Table of Contents

Biological Sciences

• Biochemistry

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    Transcription initiation defines kinetoplast RNA boundaries

    François M. Sement, Takuma Suematsu, Liye Zhang, Tian Yu, Lan Huang, Inna Aphasizheva, and Ruslan Aphasizhev

    PNAS October 30, 2018 115 (44) E10323-E10332; first published October 17, 2018. https://doi.org/10.1073/pnas.1808981115
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    Mechanism of tRNA-mediated +1 ribosomal frameshifting

    • Cozzarelli Prize Winner

    Samuel Hong, S. Sunita, Tatsuya Maehigashi, Eric D. Hoffer, Jack A. Dunkle, and Christine M. Dunham

    PNAS October 30, 2018 115 (44) 11226-11231; first published September 27, 2018. https://doi.org/10.1073/pnas.1809319115

    See companion article:

    • Culmination of a half-century quest reveals insight into mutant tRNA-mediated frameshifting after tRNA departure from the decoding site

      - Oct 19, 2018
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    Extracellularly oxidative activation and inactivation of matured prodrug for cryptic self-resistance in naphthyridinomycin biosynthesis

    Yue Zhang, Wan-Hong Wen, Jin-Yue Pu, Man-Cheng Tang, Liwen Zhang, Chao Peng, Yuquan Xu, and Gong-Li Tang

    PNAS October 30, 2018 115 (44) 11232-11237; first published October 16, 2018. https://doi.org/10.1073/pnas.1800502115

• Biophysics and Computational Biology

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    Ultrafast epithelial contractions provide insights into contraction speed limits and tissue integrity

    Shahaf Armon, Matthew Storm Bull, Andres Aranda-Diaz, and Manu Prakash

    PNAS October 30, 2018 115 (44) E10333-E10341; first published October 11, 2018. https://doi.org/10.1073/pnas.1802934115
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    Peptide design by optimization on a data-parameterized protein interaction landscape

    Justin M. Jenson, Vincent Xue, Lindsey Stretz, Tirtha Mandal, Lothar “Luther” Reich, and Amy E. Keating

    PNAS October 30, 2018 115 (44) E10342-E10351; first published October 15, 2018. https://doi.org/10.1073/pnas.1812939115
  • Open Access

    Pathological transitions in myelin membranes driven by environmental and multiple sclerosis conditions

    Rona Shaharabani, Maor Ram-On, Yeshayahu Talmon, and Roy Beck

    PNAS October 30, 2018 115 (44) 11156-11161; first published October 15, 2018. https://doi.org/10.1073/pnas.1804275115
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    Hypertrophic cardiomyopathy R403Q mutation in rabbit β-myosin reduces contractile function at the molecular and myofibrillar levels

    Susan Lowey, Vera Bretton, Peteranne B. Joel, Kathleen M. Trybus, James Gulick, Jeffrey Robbins, Albert Kalganov, Anabelle S. Cornachione, and Dilson E. Rassier

    PNAS October 30, 2018 115 (44) 11238-11243; first published October 15, 2018. https://doi.org/10.1073/pnas.1802967115

• Cell Biology

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    RPA1 binding to NRF2 switches ARE-dependent transcriptional activation to ARE-NRE–dependent repression

    Pengfei Liu, Montserrat Rojo de la Vega, Saad Sammani, Joseph B. Mascarenhas, Michael Kerins, Matthew Dodson, Xiaoguang Sun, Ting Wang, Aikseng Ooi, Joe G. N. Garcia, and Donna D. Zhang

    PNAS October 30, 2018 115 (44) E10352-E10361; first published October 11, 2018. https://doi.org/10.1073/pnas.1812125115
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    mTORC1 signaling suppresses Wnt/β-catenin signaling through DVL-dependent regulation of Wnt receptor FZD level

    Hao Zeng, Bo Lu, Raffaella Zamponi, Zinger Yang, Kristie Wetzel, Joseph Loureiro, Sina Mohammadi, Martin Beibel, Sebastian Bergling, John Reece-Hoyes, Carsten Russ, Guglielmo Roma, Jan S. Tchorz, Paola Capodieci, and Feng Cong

    PNAS October 30, 2018 115 (44) E10362-E10369; first published October 8, 2018. https://doi.org/10.1073/pnas.1808575115

• Developmental Biology

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    TRPM7 and Ca_V3.2 channels mediate Ca²⁺ influx required for egg activation at fertilization

    Miranda L. Bernhardt, Paula Stein, Ingrid Carvacho, Christopher Krapp, Goli Ardestani, Aujan Mehregan, David M. Umbach, Marisa S. Bartolomei, Rafael A. Fissore, and Carmen J. Williams

    PNAS October 30, 2018 115 (44) E10370-E10378; first published October 15, 2018. https://doi.org/10.1073/pnas.1810422115
  • Open Access

    Frequent monoallelic or skewed expression for developmental genes in CNS-derived cells and evidence for balancing selection

    Sergio Branciamore, Zuzana Valo, Min Li, Jinhui Wang, Arthur D. Riggs, and Judith Singer-Sam

    PNAS October 30, 2018 115 (44) E10379-E10386; first published October 15, 2018. https://doi.org/10.1073/pnas.1808652115
  • Open Access

    Ubiquitin ligase COP1 coordinates transcriptional programs that control cell type specification in the developing mouse brain

    Kim Newton, Debra L. Dugger, Arundhati Sengupta-Ghosh, Ronald E. Ferrando, Felix Chu, Janet Tao, Wendy Lam, Susan Haller, Sara Chan, Susan Sa, Debra Dunlap, Jeffrey Eastham-Anderson, Hai Ngu, Jeffrey Hung, Dorothy M. French, Joshua D. Webster, Brad Bolon, Jinfeng Liu, Rohit Reja, Sarah Kummerfeld, Ying-Jiun Chen, Zora Modrusan, Joseph W. Lewcock, and Vishva M. Dixit

    PNAS October 30, 2018 115 (44) 11244-11249; first published October 15, 2018. https://doi.org/10.1073/pnas.1805033115
  • Open Access

    Ribonuclease activity of MARF1 controls oocyte RNA homeostasis and genome integrity in mice

    Qingqing Yao, Guangyi Cao, Mingzhe Li, Baixing Wu, Xiaoyun Zhang, Teng Zhang, Jing Guo, Hong Yin, Lanying Shi, Jiayi Chen, Xiang Yu, Lina Zheng, Jinbiao Ma, and You-Qiang Su

    PNAS October 30, 2018 115 (44) 11250-11255; first published October 17, 2018. https://doi.org/10.1073/pnas.1809744115

• Ecology

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    Collective decision making by rational individuals

    Richard P. Mann

    PNAS October 30, 2018 115 (44) E10387-E10396; first published October 15, 2018. https://doi.org/10.1073/pnas.1811964115
  • Open Access

    Climate-driven declines in arthropod abundance restructure a rainforest food web

    Bradford C. Lister and Andres Garcia

    PNAS October 30, 2018 115 (44) E10397-E10406; first published October 15, 2018. https://doi.org/10.1073/pnas.1722477115

    See companion article:

    • Reply to Willig et al.: Long-term population trends in the Luquillo Rainforest

      - May 29, 2019
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    Multistability of model and real dryland ecosystems through spatial self-organization

    Robbin Bastiaansen, Olfa Jaïbi, Vincent Deblauwe, Maarten B. Eppinga, Koen Siteur, Eric Siero, Stéphane Mermoz, Alexandre Bouvet, Arjen Doelman, and Max Rietkerk

    PNAS October 30, 2018 115 (44) 11256-11261; first published October 15, 2018. https://doi.org/10.1073/pnas.1804771115
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    Mammal diversity will take millions of years to recover from the current biodiversity crisis

    • From the Cover

    Matt Davis, Søren Faurby, and Jens-Christian Svenning

    PNAS October 30, 2018 115 (44) 11262-11267; first published October 15, 2018. https://doi.org/10.1073/pnas.1804906115
  • Open Access

    Density-dependent adult recruitment in a low-density tropical tree

    James R. Kellner and Stephen P. Hubbell

    PNAS October 30, 2018 115 (44) 11268-11273; first published October 15, 2018. https://doi.org/10.1073/pnas.1800353115
  • Open Access

    Microbiome-assisted carrion preservation aids larval development in a burying beetle

    Shantanu P. Shukla, Camila Plata, Michael Reichelt, Sandra Steiger, David G. Heckel, Martin Kaltenpoth, Andreas Vilcinskas, and Heiko Vogel

    PNAS October 30, 2018 115 (44) 11274-11279; first published October 15, 2018. https://doi.org/10.1073/pnas.1812808115
  • Open Access

    Dispersal increases ecological selection by increasing effective community size

    Ronen Ron, Ori Fragman-Sapir, and Ronen Kadmon

    PNAS October 30, 2018 115 (44) 11280-11285; first published October 15, 2018. https://doi.org/10.1073/pnas.1812511115

• Evolution

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    Adaptation limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources

    Benjamin H. Good, Stephen Martis, and Oskar Hallatschek

    PNAS October 30, 2018 115 (44) E10407-E10416; first published October 15, 2018. https://doi.org/10.1073/pnas.1807530115
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    On the deformability of an empirical fitness landscape by microbial evolution

    Djordje Bajić, Jean C. C. Vila, Zachary D. Blount, and Alvaro Sánchez

    PNAS October 30, 2018 115 (44) 11286-11291; first published October 15, 2018. https://doi.org/10.1073/pnas.1808485115

• Genetics

  • Open Access

    Molecular profiling of nonalcoholic fatty liver disease-associated hepatocellular carcinoma using SB transposon mutagenesis

    Takahiro Kodama, Jing Yi, Justin Y. Newberg, Jean C. Tien, Hao Wu, Milton J. Finegold, Michiko Kodama, Zhubo Wei, Takeshi Tamura, Tetsuo Takehara, Randy L. Johnson, Nancy A. Jenkins, and Neal G. Copeland

    PNAS October 30, 2018 115 (44) E10417-E10426; first published October 16, 2018. https://doi.org/10.1073/pnas.1808968115
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    Single-molecule DNA-mapping and whole-genome sequencing of individual cells

    Rodolphe Marie, Jonas N. Pedersen, Loic Bærlocher, Kamila Koprowska, Marie Pødenphant, Céline Sabatel, Maksim Zalkovskij, Andrej Mironov, Brian Bilenberg, Neil Ashley, Henrik Flyvbjerg, Walter F. Bodmer, Anders Kristensen, and Kalim U. Mir

    PNAS October 30, 2018 115 (44) 11192-11197; first published October 15, 2018. https://doi.org/10.1073/pnas.1804194115

• Immunology and Inflammation

  • Open Access

    Herpesvirus trigger accelerates neuroinflammation in a nonhuman primate model of multiple sclerosis

    Emily C. Leibovitch, Breanna Caruso, Seung Kwon Ha, Matthew K. Schindler, Nathanael J. Lee, Nicholas J. Luciano, Bridgette J. Billioux, Joseph R. Guy, Cecil Yen, Pascal Sati, Afonso C. Silva, Daniel S. Reich, and Steven Jacobson

    PNAS October 30, 2018 115 (44) 11292-11297; first published October 15, 2018. https://doi.org/10.1073/pnas.1811974115

    See companion article:

    • Reply to Zahednasab et al.: HHV-6 and marmoset EAE

      - Dec 11, 2018

• Medical Sciences

  • Open Access

    Shift from androgen to estrogen action causes abdominal muscle fibrosis, atrophy, and inguinal hernia in a transgenic male mouse model

    Hong Zhao, Ling Zhou, Lin Li, John Coon V, Robert T. Chatterton, David C. Brooks, Enze Jiang, Li Liu, Xia Xu, Zhiyong Dong, Francesco J. DeMayo, Jonah J. Stulberg, Warren G. Tourtellotte, and Serdar E. Bulun

    PNAS October 30, 2018 115 (44) E10427-E10436; first published October 16, 2018. https://doi.org/10.1073/pnas.1807765115
  • Open Access

    Impaired hematopoiesis and leukemia development in mice with a conditional knock-in allele of a mutant splicing factor gene U2af1

    Dennis Liang Fei, Tao Zhen, Benjamin Durham, John Ferrarone, Tuo Zhang, Lisa Garrett, Akihide Yoshimi, Omar Abdel-Wahab, Robert K. Bradley, Paul Liu, and Harold Varmus

    PNAS October 30, 2018 115 (44) E10437-E10446; first published October 15, 2018. https://doi.org/10.1073/pnas.1812669115
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    Alterations of tumor microenvironment by nitric oxide impedes castration-resistant prostate cancer growth

    Himanshu Arora, Kush Panara, Manish Kuchakulla, Shathiyah Kulandavelu, Kerry L. Burnstein, Andrew V. Schally, Joshua M. Hare, and Ranjith Ramasamy

    PNAS October 30, 2018 115 (44) 11298-11303; first published October 15, 2018. https://doi.org/10.1073/pnas.1812704115

• Microbiology

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    Prevalent reliance of bacterioplankton on exogenous vitamin B1 and precursor availability

    Ryan W. Paerl, John Sundh, Demeng Tan, Sine L. Svenningsen, Samuel Hylander, Jarone Pinhassi, Anders F. Andersson, and Lasse Riemann

    PNAS October 30, 2018 115 (44) E10447-E10456; first published October 15, 2018. https://doi.org/10.1073/pnas.1806425115
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    ADP-ribosyl–binding and hydrolase activities of the alphavirus nsP3 macrodomain are critical for initiation of virus replication

    Rachy Abraham, Debra Hauer, Robert Lyle McPherson, Age Utt, Ilsa T. Kirby, Michael S. Cohen, Andres Merits, Anthony K. L. Leung, and Diane E. Griffin

    PNAS October 30, 2018 115 (44) E10457-E10466; first published October 15, 2018. https://doi.org/10.1073/pnas.1812130115

• Neuroscience

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    Alleviating catastrophic forgetting using context-dependent gating and synaptic stabilization

    Nicolas Y. Masse, Gregory D. Grant, and David J. Freedman

    PNAS October 30, 2018 115 (44) E10467-E10475; first published October 12, 2018. https://doi.org/10.1073/pnas.1803839115
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    Control of movement vigor and decision making during foraging

    Tehrim Yoon, Robert B. Geary, Alaa A. Ahmed, and Reza Shadmehr

    PNAS October 30, 2018 115 (44) E10476-E10485; first published October 15, 2018. https://doi.org/10.1073/pnas.1812979115
  • Open Access

    Lawful tracking of visual motion in humans, macaques, and marmosets in a naturalistic, continuous, and untrained behavioral context

    • From the Cover

    Jonas Knöll, Jonathan W. Pillow, and Alexander C. Huk

    PNAS October 30, 2018 115 (44) E10486-E10494; first published October 15, 2018. https://doi.org/10.1073/pnas.1807192115

    See companion article:

    • Rapid assessment of natural visual motion integration across primate species

      - Oct 22, 2018
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    Mutant UBQLN2 promotes toxicity by modulating intrinsic self-assembly

    Lisa M. Sharkey, Nathaniel Safren, Amit S. Pithadia, Julia E. Gerson, Mark Dulchavsky, Svetlana Fischer, Ronak Patel, Gabrielle Lantis, Naila Ashraf, John H. Kim, Alia Meliki, Eiko N. Minakawa, Sami J. Barmada, Magdalena I. Ivanova, and Henry L. Paulson

    PNAS October 30, 2018 115 (44) E10495-E10504; first published October 17, 2018. https://doi.org/10.1073/pnas.1810522115
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    Flow stimuli reveal ecologically appropriate responses in mouse visual cortex

    Luciano Dyballa, Mahmood S. Hoseini, Maria C. Dadarlat, Steven W. Zucker, and Michael P. Stryker

    PNAS October 30, 2018 115 (44) 11304-11309; first published October 16, 2018. https://doi.org/10.1073/pnas.1811265115
  • Open Access

    Color opponency with a single kind of bistable opsin in the zebrafish pineal organ

    Seiji Wada, Baoguo Shen, Emi Kawano-Yamashita, Takashi Nagata, Masahiko Hibi, Satoshi Tamotsu, Mitsumasa Koyanagi, and Akihisa Terakita

    PNAS October 30, 2018 115 (44) 11310-11315; first published October 15, 2018. https://doi.org/10.1073/pnas.1802592115
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    Focal adhesion molecules regulate astrocyte morphology and glutamate transporters to suppress seizure-like behavior

    Sukhee Cho, Allie K. Muthukumar, Tobias Stork, Jaeda C. Coutinho-Budd, and Marc R. Freeman

    PNAS October 30, 2018 115 (44) 11316-11321; first published October 16, 2018. https://doi.org/10.1073/pnas.1800830115
  • Open Access

    Mammalian behavior and physiology converge to confirm sharper cochlear tuning in humans

    Christian J. Sumner, Toby T. Wells, Christopher Bergevin, Joseph Sollini, Heather A. Kreft, Alan R. Palmer, Andrew J. Oxenham, and Christopher A. Shera

    PNAS October 30, 2018 115 (44) 11322-11326; first published October 15, 2018. https://doi.org/10.1073/pnas.1810766115

• Pharmacology

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    Discovery of a small-molecule inhibitor of specific serine residue BAD phosphorylation

    Vijay Pandey, Baocheng Wang, Chakrabhavi Dhananjaya Mohan, Ainiah Rushdiana Raquib, Shobith Rangappa, Venkatachalaiah Srinivasa, Julian E. Fuchs, Kesturu S. Girish, Tao Zhu, Andreas Bender, Lan Ma, Zhinan Yin, Basappa, Kanchugarakoppal S. Rangappa, and Peter E. Lobie

    PNAS October 30, 2018 115 (44) E10505-E10514; first published October 11, 2018. https://doi.org/10.1073/pnas.1804897115

• Plant Biology

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    Identification of SLAC1 anion channel residues required for CO₂/bicarbonate sensing and regulation of stomatal movements

    • Inaugural Article

    Jingbo Zhang, Nuo Wang, Yinglong Miao, Felix Hauser, J. Andrew McCammon, Wouter-Jan Rappel, and Julian I. Schroeder

    PNAS October 30, 2018 115 (44) 11129-11137; first published October 9, 2018. https://doi.org/10.1073/pnas.1807624115

    See companion article:

    • Profile of Julian I. Schroeder

      - Oct 15, 2018
  • Open Access

    Mutations in the DNA demethylase OsROS1 result in a thickened aleurone and improved nutritional value in rice grains

    • From the Cover

    Jinxin Liu, Xiaoba Wu, Xuefeng Yao, Ronald Yu, Philip J. Larkin, and Chun-Ming Liu

    PNAS October 30, 2018 115 (44) 11327-11332; first published October 1, 2018. https://doi.org/10.1073/pnas.1806304115

    See companion article:

    • A role of OsROS1 in aleurone development and nutrient improvement in rice

      - Nov 01, 2018

• Psychological and Cognitive Sciences

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    Potential downside of high initial visual acuity

    Lukas Vogelsang, Sharon Gilad-Gutnick, Evan Ehrenberg, Albert Yonas, Sidney Diamond, Richard Held, and Pawan Sinha

    PNAS October 30, 2018 115 (44) 11333-11338; first published October 15, 2018. https://doi.org/10.1073/pnas.1800901115

    See companion article:

    • Response to Katzhendler and Weinshall: Initial visual degradation during development may be adaptive

      - Aug 22, 2019

• Sustainability Science

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    Three pillars of sustainability in fisheries

    • From the Cover

    Frank Asche, Taryn M. Garlock, James L. Anderson, Simon R. Bush, Martin D. Smith, Christopher M. Anderson, Jingjie Chu, Karen A. Garrett, Audun Lem, Kai Lorenzen, Atle Oglend, Sigbjørn Tveteras, and Stefania Vannuccini

    PNAS October 30, 2018 115 (44) 11221-11225; first published September 24, 2018. https://doi.org/10.1073/pnas.1807677115

    See companion article:

    • Strengthening sustainability through data

      - Oct 19, 2018

• Systems Biology

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    Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice

    Bin Du, Daniel C. Zielinski, Jonathan M. Monk, and Bernhard O. Palsson

    PNAS October 30, 2018 115 (44) 11339-11344; first published October 11, 2018. https://doi.org/10.1073/pnas.1805367115