Fwd: PNAS Section Alert for March 8, 2016

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Proceedings of the National Academy of Sciences Section Alert for March 8, 2016 Agricultural Sciences Impaired imprinted X chromosome inactivation is responsible for the skewed sex ratio following in vitro fertilization Kun Tan, Lei An, Kai Miao, Likun Ren, Zhuocheng Hou, Li Tao, Zhenni Zhang, Xiaodong Wang, Wei Xia, Jinghao Liu, Zhuqing Wang, Guangyin Xi, Shuai Gao, Linlin Sui, De-Sheng Zhu, Shumin Wang, Zhonghong Wu, Ingolf Bach, Dong-bao Chen, and Jianhui Tian A mutualistic symbiosis between a parasitic mite and a pathogenic virus undermines honey bee immunity and health  Gennaro Di Prisco, Desiderato Annoscia, Marina Margiotta, Rosalba Ferrara, Paola Varricchio, Virginia Zanni, Emilio Caprio, Francesco Nazzi, and Francesco Pennacchio Genetics LNA modification of single-stranded DNA oligonucleotides allows subtle gene modification in mismatch-repair-proficient cells Thomas W. van Ravesteyn, Marleen Dekker, Alexander Fish, Titia K. Sixma, Astrid Wolters, Rob J. Dekker, and Hein P. J. te Riele Whole-exome sequencing identifies MST1R as a genetic susceptibility gene in nasopharyngeal carcinoma Wei Dai, Hong Zheng, Arthur Kwok Leung Cheung, Clara Sze-man Tang, Josephine Mun Yee Ko, Bonnie Wing Yan Wong, Merrin Man Long Leong, Pak Chung Sham, Florence Cheung, Dora Lai-Wan Kwong, Roger Kai Cheong Ngan, Wai Tong Ng, Chun Chung Yau, Jianji Pan, Xun Peng, Stewart Tung, Zengfeng Zhang, Mingfang Ji, Alan Kwok-Shing Chiang, Anne Wing-Mui Lee, Victor Ho-fun Lee, Ka-On Lam, Kwok Hung Au, Hoi Ching Cheng, Harry Ho-Yin Yiu, and Maria Li Lung Oligonucleotide-directed mutagenesis screen to identify pathogenic Lynch syndrome-associated MSH2 DNA mismatch repair gene variants Hellen Houlleberghs, Marleen Dekker, Hildo Lantermans, Roos Kleinendorst, Hendrikus Jan Dubbink, Robert M. W. Hofstra, Senno Verhoef, and Hein te Riele Functions for diverse metabolic activities in heterochromatin Xue Bessie Su and Lorraine Pillus Anthropology Polygyny and child health revisited Matthias Rieger and Natascha Wagner Reply to Rieger and Wagner: Context matters when studying purportedly harmful cultural practices David W. Lawson, Susan James, Esther Ngadaya, Bernard Ngowi, Sayoki G. M. Mfinanga, and Monique Borgerhoff Mulder Immunology and Inflammation Autoantibody-boosted T-cell reactivation in the target organ triggers manifestation of autoimmune CNS disease Anne-Christine Flach, Tanja Litke, Judith Strauss, Michael Haberl, César Cordero Gómez, Markus Reindl, Albert Saiz, Hans-Jörg Fehling, Jürgen Wienands, Francesca Odoardi, Fred Lühder, and Alexander Flügel Sialic acid-modified antigens impose tolerance via inhibition of T-cell proliferation and de novo induction of regulatory T cells  Maurizio Perdicchio, Juan M. Ilarregui, Marleen I. Verstege, Lenneke A. M. Cornelissen, Sjoerd T. T. Schetters, Steef Engels, Martino Ambrosini, Hakan Kalay, Henrike Veninga, Joke M. M. den Haan, Lisette A. van Berkel, Janneke N. Samsom, Paul R. Crocker, Tim Sparwasser, Luciana Berod, Juan J. Garcia-Vallejo, Yvette van Kooyk, and Wendy W. J. Unger Cell-type–restricted anti-cytokine therapy: TNF inhibition from one pathogenic source Grigory A. Efimov, Andrei A. Kruglov, Zoya V. Khlopchatnikova, Fedor N. Rozov, Vladislav V. Mokhonov, Stefan Rose-John, Jürgen Scheller, Siamon Gordon, Martin Stacey, Marina S. Drutskaya, Sergei V. Tillib, and Sergei A. Nedospasov Applied Biological Sciences Morphogenesis of 3D vascular networks is regulated by tensile forces Dekel Rosenfeld, Shira Landau, Yulia Shandalov, Noa Raindel, Alina Freiman, Erez Shor, Yaron Blinder, Herman H. Vandenburgh, David J. Mooney, and Shulamit Levenberg Overcoming heterologous protein interdependency to optimize P450-mediated Taxol precursor synthesis in Escherichia coli Bradley Walters Biggs, Chin Giaw Lim, Kristen Sagliani, Smriti Shankar, Gregory Stephanopoulos, Marjan De Mey, and Parayil Kumaran Ajikumar Integrated bioprocess for conversion of gaseous substrates to liquids Peng Hu, Sagar Chakraborty, Amit Kumar, Benjamin Woolston, Hongjuan Liu, David Emerson, and Gregory Stephanopoulos Applied Physical Sciences Energy landscape in protein folding and unfolding Francesco Mallamace, Carmelo Corsaro, Domenico Mallamace, Sebastiano Vasi, Cirino Vasi, Piero Baglioni, Sergey V. Buldyrev, Sow-Hsin Chen, and H. Eugene Stanley Microbiology Human symbionts inject and neutralize antibacterial toxins to persist in the gut  Aaron G. Wexler, Yiqiao Bao, John C. Whitney, Louis-Marie Bobay, Joao B. Xavier, Whitman B. Schofield, Natasha A. Barry, Alistair B. Russell, Bao Q. Tran, Young Ah Goo, David R. Goodlett, Howard Ochman, Joseph D. Mougous, and Andrew L. Goodman The source of high signal cooperativity in bacterial chemosensory arrays Germán E. Piñas, Vered Frank, Ady Vaknin, and John S. Parkinson Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species Maria Chatzidaki-Livanis, Naama Geva-Zatorsky, and Laurie E. Comstock ppGpp negatively impacts ribosome assembly affecting growth and antimicrobial tolerance in Gram-positive bacteria  Rebecca M. Corrigan, Lauren E. Bellows, Alison Wood, and Angelika Gründling Neuroscience Yes, there is a female and a male brain: Morphology versus functionality Marek Glezerman Reply to Glezerman: Why differences between brains of females and brains of males do not "add up" to create two types of brains Daphna Joel, Jürgen Hänggi, and Jared Pool Mutually repressive interaction between Brn1/2 and Rorb contributes to the establishment of neocortical layer 2/3 and layer 4 Koji Oishi, Michihiko Aramaki, and Kazunori Nakajima Neuronal profilins in health and disease: Relevance for spine plasticity and Fragile X syndrome Kristin Michaelsen-Preusse, Sabine Zessin, Gayane Grigoryan, Franziska Scharkowski, Jonas Feuge, Anita Remus, and Martin Korte Focal expression of mutant huntingtin in the songbird basal ganglia disrupts cortico-basal ganglia networks and vocal sequences  Masashi Tanaka, Jonnathan Singh Alvarado, Malavika Murugan, and Richard Mooney Ablation of huntingtin in adult neurons is nondeleterious but its depletion in young mice causes acute pancreatitis Guohao Wang, Xudong Liu, Marta A. Gaertig, Shihua Li, and Xiao-Jiang Li PP2A methylation controls sensitivity and resistance to β-amyloid–induced cognitive and electrophysiological impairments Russell E. Nicholls, Jean-Marie Sontag, Hong Zhang, Agnieszka Staniszewski, Shijun Yan, Carla Y. Kim, Michael Yim, Caitlin M. Woodruff, Erland Arning, Brandi Wasek, Deqi Yin, Teodoro Bottiglieri, Estelle Sontag, Eric R. Kandel, and Ottavio Arancio Behavioral response inhibition and maturation of goal representation in prefrontal cortex after puberty Xin Zhou, Dantong Zhu, Samson G. King, Cynthia J. Lees, Allyson J. Bennett, Emilio Salinas, Terrence R. Stanford, and Christos Constantinidis Assessing the sensitivity of diffusion MRI to detect neuronal activity directly Ruiliang Bai, Craig V. Stewart, Dietmar Plenz, and Peter J. Basser Biochemistry Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing Marina Falaleeva, Amadis Pages, Zaneta Matuszek, Sana Hidmi, Lily Agranat-Tamir, Konstantin Korotkov, Yuval Nevo, Eduardo Eyras, Ruth Sperling, and Stefan Stamm Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides Helena Safavi-Hemami, Qing Li, Ronneshia L. Jackson, Albert S. Song, Wouter Boomsma, Pradip K. Bandyopadhyay, Christian W. Gruber, Anthony W. Purcell, Mark Yandell, Baldomero M. Olivera, and Lars Ellgaard EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression Nara Lee, Therese A. Yario, Jessica S. Gao, and Joan A. Steitz Posttranslational regulation of coordinated enzyme activities in the Pup-proteasome system Yifat Elharar, Ziv Roth, Nir Hecht, Ron Rotkopf, Isam Khalaila, and Eyal Gur Conformational dynamics of a membrane protein chaperone enables spatially regulated substrate capture and release Fu-Cheng Liang, Gerard Kroon, Camille Z. McAvoy, Chris Chi, Peter E. Wright, and Shu-ou Shan Novel family of terpene synthases evolved from trans-isoprenyl diphosphate synthases in a flea beetle Franziska Beran, Peter Rahfeld, Katrin Luck, Raimund Nagel, Heiko Vogel, Natalie Wielsch, Sandra Irmisch, Srinivasan Ramasamy, Jonathan Gershenzon, David G. Heckel, and Tobias G. Köllner Biophysics and Computational Biology Atomic resolution probe for allostery in the regulatory thin filament Michael R. Williams, Sarah J. Lehman, Jil C. Tardiff, and Steven D. Schwartz Orange carotenoid protein burrows into the phycobilisome to provide photoprotection Dvir Harris, Ofir Tal, Denis Jallet, Adjélé Wilson, Diana Kirilovsky, and Noam Adir Microscopic interpretation of folding ϕ-values using the transition path ensemble Robert B. Best and Gerhard Hummer Energy landscape in protein folding and unfolding Francesco Mallamace, Carmelo Corsaro, Domenico Mallamace, Sebastiano Vasi, Cirino Vasi, Piero Baglioni, Sergey V. Buldyrev, Sow-Hsin Chen, and H. Eugene Stanley Population-based 3D genome structure analysis reveals driving forces in spatial genome organization  Harianto Tjong, Wenyuan Li, Reza Kalhor, Chao Dai, Shengli Hao, Ke Gong, Yonggang Zhou, Haochen Li, Xianghong Jasmine Zhou, Mark A. Le Gros, Carolyn A. Larabell, Lin Chen, and Frank Alber Noise-driven growth rate gain in clonal cellular populations Mikihiro Hashimoto, Takashi Nozoe, Hidenori Nakaoka, Reiko Okura, Sayo Akiyoshi, Kunihiko Kaneko, Edo Kussell, and Yuichi Wakamoto Dynamic control of strand excision during human DNA mismatch repair  Yongmoon Jeon, Daehyung Kim, Juana V. Martín-López, Ryanggeun Lee, Jungsic Oh, Jeungphill Hanne, Richard Fishel, and Jong-Bong Lee Structure and mechanism of the phage T4 recombination mediator protein UvsY  Stefan Gajewski, Michael Brett Waddell, Sivaraja Vaithiyalingam, Amanda Nourse, Zhenmei Li, Nils Woetzel, Nathan Alexander, Jens Meiler, and Stephen W. White Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance Daniel G. Schep, Jianhua Zhao, and John L. Rubinstein Blocking rapid ice crystal growth through nonbasal plane adsorption of antifreeze proteins  Luuk L. C. Olijve, Konrad Meister, Arthur L. DeVries, John G. Duman, Shuaiqi Guo, Huib J. Bakker, and Ilja K. Voets Leukocyte integrin αLβ2 headpiece structures: The αI domain, the pocket for the internal ligand, and concerted movements of its loops Timothy A. Springer and Mehmet Sen Physics Quantum communication complexity advantage implies violation of a Bell inequality Harry Buhrman, Łukasz Czekaj, Andrzej Grudka, Michał Horodecki, Paweł Horodecki, Marcin Markiewicz, Florian Speelman, and Sergii Strelchuk Cell Biology Topologically associated domains enriched for lineage-specific genes reveal expression-dependent nuclear topologies during myogenesis  Daniel S. Neems, Arturo G. Garza-Gongora, Erica D. Smith, and Steven T. Kosak Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells Yurong Xin, Jinrang Kim, Min Ni, Yi Wei, Haruka Okamoto, Joseph Lee, Christina Adler, Katie Cavino, Andrew J. Murphy, George D. Yancopoulos, Hsin Chieh Lin, and Jesper Gromada Oscillation helps to get division right David J. Sherratt Physiology Forkhead box A3 mediates glucocorticoid receptor function in adipose tissue  Xinran Ma, Lingyan Xu, and Elisabetta Mueller Chemistry Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation Suriyanarayanan Vaikuntanathan, Grant Rotskoff, Alexander Hudson, and Phillip L. Geissler Blocking rapid ice crystal growth through nonbasal plane adsorption of antifreeze proteins  Luuk L. C. Olijve, Konrad Meister, Arthur L. DeVries, John G. Duman, Shuaiqi Guo, Huib J. Bakker, and Ilja K. Voets Plant Biology Cell-to-cell movement of mitochondria in plants  Csanad Gurdon, Zora Svab, Yaping Feng, Dibyendu Kumar, and Pal Maliga NbCSPR underlies age-dependent immune responses to bacterial cold shock protein in Nicotiana benthamiana Isabel M. L. Saur, Yasuhiro Kadota, Jan Sklenar, Nicholas J. Holton, Elwira Smakowska, Youssef Belkhadir, Cyril Zipfel, and John P. Rathjen Computer Sciences Computer vision cracks the leaf code Peter Wilf, Shengping Zhang, Sharat Chikkerur, Stefan A. Little, Scott L. Wing, and Thomas Serre Earth, Atmospheric, and Planetary Sciences Deciphering ocean carbon in a changing world  Mary Ann Moran, Elizabeth B. Kujawinski, Aron Stubbins, Rob Fatland, Lihini I. Aluwihare, Alison Buchan, Byron C. Crump, Pieter C. Dorrestein, Sonya T. Dyhrman, Nancy J. Hess, Bill Howe, Krista Longnecker, Patricia M. Medeiros, Jutta Niggemann, Ingrid Obernosterer, Daniel J. Repeta, and Jacob R. Waldbauer Reduced interdecadal variability of Atlantic Meridional Overturning Circulation under global warming  Jun Cheng, Zhengyu Liu, Shaoqing Zhang, Wei Liu, Lina Dong, Peng Liu, and Hongli Li Shipwreck rates reveal Caribbean tropical cyclone response to past radiative forcing Valerie Trouet, Grant L. Harley, and Marta Domínguez-Delmás Satellite retrieval of cloud condensation nuclei concentrations by using clouds as CCN chambers Daniel Rosenfeld, Youtong Zheng, Eyal Hashimshoni, Mira L. Pöhlker, Anne Jefferson, Christopher Pöhlker, Xing Yu, Yannian Zhu, Guihua Liu, Zhiguo Yue, Baruch Fischman, Zhanqing Li, David Giguzin, Tom Goren, Paulo Artaxo, Henrique M. J. Barbosa, Ulrich Pöschl, and Meinrat O. Andreae Psychological and Cognitive Sciences Perceptual learning of degraded speech by minimizing prediction error Ediz Sohoglu and Matthew H. Davis Infants ask for help when they know they don't know  Louise Goupil, Margaux Romand-Monnier, and Sid Kouider Ecology Changing fisheries productivity and food security Cody S. Szuwalski Reply to Szuwalski: Recognizing ecological income inequality in the ocean Gregory L. Britten, Michael Dowd, and Boris Worm Discovery of a spawning ground reveals diverse migration strategies in Atlantic bluefin tuna (Thunnus thynnus)  David E. Richardson, Katrin E. Marancik, Jeffrey R. Guyon, Molly E. Lutcavage, Benjamin Galuardi, Chi Hin Lam, Harvey J. Walsh, Sharon Wildes, Douglas A. Yates, and Jonathan A. Hare Social Sciences Polygyny and child health revisited Matthias Rieger and Natascha Wagner Reply to Rieger and Wagner: Context matters when studying purportedly harmful cultural practices David W. Lawson, Susan James, Esther Ngadaya, Bernard Ngowi, Sayoki G. M. Mfinanga, and Monique Borgerhoff Mulder Engineering Three-dimensional bioprinting of thick vascularized tissues  David B. Kolesky, Kimberly A. Homan, Mark A. Skylar-Scott, and Jennifer A. Lewis Layered hydrogels accelerate iPSC-derived neuronal maturation and reveal migration defects caused by MeCP2 dysfunction  Zhen-Ning Zhang, Beatriz C. Freitas, Hao Qian, Jacques Lux, Allan Acab, Cleber A. Trujillo, Roberto H. Herai, Viet Anh Nguyen Huu, Jessica H. Wen, Shivanjali Joshi-Barr, Jerome V. Karpiak, Adam J. Engler, Xiang-Dong Fu, Alysson R. Muotri, and Adah Almutairi Sustainability Science Changing fisheries productivity and food security Cody S. Szuwalski Reply to Szuwalski: Recognizing ecological income inequality in the ocean Gregory L. Britten, Michael Dowd, and Boris Worm Analysis of data on endangered species consultations reveals nothing regarding their economic impacts Paul S. Weiland, Alan Glen, Sue Meyer, Steve Quarles, Robert Thornton, and Brooke Wahlberg Reply to Weiland et al.: The point is to bring data to inform policy, not to rely solely on anecdotes Jacob W. Malcom and Ya-Wei Li Environmental Sciences Deciphering ocean carbon in a changing world  Mary Ann Moran, Elizabeth B. Kujawinski, Aron Stubbins, Rob Fatland, Lihini I. Aluwihare, Alison Buchan, Byron C. Crump, Pieter C. Dorrestein, Sonya T. Dyhrman, Nancy J. Hess, Bill Howe, Krista Longnecker, Patricia M. Medeiros, Jutta Niggemann, Ingrid Obernosterer, Daniel J. Repeta, and Jacob R. Waldbauer Systems Biology Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements  Dan Davidi, Elad Noor, Wolfram Liebermeister, Arren Bar-Even, Avi Flamholz, Katja Tummler, Uri Barenholz, Miki Goldenfeld, Tomer Shlomi, and Ron Milo Discovery and dissection of metabolic oscillations in the microaerobic nitric oxide response network of Escherichia coli Jonathan L. Robinson and Mark P. Brynildsen Evolution Computer vision cracks the leaf code Peter Wilf, Shengping Zhang, Sharat Chikkerur, Stefan A. Little, Scott L. Wing, and Thomas Serre Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses Richard A. Neher, Trevor Bedford, Rodney S. Daniels, Colin A. Russell, and Boris I. Shraiman Perspectives Deciphering ocean carbon in a changing world  Mary Ann Moran, Elizabeth B. Kujawinski, Aron Stubbins, Rob Fatland, Lihini I. Aluwihare, Alison Buchan, Byron C. Crump, Pieter C. Dorrestein, Sonya T. Dyhrman, Nancy J. Hess, Bill Howe, Krista Longnecker, Patricia M. Medeiros, Jutta Niggemann, Ingrid Obernosterer, Daniel J. Repeta, and Jacob R. Waldbauer In This Issue In This Issue Letters and Replies Yes, there is a female and a male brain: Morphology versus functionality Marek Glezerman Reply to Glezerman: Why differences between brains of females and brains of males do not "add up" to create two types of brains Daphna Joel, Jürgen Hänggi, and Jared Pool Changing fisheries productivity and food security Cody S. Szuwalski Reply to Szuwalski: Recognizing ecological income inequality in the ocean Gregory L. Britten, Michael Dowd, and Boris Worm Polygyny and child health revisited Matthias Rieger and Natascha Wagner Reply to Rieger and Wagner: Context matters when studying purportedly harmful cultural practices David W. Lawson, Susan James, Esther Ngadaya, Bernard Ngowi, Sayoki G. M. Mfinanga, and Monique Borgerhoff Mulder Analysis of data on endangered species consultations reveals nothing regarding their economic impacts Paul S. Weiland, Alan Glen, Sue Meyer, Steve Quarles, Robert Thornton, and Brooke Wahlberg Reply to Weiland et al.: The point is to bring data to inform policy, not to rely solely on anecdotes Jacob W. Malcom and Ya-Wei Li Open Access From the Cover Inaugural Article Classic Cozzarelli Prize Winner Front Matter This message was sent to pascal.alter@gmail.com. (....) Copyright © 2016 by the National Academy of Sciences