Table of Contents

Biological Sciences

• Applied Biological Sciences

  • Open Access

    Modulating cell state to enhance suspension expansion of human pluripotent stem cells

    Yonatan Y. Lipsitz, Curtis Woodford, Ting Yin, Jacob H. Hanna, and Peter W. Zandstra

    PNAS June 19, 2018 115 (25) 6369-6374; first published June 4, 2018. https://doi.org/10.1073/pnas.1714099115

• Biochemistry

  • Open Access

    Targeting the potent Beclin 1–UVRAG coiled-coil interaction with designed peptides enhances autophagy and endolysosomal trafficking

    Shuai Wu, Yunjiao He, Xianxiu Qiu, Wenchao Yang, Wenchao Liu, Xiaohua Li, Yan Li, Han-Ming Shen, Renxiao Wang, Zhenyu Yue, and Yanxiang Zhao

    PNAS June 19, 2018 115 (25) E5669-E5678; first published June 4, 2018. https://doi.org/10.1073/pnas.1721173115
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    A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure

    Anna-Lena Steckelberg, Benjamin M. Akiyama, David A. Costantino, Tim L. Sit, Jay C. Nix, and Jeffrey S. Kieft

    PNAS June 19, 2018 115 (25) 6404-6409; first published June 4, 2018. https://doi.org/10.1073/pnas.1802429115

• Biophysics and Computational Biology

  • Open Access

    Individuality and slow dynamics in bacterial growth homeostasis

    Lee Susman, Maryam Kohram, Harsh Vashistha, Jeffrey T. Nechleba, Hanna Salman, and Naama Brenner

    PNAS June 19, 2018 115 (25) E5679-E5687; first published June 5, 2018. https://doi.org/10.1073/pnas.1615526115
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    Robust nonequilibrium pathways to microcompartment assembly

    Grant M. Rotskoff and Phillip L. Geissler

    PNAS June 19, 2018 115 (25) 6341-6346; first published June 4, 2018. https://doi.org/10.1073/pnas.1802499115

• Cell Biology

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    In vitro biomimetic engineering of a human hematopoietic niche with functional properties

    Paul E. Bourgine, Thibaut Klein, Anna M. Paczulla, Takafumi Shimizu, Leo Kunz, Konstantinos D. Kokkaliaris, Daniel L. Coutu, Claudia Lengerke, Radek Skoda, Timm Schroeder, and Ivan Martin

    PNAS June 19, 2018 115 (25) E5688-E5695; first published June 4, 2018. https://doi.org/10.1073/pnas.1805440115
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    Spatially modulated ephrinA1:EphA2 signaling increases local contractility and global focal adhesion dynamics to promote cell motility

    Zhongwen Chen, Dongmyung Oh, Kabir H. Biswas, Cheng-Han Yu, Ronen Zaidel-Bar, and Jay T. Groves

    PNAS June 19, 2018 115 (25) E5696-E5705; first published June 4, 2018. https://doi.org/10.1073/pnas.1719961115
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    Minimizing ATP depletion by oxygen scavengers for single-molecule fluorescence imaging in live cells

    Seung-Ryoung Jung, Yi Deng, Christopher Kushmerick, Charles L. Asbury, Bertil Hille, and Duk-Su Koh

    PNAS June 19, 2018 115 (25) E5706-E5715; first published June 4, 2018. https://doi.org/10.1073/pnas.1717724115
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    Altered p53 functionality in cancer-associated fibroblasts contributes to their cancer-supporting features

    Sharathchandra Arandkar, Noa Furth, Yair Elisha, Nishanth Belugali Nataraj, Heiko van der Kuip, Yosef Yarden, Walter Aulitzky, Igor Ulitsky, Benjamin Geiger, and Moshe Oren

    PNAS June 19, 2018 115 (25) 6410-6415; first published June 4, 2018. https://doi.org/10.1073/pnas.1719076115

• Ecology

  • Open Access

    Automatically identifying, counting, and describing wild animals in camera-trap images with deep learning

    • From the Cover

    Mohammad Sadegh Norouzzadeh, Anh Nguyen, Margaret Kosmala, Alexandra Swanson, Meredith S. Palmer, Craig Packer, and Jeff Clune

    PNAS June 19, 2018 115 (25) E5716-E5725; first published June 5, 2018. https://doi.org/10.1073/pnas.1719367115
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    Distance-dependent defensive coloration in the poison frog Dendrobates tinctorius, Dendrobatidae

    James B. Barnett, Constantine Michalis, Nicholas E. Scott-Samuel, and Innes C. Cuthill

    PNAS June 19, 2018 115 (25) 6416-6421; first published June 4, 2018. https://doi.org/10.1073/pnas.1800826115
  • Open Access

    Exploitation drives an ontogenetic-like deepening in marine fish

    Kenneth T. Frank, Brian Petrie, William C. Leggett, and Daniel G. Boyce

    PNAS June 19, 2018 115 (25) 6422-6427; first published June 4, 2018. https://doi.org/10.1073/pnas.1802096115

    See companion article:

    • Reply to Baudron et al.: Fishing matters: Age-specific deepening is driven by exploitation

      - Jan 23, 2019

• Evolution

  • Open Access

    Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance

    Ákos Nyerges, Bálint Csörgő, Gábor Draskovits, Bálint Kintses, Petra Szili, Györgyi Ferenc, Tamás Révész, Eszter Ari, István Nagy, Balázs Bálint, Bálint Márk Vásárhelyi, Péter Bihari, Mónika Számel, Dávid Balogh, Henrietta Papp, Dorottya Kalapis, Balázs Papp, and Csaba Pál

    PNAS June 19, 2018 115 (25) E5726-E5735; first published June 5, 2018. https://doi.org/10.1073/pnas.1801646115
  • Open Access

    Evolutionary convergence in lignin-degrading enzymes

    Iván Ayuso-Fernández, Francisco J. Ruiz-Dueñas, and Angel T. Martínez

    PNAS June 19, 2018 115 (25) 6428-6433; first published June 4, 2018. https://doi.org/10.1073/pnas.1802555115

• Immunology and Inflammation

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    Cell-intrinsic regulation of murine epidermal Langerhans cells by protein S

    Yaara Tabib, Nora S. Jaber, Maria Nassar, Tal Capucha, Gabriel Mizraji, Tsipora Nir, Noam Koren, Itay Aizenbud, Avraham Maimon, Luba Eli-Berchoer, Asaf Wilensky, Tal Burstyn-Cohen, and Avi-Hai Hovav

    PNAS June 19, 2018 115 (25) E5736-E5745; first published June 5, 2018. https://doi.org/10.1073/pnas.1800303115
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    BP180 dysfunction triggers spontaneous skin inflammation in mice

    Yang Zhang, Bin-Jin Hwang, Zhen Liu, Ning Li, Kendall Lough, Scott E. Williams, Jinbo Chen, Susan W. Burette, Luis A. Diaz, Maureen A. Su, Shengxiang Xiao, and Zhi Liu

    PNAS June 19, 2018 115 (25) 6434-6439; first published June 4, 2018. https://doi.org/10.1073/pnas.1721805115

• Medical Sciences

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    Gastrointestinal stromal tumor enhancers support a transcription factor network predictive of clinical outcome

    Matthew L. Hemming, Matthew A. Lawlor, Rhamy Zeid, Tom Lesluyes, Jonathan A. Fletcher, Chandrajit P. Raut, Ewa T. Sicinska, Frédéric Chibon, Scott A. Armstrong, George D. Demetri, and James E. Bradner

    PNAS June 19, 2018 115 (25) E5746-E5755; first published June 4, 2018. https://doi.org/10.1073/pnas.1802079115
  • Open Access

    A stress-induced response complex (SIRC) shuttles miRNAs, siRNAs, and oligonucleotides to the nucleus

    Daniela Castanotto, Xiaowei Zhang, Jessica Alluin, Xizhe Zhang, Jacqueline Rüger, Brian Armstrong, John Rossi, Arthur Riggs, and C. A. Stein

    PNAS June 19, 2018 115 (25) E5756-E5765; first published June 4, 2018. https://doi.org/10.1073/pnas.1721346115
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    PHIP as a therapeutic target for driver-negative subtypes of melanoma, breast, and lung cancer

    David de Semir, Vladimir Bezrookove, Mehdi Nosrati, Altaf A. Dar, Clayton Wu, Julia Shen, Christopher Rieken, Meenakshi Venkatasubramanian, James R. Miller III, Pierre-Yves Desprez, Sean McAllister, Liliana Soroceanu, Robert J. Debs, Nathan Salomonis, Dirk Schadendorf, James E. Cleaver, and Mohammed Kashani-Sabet

    PNAS June 19, 2018 115 (25) E5766-E5775; first published June 4, 2018. https://doi.org/10.1073/pnas.1804779115
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    Trends in health inequalities in 27 European countries

    Johan P. Mackenbach, José Rubio Valverde, Barbara Artnik, Matthias Bopp, Henrik Brønnum-Hansen, Patrick Deboosere, Ramune Kalediene, Katalin Kovács, Mall Leinsalu, Pekka Martikainen, Gwenn Menvielle, Enrique Regidor, Jitka Rychtaříková, Maica Rodriguez-Sanz, Paolo Vineis, Chris White, Bogdan Wojtyniak, Yannan Hu, and Wilma J. Nusselder

    PNAS June 19, 2018 115 (25) 6440-6445; first published June 4, 2018. https://doi.org/10.1073/pnas.1800028115

• Microbiology

  • Open Access

    ABC transporter content diversity in Streptococcus pneumoniae impacts competence regulation and bacteriocin production

    Charles Y. Wang, Nisha Patel, Wei-Yun Wholey, and Suzanne Dawid

    PNAS June 19, 2018 115 (25) E5776-E5785; first published June 4, 2018. https://doi.org/10.1073/pnas.1804668115
  • Open Access

    Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia

    Ashley A. Ross, Kirsten M. Müller, J. Scott Weese, and Josh D. Neufeld

    PNAS June 19, 2018 115 (25) E5786-E5795; first published June 5, 2018. https://doi.org/10.1073/pnas.1801302115
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    Regulation of stringent factor by branched-chain amino acids

    Mingxu Fang and Carl E. Bauer

    PNAS June 19, 2018 115 (25) 6446-6451; first published June 4, 2018. https://doi.org/10.1073/pnas.1803220115
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    Synthetic bottom-up approach reveals the complex interplay of Shigella effectors in regulation of epithelial cell death

    Xiangyu Mou, Skye Souter, Juan Du, Analise Z. Reeves, and Cammie F. Lesser

    PNAS June 19, 2018 115 (25) 6452-6457; first published June 4, 2018. https://doi.org/10.1073/pnas.1801310115
  • Open Access

    Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks

    Filipe De Vadder, Estelle Grasset, Louise Mannerås Holm, Gérard Karsenty, Andrew J. Macpherson, Louise E. Olofsson, and Fredrik Bäckhed

    PNAS June 19, 2018 115 (25) 6458-6463; first published June 4, 2018. https://doi.org/10.1073/pnas.1720017115
  • Open Access

    Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response

    Elias R. Gerrick, Thibault Barbier, Michael R. Chase, Raylin Xu, Josie François, Vincent H. Lin, Matthew J. Szucs, Jeremy M. Rock, Rushdy Ahmad, Brian Tjaden, Jonathan Livny, and Sarah M. Fortune

    PNAS June 19, 2018 115 (25) 6464-6469; first published June 5, 2018. https://doi.org/10.1073/pnas.1718003115

• Neuroscience

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    Stimulation-induced increases in cerebral blood flow and local capillary vasoconstriction depend on conducted vascular responses

    Changsi Cai, Jonas C. Fordsmann, Sofie H. Jensen, Bodil Gesslein, Micael Lønstrup, Bjørn O. Hald, Stefan A. Zambach, Birger Brodin, and Martin J. Lauritzen

    PNAS June 19, 2018 115 (25) E5796-E5804; first published June 4, 2018. https://doi.org/10.1073/pnas.1707702115
  • Open Access

    Rapid, experience-dependent translation of neurogranin enables memory encoding

    Kendrick J. Jones, Sebastian Templet, Khaled Zemoura, Bozena Kuzniewska, Franciso X. Pena, Hongik Hwang, Ding J. Lei, Henny Haensgen, Shannon Nguyen, Christopher Saenz, Michael Lewis, Magdalena Dziembowska, and Weifeng Xu

    PNAS June 19, 2018 115 (25) E5805-E5814; first published June 7, 2018. https://doi.org/10.1073/pnas.1716750115
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    Soluble epoxide hydrolase plays a key role in the pathogenesis of Parkinson’s disease

    • From the Cover

    Qian Ren, Min Ma, Jun Yang, Risa Nonaka, Akihiro Yamaguchi, Kei-ichi Ishikawa, Kenta Kobayashi, Shigeo Murayama, Sung Hee Hwang, Shinji Saiki, Wado Akamatsu, Nobutaka Hattori, Bruce D. Hammock, and Kenji Hashimoto

    PNAS June 19, 2018 115 (25) E5815-E5823; first published May 7, 2018. https://doi.org/10.1073/pnas.1802179115

    See companion article:

    • Fatty acid chemical mediator provides insights into the pathology and treatment of Parkinson’s disease

      - May 30, 2018
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    Human midcingulate cortex encodes distributed representations of task progress

    Clay B. Holroyd, José J. F. Ribas-Fernandes, Danesh Shahnazian, Massimo Silvetti, and Tom Verguts

    PNAS June 19, 2018 115 (25) 6398-6403; first published June 4, 2018. https://doi.org/10.1073/pnas.1803650115
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    Transdifferentiation of human adult peripheral blood T cells into neurons

    Koji Tanabe, Cheen Euong Ang, Soham Chanda, Victor Hipolito Olmos, Daniel Haag, Douglas F. Levinson, Thomas C. Südhof, and Marius Wernig

    PNAS June 19, 2018 115 (25) 6470-6475; first published June 4, 2018. https://doi.org/10.1073/pnas.1720273115
  • Open Access

    TMS-induced neuronal plasticity enables targeted remodeling of visual cortical maps

    Vladislav Kozyrev, Robert Staadt, Ulf T. Eysel, and Dirk Jancke

    PNAS June 19, 2018 115 (25) 6476-6481; first published June 4, 2018. https://doi.org/10.1073/pnas.1802798115

• Plant Biology

  • Open Access

    A shared cis-regulatory module activates transcription in the suspensor of plant embryos

    Kelli F. Henry, Anhthu Q. Bui, Tomokazu Kawashima, and Robert B. Goldberg

    PNAS June 19, 2018 115 (25) E5824-E5833; first published June 4, 2018. https://doi.org/10.1073/pnas.1805802115
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    Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors

    Hui Shi, Mohan Lyu, Yiwen Luo, Shoucheng Liu, Yue Li, Hang He, Ning Wei, Xing Wang Deng, and Shangwei Zhong

    PNAS June 19, 2018 115 (25) 6482-6487; first published May 29, 2018. https://doi.org/10.1073/pnas.1803861115
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    Uncovering pH at both sides of the root plasma membrane interface using noninvasive imaging

    Alexandre Martinière, Rémy Gibrat, Hervé Sentenac, Xavier Dumont, Isabelle Gaillard, and Nadine Paris

    PNAS June 19, 2018 115 (25) 6488-6493; first published June 4, 2018. https://doi.org/10.1073/pnas.1721769115
  • Open Access

    Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants

    • From the Cover

    Kranthi Varala, Amy Marshall-Colón, Jacopo Cirrone, Matthew D. Brooks, Angelo V. Pasquino, Sophie Léran, Shipra Mittal, Tara M. Rock, Molly B. Edwards, Grace J. Kim, Sandrine Ruffel, W. Richard McCombie, Dennis Shasha, and Gloria M. Coruzzi

    PNAS June 19, 2018 115 (25) 6494-6499; first published May 16, 2018. https://doi.org/10.1073/pnas.1721487115

    See companion article:

    • Time to build on good design: Resolving the temporal dynamics of gene regulatory networks

      - Jun 05, 2018

• Psychological and Cognitive Sciences

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    Memory-related hippocampal activation in the sleeping toddler

    Janani Prabhakar, Elliott G. Johnson, Christine Wu Nordahl, and Simona Ghetti

    PNAS June 19, 2018 115 (25) 6500-6505; first published June 4, 2018. https://doi.org/10.1073/pnas.1805572115

• Systems Biology

  • Open Access

    The biomass distribution on Earth

    • From the Cover

    Yinon M. Bar-On, Rob Phillips, and Ron Milo

    PNAS June 19, 2018 115 (25) 6506-6511; first published May 21, 2018. https://doi.org/10.1073/pnas.1711842115

    See companion article:

    • The scale of life and its lessons for humanity

      - May 23, 2018