Cień dnia (1): Fwd: PNAS Table of Contents for 30 July 2013; Vol. 110, No. 31

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Proceedings of the National Academy of Sciences

30 July 2013; Vol. 110, No. 31

This Week in PNAS

In This Issue

Letters (Online Only)

Declining snow cover may affect spring phenological trend on the Tibetan Plateau: Tao Wang, Shushi Peng, Xin Lin, and Jinfeng Chang

Reply to Wang et al.: Snow cover and air temperature affect the rate of changes in spring phenology in the Tibetan Plateau: Jinwei Dong, Geli Zhang, Yangjian Zhang, and Xiangming Xiao

Improved empirical tests of area-heterogeneity tradeoffs: Jofre Carnicer, Lluís Brotons, Sergi Herrando, and Daniel Sol

Reply to Carnicer et al.: Environmental heterogeneity reduces breeding bird richness in Catalonia by increasing extinction rates: Omri Allouche, Michael Kalyuzhny, Gregorio Moreno-Rueda, Manuel Pizarro, and Ronen Kadmon

Cultivated hay and fallow/idle cropland confound analysis of grassland conversion in the Western Corn Belt: Keith L. Kline, Nagendra Singh, and Virginia H. Dale

Reply to Kline et al.: Cropland data layer provides a valid assessment of recent grassland conversion in the Western Corn Belt: Christopher K. Wright and Michael C. Wimberly

QnAs

QnAs with Lynn M. Riddiford: Sujata Gupta

Commentaries

Oncogenic herpesviruses sending mixed signals: D. Michiel Pegtel

Drops on soft surfaces learn the hard way: Todd M. Squires

Mutation that causes hypertrophic cardiomyopathy increases force production in human β-cardiac myosin: Joseph M. Muretta and David D. Thomas

Neutrophils enlist IL-22 to restore order in the gut: Timothy L. Denning and Charles A. Parkos

PNAS Plus Significance Statements

PNAS Plus Significance Statements

Perspective

The case for distributed irrigation as a development priority in sub-Saharan Africa: Jennifer A. Burney, Rosamond L. Naylor, and Sandra L. Postel

Feature Article

mTOR complex 2-Akt signaling at mitochondria-associated endoplasmic reticulum membranes (MAM) regulates mitochondrial physiology OPEN ACCESS ARTICLE: Charles Betz, Daniele Stracka, Cristina Prescianotto-Baschong, Maud Frieden, Nicolas Demaurex, and Michael N. Hall

Physical Sciences

Applied Mathematics

Empirical intrinsic geometry for nonlinear modeling and time series filtering: Ronen Talmon and Ronald R. Coifman

Applied Physical Sciences

Patterning droplets with durotaxis: Robert W. Style, Yonglu Che, Su Ji Park, Byung Mook Weon, Jung Ho Je, Callen Hyland, Guy K. German, Michael P. Power, Larry A. Wilen, John S. Wettlaufer, and Eric R. Dufresne

Digital instability of a confined elastic meniscus: John S. Biggins, Baudouin Saintyves, Zhiyan Wei, Elisabeth Bouchaud, and L. Mahadevan

Acoustophoretic contactless transport and handling of matter in air: Daniele Foresti, Majid Nabavi, Mirko Klingauf, Aldo Ferrari, and Dimos Poulikakos

Chemistry

Temperature-memory polymer actuators OPEN ACCESS ARTICLE: Marc Behl, Karl Kratz, Ulrich Noechel, Tilman Sauter, and Andreas Lendlein

Earth, Atmospheric, and Planetary Sciences

Physical evidence of predatory behavior in Tyrannosaurus rex: Robert A. DePalma II, David A. Burnham, Larry D. Martin, Bruce M. Rothschild, and Peter L. Larson

Export of submicron particulate organic matter to mesopelagic depth in an oligotrophic gyre: Hilary G. Close, Sunita R. Shah, Anitra E. Ingalls, Aaron F. Diefendorf, Eoin L. Brodie, Roberta L. Hansman, Katherine H. Freeman, Lihini I. Aluwihare, and Ann Pearson

Reducing spread in climate model projections of a September ice-free Arctic: Jiping Liu, Mirong Song, Radley M. Horton, and Yongyun Hu

Engineering

Generation of functionally competent and durable engineered blood vessels from human induced pluripotent stem cells OPEN ACCESS ARTICLE: Rekha Samuel, Laurence Daheron, Shan Liao, Trupti Vardam, Walid S. Kamoun, Ana Batista, Christa Buecker, Richard Schäfer, Xiaoxing Han, Patrick Au, David T. Scadden, Dan G. Duda, Dai Fukumura, and Rakesh K. Jain

Physics

Cell–cell contacts confine public goods diffusion inside Pseudomonas aeruginosa clonal microcolonies OPEN ACCESS ARTICLE: Thomas Julou, Thierry Mora, Laurent Guillon, Vincent Croquette, Isabelle J. Schalk, David Bensimon, and Nicolas Desprat

Sustainability Science

Joint CO₂ and CH₄ accountability for global warming OPEN ACCESS ARTICLE: Kirk R. Smith, Manish A. Desai, Jamesine V. Rogers, and Richard A. Houghton

Social Sciences

Anthropology

Stone tools and foraging in northern Madagascar challenge Holocene extinction models: Robert E. Dewar, Chantal Radimilahy, Henry T. Wright, Zenobia Jacobs, Gwendolyn O. Kelly, and Francesco Berna

Crop manuring and intensive land management by Europe's first farmers: Amy Bogaard, Rebecca Fraser, Tim H. E. Heaton, Michael Wallace, Petra Vaiglova, Michael Charles, Glynis Jones, Richard P. Evershed, Amy K. Styring, Niels H. Andersen, Rose-Marie Arbogast, László Bartosiewicz, Armelle Gardeisen, Marie Kanstrup, Ursula Maier, Elena Marinova, Lazar Ninov, Marguerita Schäfer, and Elisabeth Stephan

Uncovering archaeological landscapes at Angkor using lidar OPEN ACCESS ARTICLE: Damian H. Evans, Roland J. Fletcher, Christophe Pottier, Jean-Baptiste Chevance, Dominique Soutif, Boun Suy Tan, Sokrithy Im, Darith Ea, Tina Tin, Samnang Kim, Christopher Cromarty, Stéphane De Greef, Kasper Hanus, Pierre Bâty, Robert Kuszinger, Ichita Shimoda, and Glenn Boornazian

Biological Sciences

Applied Biological Sciences

Self-organized vascular networks from human pluripotent stem cells in a synthetic matrix: Sravanti Kusuma, Yu-I Shen, Donny Hanjaya-Putra, Prashant Mali, Linzhao Cheng, and Sharon Gerecht

Biochemistry

mTOR complex 2-Akt signaling at mitochondria-associated endoplasmic reticulum membranes (MAM) regulates mitochondrial physiology OPEN ACCESS ARTICLE: Charles Betz, Daniele Stracka, Cristina Prescianotto-Baschong, Maud Frieden, Nicolas Demaurex, and Michael N. Hall

Molecular consequences of the R453C hypertrophic cardiomyopathy mutation on human β-cardiac myosin motor function OPEN ACCESS ARTICLE: Ruth F. Sommese, Jongmin Sung, Suman Nag, Shirley Sutton, John C. Deacon, Elizabeth Choe, Leslie A. Leinwand, Kathleen Ruppel, and James A. Spudich

Characterization of the nitric oxide reductase from Thermus thermophilus: Lici A. Schurig-Briccio, Padmaja Venkatakrishnan, James Hemp, Carlos Bricio, José Berenguer, and Robert B. Gennis

Structure and function of CarD, an essential mycobacterial transcription factor: Devendra B. Srivastava, Katherine Leon, Joseph Osmundson, Ashley L. Garner, Leslie A. Weiss, Lars F. Westblade, Michael S. Glickman, Robert Landick, Seth A. Darst, Christina L. Stallings, and Elizabeth A. Campbell

Visualizing the substrate-, superoxo-, alkylperoxo-, and product-bound states at the nonheme Fe(II) site of homogentisate dioxygenase: Jae-Hun Jeoung, Martin Bommer, Tzong-Yuan Lin, and Holger Dobbek

Biophysics and Computational Biology

Patterning droplets with durotaxis: Robert W. Style, Yonglu Che, Su Ji Park, Byung Mook Weon, Jung Ho Je, Callen Hyland, Guy K. German, Michael P. Power, Larry A. Wilen, John S. Wettlaufer, and Eric R. Dufresne

Cell–cell contacts confine public goods diffusion inside Pseudomonas aeruginosa clonal microcolonies OPEN ACCESS ARTICLE: Thomas Julou, Thierry Mora, Laurent Guillon, Vincent Croquette, Isabelle J. Schalk, David Bensimon, and Nicolas Desprat

Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria: Ivan Gushchin, Pavel Chervakov, Pavel Kuzmichev, Alexander N. Popov, Ekaterina Round, Valentin Borshchevskiy, Andrii Ishchenko, Lada Petrovskaya, Vladimir Chupin, Dmitry A. Dolgikh, Alexander A. Arseniev, Mikhail Kirpichnikov, and Valentin Gordeliy

Syntaxin1a variants lacking an N-peptide or bearing the LE mutation bind to Munc18a in a closed conformation: Karen N. Colbert, Douglas A. Hattendorf, Thomas M. Weiss, Pawel Burkhardt, Dirk Fasshauer, and William I. Weis

Cell Biology

Atg29 phosphorylation regulates coordination of the Atg17-Atg31-Atg29 complex with the Atg11 scaffold during autophagy initiation: Kai Mao, Leon H. Chew, Yuko Inoue-Aono, Heesun Cheong, Usha Nair, Hana Popelka, Calvin K. Yip, and Daniel J. Klionsky

EVI1 oncoprotein interacts with a large and complex network of proteins and integrates signals through protein phosphorylation: Emilie A. Bard-Chapeau, Jayantha Gunaratne, Pankaj Kumar, Belinda Q. Chua, Julius Muller, Frederic A. Bard, Walter Blackstock, Neal G. Copeland, and Nancy A. Jenkins

Clonal precursor of bone, cartilage, and hematopoietic niche stromal cells: Charles K. F. Chan, Paul Lindau, Wen Jiang, James Y. Chen, Lillian F. Zhang, Ching-Cheng Chen, Jun Seita, Debashis Sahoo, Jae-Beom Kim, Andrew Lee, Sujin Park, Divya Nag, Yongquan Gong, Subhash Kulkarni, Cynthia A. Luppen, Alexander A. Theologis, Derrick C. Wan, Anthony DeBoer, Eun Young Seo, Justin D. Vincent-Tompkins, Kyle Loh, Graham G. Walmsley, Daniel L. Kraft, Joseph C. Wu, Michael T. Longaker, and Irving L. Weissman

Inactivating mutations of RNF43 confer Wnt dependency in pancreatic ductal adenocarcinoma: Xiaomo Jiang, Huai-Xiang Hao, Joseph D. Growney, Steve Woolfenden, Cindy Bottiglio, Nicholas Ng, Bo Lu, Mindy H. Hsieh, Linda Bagdasarian, Ronald Meyer, Timothy R. Smith, Monika Avello, Olga Charlat, Yang Xie, Jeffery A. Porter, Shifeng Pan, Jun Liu, Margaret E. McLaughlin, and Feng Cong

CTIP2 is a negative regulator of P-TEFb: Thomas Cherrier, Valentin Le Douce, Sebastian Eilebrecht, Raphael Riclet, Céline Marban, Franck Dequiedt, Yannick Goumon, Jean-Christophe Paillart, Mathias Mericskay, Ara Parlakian, Pedro Bausero, Wasim Abbas, Georges Herbein, Siavash K. Kurdistani, Xavier Grana, Benoit Van Driessche, Christian Schwartz, Ermanno Candolfi, Arndt G. Benecke, Carine Van Lint, and Olivier Rohr

Pathological hypertrophy amelioration by PRAS40-mediated inhibition of mTORC1: Mirko Völkers, Haruhiro Toko, Shirin Doroudgar, Shabana Din, Pearl Quijada, Anya Y. Joyo, Luis Ornelas, Eri Joyo, Donna J. Thuerauf, Mathias H. Konstandin, Natalie Gude, Christopher C. Glembotski, and Mark A. Sussman

Induction of human cardiomyocyte-like cells from fibroblasts by defined factors: Rie Wada, Naoto Muraoka, Kohei Inagawa, Hiroyuki Yamakawa, Kazutaka Miyamoto, Taketaro Sadahiro, Tomohiko Umei, Ruri Kaneda, Tomoyuki Suzuki, Kaichiro Kamiya, Shugo Tohyama, Shinsuke Yuasa, Kiyokazu Kokaji, Ryo Aeba, Ryohei Yozu, Hiroyuki Yamagishi, Toshio Kitamura, Keiichi Fukuda, and Masaki Ieda

Leptin promotes K_ATP channel trafficking by AMPK signaling in pancreatic β-cells: Sun-Hyun Park, Shin-Young Ryu, Weon-Jin Yu, Young Eun Han, Young-Sun Ji, Keunhee Oh, Jong-Woo Sohn, Ajin Lim, Jae-Pyo Jeon, Hyunsu Lee, Kyu-Hee Lee, Suk-Ho Lee, Per-Olof Berggren, Ju-Hong Jeon, and Won-Kyung Ho

Oxygen-sensitive mitochondrial accumulation of cystathionine β-synthase mediated by Lon protease: Huajian Teng, Bo Wu, Kexin Zhao, Guangdong Yang, Lingyun Wu, and Rui Wang

Developmental Biology

A molt timer is involved in the metamorphic molt in Manduca sexta larvae OPEN ACCESS ARTICLE: Yuichiro Suzuki, Takashi Koyama, Kiyoshi Hiruma, Lynn M. Riddiford, and James W. Truman

Tumor suppressor gene Rb is required for self-renewal of spermatogonial stem cells in mice: Yueh-Chiang Hu, Dirk G. de Rooij, and David C. Page

Reconstituting pancreas development from purified progenitor cells reveals genes essential for islet differentiation: Takuya Sugiyama, Cecil M. Benitez, Amar Ghodasara, Lucy Liu, Graeme W. McLean, Jonghyeob Lee, Timothy A. Blauwkamp, Roeland Nusse, Christopher V. E. Wright, Guoqiang Gu, and Seung K. Kim

Reptin/Ruvbl2 is a Lrrc6/Seahorse interactor essential for cilia motility: Lu Zhao, Shiaulou Yuan, Ying Cao, Sowjanya Kallakuri, Yuanyuan Li, Norihito Kishimoto, Linda DiBella, and Zhaoxia Sun

Pomalidomide is nonteratogenic in chicken and zebrafish embryos and nonneurotoxic in vitro OPEN ACCESS ARTICLE: Chris Mahony, Lynda Erskine, Jennifer Niven, Nigel H. Greig, William Douglas Figg, and Neil Vargesson

Neural crest and Schwann cell progenitor-derived melanocytes are two spatially segregated populations similarly regulated by Foxd3: Erez Nitzan, Elise R. Pfaltzgraff, Patricia A. Labosky, and Chaya Kalcheim

Ecology

Species–fragmented area relationship OPEN ACCESS ARTICLE: Ilkka Hanski, Gustavo A. Zurita, M. Isabel Bellocq, and Joel Rybicki

Community dynamics and ecosystem simplification in a high-CO₂ ocean OPEN ACCESS ARTICLE: Kristy J. Kroeker, Maria Cristina Gambi, and Fiorenza Micheli

Determinants of plant establishment success in a multispecies introduction experiment with native and alien species: Anne Kempel, Thomas Chrobock, Markus Fischer, Rudolf Philippe Rohr, and Mark van Kleunen

Environmental Sciences

Patterns of new versus recycled primary production in the terrestrial biosphere: Cory C. Cleveland, Benjamin Z. Houlton, W. Kolby Smith, Alison R. Marklein, Sasha C. Reed, William Parton, Stephen J. Del Grosso, and Steven W. Running

Evolution

Physical evidence of predatory behavior in Tyrannosaurus rex: Robert A. DePalma II, David A. Burnham, Larry D. Martin, Bruce M. Rothschild, and Peter L. Larson

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes OPEN ACCESS ARTICLE: Thomas J. Near, Alex Dornburg, Ron I. Eytan, Benjamin P. Keck, W. Leo Smith, Kristen L. Kuhn, Jon A. Moore, Samantha A. Price, Frank T. Burbrink, Matt Friedman, and Peter C. Wainwright

Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes: Joseph J. Carter, Matthew D. Daugherty, Xiaojie Qi, Anjali Bheda-Malge, Gregory C. Wipf, Kristin Robinson, Ann Roman, Harmit S. Malik, and Denise A. Galloway

Genetics

Homologous recombination rescues ssDNA gaps generated by nucleotide excision repair and reduced translesion DNA synthesis in yeast G2 cells: Wenjian Ma, James W. Westmoreland, and Michael A. Resnick

RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee OPEN ACCESS ARTICLE: Hongmei Li-Byarlay, Yang Li, Hume Stroud, Suhua Feng, Thomas C. Newman, Megan Kaneda, Kirk K. Hou, Kim C. Worley, Christine G. Elsik, Samuel A. Wickline, Steven E. Jacobsen, Jian Ma, and Gene E. Robinson

Two-codon T-box riboswitch binding two tRNAs: Nizar Y. Saad, Vassiliki Stamatopoulou, Mélanie Brayé, Denis Drainas, Constantinos Stathopoulos, and Hubert Dominique Becker

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans: Ali R. Awan, Amanda Manfredo, and Jeffrey A. Pleiss

Immunology

Asymmetric thymocyte death underlies the CD4:CD8 T-cell ratio in the adaptive immune system OPEN ACCESS ARTICLE: Charles Sinclair, Iren Bains, Andrew J. Yates, and Benedict Seddon

Extracellular matrix of secondary lymphoid organs impacts on B-cell fate and survival: Jian Song, Zerina Lokmic, Tim Lämmermann, Julia Rolf, Chuan Wu, Xueli Zhang, Rupert Hallmann, Melanie-Jane Hannocks, Nathalie Horn, Markus A. Ruegg, Arnoud Sonnenberg, Elisabeth Georges-Labouesse, Thomas H. Winkler, John F. Kearney, Susanna Cardell, and Lydia Sorokin

IL-22–producing neutrophils contribute to antimicrobial defense and restitution of colonic epithelial integrity during colitis: Carlene L. Zindl, Jen-Feng Lai, Yun Kyung Lee, Craig L. Maynard, Stacey N. Harbour, Wenjun Ouyang, David D. Chaplin, and Casey T. Weaver

Medical Sciences

Generation of functionally competent and durable engineered blood vessels from human induced pluripotent stem cells OPEN ACCESS ARTICLE: Rekha Samuel, Laurence Daheron, Shan Liao, Trupti Vardam, Walid S. Kamoun, Ana Batista, Christa Buecker, Richard Schäfer, Xiaoxing Han, Patrick Au, David T. Scadden, Dan G. Duda, Dai Fukumura, and Rakesh K. Jain

Saturated and unsaturated fat induce hepatic insulin resistance independently of TLR-4 signaling and ceramide synthesis in vivo OPEN ACCESS ARTICLE: Thomas Galbo, Rachel J. Perry, Michael J. Jurczak, João-Paulo G. Camporez‎, Tiago C. Alves, Mario Kahn, Blas A. Guigni, Julie Serr, Dongyan Zhang, Sanjay Bhanot, Varman T. Samuel, and Gerald I. Shulman

Inhibiting the HSP90 chaperone slows cyst growth in a mouse model of autosomal dominant polycystic kidney disease: Tamina Seeger-Nukpezah, David A. Proia, Brian L. Egleston, Anna S. Nikonova, Tatiana Kent, Kathy Q. Cai, Harvey H. Hensley, Weiwen Ying, Dinesh Chimmanamada, Ilya G. Serebriiskii, and Erica A. Golemis

Microbiology

Modulation of B-cell exosome proteins by gamma herpesvirus infection: David G. Meckes, Jr., Harsha P. Gunawardena, Robert M. Dekroon, Phillip R. Heaton, Rachel H. Edwards, Sezgin Ozgur, Jack D. Griffith, Blossom Damania, and Nancy Raab-Traub

Gene expression profiles in febrile children with defined viral and bacterial infection: Xinran Hu, Jinsheng Yu, Seth D. Crosby, and Gregory A. Storch

Twelve previously unknown phage genera are ubiquitous in global oceans: Karin Holmfeldt, Natalie Solonenko, Manesh Shah, Kristen Corrier, Lasse Riemann, Nathan C. VerBerkmoes, and Matthew B. Sullivan