Table of Contents

Biological Sciences

• Anthropology

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    Dental calculus reveals Mesolithic foragers in the Balkans consumed domesticated plant foods

    Emanuela Cristiani, Anita Radini, Marija Edinborough, and Dušan Borić

    PNAS September 13, 2016 113 (37) 10298-10303; first published August 29, 2016. https://doi.org/10.1073/pnas.1603477113

• Biochemistry

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    Na⁺ coordination at the Na2 site of the Na⁺/I⁻ symporter

    Giuseppe Ferrandino, Juan Pablo Nicola, Yuly E. Sánchez, Ignacia Echeverria, Yunlong Liu, L. Mario Amzel, and Nancy Carrasco

    PNAS September 13, 2016 113 (37) E5379-E5388; first published August 25, 2016. https://doi.org/10.1073/pnas.1607231113
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    Precision glycocalyx editing as a strategy for cancer immunotherapy

    • From the Cover

    Han Xiao, Elliot C. Woods, Petar Vukojicic, and Carolyn R. Bertozzi

    PNAS September 13, 2016 113 (37) 10304-10309; first published August 22, 2016. https://doi.org/10.1073/pnas.1608069113

    See companion article:

    • Cutting back on the carbs

      - Sep 01, 2016
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    Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters

    Aaron T. Bozzi, Lukas B. Bane, Wilhelm A. Weihofen, Anne L. McCabe, Abhishek Singharoy, Christophe J. Chipot, Klaus Schulten, and Rachelle Gaudet

    PNAS September 13, 2016 113 (37) 10310-10315; first published August 29, 2016. https://doi.org/10.1073/pnas.1607734113
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    Anatomy of the β-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate

    Finn P. Maloney, Lena Gerwick, William H. Gerwick, David H. Sherman, and Janet L. Smith

    PNAS September 13, 2016 113 (37) 10316-10321; first published August 29, 2016. https://doi.org/10.1073/pnas.1607210113
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    SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells

    Matthew J. Smola, Thomas W. Christy, Kaoru Inoue, Cindo O. Nicholson, Matthew Friedersdorf, Jack D. Keene, David M. Lee, J. Mauro Calabrese, and Kevin M. Weeks

    PNAS September 13, 2016 113 (37) 10322-10327; first published August 30, 2016. https://doi.org/10.1073/pnas.1600008113

• Biophysics and Computational Biology

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    Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS

    Mikayel Aznauryan, Leonildo Delgado, Andrea Soranno, Daniel Nettels, Jie-rong Huang, Alexander M. Labhardt, Stephan Grzesiek, and Benjamin Schuler

    PNAS September 13, 2016 113 (37) E5389-E5398; first published August 26, 2016. https://doi.org/10.1073/pnas.1607193113
  • Open Access

    Mutations associated with familial Parkinson’s disease alter the initiation and amplification steps of α-synuclein aggregation

    Patrick Flagmeier, Georg Meisl, Michele Vendruscolo, Tuomas P. J. Knowles, Christopher M. Dobson, Alexander K. Buell, and Céline Galvagnion

    PNAS September 13, 2016 113 (37) 10328-10333; first published August 29, 2016. https://doi.org/10.1073/pnas.1604645113
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    Communication shapes sensory response in multicellular networks

    Garrett D. Potter, Tommy A. Byrd, Andrew Mugler, and Bo Sun

    PNAS September 13, 2016 113 (37) 10334-10339; first published August 29, 2016. https://doi.org/10.1073/pnas.1605559113
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    Interplay between hydrophobicity and the positive-inside rule in determining membrane-protein topology

    Assaf Elazar, Jonathan Jacob Weinstein, Jaime Prilusky, and Sarel Jacob Fleishman

    PNAS September 13, 2016 113 (37) 10340-10345; first published August 25, 2016. https://doi.org/10.1073/pnas.1605888113
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    Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension

    James T. MacDonald, Burak V. Kabasakal, David Godding, Sebastian Kraatz, Louie Henderson, James Barber, Paul S. Freemont, and James W. Murray

    PNAS September 13, 2016 113 (37) 10346-10351; first published August 29, 2016. https://doi.org/10.1073/pnas.1525308113
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    Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain

    Tatjana Braun, Matthijn R. Vos, Nir Kalisman, Nicholas E. Sherman, Reinhard Rachel, Reinhard Wirth, Gunnar F. Schröder, and Edward H. Egelman

    PNAS September 13, 2016 113 (37) 10352-10357; first published August 30, 2016. https://doi.org/10.1073/pnas.1607756113
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    Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC

    Hüseyin Ilgü, Jean-Marc Jeckelmann, Vytautas Gapsys, Zöhre Ucurum, Bert L. de Groot, and Dimitrios Fotiadis

    PNAS September 13, 2016 113 (37) 10358-10363; first published August 31, 2016. https://doi.org/10.1073/pnas.1605442113

• Cell Biology

  • Open Access

    Reg4⁺ deep crypt secretory cells function as epithelial niche for Lgr5⁺ stem cells in colon

    Nobuo Sasaki, Norman Sachs, Kay Wiebrands, Saskia I. J. Ellenbroek, Arianna Fumagalli, Anna Lyubimova, Harry Begthel, Maaike van den Born, Johan H. van Es, Wouter R. Karthaus, Vivian S. W. Li, Carmen López-Iglesias, Peter J. Peters, Jacco van Rheenen, Alexander van Oudenaarden, and Hans Clevers

    PNAS September 13, 2016 113 (37) E5399-E5407; first published August 29, 2016. https://doi.org/10.1073/pnas.1607327113
  • Open Access

    Highly photostable, reversibly photoswitchable fluorescent protein with high contrast ratio for live-cell superresolution microscopy

    Xi Zhang, Mingshu Zhang, Dong Li, Wenting He, Jianxin Peng, Eric Betzig, and Pingyong Xu

    PNAS September 13, 2016 113 (37) 10364-10369; first published August 25, 2016. https://doi.org/10.1073/pnas.1611038113
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    Propagation of trimethylated H3K27 regulated by polycomb protein EED is required for embryogenesis, hematopoietic maintenance, and tumor suppression

    Takeshi Ueda, Yuichiro Nakata, Akiko Nagamachi, Norimasa Yamasaki, Akinori Kanai, Yasuyuki Sera, Masato Sasaki, Hirotaka Matsui, Zen-ichiro Honda, Hideaki Oda, Linda Wolff, Toshiya Inaba, and Hiroaki Honda

    PNAS September 13, 2016 113 (37) 10370-10375; first published August 30, 2016. https://doi.org/10.1073/pnas.1600070113

• Developmental Biology

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    MRG15 is required for pre-mRNA splicing and spermatogenesis

    Naoki Iwamori, Kaoru Tominaga, Tetsuya Sato, Kevin Riehle, Tokuko Iwamori, Yasuyuki Ohkawa, Cristian Coarfa, Etsuro Ono, and Martin M. Matzuk

    PNAS September 13, 2016 113 (37) E5408-E5415; first published August 29, 2016. https://doi.org/10.1073/pnas.1611995113

• Ecology

  • Open Access

    Captivity humanizes the primate microbiome

    • From the Cover

    Jonathan B. Clayton, Pajau Vangay, Hu Huang, Tonya Ward, Benjamin M. Hillmann, Gabriel A. Al-Ghalith, Dominic A. Travis, Ha Thang Long, Bui Van Tuan, Vo Van Minh, Francis Cabana, Tilo Nadler, Barbara Toddes, Tami Murphy, Kenneth E. Glander, Timothy J. Johnson, and Dan Knights

    PNAS September 13, 2016 113 (37) 10376-10381; first published August 29, 2016. https://doi.org/10.1073/pnas.1521835113

• Evolution

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    Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis

    Filip Husnik and John P. McCutcheon

    PNAS September 13, 2016 113 (37) E5416-E5424; first published August 29, 2016. https://doi.org/10.1073/pnas.1603910113
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    Differences in cooperative behavior among Damaraland mole rats are consequences of an age-related polyethism

    Markus Zöttl, Philippe Vullioud, Rute Mendonça, Miquel Torrents Ticó, David Gaynor, Adam Mitchell, and Tim Clutton-Brock

    PNAS September 13, 2016 113 (37) 10382-10387; first published September 1, 2016. https://doi.org/10.1073/pnas.1607885113

• Genetics

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    Parent-of-origin effects of A1CF and AGO2 on testicular germ-cell tumors, testicular abnormalities, and fertilization bias

    Delphine Carouge, Valerie Blanc, Sue E. Knoblaugh, Robert J. Hunter, Nicholas O. Davidson, and Joseph H. Nadeau

    PNAS September 13, 2016 113 (37) E5425-E5433; first published August 31, 2016. https://doi.org/10.1073/pnas.1604773113

• Immunology and Inflammation

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    Cd47-Sirpα interaction and IL-10 constrain inflammation-induced macrophage phagocytosis of healthy self-cells

    Zhen Bian, Lei Shi, Ya-Lan Guo, Zhiyuan Lv, Cong Tang, Shuo Niu, Alexandra Tremblay, Mahathi Venkataramani, Courtney Culpepper, Limin Li, Zhen Zhou, Ahmed Mansour, Yongliang Zhang, Andrew Gewirtz, Koby Kidder, Ke Zen, and Yuan Liu

    PNAS September 13, 2016 113 (37) E5434-E5443; first published August 30, 2016. https://doi.org/10.1073/pnas.1521069113
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    IL2Rβ-dependent signals drive terminal exhaustion and suppress memory development during chronic viral infection

    Jean-Christophe Beltra, Sara Bourbonnais, Nathalie Bédard, Tania Charpentier, Moana Boulangé, Eva Michaud, Ines Boufaied, Julie Bruneau, Naglaa H. Shoukry, Alain Lamarre, and Hélène Decaluwe

    PNAS September 13, 2016 113 (37) E5444-E5453; first published August 29, 2016. https://doi.org/10.1073/pnas.1604256113
  • Open Access

    Functional role of T-cell receptor nanoclusters in signal initiation and antigen discrimination

    Sophie V. Pageon, Thibault Tabarin, Yui Yamamoto, Yuanqing Ma, Philip R. Nicovich, John S. Bridgeman, André Cohnen, Carola Benzing, Yijun Gao, Michael D. Crowther, Katie Tungatt, Garry Dolton, Andrew K. Sewell, David A. Price, Oreste Acuto, Robert G. Parton, J. Justin Gooding, Jérémie Rossy, Jamie Rossjohn, and Katharina Gaus

    PNAS September 13, 2016 113 (37) E5454-E5463; first published August 29, 2016. https://doi.org/10.1073/pnas.1607436113
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    Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression

    Hironori Nishitsuji, Saneyuki Ujino, Sachiyo Yoshio, Masaya Sugiyama, Masashi Mizokami, Tatsuya Kanto, and Kunitada Shimotohno

    PNAS September 13, 2016 113 (37) 10388-10393; first published August 31, 2016. https://doi.org/10.1073/pnas.1525022113
  • Open Access

    Endoplasmic reticulum-resident E3 ubiquitin ligase Hrd1 controls B-cell immunity through degradation of the death receptor CD95/Fas

    Sinyi Kong, Yi Yang, Yuanming Xu, Yajun Wang, Yusi Zhang, Johanna Melo-Cardenas, Xiangping Xu, Beixue Gao, Edward B. Thorp, Donna D. Zhang, Bin Zhang, Jianxun Song, Kezhong Zhang, Jianning Zhang, Jinping Zhang, Huabin Li, and Deyu Fang

    PNAS September 13, 2016 113 (37) 10394-10399; first published August 29, 2016. https://doi.org/10.1073/pnas.1606742113

• Medical Sciences

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    Zinc-sensitive MRI contrast agent detects differential release of Zn(II) ions from the healthy vs. malignant mouse prostate

    M. Veronica Clavijo Jordan, Su-Tang Lo, Shiuhwei Chen, Christian Preihs, Sara Chirayil, Shanrong Zhang, Payal Kapur, Wen-Hong Li, Luis M. De Leon-Rodriguez, Angelo J. M. Lubag, Neil M. Rofsky, and A. Dean Sherry

    PNAS September 13, 2016 113 (37) E5464-E5471; first published August 25, 2016. https://doi.org/10.1073/pnas.1609450113
  • Open Access

    Metabolic features of chronic fatigue syndrome

    Robert K. Naviaux, Jane C. Naviaux, Kefeng Li, A. Taylor Bright, William A. Alaynick, Lin Wang, Asha Baxter, Neil Nathan, Wayne Anderson, and Eric Gordon

    PNAS September 13, 2016 113 (37) E5472-E5480; first published August 29, 2016. https://doi.org/10.1073/pnas.1607571113

    See companion article:

    • Metabolomics and chronic fatigue syndrome

      - Nov 03, 2016
    • Metabolome of chronic fatigue syndrome

      - Jan 26, 2017
  • Open Access

    MYC-nick promotes cell migration by inducing fascin expression and Cdc42 activation

    Sarah Anderson, Kumud Raj Poudel, Minna Roh-Johnson, Thomas Brabletz, Ming Yu, Nofit Borenstein-Auerbach, William N. Grady, Jihong Bai, Cecilia B. Moens, Robert N. Eisenman, and Maralice Conacci-Sorrell

    PNAS September 13, 2016 113 (37) E5481-E5490; first published August 26, 2016. https://doi.org/10.1073/pnas.1610994113
  • Open Access

    Vitamin C increases viral mimicry induced by 5-aza-2′-deoxycytidine

    • Inaugural Article

    Minmin Liu, Hitoshi Ohtani, Wanding Zhou, Andreas Due Ørskov, Jessica Charlet, Yang W. Zhang, Hui Shen, Stephen B. Baylin, Gangning Liang, Kirsten Grønbæk, and Peter A. Jones

    PNAS September 13, 2016 113 (37) 10238-10244; first published August 29, 2016. https://doi.org/10.1073/pnas.1612262113

    See companion article:

    • Profile of Peter A. Jones

      - Nov 21, 2016

• Microbiology

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    Healthy human gut phageome

    Pilar Manrique, Benjamin Bolduc, Seth T. Walk, John van der Oost, Willem M. de Vos, and Mark J. Young

    PNAS September 13, 2016 113 (37) 10400-10405; first published August 29, 2016. https://doi.org/10.1073/pnas.1601060113
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    NADPH oxidase-derived H₂O₂ subverts pathogen signaling by oxidative phosphotyrosine conversion to PB-DOPA

    Luis A. Alvarez, Lidija Kovačič, Javier Rodríguez, Jan-Hendrik Gosemann, Malgorzata Kubica, Gratiela G. Pircalabioru, Florian Friedmacher, Ada Cean, Alina Ghişe, Mihai B. Sărăndan, Prem Puri, Simon Daff, Erika Plettner, Alex von Kriegsheim, Billy Bourke, and Ulla G. Knaus

    PNAS September 13, 2016 113 (37) 10406-10411; first published August 25, 2016. https://doi.org/10.1073/pnas.1605443113
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    Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM

    Ariane Briegel, Davi R. Ortega, Petra Mann, Andreas Kjær, Simon Ringgaard, and Grant J. Jensen

    PNAS September 13, 2016 113 (37) 10412-10417; first published August 29, 2016. https://doi.org/10.1073/pnas.1604693113

• Neuroscience

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    Merkel disc is a serotonergic synapse in the epidermis for transmitting tactile signals in mammals

    Weipang Chang, Hirosato Kanda, Ryo Ikeda, Jennifer Ling, Jennifer J. DeBerry, and Jianguo G. Gu

    PNAS September 13, 2016 113 (37) E5491-E5500; first published August 29, 2016. https://doi.org/10.1073/pnas.1610176113
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    Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding

    Huiyun Du, Wei Deng, James B. Aimone, Minyan Ge, Sarah Parylak, Keenan Walch, Wei Zhang, Jonathan Cook, Huina Song, Liping Wang, Fred H. Gage, and Yangling Mu

    PNAS September 13, 2016 113 (37) E5501-E5510; first published August 29, 2016. https://doi.org/10.1073/pnas.1606951113

• Pharmacology

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    A novel orvinol analog, BU08028, as a safe opioid analgesic without abuse liability in primates

    • From the Cover

    Huiping Ding, Paul W. Czoty, Norikazu Kiguchi, Gerta Cami-Kobeci, Devki D. Sukhtankar, Michael A. Nader, Stephen M. Husbands, and Mei-Chuan Ko

    PNAS September 13, 2016 113 (37) E5511-E5518; first published August 29, 2016. https://doi.org/10.1073/pnas.1605295113

    See companion article:

    • BU08028 as a safe and nonaddictive analgesic

      - Aug 29, 2016

• Plant Biology

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    FERONIA interacts with ABI2-type phosphatases to facilitate signaling cross-talk between abscisic acid and RALF peptide in Arabidopsis

    Jia Chen, Feng Yu, Ying Liu, Changqing Du, Xiushan Li, Sirui Zhu, Xianchun Wang, Wenzhi Lan, Pedro L. Rodriguez, Xuanming Liu, Dongping Li, Liangbi Chen, and Sheng Luan

    PNAS September 13, 2016 113 (37) E5519-E5527; first published August 26, 2016. https://doi.org/10.1073/pnas.1608449113
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    Histone deacetylase HDA6 enhances brassinosteroid signaling by inhibiting the BIN2 kinase

    Yuhan Hao, Haijiao Wang, Shenglong Qiao, Linna Leng, and Xuelu Wang

    PNAS September 13, 2016 113 (37) 10418-10423; first published August 25, 2016. https://doi.org/10.1073/pnas.1521363113
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    RPT2/NCH1 subfamily of NPH3-like proteins is essential for the chloroplast accumulation response in land plants

    Noriyuki Suetsugu, Atsushi Takemiya, Sam-Geun Kong, Takeshi Higa, Aino Komatsu, Ken-ichiro Shimazaki, Takayuki Kohchi, and Masamitsu Wada

    PNAS September 13, 2016 113 (37) 10424-10429; first published August 30, 2016. https://doi.org/10.1073/pnas.1602151113

• Sustainability Science

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    Land-use change reduces habitat suitability for supporting managed honey bee colonies in the Northern Great Plains

    Clint R. V. Otto, Cali L. Roth, Benjamin L. Carlson, and Matthew D. Smart

    PNAS September 13, 2016 113 (37) 10430-10435; first published August 29, 2016. https://doi.org/10.1073/pnas.1603481113

• Systems Biology

  • Open Access

    Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing

    Yuchao Jiang, Yu Qiu, Andy J. Minn, and Nancy R. Zhang

    PNAS September 13, 2016 113 (37) E5528-E5537; first published August 29, 2016. https://doi.org/10.1073/pnas.1522203113
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    Oncometabolite d-2-hydroxyglutarate impairs α-ketoglutarate dehydrogenase and contractile function in rodent heart

    Anja Karlstaedt, Xiaotian Zhang, Heidi Vitrac, Romain Harmancey, Hernan Vasquez, Jing Han Wang, Margaret A. Goodell, and Heinrich Taegtmeyer

    PNAS September 13, 2016 113 (37) 10436-10441; first published August 31, 2016. https://doi.org/10.1073/pnas.1601650113
  • Open Access

    Prediction of multidimensional drug dose responses based on measurements of drug pairs

    • From the Cover

    Anat Zimmer, Itay Katzir, Erez Dekel, Avraham E. Mayo, and Uri Alon

    PNAS September 13, 2016 113 (37) 10442-10447; first published August 25, 2016. https://doi.org/10.1073/pnas.1606301113

    See companion article:

    • Battling combinatorics in multidrug therapies

      - Sep 01, 2016