PNAS Table of Contents for February 18, 2020; Vol. 117, No. 7

[PNAS] [Chemistry Portal](/cgi/adclick/?ad=54707&adclick=true&url=http%3A%2F%2Fchemistry.pnas.org%2F)   [February 18, 2020; Vol. 117, No. 7]( ) This Week in PNAS [In This Issue]( --------------------------------------------------------------- At the National Academies [Meanwhile, back “At the National Academies”]( May R. Berenbaum and Marcia McNutt --------------------------------------------------------------- News Feature [News Feature: Editing the microbiome]( Jyoti Madhusoodanan An in-depth look at trending science issues. --------------------------------------------------------------- Commentaries [Cofilin-induced structural changes in actin filaments stay local]( Shoichiro Ono [Dynamics and clustering of IRE1α during ER stress]( T. Kelly Rainbolt and Judith Frydman [The mystery of ornate offspring]( Douglas W. Mock [Fijian farming ants resolve the guns-or-butter dilemma for their crop plants]( William T. Wcislo [Inorganic ions regulate amorphous-to-crystal shape preservation in biomineralization]( Jeffrey D. Rimer --------------------------------------------------------------- Letters [The small molecule BI-2852 induces a nonfunctional dimer of KRAS]( Timothy H. Tran, Patrick Alexander, Srisathiyanarayanan Dharmaiah, Constance Agamasu, Dwight V. Nissley, Frank McCormick, Dominic Esposito, Dhirendra K. Simanshu, Andrew G. Stephen, and Trent E. Balius [Reply to Tran et al.: Dimeric KRAS protein–protein interaction stabilizers]( Dirk Kessler, Andreas Gollner, Michael Gmachl, Andreas Mantoulidis, Laetitia J. Martin, Andreas Zoephel, Moriz Mayer, David Covini, Silke Fischer, Thomas Gerstberger, Teresa Gmaschitz, Craig Goodwin, Peter Greb, Daniela Häring, Wolfgang Hela, Johann Hoffmann, Jale Karolyi-Oezguer, Petr Knesl, Stefan Kornigg, Manfred Koegl, Roland Kousek, Lyne Lamarre, Franziska Moser, Silvia Munico-Martinez, Christoph Peinsipp, Jason Phan, Jörg Rinnenthal, Jiqing Sai, Christian Salamon, Yvonne Scherbantin, Katharina Schipany, Renate Schnitzer, Andreas Schrenk, Bernadette Sharps, Gabriella Siszler, Qi Sun, Alex Waterson, Bernhard Wolkerstorfer, Markus Zeeb, Mark Pearson, Stephen W. Fesik, and Darryl B. McConnell [Species richness and composition are not sufficient for determining the functionality of ancient ecosystems]( Tom Weihmann [Reply to Weihmann: Fifty gazelles do not equal an elephant, and other ecological misunderstandings]( J. Tyler Faith, John Rowan, and Andrew Du --------------------------------------------------------------- Brief Report [On the collision of rods in a quiescent fluid]( Jonasz Słomka and Roman Stocker --------------------------------------------------------------- Physical Sciences Applied Physical Sciences [Formation of stable aggregates by fluid-assembled solid bridges]( Ali Seiphoori, Xiao-guang Ma, Paulo E. Arratia, and Douglas J. Jerolmack [Packing structure of semiflexible rings]( Leopoldo R. Gómez, Nicolás A. García, and Thorsten Pöschel Biophysics and Computational Biology [Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness]( Ian M. Walsh, Micayla A. Bowman, Iker F. Soto Santarriaga, Anabel Rodriguez, and Patricia L. Clark [Dynamic clamp constructed phase diagram for the Hodgkin and Huxley model of excitability]( Hillel Ori, Hananel Hazan, Eve Marder, and Shimon Marom Chemistry [All-digital histopathology by infrared-optical hybrid microscopy]( Martin Schnell, Shachi Mittal, Kianoush Falahkheirkhah, Anirudh Mittal, Kevin Yeh, Seth Kenkel, Andre Kajdacsy-Balla, P. Scott Carney, and Rohit Bhargava [Shape-preserving amorphous-to-crystalline transformation of CaCO3 revealed by in situ TEM]( Zhaoming Liu, Zhisen Zhang, Zheming Wang, Biao Jin, Dongsheng Li, Jinhui Tao, Ruikang Tang, and James J. De Yoreo [Selective targeting of nanomedicine to inflamed cerebral vasculature to enhance the blood–brain barrier]( Oscar A. Marcos-Contreras, Colin F. Greineder, Raisa Yu Kiseleva, Hamideh Parhiz, Landis R. Walsh, Viviana Zuluaga-Ramirez, Jacob W. Myerson, Elizabeth D. Hood, Carlos H. Villa, Istvan Tombacz, Norbert Pardi, Alecia Seliga, Barbara L. Mui, Ying K. Tam, Patrick M. Glassman, Vladimir V. Shuvaev, Jia Nong, Jacob S. Brenner, Makan Khoshnejad, Tom Madden, Drew Weissmann, Yuri Persidsky, and Vladimir R. Muzykantov [Anisotropic viscoelastic phase separation in polydisperse hard rods leads to nonsticky gelation]( Claudia Ferreiro-Córdova, C. Patrick Royall, and Jeroen S. van Duijneveldt [The displacement field associated with the freezing of a melt and its role in determining crystal growth kinetics]( Gang Sun, Alexander Hawken, and Peter Harrowell Earth, Atmospheric, and Planetary Sciences [Remarkable nucleation and growth of ultrafine particles from vehicular exhaust]( Song Guo, Min Hu, Jianfei Peng, Zhijun Wu, Misti L. Zamora, Dongjie Shang, Zhuofei Du, Jing Zheng, Xin Fang, Rongzhi Tang, Yusheng Wu, Limin Zeng, Shijin Shuai, Wenbin Zhang, Yuan Wang, Yuemeng Ji, Yixin Li, Annie L. Zhang, Weigang Wang, Fang Zhang, Jiayun Zhao, Xiaoli Gong, Chunyu Wang, Mario J. Molina, and Renyi Zhang [Dark biological superoxide production as a significant flux and sink of marine dissolved oxygen]( Kevin M. Sutherland, Scott D. Wankel, and Colleen M. Hansel Engineering [Unsaturated nanoporomechanics]( Hoang Nguyen, Saeed Rahimi-Aghdam, and Zdeněk P. Bažant [A self-adjusting platinum surface for acetone hydrogenation]( Benginur Demir, Thomas Kropp, Keishla R. Rivera-Dones, Elise B. Gilcher, George W. Huber, Manos Mavrikakis, and James A. Dumesic [Measuring the effectiveness of high-performance Co-Optima biofuels on suppressing soot formation at high temperature]( Samuel Barak, Ramees K. Rahman, Sneha Neupane, Erik Ninnemann, Farhan Arafin, Andrew Laich, Anthony C. Terracciano, and Subith S. Vasu [High-Reynolds-number fractal signature of nascent turbulence during transition]( Zhao Wu, Tamer A. Zaki, and Charles Meneveau [Acoustically powered surface-slipping mobile microrobots]( Amirreza Aghakhani, Oncay Yasa, Paul Wrede, and Metin Sitti [High-throughput quantitative microscopy-based half-life measurements of intravenously injected agents]( Laura G. Bracaglia, Alexandra S. Piotrowski-Daspit, Chun-Yu Lin, Zoe M. Moscato, Yongheng Wang, Gregory T. Tietjen, and W. Mark Saltzman [Real-time particle-by-particle detection of erythrocyte-camouflaged microsensor with extended circulation time in the bloodstream]( Wenjun Di, Xuefei Tan, Isen Andrew C. Calderon, Ashlyn E. Neal Reilly, Mark Niedre, and Heather A. Clark [Transdermal cold atmospheric plasma-mediated immune checkpoint blockade therapy]( Guojun Chen, Zhitong Chen, Di Wen, Zejun Wang, Hongjun Li, Yi Zeng, Gianpietro Dotti, Richard E. Wirz, and Zhen Gu [Combining microenvironment normalization strategies to improve cancer immunotherapy]( Fotios Mpekris, Chrysovalantis Voutouri, James W. Baish, Dan G. Duda, Lance L. Munn, Triantafyllos Stylianopoulos, and Rakesh K. Jain Environmental Sciences [Impacts of current and future large dams on the geographic range connectivity of freshwater fish worldwide]( Valerio Barbarossa, Rafael J. P. Schmitt, Mark A. J. Huijbregts, Christiane Zarfl, Henry King, and Aafke M. Schipper [Shale gas development has limited effects on stream biology and geochemistry in a gradient-based, multiparameter study in Pennsylvania]( Adam C. Mumford, Kelly O. Maloney, Denise M. Akob, Sarah Nettemann, Arianne Proctor, Jason Ditty, Luke Ulsamer, Josh Lookenbill, and Isabelle M. Cozzarelli Physics [Energy dissipation bounds for autonomous thermodynamic cycles]( Samuel J. Bryant and Benjamin B. Machta --------------------------------------------------------------- Social Sciences Psychological and Cognitive Sciences [Parent coaching increases conversational turns and advances infant language development]( Naja Ferjan Ramírez, Sarah Roseberry Lytle, and Patricia K. Kuhl [Functional connectivity predicts changes in attention observed across minutes, days, and months]( Monica D. Rosenberg, Dustin Scheinost, Abigail S. Greene, Emily W. Avery, Young Hye Kwon, Emily S. Finn, Ramachandran Ramani, Maolin Qiu, R. Todd Constable, and Marvin M. Chun --------------------------------------------------------------- Biological Sciences Agricultural Sciences [Canine olfactory detection of a vectored phytobacterial pathogen, Liberibacter asiaticus, and integration with disease control]( Timothy Gottwald, Gavin Poole, Thomas McCollum, David Hall, John Hartung, Jinhe Bai, Weiqi Luo, Drew Posny, Yong-Ping Duan, Earl Taylor, John da Graça, MaryLou Polek, Frank Louws, and William Schneider Applied Biological Sciences [High-throughput quantitative microscopy-based half-life measurements of intravenously injected agents]( Laura G. Bracaglia, Alexandra S. Piotrowski-Daspit, Chun-Yu Lin, Zoe M. Moscato, Yongheng Wang, Gregory T. Tietjen, and W. Mark Saltzman [Real-time particle-by-particle detection of erythrocyte-camouflaged microsensor with extended circulation time in the bloodstream]( Wenjun Di, Xuefei Tan, Isen Andrew C. Calderon, Ashlyn E. Neal Reilly, Mark Niedre, and Heather A. Clark [Spatiotemporal dynamic monitoring of fatty acid–receptor interaction on single living cells by multiplexed Raman imaging]( Wei Zhang, Fangjun Lin, Yan Liu, Han Zhang, Timothy A. Gilbertson, and Anhong Zhou Biochemistry [Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness]( Ian M. Walsh, Micayla A. Bowman, Iker F. Soto Santarriaga, Anabel Rodriguez, and Patricia L. Clark [Human MutLγ, the MLH1–MLH3 heterodimer, is an endonuclease that promotes DNA expansion]( Lyudmila Y. Kadyrova, Vaibhavi Gujar, Vickers Burdett, Paul L. Modrich, and Farid A. Kadyrov [Role of a DEF/Y motif in histone H2A-H2B recognition and nucleosome editing]( Yan Huang, Lu Sun, Leonidas Pierrakeas, Linchang Dai, Lu Pan, Ed Luk, and Zheng Zhou [Unique subsite specificity and potential natural function of a chitosan deacetylase from the human pathogen Cryptococcus neoformans]( Lea Hembach, Martin Bonin, Christian Gorzelanny, and Bruno M. Moerschbacher [Np4A alarmones function in bacteria as precursors to RNA caps]( Daniel J. Luciano and Joel G. Belasco [Control of XPR1-dependent cellular phosphate efflux by InsP8 is an exemplar for functionally-exclusive inositol pyrophosphate signaling]( Xingyao Li, Chunfang Gu, Sarah Hostachy, Soumyadip Sahu, Christopher Wittwer, Henning J. Jessen, Dorothea Fiedler, Huanchen Wang, and Stephen B. Shears Biophysics and Computational Biology [Energy dissipation bounds for autonomous thermodynamic cycles]( Samuel J. Bryant and Benjamin B. Machta [Dynamic clamp constructed phase diagram for the Hodgkin and Huxley model of excitability]( Hillel Ori, Hananel Hazan, Eve Marder, and Shimon Marom [M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus]( Hedieh Torabifard, Afra Panahi, and Charles L. Brooks III [The α-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structure]( David R. Boyer, Binsen Li, Chuanqi Sun, Weijia Fan, Kang Zhou, Michael P. Hughes, Michael R. Sawaya, Lin Jiang, and David S. Eisenberg [Drosophila YBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs]( Fan Zou, Renjun Tu, Bo Duan, Zhenlin Yang, Zhaohua Ping, Xiaoqing Song, Shiyuan Chen, Andrew Price, Hua Li, Allison Scott, Anoja Perera, Sisi Li, and Ting Xie [Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection]( Justin C. Morse, Dylan Girodat, Benjamin J. Burnett, Mikael Holm, Roger B. Altman, Karissa Y. Sanbonmatsu, Hans-Joachim Wieden, and Scott C. Blanchard Cell Biology [Selective targeting of TET catalytic domain promotes somatic cell reprogramming]( Anup Kumar Singh, Bo Zhao, Xiuhua Liu, Xin Wang, Hongzhi Li, Hanjun Qin, Xiwei Wu, Yuelong Ma, David Horne, and Xiaochun Yu [Splice switching an oncogenic ratio of SmgGDS isoforms as a strategy to diminish malignancy]( Anthony C. Brandt, Lisa McNally, Ellen L. Lorimer, Bethany Unger, Olivia J. Koehn, Kiall F. Suazo, Lisa Rein, Aniko Szabo, Shirng-Wern Tsaih, Mark D. Distefano, Michael J. Flister, Frank Rigo, Mark T. McNally, and Carol L. Williams [TIP5 primes prostate luminal cells for the oncogenic transformation mediated by PTEN-loss]( Karolina Pietrzak, Rostyslav Kuzyakiv, Ronald Simon, Marco Bolis, Dominik Bär, Rossana Aprigliano, Jean-Philippe Theurillat, Guido Sauter, and Raffaella Santoro Ecology [Impacts of current and future large dams on the geographic range connectivity of freshwater fish worldwide]( Valerio Barbarossa, Rafael J. P. Schmitt, Mark A. J. Huijbregts, Christiane Zarfl, Henry King, and Aafke M. Schipper [Ecological drivers of bacterial community assembly in synthetic phycospheres]( He Fu, Mario Uchimiya, Jeff Gore, and Mary Ann Moran [Mismatches between demographic niches and geographic distributions are strongest in poorly dispersed and highly persistent plant species]( Jörn Pagel, Martina Treurnicht, William J. Bond, Tineke Kraaij, Henning Nottebrock, AnneLise Schutte-Vlok, Jeanne Tonnabel, Karen J. Esler, and Frank M. Schurr Environmental Sciences [Shale gas development has limited effects on stream biology and geochemistry in a gradient-based, multiparameter study in Pennsylvania]( Adam C. Mumford, Kelly O. Maloney, Denise M. Akob, Sarah Nettemann, Arianne Proctor, Jason Ditty, Luke Ulsamer, Josh Lookenbill, and Isabelle M. Cozzarelli Evolution [Whole-proteome tree of life suggests a deep burst of organism diversity]( JaeJin Choi and Sung-Hou Kim Immunology and Inflammation [Transdermal cold atmospheric plasma-mediated immune checkpoint blockade therapy]( Guojun Chen, Zhitong Chen, Di Wen, Zejun Wang, Hongjun Li, Yi Zeng, Gianpietro Dotti, Richard E. Wirz, and Zhen Gu [Glioblastomas exploit truncated O-linked glycans for local and distant immune modulation via the macrophage galactose-type lectin]( Sophie A. Dusoswa, Jan Verhoeff, Erik Abels, Santiago P. Méndez-Huergo, Diego O. Croci, Lisan H. Kuijper, Elena de Miguel, Valerie M. C. J. Wouters, Myron G. Best, Ernesto Rodriguez, Lenneke A. M. Cornelissen, Sandra J. van Vliet, Pieter Wesseling, Xandra O. Breakefield, David P. Noske, Thomas Würdinger, Marike L. D. Broekman, Gabriel A. Rabinovich, Yvette van Kooyk, and Juan J. Garcia-Vallejo [Defective HIV-1 proviruses produce viral proteins]( Hiromi Imamichi, Mindy Smith, Joseph W. Adelsberger, Taisuke Izumi, Francesca Scrimieri, Brad T. Sherman, Catherine A. Rehm, Tomozumi Imamichi, Alice Pau, Marta Catalfamo, Anthony S. Fauci, and H. Clifford Lane [Activation of mosquito immunity blocks the development of transmission-stage filarial nematodes]( Elizabeth B. Edgerton, Abigail R. McCrea, Corbett T. Berry, Jenny Y. Kwok, Letitia K. Thompson, Brittany Watson, Elizabeth M. Fuller, Thomas J. Nolan, James B. Lok, and Michael Povelones [An ontogenetic switch drives the positive and negative selection of B cells]( Xijin Xu, Mukta Deobagkar-Lele, Katherine R. Bull, Tanya L. Crockford, Adam J. Mead, Adam P. Cribbs, David Sims, Consuelo Anzilotti, and Richard J. Cornall Medical Sciences [All-digital histopathology by infrared-optical hybrid microscopy]( Martin Schnell, Shachi Mittal, Kianoush Falahkheirkhah, Anirudh Mittal, Kevin Yeh, Seth Kenkel, Andre Kajdacsy-Balla, P. Scott Carney, and Rohit Bhargava [Combining microenvironment normalization strategies to improve cancer immunotherapy]( Fotios Mpekris, Chrysovalantis Voutouri, James W. Baish, Dan G. Duda, Lance L. Munn, Triantafyllos Stylianopoulos, and Rakesh K. Jain [NAD deficiency due to environmental factors or gene–environment interactions causes congenital malformations and miscarriage in mice]( Hartmut Cuny, Melissa Rapadas, Jessica Gereis, Ella M. M. A. Martin, Rosemary B. Kirk, Hongjun Shi, and Sally L. Dunwoodie [Hsp47 promotes cancer metastasis by enhancing collagen-dependent cancer cell-platelet interaction]( Gaofeng Xiong, Jie Chen, Guoying Zhang, Shike Wang, Kunito Kawasaki, Jieqing Zhu, Yan Zhang, Kazuhiro Nagata, Zhenyu Li, Binhua P. Zhou, and Ren Xu Microbiology [Repair of a previously uncharacterized second host-range gene contributes to full replication of modified vaccinia virus Ankara (MVA) in human cells]( Chen Peng and Bernard Moss [Development of an antibody cocktail for treatment of Sudan virus infection]( Andrew S. Herbert, Jeffery W. Froude, Ramon A. Ortiz, Ana I. Kuehne, Danielle E. Dorosky, Russell R. Bakken, Samantha E. Zak, Nicole M. Josleyn, Konstantin Musiychuk, R. Mark Jones, Brian Green, Stephen J. Streatfield, Anna Z. Wec, Natasha Bohorova, Ognian Bohorov, Do H. Kim, Michael H. Pauly, Jesus Velasco, Kevin J. Whaley, Spencer W. Stonier, Zachary A. Bornholdt, Kartik Chandran, Larry Zeitlin, Darryl Sampey, Vidadi Yusibov, and John M. Dye [Facilitative and synergistic interactions between fungal and plant viruses]( Ruiling Bian, Ida Bagus Andika, Tianxing Pang, Ziqian Lian, Shuang Wei, Erbo Niu, Yunfeng Wu, Hideki Kondo, Xili Liu, and Liying Sun [Listeria monocytogenes exploits host exocytosis to promote cell-to-cell spread]( Georgina C. Dowd, Roman Mortuza, Manmeet Bhalla, Hoan Van Ngo, Yang Li, Luciano A. Rigano, and Keith Ireton Neuroscience [Functional connectivity predicts changes in attention observed across minutes, days, and months]( Monica D. Rosenberg, Dustin Scheinost, Abigail S. Greene, Emily W. Avery, Young Hye Kwon, Emily S. Finn, Ramachandran Ramani, Maolin Qiu, R. Todd Constable, and Marvin M. Chun [Individual-specific functional connectivity of the amygdala: A substrate for precision psychiatry]( Chad M. Sylvester, Qiongru Yu, A. Benjamin Srivastava, Scott Marek, Annie Zheng, Dimitrios Alexopoulos, Christopher D. Smyser, Joshua S. Shimony, Mario Ortega, Donna L. Dierker, Gaurav H. Patel, Steven M. Nelson, Adrian W. Gilmore, Kathleen B. McDermott, Jeffrey J. Berg, Andrew T. Drysdale, Michael T. Perino, Abraham Z. Snyder, Ryan V. Raut, Timothy O. Laumann, Evan M. Gordon, Deanna M. Barch, Cynthia E. Rogers, Deanna J. Greene, Marcus E. Raichle, and Nico U. F. Dosenbach [Synaptotagmin 1 oligomers clamp and regulate different modes of neurotransmitter release]( Erica Tagliatti, Oscar D. Bello, Philipe R. F. Mendonça, Dimitrios Kotzadimitriou, Elizabeth Nicholson, Jeff Coleman, Yulia Timofeeva, James E. Rothman, Shyam S. Krishnakumar, and Kirill E. Volynski [Protection of cochlear synapses from noise-induced excitotoxic trauma by blockade of Ca2+-permeable AMPA receptors]( Ning Hu, Mark A. Rutherford, and Steven H. Green [Conformational spread and dynamics in allostery of NMDA receptors]( Ryan J. Durham, Nabina Paudyal, Elisa Carrillo, Nidhi Kaur Bhatia, David M. Maclean, Vladimir Berka, Drew M. Dolino, Alemayehu A. Gorfe, and Vasanthi Jayaraman Pharmacology [Positive allosteric modulation of indoleamine 2,3-dioxygenase 1 restrains neuroinflammation]( Giada Mondanelli, Alice Coletti, Francesco Antonio Greco, Maria Teresa Pallotta, Ciriana Orabona, Alberta Iacono, Maria Laura Belladonna, Elisa Albini, Eleonora Panfili, Francesca Fallarino, Marco Gargaro, Giorgia Manni, Davide Matino, Agostinho Carvalho, Cristina Cunha, Patricia Maciel, Massimiliano Di Filippo, Lorenzo Gaetani, Roberta Bianchi, Carmine Vacca, Ioana Maria Iamandii, Elisa Proietti, Francesca Boscia, Lucio Annunziato, Maikel Peppelenbosch, Paolo Puccetti, Paolo Calabresi, Antonio Macchiarulo, Laura Santambrogio, Claudia Volpi, and Ursula Grohmann Physiology [Kv2.1 channels play opposing roles in regulating membrane potential, Ca2+ channel function, and myogenic tone in arterial smooth muscle]( Samantha C. O’Dwyer, Stephanie Palacio, Collin Matsumoto, Laura Guarina, Nicholas R. Klug, Sendoa Tajada, Barbara Rosati, David McKinnon, James S. Trimmer, and L. Fernando Santana Plant Biology [The versatile functions of OsALDH2B1 provide a genic basis for growth–defense trade-offs in rice]( Yinggen Ke, Meng Yuan, Hongbo Liu, Shugang Hui, Xiaofeng Qin, Jie Chen, Qinglu Zhang, Xianghua Li, Jinghua Xiao, Qifa Zhang, and Shiping Wang [Rhizosphere microbiome mediates systemic root metabolite exudation by root-to-root signaling]( Elisa Korenblum, Yonghui Dong, Jedrzej Szymanski, Sayantan Panda, Adam Jozwiak, Hassan Massalha, Sagit Meir, Ilana Rogachev, and Asaph Aharoni [Cover] --------------------------------------------------------------- This message was sent to {EMAIL}. [Unsubscribe]( from or [edit]( your subscription for this service. Or by mail: Customer Service * 15575-A Los Gatos Blvd * Los Gatos, CA 95032 * U.S.A. Copyright © 2020 by the National Academy of Sciences