Table of Contents

Biological Sciences

• Applied Biological Sciences

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    Artificial riboswitches for gene expression and replication control of DNA and RNA viruses

    Patrick Ketzer, Johanna K. Kaufmann, Sarah Engelhardt, Sascha Bossow, Christof von Kalle, Jörg S. Hartig, Guy Ungerechts, and Dirk M. Nettelbeck

    PNAS February 4, 2014 111 (5) E554-E562; https://doi.org/10.1073/pnas.1318563111
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    A general approach to site-specific antibody drug conjugates

    Feng Tian, Yingchun Lu, Anthony Manibusan, Aaron Sellers, Hon Tran, Ying Sun, Trung Phuong, Richard Barnett, Brad Hehli, Frank Song, Michael J. DeGuzman, Semsi Ensari, Jason K. Pinkstaff, Lorraine M. Sullivan, Sandra L. Biroc, Ho Cho, Peter G. Schultz, John DiJoseph, Maureen Dougher, Dangshe Ma, Russell Dushin, Mauricio Leal, Lioudmila Tchistiakova, Eric Feyfant, Hans-Peter Gerber, and Puja Sapra

    PNAS February 4, 2014 111 (5) 1766-1771; https://doi.org/10.1073/pnas.1321237111

• Biochemistry

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    Role of clusters in nonclassical nucleation and growth of protein crystals

    Mike Sleutel and Alexander E. S. Van Driessche

    PNAS February 4, 2014 111 (5) E546-E553; https://doi.org/10.1073/pnas.1309320111
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    Structure, domain organization, and different conformational states of stem cell factor-induced intact KIT dimers

    Yarden Opatowsky, Irit Lax, Francisco Tomé, Franziska Bleichert, Vinzenz M. Unger, and Joseph Schlessinger

    PNAS February 4, 2014 111 (5) 1772-1777; https://doi.org/10.1073/pnas.1323254111
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    Inhibition of master transcription factors in pluripotent cells induces early stage differentiation

    Debojyoti De, Myong-Ho Jeong, Young-Eun Leem, Dmitri I. Svergun, David E. Wemmer, Jong-Sun Kang, Kyeong Kyu Kim, and Sung-Hou Kim

    PNAS February 4, 2014 111 (5) 1778-1783; https://doi.org/10.1073/pnas.1323386111
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    Structure of sugar-bound LacY

    Hemant Kumar, Vladimir Kasho, Irina Smirnova, Janet S. Finer-Moore, H. Ronald Kaback, and Robert M. Stroud

    PNAS February 4, 2014 111 (5) 1784-1788; https://doi.org/10.1073/pnas.1324141111
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    Variants of mouse DNA polymerase κ reveal a mechanism of efficient and accurate translesion synthesis past a benzo[a]pyrene dG adduct

    Yang Liu, Yeran Yang, Tie-Shan Tang, Hui Zhang, Zhifeng Wang, Errol Friedberg, Wei Yang, and Caixia Guo

    PNAS February 4, 2014 111 (5) 1789-1794; https://doi.org/10.1073/pnas.1324168111
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    CRL4-like Clr4 complex in Schizosaccharomyces pombe depends on an exposed surface of Dos1 for heterochromatin silencing

    Canan Kuscu, Mikel Zaratiegui, Hyun Soo Kim, David A. Wah, Robert A. Martienssen, Thomas Schalch, and Leemor Joshua-Tor

    PNAS February 4, 2014 111 (5) 1795-1800; https://doi.org/10.1073/pnas.1313096111
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    Probing large conformational rearrangements in wild-type and mutant spectrin using structural mass spectrometry

    Sira Sriswasdi, Sandra L. Harper, Hsin-Yao Tang, Patrick G. Gallagher, and David W. Speicher

    PNAS February 4, 2014 111 (5) 1801-1806; https://doi.org/10.1073/pnas.1317620111

• Biophysics and Computational Biology

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    Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

    Ryan R. Cheng, Faruck Morcos, Herbert Levine, and José N. Onuchic

    PNAS February 4, 2014 111 (5) E563-E571; https://doi.org/10.1073/pnas.1323734111
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    Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins

    Silvia Rinaldi, Federico Melaccio, Samer Gozem, Francesca Fanelli, and Massimo Olivucci

    PNAS February 4, 2014 111 (5) 1714-1719; https://doi.org/10.1073/pnas.1309508111
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    Nonautonomous contact guidance signaling during collective cell migration

    Camila Londono, M. Jimena Loureiro, Benjamin Slater, Petra B. Lücker, John Soleas, Suthamathy Sathananthan, J. Stewart Aitchison, Alexandre J. Kabla, and Alison P. McGuigan

    PNAS February 4, 2014 111 (5) 1807-1812; https://doi.org/10.1073/pnas.1321852111
  • Open Access

    Structure and mechanism of a eukaryotic transmembrane ascorbate-dependent oxidoreductase

    Peilong Lu, Dan Ma, Chuangye Yan, Xinqi Gong, Mingjian Du, and Yigong Shi

    PNAS February 4, 2014 111 (5) 1813-1818; https://doi.org/10.1073/pnas.1323931111
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    Water access points and hydration pathways in CLC H⁺/Cl⁻ transporters

    • From the Cover

    Wei Han, Ricky C. Cheng, Merritt C. Maduke, and Emad Tajkhorshid

    PNAS February 4, 2014 111 (5) 1819-1824; https://doi.org/10.1073/pnas.1317890111

    See companion article:

    • Proton pathways in bacterial Cl⁻/H⁺ transporters

      - Jan 23, 2014
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    Functional map of arrestin-1 at single amino acid resolution

    Martin K. Ostermaier, Christian Peterhans, Rolf Jaussi, Xavier Deupi, and Jörg Standfuss

    PNAS February 4, 2014 111 (5) 1825-1830; https://doi.org/10.1073/pnas.1319402111
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    Dynamics transitions at the outer vestibule of the KcsA potassium channel during gating

    H. Raghuraman, Shahidul M. Islam, Soumi Mukherjee, Benoit Roux, and Eduardo Perozo

    PNAS February 4, 2014 111 (5) 1831-1836; https://doi.org/10.1073/pnas.1314875111
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    Comprehensive structural model of the mechanochemical cycle of a mitotic motor highlights molecular adaptations in the kinesin family

    Adeline Goulet, Jennifer Major, Yonggun Jun, Steven P. Gross, Steven S. Rosenfeld, and Carolyn A. Moores

    PNAS February 4, 2014 111 (5) 1837-1842; https://doi.org/10.1073/pnas.1319848111

• Cell Biology

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    Induced multipotency in adult keratinocytes through down-regulation of ΔNp63 or DGCR8

    Deepavali Chakravarti, Xiaohua Su, Min Soon Cho, Ngoc Hoang Bao Bui, Cristian Coarfa, Avinashnarayan Venkatanarayan, Ashley L. Benham, Ramón E. Flores González, Jennifer Alana, Weimin Xiao, Marco L. Leung, Harina Vin, Io Long Chan, Arianexys Aquino, Nicole Müller, Hongran Wang, Austin J. Cooney, Jan Parker-Thornburg, Kenneth Y. Tsai, Preethi H. Gunaratne, and Elsa R. Flores

    PNAS February 4, 2014 111 (5) E572-E581; https://doi.org/10.1073/pnas.1319743111
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    Sel1L is indispensable for mammalian endoplasmic reticulum-associated degradation, endoplasmic reticulum homeostasis, and survival

    Shengyi Sun, Guojun Shi, Xuemei Han, Adam B. Francisco, Yewei Ji, Nuno Mendonça, Xiaojing Liu, Jason W. Locasale, Kenneth W. Simpson, Gerald E. Duhamel, Sander Kersten, John R. Yates III, Qiaoming Long, and Ling Qi

    PNAS February 4, 2014 111 (5) E582-E591; https://doi.org/10.1073/pnas.1318114111
  • Open Access

    TAp73 is required for spermatogenesis and the maintenance of male fertility

    Satoshi Inoue, Richard Tomasini, Alessandro Rufini, Andrew J. Elia, Massimiliano Agostini, Ivano Amelio, Dave Cescon, David Dinsdale, Lily Zhou, Isaac S. Harris, Sophie Lac, Jennifer Silvester, Wanda Y. Li, Masato Sasaki, Jillian Haight, Anne Brüstle, Andrew Wakeham, Colin Mckerlie, Andrea Jurisicova, Gerry Melino, and Tak W. Mak

    PNAS February 4, 2014 111 (5) 1843-1848; https://doi.org/10.1073/pnas.1323416111
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    Membrane adhesion dictates Golgi stacking and cisternal morphology

    Intaek Lee, Neeraj Tiwari, Myun Hwa Dunlop, Morven Graham, Xinran Liu, and James E. Rothman

    PNAS February 4, 2014 111 (5) 1849-1854; https://doi.org/10.1073/pnas.1323895111
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    Different modes of endothelial–smooth muscle cell interaction elicit differential β-catenin phosphorylations and endothelial functions

    Shun-Fu Chang, Li-Jing Chen, Pei-Ling Lee, Ding-Yu Lee, Shu Chien, and Jeng-Jiann Chiu

    PNAS February 4, 2014 111 (5) 1855-1860; https://doi.org/10.1073/pnas.1323761111
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    Processing of microRNA primary transcripts requires heme in mammalian cells

    Sara H. Weitz, Ming Gong, Ian Barr, Shimon Weiss, and Feng Guo

    PNAS February 4, 2014 111 (5) 1861-1866; https://doi.org/10.1073/pnas.1309915111

• Developmental Biology

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    In vitro analysis suggests that difference in cell movement during direct interaction can generate various pigment patterns in vivo

    Hiroaki Yamanaka and Shigeru Kondo

    PNAS February 4, 2014 111 (5) 1867-1872; https://doi.org/10.1073/pnas.1315416111
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    Paternally induced transgenerational inheritance of susceptibility to diabetes in mammals

    Yanchang Wei, Cai-Rong Yang, Yan-Ping Wei, Zhen-Ao Zhao, Yi Hou, Heide Schatten, and Qing-Yuan Sun

    PNAS February 4, 2014 111 (5) 1873-1878; https://doi.org/10.1073/pnas.1321195111

• Ecology

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    Gene-centric approach to integrating environmental genomics and biogeochemical models

    Daniel C. Reed, Christopher K. Algar, Julie A. Huber, and Gregory J. Dick

    PNAS February 4, 2014 111 (5) 1879-1884; https://doi.org/10.1073/pnas.1313713111
  • Open Access

    Complementary molecular information changes our perception of food web structure

    Helena K. Wirta, Paul D. N. Hebert, Riikka Kaartinen, Sean W. Prosser, Gergely Várkonyi, and Tomas Roslin

    PNAS February 4, 2014 111 (5) 1885-1890; https://doi.org/10.1073/pnas.1316990111

• Environmental Sciences

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    Quantifying the distribution of nanodiamonds in pre-Younger Dryas to recent age deposits along Bull Creek, Oklahoma Panhandle, USA

    Leland C. Bement, Andrew S. Madden, Brian J. Carter, Alexander R. Simms, Andrew L. Swindle, Hanna M. Alexander, Scott Fine, and Mourad Benamara

    PNAS February 4, 2014 111 (5) 1726-1731; https://doi.org/10.1073/pnas.1309734111

• Evolution

  • Open Access

    Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes

    • Inaugural Article

    Lakshminarayan M. Iyer, Dapeng Zhang, Robson F. de Souza, Patricia J. Pukkila, Anjana Rao, and L. Aravind

    PNAS February 4, 2014 111 (5) 1676-1683; https://doi.org/10.1073/pnas.1321818111

• Genetics

  • Open Access

    Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations

    Glenn K. Fu, Weihong Xu, Julie Wilhelmy, Michael N. Mindrinos, Ronald W. Davis, Wenzhong Xiao, and Stephen P. A. Fodor

    PNAS February 4, 2014 111 (5) 1891-1896; https://doi.org/10.1073/pnas.1323732111
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    Mutational landscape of yeast mutator strains

    Alexandre Serero, Claire Jubin, Sophie Loeillet, Patricia Legoix-Né, and Alain G. Nicolas

    PNAS February 4, 2014 111 (5) 1897-1902; https://doi.org/10.1073/pnas.1314423111
  • Open Access

    Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe

    William R. A. Brown, Geraint Thomas, Nicholas C. O. Lee, Martin Blythe, Gianni Liti, Jonas Warringer, and Matthew W. Loose

    PNAS February 4, 2014 111 (5) 1903-1908; https://doi.org/10.1073/pnas.1216934111

• Immunology

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    Novel antiviral host factor, TNK1, regulates IFN signaling through serine phosphorylation of STAT1

    Ee Lyn Ooi, Stephanie T. Chan, Noell E. Cho, Courtney Wilkins, Jessica Woodward, Meng Li, Ushio Kikkawa, Timothy Tellinghuisen, Michael Gale Jr., and Takeshi Saito

    PNAS February 4, 2014 111 (5) 1909-1914; https://doi.org/10.1073/pnas.1314268111
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    Characterization of the IL-15 niche in primary and secondary lymphoid organs in vivo

    Guangwei Cui, Takahiro Hara, Szandor Simmons, Keisuke Wagatsuma, Akifumi Abe, Hitoshi Miyachi, Satsuki Kitano, Masaru Ishii, Shizue Tani-ichi, and Koichi Ikuta

    PNAS February 4, 2014 111 (5) 1915-1920; https://doi.org/10.1073/pnas.1318281111

• Medical Sciences

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    Prostatic inflammation enhances basal-to-luminal differentiation and accelerates initiation of prostate cancer with a basal cell origin

    Oh-Joon Kwon, Li Zhang, Michael M. Ittmann, and Li Xin

    PNAS February 4, 2014 111 (5) E592-E600; https://doi.org/10.1073/pnas.1318157111

    See companion article:

    • Inflammation promotes prostate differentiation

      - Jan 23, 2014
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    Elevated expression of TANK-binding kinase 1 enhances tamoxifen resistance in breast cancer

    Congwen Wei, Yuan Cao, Xiaoli Yang, Zirui Zheng, Kai Guan, Qiang Wang, Yanhong Tai, Yanhong Zhang, Shengli Ma, Ye Cao, Xiaoxing Ge, Changzhi Xu, Jia Li, Hui Yan, Youguo Ling, Ting Song, Lin Zhu, Buchang Zhang, Quanbin Xu, Chengjin Hu, Xiu-wu Bian, Xiang He, and Hui Zhong

    PNAS February 4, 2014 111 (5) E601-E610; https://doi.org/10.1073/pnas.1316255111
  • Open Access

    Empirical prediction of genomic susceptibilities for multiple cancer classes

    Minseung Kim and Sung-Hou Kim

    PNAS February 4, 2014 111 (5) 1921-1926; https://doi.org/10.1073/pnas.1318383110
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    Conformal piezoelectric energy harvesting and storage from motions of the heart, lung, and diaphragm

    Canan Dagdeviren, Byung Duk Yang, Yewang Su, Phat L. Tran, Pauline Joe, Eric Anderson, Jing Xia, Vijay Doraiswamy, Behrooz Dehdashti, Xue Feng, Bingwei Lu, Robert Poston, Zain Khalpey, Roozbeh Ghaffari, Yonggang Huang, Marvin J. Slepian, and John A. Rogers

    PNAS February 4, 2014 111 (5) 1927-1932; https://doi.org/10.1073/pnas.1317233111
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    Differential expression of estrogen receptor α, β1, and β2 in lobular and ductal breast cancer

    Bo Huang, Yoko Omoto, Hirotaka Iwase, Hiroko Yamashita, Tatsuya Toyama, Raoul Charles Coombes, Aleksandra Filipovic, Margaret Warner, and Jan-Åke Gustafsson

    PNAS February 4, 2014 111 (5) 1933-1938; https://doi.org/10.1073/pnas.1323719111

• Microbiology

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    Hydrodynamics and collective behavior of the tethered bacterium Thiovulum majus

    Alexander Petroff and Albert Libchaber

    PNAS February 4, 2014 111 (5) E537-E545; https://doi.org/10.1073/pnas.1322092111
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    HSV-1 degrades, stabilizes, requires, or is stung by STING depending on ICP0, the US3 protein kinase, and cell derivation

    Maria Kalamvoki and Bernard Roizman

    PNAS February 4, 2014 111 (5) E611-E617; https://doi.org/10.1073/pnas.1323414111
  • Open Access

    Dengue virus envelope protein domain I/II hinge determines long-lived serotype-specific dengue immunity

    • From the Cover

    William B. Messer, Ruklanthi de Alwis, Boyd L. Yount, Scott R. Royal, Jeremy P. Huynh, Scott A. Smith, James E. Crowe Jr., Benjamin J. Doranz, Kristen M. Kahle, Jennifer M. Pfaff, Laura J. White, Carlos A. Sariol, Aravinda M. de Silva, and Ralph S. Baric

    PNAS February 4, 2014 111 (5) 1939-1944; first published January 2, 2014. https://doi.org/10.1073/pnas.1317350111

    See companion article:

    • Dengue neutralizing epitope recognized by humans

      - Jan 17, 2014
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    Self-poisoning of Mycobacterium tuberculosis by interrupting siderophore recycling

    Christopher M. Jones, Ryan M. Wells, Ashoka V. R. Madduri, Matthew B. Renfrow, Colin Ratledge, D. Branch Moody, and Michael Niederweis

    PNAS February 4, 2014 111 (5) 1945-1950; https://doi.org/10.1073/pnas.1311402111
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    ChREBP, a glucose-responsive transcriptional factor, enhances glucose metabolism to support biosynthesis in human cytomegalovirus-infected cells

    Yongjun Yu, Tobi G. Maguire, and James C. Alwine

    PNAS February 4, 2014 111 (5) 1951-1956; https://doi.org/10.1073/pnas.1310779111
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    Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A

    Kazuya Yamanaka, Kirk A. Reynolds, Roland D. Kersten, Katherine S. Ryan, David J. Gonzalez, Victor Nizet, Pieter C. Dorrestein, and Bradley S. Moore

    PNAS February 4, 2014 111 (5) 1957-1962; https://doi.org/10.1073/pnas.1319584111
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    PhoPQ regulates acidic glycerophospholipid content of the Salmonella Typhimurium outer membrane

    Zachary D. Dalebroux, Susana Matamouros, Dale Whittington, Russell E. Bishop, and Samuel I. Miller

    PNAS February 4, 2014 111 (5) 1963-1968; https://doi.org/10.1073/pnas.1316901111
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    Programmed Allee effect in bacteria causes a tradeoff between population spread and survival

    Robert Smith, Cheemeng Tan, Jaydeep K. Srimani, Anand Pai, Katherine A. Riccione, Hao Song, and Lingchong You

    PNAS February 4, 2014 111 (5) 1969-1974; https://doi.org/10.1073/pnas.1315954111
  • Open Access

    Quorum sensing controls hyphal initiation in Candida albicans through Ubr1-mediated protein degradation

    Yang Lu, Chang Su, Ohimai Unoje, and Haoping Liu

    PNAS February 4, 2014 111 (5) 1975-1980; https://doi.org/10.1073/pnas.1318690111

• Neuroscience

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    Decision-related pupil dilation reflects upcoming choice and individual bias

    Jan Willem de Gee, Tomas Knapen, and Tobias H. Donner

    PNAS February 4, 2014 111 (5) E618-E625; https://doi.org/10.1073/pnas.1317557111
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    Differences in the right inferior longitudinal fasciculus but no general disruption of white matter tracts in children with autism spectrum disorder

    Kami Koldewyn, Anastasia Yendiki, Sarah Weigelt, Hyowon Gweon, Joshua Julian, Hilary Richardson, Caitlin Malloy, Rebecca Saxe, Bruce Fischl, and Nancy Kanwisher

    PNAS February 4, 2014 111 (5) 1981-1986; https://doi.org/10.1073/pnas.1324037111
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    Common polymorphism in the oxytocin receptor gene (OXTR) is associated with human social recognition skills

    • From the Cover

    David H. Skuse, Adriana Lori, Joseph F. Cubells, Irene Lee, Karen N. Conneely, Kaija Puura, Terho Lehtimäki, Elisabeth B. Binder, and Larry J. Young

    PNAS February 4, 2014 111 (5) 1987-1992; https://doi.org/10.1073/pnas.1302985111

    See companion article:

    • Genetics and behavior

      - Jan 21, 2014
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    PIKE is essential for oligodendroglia development and CNS myelination

    Chi Bun Chan, Xia Liu, Lixia Zhao, Guanglu Liu, Chi Wai Lee, Yue Feng, and Keiqang Ye

    PNAS February 4, 2014 111 (5) 1993-1998; https://doi.org/10.1073/pnas.1318185111
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    Spatiotemporal pattern of action potential firing in developing inner hair cells of the mouse cochlea

    Gaston Sendin, Jérôme Bourien, François Rassendren, Jean-Luc Puel, and Régis Nouvian

    PNAS February 4, 2014 111 (5) 1999-2004; https://doi.org/10.1073/pnas.1319615111
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    Essential role of poly(ADP-ribosyl)ation in cocaine action

    Kimberly N. Scobie, Diane Damez-Werno, HaoSheng Sun, NingYi Shao, Amy Gancarz, Clarisse H. Panganiban, Caroline Dias, JaWook Koo, Paola Caiafa, Lewis Kaufman, Rachael L. Neve, David M. Dietz, Li Shen, and Eric J. Nestler

    PNAS February 4, 2014 111 (5) 2005-2010; https://doi.org/10.1073/pnas.1319703111

• Pharmacology

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    Doxorubicin-induced carbonylation and degradation of cardiac myosin binding protein C promote cardiotoxicity

    Baikuntha Aryal, Jinsook Jeong, and V. Ashutosh Rao

    PNAS February 4, 2014 111 (5) 2011-2016; https://doi.org/10.1073/pnas.1321783111

• Plant Biology

  • Open Access

    Inheritance of Trans Chromosomal Methylation patterns from Arabidopsis F1 hybrids

    Ian K. Greaves, Michael Groszmann, Aihua Wang, W. James Peacock, and Elizabeth S. Dennis

    PNAS February 4, 2014 111 (5) 2017-2022; https://doi.org/10.1073/pnas.1323656111
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    Tetrapyrrole biosynthetic enzyme protoporphyrinogen IX oxidase 1 is required for plastid RNA editing

    Fan Zhang, Weijiang Tang, Boris Hedtke, Linlin Zhong, Lin Liu, Lianwei Peng, Congming Lu, Bernhard Grimm, and Rongcheng Lin

    PNAS February 4, 2014 111 (5) 2023-2028; https://doi.org/10.1073/pnas.1316183111
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    CLE-CLAVATA1 peptide-receptor signaling module regulates the expansion of plant root systems in a nitrogen-dependent manner

    Takao Araya, Mayu Miyamoto, Juliarni Wibowo, Akinori Suzuki, Soichi Kojima, Yumiko N. Tsuchiya, Shinichiro Sawa, Hiroo Fukuda, Nicolaus von Wirén, and Hideki Takahashi

    PNAS February 4, 2014 111 (5) 2029-2034; https://doi.org/10.1073/pnas.1319953111

• Psychological and Cognitive Sciences

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    Development of pattern vision following early and extended blindness

    Amy Kalia, Luis Andres Lesmes, Michael Dorr, Tapan Gandhi, Garga Chatterjee, Suma Ganesh, Peter J. Bex, and Pawan Sinha

    PNAS February 4, 2014 111 (5) 2035-2039; https://doi.org/10.1073/pnas.1311041111

• Systems Biology

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    Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles

    Sameer S. Bajikar, Christiane Fuchs, Andreas Roller, Fabian J. Theis, and Kevin A. Janes

    PNAS February 4, 2014 111 (5) E626-E635; https://doi.org/10.1073/pnas.1311647111
  • Open Access

    Spatiotemporal separation of PER and CRY posttranslational regulation in the mammalian circadian clock

    Peter C. St. John, Tsuyoshi Hirota, Steve A. Kay, and Francis J. Doyle III

    PNAS February 4, 2014 111 (5) 2040-2045; https://doi.org/10.1073/pnas.1323618111