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Fwd: PNAS Early Edition for 25 Jun 2015


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Date: Fri, Jun 26, 2015 at 8:13 AM
Subject: PNAS Early Edition for 25 Jun 2015
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PNAS    Proceedings of the National Academy of Sciences
Letters (Online Only)

QnAs
QnAs with James J. Collins
Tinsley H. Davis

Commentaries

Physical Sciences
Applied Physical Sciences
Tissue stiffness regulates serine/arginine-rich protein-mediated splicing of the extra domain B-fibronectin isoform in tumors
Francois Bordeleau, Joseph P. Califano, Yashira L. Negrón Abril, Brooke N. Mason, Danielle J. LaValley, Sandra J. Shin, Robert S. Weiss, and Cynthia A. Reinhart-King
Pathways to dewetting in hydrophobic confinement
Richard C. Remsing, Erte Xi, Srivathsan Vembanur, Sumit Sharma, Pablo G. Debenedetti, Shekhar Garde, and Amish J. Patel
Chemistry
Self-reproducing catalyst drives repeated phospholipid synthesis and membrane growth
Michael D. Hardy, Jun Yang, Jangir Selimkhanov, Christian M. Cole, Lev S. Tsimring, and Neal K. Devaraj
Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)
Sandra C. Koch, Jochen Kuper, Karola L. Gasteiger, Nina Simon, Ralf Strasser, David Eisen, Simon Geiger, Sabine Schneider, Caroline Kisker, and Thomas Carell
Earth, Atmospheric, and Planetary Sciences
Physics
Cooperative strings and glassy interfaces
Thomas Salez, Justin Salez, Kari Dalnoki-Veress, Elie Raphaël, and James A. Forrest
Solid−liquid critical behavior of water in nanopores
Kenji Mochizuki and Kenichiro Koga
Relationship between thermoelectric figure of merit and energy conversion efficiency
Hee Seok Kim, Weishu Liu, Gang Chen, Ching-Wu Chu, and Zhifeng Ren
Effect of salt on the H-bond symmetrization in ice Open Access Article
Livia Eleonora Bove, Richard Gaal, Zamaan Raza, Adriaan-Alexander Ludl, Stefan Klotz, Antonino Marco Saitta, Alexander F. Goncharov, and Philippe Gillet
Developed turbulence and nonlinear amplification of magnetic fields in laboratory and astrophysical plasmas
Jena Meinecke, Petros Tzeferacos, Anthony Bell, Robert Bingham, Robert Clarke, Eugene Churazov, Robert Crowston, Hugo Doyle, R. Paul Drake, Robert Heathcote, Michel Koenig, Yasuhiro Kuramitsu, Carolyn Kuranz, Dongwook Lee, Michael MacDonald, Christopher Murphy, Margaret Notley, Hye-Sook Park, Alexander Pelka, Alessandra Ravasio, Brian Reville, Youichi Sakawa, Willow Wan, Nigel Woolsey, Roman Yurchak, Francesco Miniati, Alexander Schekochihin, Don Lamb, and Gianluca Gregori

Social Sciences
Anthropology
Human population dynamics in Europe over the Last Glacial Maximum
Miikka Tallavaara, Miska Luoto, Natalia Korhonen, Heikki Järvinen, and Heikki Seppä
Early procurement of scarlet macaws and the emergence of social complexity in Chaco Canyon, NM Open Access Article
Adam S. Watson, Stephen Plog, Brendan J. Culleton, Patricia A. Gilman, Steven A. LeBlanc, Peter M. Whiteley, Santiago Claramunt, and Douglas J. Kennett
Psychological and Cognitive Sciences
Top-down control of the phase of alpha-band oscillations as a mechanism for temporal prediction
Jason Samaha, Phoebe Bauer, Sawyer Cimaroli, and Bradley R. Postle
Adolescent impatience decreases with increased frontostriatal connectivity
Wouter van den Bos, Christian A. Rodriguez, Julie B. Schweitzer, and Samuel M. McClure
The self-control consequences of political ideology
Joshua J. Clarkson, John R. Chambers, Edward R. Hirt, Ashley S. Otto, Frank R. Kardes, and Christopher Leone
Individual olfactory perception reveals meaningful nonolfactory genetic information Open Access Article
Lavi Secundo, Kobi Snitz, Kineret Weissler, Liron Pinchover, Yehuda Shoenfeld, Ron Loewenthal, Nancy Agmon-Levin, Idan Frumin, Dana Bar-Zvi, Sagit Shushan, and Noam Sobel

Biological Sciences
Anthropology
Human population dynamics in Europe over the Last Glacial Maximum
Miikka Tallavaara, Miska Luoto, Natalia Korhonen, Heikki Järvinen, and Heikki Seppä
Applied Biological Sciences
Engineering Escherichia coli coculture systems for the production of biochemical products Open Access Article
Haoran Zhang, Brian Pereira, Zhengjun Li, and Gregory Stephanopoulos
Microneedle-array patches loaded with hypoxia-sensitive vesicles provide fast glucose-responsive insulin delivery
Jicheng Yu, Yuqi Zhang, Yanqi Ye, Rocco DiSanto, Wujin Sun, Davis Ranson, Frances S. Ligler, John B. Buse, and Zhen Gu
Biochemistry
A retro-biosynthetic approach to the prediction of biosynthetic pathways from position-specific isotope analysis as shown for tramadol
Katarzyna M. Romek, Pierrick Nun, Gérald S. Remaud, Virginie Silvestre, Germain Sotoing Taïwe, Florine Lecerf-Schmidt, Ahcène Boumendjel, Michel De Waard, and Richard J. Robins
DNA polymerase from temperate phage Bam35 is endowed with processive polymerization and abasic sites translesion synthesis capacity
Mónica Berjón-Otero, Laurentino Villar, Miguel de Vega, Margarita Salas, and Modesto Redrejo-Rodríguez
Generating new prions by targeted mutation or segment duplication
Kacy R. Paul, Connor G. Hendrich, Aubrey Waechter, Madison R. Harman, and Eric D. Ross
Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)
Sandra C. Koch, Jochen Kuper, Karola L. Gasteiger, Nina Simon, Ralf Strasser, David Eisen, Simon Geiger, Sabine Schneider, Caroline Kisker, and Thomas Carell
Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition
Irene Garcia-Ferrer, Pedro Arêde, Josué Gómez-Blanco, Daniel Luque, Stephane Duquerroy, José R. Castón, Theodoros Goulas, and F. Xavier Gomis-Rüth
Discovery of an intrinsic tenase complex inhibitor: Pure nonasaccharide from fucosylated glycosaminoglycan
Longyan Zhao, Mingyi Wu, Chuang Xiao, Lian Yang, Lutan Zhou, Na Gao, Zi Li, Jun Chen, Jianchao Chen, Jikai Liu, Hongbo Qin, and Jinhua Zhao
Biophysics and Computational Biology
Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape
Hao Yu, Derek R. Dee, Xia Liu, Angela M. Brigley, Iveta Sosova, and Michael T. Woodside
Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics
Joseph A. Liberman, Krishna C. Suddala, Asaminew Aytenfisu, Dalen Chan, Ivan A. Belashov, Mohammad Salim, David H. Mathews, Robert C. Spitale, Nils G. Walter, and Joseph E. Wedekind
Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar
Michael C. Baxa, Wookyung Yu, Aashish N. Adhikari, Liang Ge, Zhen Xia, Ruhong Zhou, Karl F. Freed, and Tobin R. Sosnick
Antibiotic efficacy is linked to bacterial cellular respiration Open Access Article Inaugural Article
Michael A. Lobritz, Peter Belenky, Caroline B. M. Porter, Arnaud Gutierrez, Jason H. Yang, Eric G. Schwarz, Daniel J. Dwyer, Ahmad S. Khalil, and James J. Collins
Cell Biology
The Bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation
Chiara Pastori, Philipp Kapranov, Clara Penas, Veronica Peschansky, Claude-Henry Volmar, Jann N. Sarkaria, Amade Bregy, Ricardo Komotar, Georges St. Laurent, Nagi G. Ayad, and Claes Wahlestedt
Vimentin filament precursors exchange subunits in an ATP-dependent manner
Amélie Robert, Molly J. Rossow, Caroline Hookway, Stephen A. Adam, and Vladimir I. Gelfand
Engineered cellular gene-replacement platform for selective and inducible proteolytic profiling
Charles W. Morgan, Juan E. Diaz, Samantha G. Zeitlin, Daniel C. Gray, and James A. Wells
Tissue stiffness regulates serine/arginine-rich protein-mediated splicing of the extra domain B-fibronectin isoform in tumors
Francois Bordeleau, Joseph P. Califano, Yashira L. Negrón Abril, Brooke N. Mason, Danielle J. LaValley, Sandra J. Shin, Robert S. Weiss, and Cynthia A. Reinhart-King
BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase
Abid Khan, Sumanprava Giri, Yating Wang, Arindam Chakraborty, Archit K. Ghosh, Aparna Anantharaman, Vasudha Aggarwal, Kizhakke M. Sathyan, Taekjip Ha, Kannanganattu V. Prasanth, and Supriya G. Prasanth
Single-molecule imaging of Hedgehog pathway protein Smoothened in primary cilia reveals binding events regulated by Patched1
Ljiljana Milenkovic, Lucien E. Weiss, Joshua Yoon, Theodore L. Roth, YouRong S. Su, Steffen J. Sahl, Matthew P. Scott, and W. E. Moerner
Paternal allelic mutation at the Kcnq1 locus reduces pancreatic β-cell mass by epigenetic modification of Cdkn1c Open Access Article
Shun-ichiro Asahara, Hiroaki Etoh, Hiroyuki Inoue, Kyoko Teruyama, Yuki Shibutani, Yuka Ihara, Yukina Kawada, Alberto Bartolome, Naoko Hashimoto, Tomokazu Matsuda, Maki Koyanagi-Kimura, Ayumi Kanno, Yushi Hirota, Tetsuya Hosooka, Kazuaki Nagashima, Wataru Nishimura, Hiroshi Inoue, Michihiro Matsumoto, Michael J. Higgins, Kazuki Yasuda, Nobuya Inagaki, Susumu Seino, Masato Kasuga, and Yoshiaki Kido
DNA damage during the G0/G1 phase triggers RNA-templated, Cockayne syndrome B-dependent homologous recombination Open Access Article
Leizhen Wei, Satoshi Nakajima, Stefanie Böhm, Kara A. Bernstein, Zhiyuan Shen, Michael Tsang, Arthur S. Levine, and Li Lan
Ecology
Backbones of evolutionary history test biodiversity theory for microbes Open Access Article
James P. O'Dwyer, Steven W. Kembel, and Thomas J. Sharpton
Assessing niche width of endothermic fish from genes to ecosystem
Daniel J. Madigan, Aaron B. Carlisle, Luke D. Gardner, Nishad Jayasundara, Fiorenza Micheli, Kurt M. Schaefer, Daniel W. Fuller, and Barbara A. Block
Climate-driven diversity loss in a grassland community
Susan P. Harrison, Elise S. Gornish, and Stella Copeland
Evolution
The butterfly plant arms-race escalated by gene and genome duplications Open Access Article
Patrick P. Edger, Hanna M. Heidel-Fischer, Michaël Bekaert, Jadranka Rota, Gernot Glöckner, Adrian E. Platts, David G. Heckel, Joshua P. Der, Eric K. Wafula, Michelle Tang, Johannes A. Hofberger, Ann Smithson, Jocelyn C. Hall, Matthieu Blanchette, Thomas E. Bureau, Stephen I. Wright, Claude W. dePamphilis, M. Eric Schranz, Michael S. Barker, Gavin C. Conant, Niklas Wahlberg, Heiko Vogel, J. Chris Pires, and Christopher W. Wheat
Swimming muscles power suction feeding in largemouth bass
Ariel L. Camp, Thomas J. Roberts, and Elizabeth L. Brainerd
Genetics
Genetic architecture of natural variation in Drosophila melanogaster aggressive behavior Open Access Article
John Shorter, Charlene Couch, Wen Huang, Mary Anna Carbone, Jason Peiffer, Robert R. H. Anholt, and Trudy F. C. Mackay
The histone methyltransferase SETDB1 represses endogenous and exogenous retroviruses in B lymphocytes
Patrick L. Collins, Katherine E. Kyle, Takeshi Egawa, Yoichi Shinkai, and Eugene M. Oltz
Genome-wide binding and mechanistic analyses of Smchd1-mediated epigenetic regulation Open Access Article
Kelan Chen, Jiang Hu, Darcy L. Moore, Ruijie Liu, Sarah A. Kessans, Kelsey Breslin, Isabelle S. Lucet, Andrew Keniry, Huei San Leong, Clare L. Parish, Douglas J. Hilton, Richard J. L. F. Lemmers, Silvère M. van der Maarel, Peter E. Czabotar, Renwick C. J. Dobson, Matthew E. Ritchie, Graham F. Kay, James M. Murphy, and Marnie E. Blewitt
Immunology and Inflammation
Platelet microparticles are internalized in neutrophils via the concerted activity of 12-lipoxygenase and secreted phospholipase A2-IIA
Anne-Claire Duchez, Luc H. Boudreau, James Bollinger, Clémence Belleannée, Nathalie Cloutier, Benoit Laffont, Raifish E. Mendoza-Villarroel, Tania Lévesque, Emmanuelle Rollet-Labelle, Matthieu Rousseau, Isabelle Allaeys, Jacques J. Tremblay, Patrice E. Poubelle, Gérard Lambeau, Marc Pouliot, Patrick Provost, Denis Soulet, Michael H. Gelb, and Eric Boilard
Cellular immune correlates analysis of an HIV-1 preexposure prophylaxis trial Open Access Article
Peter J. Kuebler, Megha L. Mehrotra, J. Jeff McConnell, Sara J. Holditch, Brian I. Shaw, Leandro F. Tarosso, Kaitlyn S. Leadabrand, Jeffrey M. Milush, Vanessa A. York, Rui André Saraiva Raposo, Rex G. Cheng, Emily M. Eriksson, Vanessa McMahan, David V. Glidden, Stephen Shiboski, Robert M. Grant, Douglas F. Nixon, and Esper G. Kallás
Medical Sciences
Sulindac metabolites decrease cerebrovascular malformations in CCM3-knockout mice
Luca Bravi, Noemi Rudini, Roberto Cuttano, Costanza Giampietro, Luigi Maddaluno, Luca Ferrarini, Ralf H. Adams, Monica Corada, Gwenola Boulday, Elizabeth Tournier-Lasserve, Elisabetta Dejana, and Maria Grazia Lampugnani
Rescue of the Stargardt phenotype in Abca4 knockout mice through inhibition of vitamin A dimerization Open Access Article
Peter Charbel Issa, Alun R. Barnard, Philipp Herrmann, Ilyas Washington, and Robert E. MacLaren
Disruption of prostaglandin E2 receptor EP4 impairs urinary concentration via decreasing aquaporin 2 in renal collecting ducts
Min Gao, Rong Cao, Shengnan Du, Xiao Jia, Senfeng Zheng, Shizheng Huang, Qifei Han, Jia Liu, Xiaoyan Zhang, Yifei Miao, Jihong Kang, Jan-Åke Gustafsson, and Youfei Guan
Selective resistance to the PARP inhibitor olaparib in a mouse model for BRCA1-deficient metaplastic breast cancer
Linda Henneman, Martine H. van Miltenburg, Ewa M. Michalak, Tanya M. Braumuller, Janneke E. Jaspers, Anne Paulien Drenth, Renske de Korte-Grimmerink, Ewa Gogola, Karoly Szuhai, Andreas Schlicker, Rahmen Bin Ali, Colin Pritchard, Ivo J. Huijbers, Anton Berns, Sven Rottenberg, and Jos Jonkers
Microbiology
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health Open Access Article
Kathryn E. Holt, Heiman Wertheim, Ruth N. Zadoks, Stephen Baker, Chris A. Whitehouse, David Dance, Adam Jenney, Thomas R. Connor, Li Yang Hsu, Juliëtte Severin, Sylvain Brisse, Hanwei Cao, Jonathan Wilksch, Claire Gorrie, Mark B. Schultz, David J. Edwards, Kinh Van Nguyen, Trung Vu Nguyen, Trinh Tuyet Dao, Martijn Mensink, Vien Le Minh, Nguyen Thi Khanh Nhu, Constance Schultsz, Kuntaman Kuntaman, Paul N. Newton, Catrin E. Moore, Richard A. Strugnell, and Nicholas R. Thomson
A self-lysis pathway that enhances the virulence of a pathogenic bacterium
Kirsty A. McFarland, Emily L. Dolben, Michele LeRoux, Tracy K. Kambara, Kathryn M. Ramsey, Robin L. Kirkpatrick, Joseph D. Mougous, Deborah A. Hogan, and Simon L. Dove
Neuroscience
Activity-dependent synaptic GRIP1 accumulation drives synaptic scaling up in response to action potential blockade
Melanie A. Gainey, Vedakumar Tatavarty, Marc Nahmani, Heather Lin, and Gina G. Turrigiano
Ongoing dynamics in large-scale functional connectivity predict perception
Sepideh Sadaghiani, Jean-Baptiste Poline, Andreas Kleinschmidt, and Mark D'Esposito
Top-down control of the phase of alpha-band oscillations as a mechanism for temporal prediction
Jason Samaha, Phoebe Bauer, Sawyer Cimaroli, and Bradley R. Postle
RNA ligation in neurons by RtcB inhibits axon regeneration
Sara Guckian Kosmaczewski, Sung Min Han, Bingjie Han, Benjamin Irving Meyer, Huma S. Baig, Wardah Athar, Alexander T. Lin-Moore, Michael R. Koelle, and Marc Hammarlund
Theta–gamma coordination between anterior cingulate and prefrontal cortex indexes correct attention shifts
Benjamin Voloh, Taufik A. Valiante, Stefan Everling, and Thilo Womelsdorf
Individual olfactory perception reveals meaningful nonolfactory genetic information Open Access Article
Lavi Secundo, Kobi Snitz, Kineret Weissler, Liron Pinchover, Yehuda Shoenfeld, Ron Loewenthal, Nancy Agmon-Levin, Idan Frumin, Dana Bar-Zvi, Sagit Shushan, and Noam Sobel
Pharmacology
A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels Open Access Article
Luisa Maria Rosaria Napolitano, Ina Bisha, Matteo De March, Arin Marchesi, Manuel Arcangeletti, Nicola Demitri, Monica Mazzolini, Alex Rodriguez, Alessandra Magistrato, Silvia Onesti, Alessandro Laio, and Vincent Torre
Allosteric interactions between agonists and antagonists within the adenosine A2A receptor-dopamine D2 receptor heterotetramer
Jordi Bonaventura, Gemma Navarro, Verònica Casadó-Anguera, Karima Azdad, William Rea, Estefanía Moreno, Marc Brugarolas, Josefa Mallol, Enric I. Canela, Carme Lluís, Antoni Cortés, Nora D. Volkow, Serge N. Schiffmann, Sergi Ferré, and Vicent Casadó
N-linked glycosylation of protease-activated receptor-1 at extracellular loop 2 regulates G-protein signaling bias
Antonio G. Soto, Thomas H. Smith, Buxin Chen, Supriyo Bhattacharya, Isabel Canto Cordova, Terry Kenakin, Nagarajan Vaidehi, and JoAnn Trejo
Plant Biology
Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis
Jack P. Wang, Ling Chuang, Philip L. Loziuk, Hao Chen, Ying-Chung Lin, Rui Shi, Guan-Zheng Qu, David C. Muddiman, Ronald R. Sederoff, and Vincent L. Chiang
Trp triad-dependent rapid photoreduction is not required for the function of Arabidopsis CRY1
Jie Gao, Xu Wang, Meng Zhang, Mingdi Bian, Weixian Deng, Zecheng Zuo, Zhenming Yang, Dongping Zhong, and Chentao Lin
Osmotic stress induces phosphorylation of histone H3 at threonine 3 in pericentromeric regions of Arabidopsis thaliana
Zhen Wang, Juan Armando Casas-Mollano, Jianping Xu, Jean-Jack M. Riethoven, Chi Zhang, and Heriberto Cerutti
Psychological and Cognitive Sciences
Adolescent impatience decreases with increased frontostriatal connectivity
Wouter van den Bos, Christian A. Rodriguez, Julie B. Schweitzer, and Samuel M. McClure
Systems Biology
Synaptic clusters function as odor operators in the olfactory bulb
Michele Migliore, Francesco Cavarretta, Addolorata Marasco, Eleonora Tulumello, Michael L. Hines, and Gordon M. Shepherd
Integrated, systems metabolic picture of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum
Chen Liao, Seung-Oh Seo, Venhar Celik, Huaiwei Liu, Wentao Kong, Yi Wang, Hans Blaschek, Yong-Su Jin, and Ting Lu

Corrections

SI Correction
Open Access
From the Cover
Inaugural Article
Classic
Cozzarelli Prize Winner
Front Matter

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