Table of Contents

Biological Sciences

• Biochemistry

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    Tissue-based metabolic labeling of polysialic acids in living primary hippocampal neurons

    Kyungtae Kang, Sunghoon Joo, Ji Yu Choi, Sujeong Geum, Seok-Pyo Hong, Seung-Yeul Lee, Yong Ho Kim, Seong-Min Kim, Myung-Han Yoon, Yoonkey Nam, Kyung-Bok Lee, Hee-Yoon Lee, and Insung S. Choi

    PNAS January 20, 2015 112 (3) E241-E248; first published January 6, 2015. https://doi.org/10.1073/pnas.1419683112
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    Cdc45 (cell division cycle protein 45) guards the gate of the Eukaryote Replisome helicase stabilizing leading strand engagement

    Tatjana Petojevic, James J. Pesavento, Alessandro Costa, Jingdan Liang, Zhijun Wang, James M. Berger, and Michael R. Botchan

    PNAS January 20, 2015 112 (3) E249-E258; first published January 5, 2015. https://doi.org/10.1073/pnas.1422003112
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    Flies expand the repertoire of protein structures that bind ice

    Koli Basu, Laurie A. Graham, Robert L. Campbell, and Peter L. Davies

    PNAS January 20, 2015 112 (3) 737-742; first published January 5, 2015. https://doi.org/10.1073/pnas.1422272112

• Biophysics and Computational Biology

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    Modulation of folding energy landscape by charge–charge interactions: Linking experiments with computational modeling

    Franco O. Tzul, Katrina L. Schweiker, and George I. Makhatadze

    PNAS January 20, 2015 112 (3) E259-E266; first published January 6, 2015. https://doi.org/10.1073/pnas.1410424112
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    Programmable motion of DNA origami mechanisms

    Alexander E. Marras, Lifeng Zhou, Hai-Jun Su, and Carlos E. Castro

    PNAS January 20, 2015 112 (3) 713-718; first published January 5, 2015. https://doi.org/10.1073/pnas.1408869112
  • Open Access

    Trigger loop folding determines transcription rate of Escherichia coli’s RNA polymerase

    Yara X. Mejia, Evgeny Nudler, and Carlos Bustamante

    PNAS January 20, 2015 112 (3) 743-748; first published December 31, 2014. https://doi.org/10.1073/pnas.1421067112
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    Protein design algorithms predict viable resistance to an experimental antifolate

    Stephanie M. Reeve, Pablo Gainza, Kathleen M. Frey, Ivelin Georgiev, Bruce R. Donald, and Amy C. Anderson

    PNAS January 20, 2015 112 (3) 749-754; first published December 31, 2014. https://doi.org/10.1073/pnas.1411548112
  • Open Access

    Antimalarial 4(1H)-pyridones bind to the Q_i site of cytochrome bc₁

    Michael J. Capper, Paul M. O’Neill, Nicholas Fisher, Richard W. Strange, Darren Moss, Stephen A. Ward, Neil G. Berry, Alexandre S. Lawrenson, S. Samar Hasnain, Giancarlo A. Biagini, and Svetlana V. Antonyuk

    PNAS January 20, 2015 112 (3) 755-760; first published January 6, 2015. https://doi.org/10.1073/pnas.1416611112

• Cell Biology

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    Single-molecule tracking of small GTPase Rac1 uncovers spatial regulation of membrane translocation and mechanism for polarized signaling

    Sulagna Das, Taofei Yin, Qingfen Yang, Jingqiao Zhang, Yi I. Wu, and Ji Yu

    PNAS January 20, 2015 112 (3) E267-E276; first published January 5, 2015. https://doi.org/10.1073/pnas.1409667112
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    VEGFR3 does not sustain retinal angiogenesis without VEGFR2

    Georgia Zarkada, Krista Heinolainen, Taija Makinen, Yoshiaki Kubota, and Kari Alitalo

    PNAS January 20, 2015 112 (3) 761-766; first published January 5, 2015. https://doi.org/10.1073/pnas.1423278112
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    In vivo, Argonaute-bound microRNAs exist predominantly in a reservoir of low molecular weight complexes not associated with mRNA

    Gaspare La Rocca, Scott H. Olejniczak, Alvaro J. González, Daniel Briskin, Joana A. Vidigal, Lee Spraggon, Raymond G. DeMatteo, Megan R. Radler, Tullia Lindsten, Andrea Ventura, Thomas Tuschl, Christina S. Leslie, and Craig B. Thompson

    PNAS January 20, 2015 112 (3) 767-772; first published January 7, 2015. https://doi.org/10.1073/pnas.1424217112
  • Open Access

    Loss of autophagy causes a synthetic lethal deficiency in DNA repair

    Emma Y. Liu, Naihan Xu, Jim O’Prey, Laurence Y. Lao, Sanket Joshi, Jaclyn S. Long, Margaret O’Prey, Daniel R. Croft, Florian Beaumatin, Alice D. Baudot, Michaela Mrschtik, Mathias Rosenfeldt, Yaou Zhang, David A. Gillespie, and Kevin M. Ryan

    PNAS January 20, 2015 112 (3) 773-778; first published January 7, 2015. https://doi.org/10.1073/pnas.1409563112
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    K-Ras4A splice variant is widely expressed in cancer and uses a hybrid membrane-targeting motif

    Frederick D. Tsai, Mathew S. Lopes, Mo Zhou, Helen Court, Odis Ponce, James J. Fiordalisi, Jessica J. Gierut, Adrienne D. Cox, Kevin M. Haigis, and Mark R. Philips

    PNAS January 20, 2015 112 (3) 779-784; first published January 5, 2015. https://doi.org/10.1073/pnas.1412811112

• Developmental Biology

  • Open Access

    Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo

    Max V. Staller, Ben J. Vincent, Meghan D. J. Bragdon, Tara Lydiard-Martin, Zeba Wunderlich, Javier Estrada, and Angela H. DePace

    PNAS January 20, 2015 112 (3) 785-790; first published January 6, 2015. https://doi.org/10.1073/pnas.1413877112
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    Calcium waves occur as Drosophila oocytes activate

    Taro Kaneuchi, Caroline V. Sartain, Satomi Takeo, Vanessa L. Horner, Norene A. Buehner, Toshiro Aigaki, and Mariana F. Wolfner

    PNAS January 20, 2015 112 (3) 791-796; first published January 6, 2015. https://doi.org/10.1073/pnas.1420589112

• Ecology

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    Inference for dynamic and latent variable models via iterated, perturbed Bayes maps

    Edward L. Ionides, Dao Nguyen, Yves Atchadé, Stilian Stoev, and Aaron A. King

    PNAS January 20, 2015 112 (3) 719-724; first published January 7, 2015. https://doi.org/10.1073/pnas.1410597112
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    Plant functional traits and the multidimensional nature of species coexistence

    Nathan J. B. Kraft, Oscar Godoy, and Jonathan M. Levine

    PNAS January 20, 2015 112 (3) 797-802; first published January 5, 2015. https://doi.org/10.1073/pnas.1413650112

• Evolution

  • Open Access

    Deep conservation of wrist and digit enhancers in fish

    Andrew R. Gehrke, Igor Schneider, Elisa de la Calle-Mustienes, Juan J. Tena, Carlos Gomez-Marin, Mayuri Chandran, Tetsuya Nakamura, Ingo Braasch, John H. Postlethwait, José Luis Gómez-Skarmeta, and Neil H. Shubin

    PNAS January 20, 2015 112 (3) 803-808; first published December 22, 2014. https://doi.org/10.1073/pnas.1420208112
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    Adaptive simplification and the evolution of gecko locomotion: Morphological and biomechanical consequences of losing adhesion

    • From the Cover

    Timothy E. Higham, Aleksandra V. Birn-Jeffery, Clint E. Collins, C. Darrin Hulsey, and Anthony P. Russell

    PNAS January 20, 2015 112 (3) 809-814; first published December 29, 2014. https://doi.org/10.1073/pnas.1418979112
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    Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets

    Laura C. Norris, Bradley J. Main, Yoosook Lee, Travis C. Collier, Abdrahamane Fofana, Anthony J. Cornel, and Gregory C. Lanzaro

    PNAS January 20, 2015 112 (3) 815-820; first published January 5, 2015. https://doi.org/10.1073/pnas.1418892112
  • Open Access

    Dried whole-plant Artemisia annua slows evolution of malaria drug resistance and overcomes resistance to artemisinin

    Mostafa A. Elfawal, Melissa J. Towler, Nicholas G. Reich, Pamela J. Weathers, and Stephen M. Rich

    PNAS January 20, 2015 112 (3) 821-826; first published January 5, 2015. https://doi.org/10.1073/pnas.1413127112

• Genetics

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    Uncoupling lifespan and healthspan in Caenorhabditis elegans longevity mutants

    Ankita Bansal, Lihua J. Zhu, Kelvin Yen, and Heidi A. Tissenbaum

    PNAS January 20, 2015 112 (3) E277-E286; first published January 5, 2015. https://doi.org/10.1073/pnas.1412192112
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    Control of stem cell self-renewal and differentiation by the heterochronic genes and the cellular asymmetry machinery in Caenorhabditis elegans

    Omid F. Harandi and Victor R. Ambros

    PNAS January 20, 2015 112 (3) E287-E296; first published January 5, 2015. https://doi.org/10.1073/pnas.1422852112

• Immunology and Inflammation

  • Open Access

    Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs

    Nasun Hah, Chris Benner, Ling-Wa Chong, Ruth T. Yu, Michael Downes, and Ronald M. Evans

    PNAS January 20, 2015 112 (3) E297-E302; first published January 6, 2015. https://doi.org/10.1073/pnas.1424028112
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    Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells

    • From the Cover

    Ellen F. Foxman, James A. Storer, Megan E. Fitzgerald, Bethany R. Wasik, Lin Hou, Hongyu Zhao, Paul E. Turner, Anna Marie Pyle, and Akiko Iwasaki

    PNAS January 20, 2015 112 (3) 827-832; first published January 5, 2015. https://doi.org/10.1073/pnas.1411030112
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    Structure of FcγRI in complex with Fc reveals the importance of glycan recognition for high-affinity IgG binding

    Jinghua Lu, Jonathan Chu, Zhongcheng Zou, Nels B. Hamacher, Mark W. Rixon, and Peter D. Sun

    PNAS January 20, 2015 112 (3) 833-838; first published January 5, 2015. https://doi.org/10.1073/pnas.1418812112

• Medical Sciences

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    Examination of HER3 targeting in cancer using monoclonal antibodies

    Nadège Gaborit, Ali Abdul-Hai, Maicol Mancini, Moshit Lindzen, Sara Lavi, Orith Leitner, Lucile Mounier, Myriam Chentouf, Sai Dunoyer, Manjusha Ghosh, Christel Larbouret, Thierry Chardès, Hervé Bazin, André Pèlegrin, Michael Sela, and Yosef Yarden

    PNAS January 20, 2015 112 (3) 839-844; first published January 6, 2015. https://doi.org/10.1073/pnas.1423645112
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    A KIR B centromeric region present in Africans but not Europeans protects pregnant women from pre-eclampsia

    Annettee Nakimuli, Olympe Chazara, Susan E. Hiby, Lydia Farrell, Stephen Tukwasibwe, Jyothi Jayaraman, James A. Traherne, John Trowsdale, Francesco Colucci, Emma Lougee, Robert W. Vaughan, Alison M. Elliott, Josaphat Byamugisha, Pontiano Kaleebu, Florence Mirembe, Neda Nemat-Gorgani, Peter Parham, Paul J. Norman, and Ashley Moffett

    PNAS January 20, 2015 112 (3) 845-850; first published January 5, 2015. https://doi.org/10.1073/pnas.1413453112
  • Open Access

    Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity

    Mona Meyer, Jüri Reimand, Xiaoyang Lan, Renee Head, Xueming Zhu, Michelle Kushida, Jane Bayani, Jessica C. Pressey, Anath C. Lionel, Ian D. Clarke, Michael Cusimano, Jeremy A. Squire, Stephen W. Scherer, Mark Bernstein, Melanie A. Woodin, Gary D. Bader, and Peter B. Dirks

    PNAS January 20, 2015 112 (3) 851-856; first published January 5, 2015. https://doi.org/10.1073/pnas.1320611111

• Microbiology

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    Single-cell, real-time detection of oxidative stress induced in Escherichia coli by the antimicrobial peptide CM15

    Heejun Choi, Zhilin Yang, and James C. Weisshaar

    PNAS January 20, 2015 112 (3) E303-E310; first published January 5, 2015. https://doi.org/10.1073/pnas.1417703112
  • Open Access

    Terpene synthases are widely distributed in bacteria

    Yuuki Yamada, Tomohisa Kuzuyama, Mamoru Komatsu, Kazuo Shin-ya, Satoshi Omura, David E. Cane, and Haruo Ikeda

    PNAS January 20, 2015 112 (3) 857-862; first published December 22, 2014. https://doi.org/10.1073/pnas.1422108112
  • Open Access

    Patterns of genome evolution that have accompanied host adaptation in Salmonella

    • From the Cover

    Gemma C. Langridge, Maria Fookes, Thomas R. Connor, Theresa Feltwell, Nicholas Feasey, Bryony N. Parsons, Helena M. B. Seth-Smith, Lars Barquist, Anna Stedman, Tom Humphrey, Paul Wigley, Sarah E. Peters, Duncan J. Maskell, Jukka Corander, Jose A. Chabalgoity, Paul Barrow, Julian Parkhill, Gordon Dougan, and Nicholas R. Thomson

    PNAS January 20, 2015 112 (3) 863-868; first published December 22, 2014. https://doi.org/10.1073/pnas.1416707112

    See companion article:

    • Reconstructing pathogen evolution from the ruins

      - Jan 07, 2015
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    Clofazimine shortens the duration of the first-line treatment regimen for experimental chemotherapy of tuberculosis

    Sandeep Tyagi, Nicole C. Ammerman, Si-Yang Li, John Adamson, Paul J. Converse, Rosemary V. Swanson, Deepak V. Almeida, and Jacques H. Grosset

    PNAS January 20, 2015 112 (3) 869-874; first published January 5, 2015. https://doi.org/10.1073/pnas.1416951112

• Neuroscience

  • Open Access

    Genetic dissection of pheromone processing reveals main olfactory system-mediated social behaviors in mice

    Tomohiko Matsuo, Tatsuya Hattori, Akari Asaba, Naokazu Inoue, Nobuhiro Kanomata, Takefumi Kikusui, Reiko Kobayakawa, and Ko Kobayakawa

    PNAS January 20, 2015 112 (3) E311-E320; first published January 6, 2015. https://doi.org/10.1073/pnas.1416723112
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    Acceleration of conduction velocity linked to clustering of nodal components precedes myelination

    Sean A. Freeman, Anne Desmazières, Jean Simonnet, Marie Gatta, Friederike Pfeiffer, Marie Stéphane Aigrot, Quentin Rappeneau, Serge Guerreiro, Patrick Pierre Michel, Yuchio Yanagawa, Gilles Barbin, Peter J. Brophy, Desdemona Fricker, Catherine Lubetzki, and Nathalie Sol-Foulon

    PNAS January 20, 2015 112 (3) E321-E328; first published January 5, 2015. https://doi.org/10.1073/pnas.1419099112
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    Novel neural circuit mechanism for visual edge detection

    Charles F. Stevens

    PNAS January 20, 2015 112 (3) 875-880; first published January 5, 2015. https://doi.org/10.1073/pnas.1422673112
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    Enduring good memories of infant trauma: Rescue of adult neurobehavioral deficits via amygdala serotonin and corticosterone interaction

    Millie Rincón-Cortés, Gordon A. Barr, Anne Marie Mouly, Kiseko Shionoya, Bestina S. Nuñez, and Regina M. Sullivan

    PNAS January 20, 2015 112 (3) 881-886; first published January 5, 2015. https://doi.org/10.1073/pnas.1416065112
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    Signature of consciousness in the dynamics of resting-state brain activity

    Pablo Barttfeld, Lynn Uhrig, Jacobo D. Sitt, Mariano Sigman, Béchir Jarraya, and Stanislas Dehaene

    PNAS January 20, 2015 112 (3) 887-892; first published January 5, 2015. https://doi.org/10.1073/pnas.1418031112
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    Targeted ablation of cholinergic interneurons in the dorsolateral striatum produces behavioral manifestations of Tourette syndrome

    Meiyu Xu, Andrew Kobets, Jung-Chieh Du, Jessica Lennington, Lina Li, Mounira Banasr, Ronald S. Duman, Flora M. Vaccarino, Ralph J. DiLeone, and Christopher Pittenger

    PNAS January 20, 2015 112 (3) 893-898; first published January 5, 2015. https://doi.org/10.1073/pnas.1419533112

• Physiology

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    Intracellular Cl⁻ as a signaling ion that potently regulates Na⁺/HCO3⁻ transporters

    Nikolay Shcheynikov, Aran Son, Jeong Hee Hong, Osamu Yamazaki, Ehud Ohana, Ira Kurtz, Dong Min Shin, and Shmuel Muallem

    PNAS January 20, 2015 112 (3) E329-E337; first published January 5, 2015. https://doi.org/10.1073/pnas.1415673112
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    Central role of SIAH inhibition in DCC-dependent cardioprotection provoked by netrin-1/NO

    Qiang Li, Ping Wang, Keqiang Ye, and Hua Cai

    PNAS January 20, 2015 112 (3) 899-904; first published January 5, 2015. https://doi.org/10.1073/pnas.1420695112

• Plant Biology

  • Open Access

    Natural diversity in daily rhythms of gene expression contributes to phenotypic variation

    Amaury de Montaigu, Antonis Giakountis, Matthew Rubin, Réka Tóth, Frédéric Cremer, Vladislava Sokolova, Aimone Porri, Matthieu Reymond, Cynthia Weinig, and George Coupland

    PNAS January 20, 2015 112 (3) 905-910; first published December 29, 2014. https://doi.org/10.1073/pnas.1422242112
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    DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis

    Xuehua Zhong, Christopher J. Hale, Minh Nguyen, Israel Ausin, Martin Groth, Jonathan Hetzel, Ajay A. Vashisht, Ian R. Henderson, James A. Wohlschlegel, and Steven E. Jacobsen

    PNAS January 20, 2015 112 (3) 911-916; first published January 5, 2015. https://doi.org/10.1073/pnas.1423603112
  • Open Access

    Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana

    Donna M. Bond and David C. Baulcombe

    PNAS January 20, 2015 112 (3) 917-922; first published January 5, 2015. https://doi.org/10.1073/pnas.1413053112
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    Translatome analyses capture of opposing tissue-specific brassinosteroid signals orchestrating root meristem differentiation

    Kristina Vragović, Ayala Sela, Lilach Friedlander-Shani, Yulia Fridman, Yael Hacham, Neta Holland, Elizabeth Bartom, Todd C. Mockler, and Sigal Savaldi-Goldstein

    PNAS January 20, 2015 112 (3) 923-928; first published January 5, 2015. https://doi.org/10.1073/pnas.1417947112

• Systems Biology

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    Model-driven discovery of underground metabolic functions in Escherichia coli

    Gabriela I. Guzmán, José Utrilla, Sergey Nurk, Elizabeth Brunk, Jonathan M. Monk, Ali Ebrahim, Bernhard O. Palsson, and Adam M. Feist

    PNAS January 20, 2015 112 (3) 929-934; first published January 6, 2015. https://doi.org/10.1073/pnas.1414218112