguez, James P. Noonan, RETRACTION and Pasko Rakic 14956 Trial-to-trial variability in the responses of neurons BIOCHEMISTRY carries information about stimulus location in the 15010 Identification of an RNA-dependent RNA polymerase rat whisker thalamus in Drosophila involved in RNAi and Alessandro Scaglione, Karen A. Moxon, Juan Aguilar, transposon suppression and Guglielmo Foffani Concetta Lipardi and Bruce M. Paterson

viii u www.pnas.org Downloaded by guest on September 24, 2021 GENETICS CORRECTIONS 15010 Efficient generation of a biallelic knockout in pigs using zinc-finger nucleases BIOCHEMISTRY Janet Hauschild, Bjoern Petersen, Yolanda Santiago, 15010 RNA-guided complex from a bacterial immune system Anna-Lisa Queisser, Joseph W. Carnwath, Andrea enhances target recognition through seed Lucas-Hahn, Lei Zhang, Xiangdong Meng, Philip D. sequence interactions Gregory, Reinhard Schwinzer, Gregory J. Cost, Blake Wiedenheft, Esther van Duijn, Jelle Bultema, and Heiner Niemann Sakharam Waghmare, Kaihong Zhou, Arjan Barendregt, Wiebke Westphal, Albert Heck, Egbert Boekema, Mark Dickman, and Jennifer A. Doudna xi Subscription Form

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