Table of Contents

Biological Sciences

• Agricultural Sciences

  • Open Access

    Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection

    • From the Cover

    Adriana García-Ruiz, John B. Cole, Paul M. VanRaden, George R. Wiggans, Felipe J. Ruiz-López, and Curtis P. Van Tassell

    PNAS July 12, 2016 113 (28) E3995-E4004; first published June 27, 2016. https://doi.org/10.1073/pnas.1519061113

    See companion article:

    • Holsteins are the genomic selection poster cows

      - Jul 12, 2016

• Anthropology

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    Faster reproductive rates trade off against offspring growth in wild chimpanzees

    Melissa Emery Thompson, Martin N. Muller, Kris Sabbi, Zarin P. Machanda, Emily Otali, and Richard W. Wrangham

    PNAS July 12, 2016 113 (28) 7780-7785; first published June 27, 2016. https://doi.org/10.1073/pnas.1522168113

• Biochemistry

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    Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation

    Bo Shu and Peng Gong

    PNAS July 12, 2016 113 (28) E4005-E4014; first published June 23, 2016. https://doi.org/10.1073/pnas.1602591113
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    Htm1p–Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation

    Yi-Chang Liu, Danica Galonić Fujimori, and Jonathan S. Weissman

    PNAS July 12, 2016 113 (28) E4015-E4024; first published June 28, 2016. https://doi.org/10.1073/pnas.1608795113
  • Open Access

    Gpr161 anchoring of PKA consolidates GPCR and cAMP signaling

    Verena A. Bachmann, Johanna E. Mayrhofer, Ronit Ilouz, Philipp Tschaikner, Philipp Raffeiner, Ruth Röck, Mathieu Courcelles, Federico Apelt, Tsan-Wen Lu, George S. Baillie, Pierre Thibault, Pia Aanstad, Ulrich Stelzl, Susan S. Taylor, and Eduard Stefan

    PNAS July 12, 2016 113 (28) 7786-7791; first published June 28, 2016. https://doi.org/10.1073/pnas.1608061113
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    Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair

    Chenxu Zhu, Lining Lu, Jun Zhang, Zongwei Yue, Jinghui Song, Shuai Zong, Menghao Liu, Olivia Stovicek, Yi Qin Gao, and Chengqi Yi

    PNAS July 12, 2016 113 (28) 7792-7797; first published June 27, 2016. https://doi.org/10.1073/pnas.1604591113
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    Substrate-assisted mechanism of RNP disruption by the spliceosomal Brr2 RNA helicase

    Matthias Theuser, Claudia Höbartner, Markus C. Wahl, and Karine F. Santos

    PNAS July 12, 2016 113 (28) 7798-7803; first published June 27, 2016. https://doi.org/10.1073/pnas.1524616113

• Biophysics and Computational Biology

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    Algorithmic methods to infer the evolutionary trajectories in cancer progression

    Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti, Rebeca Sanz-Pamplona, Luca De Sano, Giancarlo Mauri, Victor Moreno, Marco Antoniotti, and Bud Mishra

    PNAS July 12, 2016 113 (28) E4025-E4034; first published June 28, 2016. https://doi.org/10.1073/pnas.1520213113
  • Open Access

    Biomechanics of red blood cells in human spleen and consequences for physiology and disease

    Igor V. Pivkin, Zhangli Peng, George E. Karniadakis, Pierre A. Buffet, Ming Dao, and Subra Suresh

    PNAS July 12, 2016 113 (28) 7804-7809; first published June 27, 2016. https://doi.org/10.1073/pnas.1606751113
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    Analyzing the electrogenicity of cytochrome c oxidase

    Ilsoo Kim and Arieh Warshel

    PNAS July 12, 2016 113 (28) 7810-7815; first published June 28, 2016. https://doi.org/10.1073/pnas.1608118113
  • Open Access

    Structure of the human 26S proteasome at a resolution of 3.9 Å

    Andreas Schweitzer, Antje Aufderheide, Till Rudack, Florian Beck, Günter Pfeifer, Jürgen M. Plitzko, Eri Sakata, Klaus Schulten, Friedrich Förster, and Wolfgang Baumeister

    PNAS July 12, 2016 113 (28) 7816-7821; first published June 24, 2016. https://doi.org/10.1073/pnas.1608050113
  • Open Access

    Enzyme surface rigidity tunes the temperature dependence of catalytic rates

    Geir Villy Isaksen, Johan Åqvist, and Bjørn Olav Brandsdal

    PNAS July 12, 2016 113 (28) 7822-7827; first published June 27, 2016. https://doi.org/10.1073/pnas.1605237113

• Cell Biology

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    Modular elements of the TPR domain in the Mps1 N terminus differentially target Mps1 to the centrosome and kinetochore

    Joseph R. Marquardt, Jennifer L. Perkins, Kyle J. Beuoy, and Harold A. Fisk

    PNAS July 12, 2016 113 (28) 7828-7833; first published June 23, 2016. https://doi.org/10.1073/pnas.1607421113
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    Phospholipase Cβ1 induces membrane tubulation and is involved in caveolae formation

    Takehiko Inaba, Takuma Kishimoto, Motohide Murate, Takuya Tajima, Shota Sakai, Mitsuhiro Abe, Asami Makino, Nario Tomishige, Reiko Ishitsuka, Yasuo Ikeda, Shinji Takeoka, and Toshihide Kobayashi

    PNAS July 12, 2016 113 (28) 7834-7839; first published June 24, 2016. https://doi.org/10.1073/pnas.1603513113

• Developmental Biology

  • Open Access

    Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice

    • Inaugural Article

    Haruhiko Miyata, Julio M. Castaneda, Yoshitaka Fujihara, Zhifeng Yu, Denise R. Archambeault, Ayako Isotani, Daiji Kiyozumi, Maya L. Kriseman, Daisuke Mashiko, Takafumi Matsumura, Ryan M. Matzuk, Masashi Mori, Taichi Noda, Asami Oji, Masaru Okabe, Renata Prunskaite-Hyyrylainen, Ramiro Ramirez-Solis, Yuhkoh Satouh, Qian Zhang, Masahito Ikawa, and Martin M. Matzuk

    PNAS July 12, 2016 113 (28) 7704-7710; first published June 29, 2016. https://doi.org/10.1073/pnas.1608458113

    See companion article:

    • Profile of Martin Matzuk

      - Jul 12, 2016
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    Gene targeting of the transcription factor Mohawk in rats causes heterotopic ossification of Achilles tendon via failed tenogenesis

    • From the Cover

    Hidetsugu Suzuki, Yoshiaki Ito, Masahiro Shinohara, Satoshi Yamashita, Shizuko Ichinose, Akio Kishida, Takuya Oyaizu, Tomohiro Kayama, Ryo Nakamichi, Naoki Koda, Kazuyoshi Yagishita, Martin K. Lotz, Atsushi Okawa, and Hiroshi Asahara

    PNAS July 12, 2016 113 (28) 7840-7845; first published July 1, 2016. https://doi.org/10.1073/pnas.1522054113

• Ecology

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    Macronutrient ratios in pollen shape bumble bee (Bombus impatiens) foraging strategies and floral preferences

    Anthony D. Vaudo, Harland M. Patch, David A. Mortensen, John F. Tooker, and Christina M. Grozinger

    PNAS July 12, 2016 113 (28) E4035-E4042; first published June 28, 2016. https://doi.org/10.1073/pnas.1606101113
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    Large-scale climatic and geophysical controls on the leaf economics spectrum

    Gregory P. Asner, David E. Knapp, Christopher B. Anderson, Roberta E. Martin, and Nicholas Vaughn

    PNAS July 12, 2016 113 (28) E4043-E4051; first published June 27, 2016. https://doi.org/10.1073/pnas.1604863113
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    Detecting regional patterns of changing CO₂ flux in Alaska

    Nicholas C. Parazoo, Roisin Commane, Steven C. Wofsy, Charles D. Koven, Colm Sweeney, David M. Lawrence, Jakob Lindaas, Rachel Y.-W. Chang, and Charles E. Miller

    PNAS July 12, 2016 113 (28) 7733-7738; first published June 27, 2016. https://doi.org/10.1073/pnas.1601085113

• Evolution

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    Genetic evidence for natural selection in humans in the contemporary United States

    • From the Cover

    Jonathan P. Beauchamp

    PNAS July 12, 2016 113 (28) 7774-7779; first published July 11, 2016. https://doi.org/10.1073/pnas.1600398113

    See companion article:

    • When genes and environment disagree: Making sense of trends in recent human evolution

      - Jul 12, 2016

    See companion article:

    • Reply to Woodley of Menie: Natural selection, educational attainment, and cognitive variance components

      - Oct 04, 2016

• Genetics

  • Open Access

    Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms

    Luis Zapata, Jia Ding, Eva-Maria Willing, Benjamin Hartwig, Daniela Bezdan, Wen-Biao Jiao, Vipul Patel, Geo Velikkakam James, Maarten Koornneef, Stephan Ossowski, and Korbinian Schneeberger

    PNAS July 12, 2016 113 (28) E4052-E4060; first published June 27, 2016. https://doi.org/10.1073/pnas.1607532113

• Immunology and Inflammation

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    Highly sensitive and unbiased approach for elucidating antibody repertoires

    Sherry G. Lin, Zhaoqing Ba, Zhou Du, Yu Zhang, Jiazhi Hu, and Frederick W. Alt

    PNAS July 12, 2016 113 (28) 7846-7851; first published June 27, 2016. https://doi.org/10.1073/pnas.1608649113
  • Open Access

    Human antibody responses after dengue virus infection are highly cross-reactive to Zika virus

    Lalita Priyamvada, Kendra M. Quicke, William H. Hudson, Nattawat Onlamoon, Jaturong Sewatanon, Srilatha Edupuganti, Kovit Pattanapanyasat, Kulkanya Chokephaibulkit, Mark J. Mulligan, Patrick C. Wilson, Rafi Ahmed, Mehul S. Suthar, and Jens Wrammert

    PNAS July 12, 2016 113 (28) 7852-7857; first published June 27, 2016. https://doi.org/10.1073/pnas.1607931113
  • Open Access

    GsdmD p30 elicited by caspase-11 during pyroptosis forms pores in membranes

    Robin A. Aglietti, Alberto Estevez, Aaron Gupta, Monica Gonzalez Ramirez, Peter S. Liu, Nobuhiko Kayagaki, Claudio Ciferri, Vishva M. Dixit, and Erin C. Dueber

    PNAS July 12, 2016 113 (28) 7858-7863; first published June 23, 2016. https://doi.org/10.1073/pnas.1607769113
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    Distinct oligoclonal band antibodies in multiple sclerosis recognize ubiquitous self-proteins

    • From the Cover

    Simone M. Brändle, Birgit Obermeier, Makbule Senel, Jessica Bruder, Reinhard Mentele, Mohsen Khademi, Tomas Olsson, Hayrettin Tumani, Wolfgang Kristoferitsch, Friedrich Lottspeich, Hartmut Wekerle, Reinhard Hohlfeld, and Klaus Dornmair

    PNAS July 12, 2016 113 (28) 7864-7869; first published June 20, 2016. https://doi.org/10.1073/pnas.1522730113

    See companion article:

    • Antibodies in multiple sclerosis oligoclonal bands target debris

      - Jul 12, 2016

• Medical Sciences

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    Dose-dependent role of claudin-1 in vivo in orchestrating features of atopic dermatitis

    Reitaro Tokumasu, Kosuke Yamaga, Yuji Yamazaki, Hiroyuki Murota, Koya Suzuki, Atsushi Tamura, Kana Bando, Yasuhide Furuta, Ichiro Katayama, and Sachiko Tsukita

    PNAS July 12, 2016 113 (28) E4061-E4068; first published June 24, 2016. https://doi.org/10.1073/pnas.1525474113
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    Theranostic near-infrared fluorescent nanoplatform for imaging and systemic siRNA delivery to metastatic anaplastic thyroid cancer

    Yanlan Liu, Viswanath Gunda, Xi Zhu, Xiaoding Xu, Jun Wu, Diana Askhatova, Omid C. Farokhzad, Sareh Parangi, and Jinjun Shi

    PNAS July 12, 2016 113 (28) 7750-7755; first published June 24, 2016. https://doi.org/10.1073/pnas.1605841113

• Microbiology

  • Open Access

    Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

    Roland Hatzenpichler, Stephanie A. Connon, Danielle Goudeau, Rex R. Malmstrom, Tanja Woyke, and Victoria J. Orphan

    PNAS July 12, 2016 113 (28) E4069-E4078; first published June 28, 2016. https://doi.org/10.1073/pnas.1603757113
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    Solid tumor therapy by selectively targeting stromal endothelial cells

    Shihui Liu, Jie Liu, Qian Ma, Liu Cao, Rasem J. Fattah, Zuxi Yu, Thomas H. Bugge, Toren Finkel, and Stephen H. Leppla

    PNAS July 12, 2016 113 (28) E4079-E4087; first published June 29, 2016. https://doi.org/10.1073/pnas.1600982113
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    Septins guide microtubule protrusions induced by actin-depolymerizing toxins like Clostridium difficile transferase (CDT)

    Thilo Nölke, Carsten Schwan, Friederike Lehmann, Kristine Østevold, Olivier Pertz, and Klaus Aktories

    PNAS July 12, 2016 113 (28) 7870-7875; first published June 23, 2016. https://doi.org/10.1073/pnas.1522717113
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    A viral kinase mimics S6 kinase to enhance cell proliferation

    Aadra Prashant Bhatt, Jason P. Wong, Marc S. Weinberg, Kurtis M. Host, Louise C. Giffin, Joshua Buijnink, Evert van Dijk, Yoshihiro Izumiya, Hsing-jien Kung, Brenda R. S. Temple, and Blossom Damania

    PNAS July 12, 2016 113 (28) 7876-7881; first published June 24, 2016. https://doi.org/10.1073/pnas.1600587113
  • Open Access

    FtsK translocation permits discrimination between an endogenous and an imported Xer/dif recombination complex

    • From the Cover

    Florian Fournes, Estelles Crozat, Carine Pages, Catherine Tardin, Laurence Salomé, François Cornet, and Philippe Rousseau

    PNAS July 12, 2016 113 (28) 7882-7887; first published June 17, 2016. https://doi.org/10.1073/pnas.1523178113

    See companion article:

    • How Xer-exploiting mobile elements overcome cellular control

      - Jul 26, 2016
  • Open Access

    Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea

    Jong-Geol Kim, Soo-Je Park, Jaap S. Sinninghe Damsté, Stefan Schouten, W. Irene C. Rijpstra, Man-Young Jung, So-Jeong Kim, Joo-Han Gwak, Heeji Hong, Ok-Ja Si, SangHoon Lee, Eugene L. Madsen, and Sung-Keun Rhee

    PNAS July 12, 2016 113 (28) 7888-7893; first published June 23, 2016. https://doi.org/10.1073/pnas.1605501113
  • Open Access

    Bacterial lipids activate, synergize, and inhibit a developmental switch in choanoflagellates

    Arielle Woznica, Alexandra M. Cantley, Christine Beemelmanns, Elizaveta Freinkman, Jon Clardy, and Nicole King

    PNAS July 12, 2016 113 (28) 7894-7899; first published June 27, 2016. https://doi.org/10.1073/pnas.1605015113

• Neuroscience

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    A face-selective ventral occipito-temporal map of the human brain with intracerebral potentials

    Jacques Jonas, Corentin Jacques, Joan Liu-Shuang, Hélène Brissart, Sophie Colnat-Coulbois, Louis Maillard, and Bruno Rossion

    PNAS July 12, 2016 113 (28) E4088-E4097; first published June 27, 2016. https://doi.org/10.1073/pnas.1522033113
  • Open Access

    Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates

    Anders Eklund, Thomas E. Nichols, and Hans Knutsson

    PNAS July 12, 2016 113 (28) 7900-7905; first published June 28, 2016. https://doi.org/10.1073/pnas.1602413113

    See companion article:

    • Case for fMRI data repositories

      - Jul 12, 2016

    See companion article:

    • Reply to Brown and Behrmann, Cox, et al., and Kessler et al.: Data and code sharing is the way forward for fMRI

      - Apr 25, 2017
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    Epigenetics and energetics in ventral hippocampus mediate rapid antidepressant action: Implications for treatment resistance

    Benedetta Bigio, Aleksander A. Mathé, Vasco C. Sousa, Danielle Zelli, Per Svenningsson, Bruce S. McEwen, and Carla Nasca

    PNAS July 12, 2016 113 (28) 7906-7911; first published June 27, 2016. https://doi.org/10.1073/pnas.1603111113

    See companion article:

    • Reply to Arduini et al.: Acetyl-l-carnitine and the brain: Epigenetics, energetics, and stress

      - Sep 27, 2016
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    Physiological role for amyloid precursor protein in adult experience-dependent plasticity

    Sally A. Marik, Olav Olsen, Marc Tessier-Lavigne, and Charles D. Gilbert

    PNAS July 12, 2016 113 (28) 7912-7917; first published June 27, 2016. https://doi.org/10.1073/pnas.1604299113
  • Open Access

    Dopamine D2 receptor availability is linked to hippocampal–caudate functional connectivity and episodic memory

    Lars Nyberg, Nina Karalija, Alireza Salami, Micael Andersson, Anders Wåhlin, Neda Kaboovand, Ylva Köhncke, Jan Axelsson, Anna Rieckmann, Goran Papenberg, Douglas D. Garrett, Katrine Riklund, Martin Lövdén, Ulman Lindenberger, and Lars Bäckman

    PNAS July 12, 2016 113 (28) 7918-7923; first published June 23, 2016. https://doi.org/10.1073/pnas.1606309113

• Pharmacology

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    ATP: The crucial component of secretory vesicles

    Judith Estévez-Herrera, Natalia Domínguez, Marta R. Pardo, Ayoze González-Santana, Edward W. Westhead, Ricardo Borges, and José David Machado

    PNAS July 12, 2016 113 (28) E4098-E4106; first published June 24, 2016. https://doi.org/10.1073/pnas.1600690113
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    β-arrestin–biased signaling through the β₂-adrenergic receptor promotes cardiomyocyte contraction

    Richard Carr III, Justin Schilling, Jianliang Song, Rhonda L. Carter, Yang Du, Sungsoo M. Yoo, Christopher J. Traynham, Walter J. Koch, Joseph Y. Cheung, Douglas G. Tilley, and Jeffrey L. Benovic

    PNAS July 12, 2016 113 (28) E4107-E4116; first published June 27, 2016. https://doi.org/10.1073/pnas.1606267113