Table of Contents

Biological Sciences

• Agricultural Sciences

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    Transporters of arsenite in rice and their role in arsenic accumulation in rice grain

    Jian Feng Ma, Naoki Yamaji, Namiki Mitani, Xiao-Yan Xu, Yu-Hong Su, Steve P. McGrath, and Fang-Jie Zhao

    PNAS July 22, 2008 105 (29) 9931-9935; https://doi.org/10.1073/pnas.0802361105

    See companion article:

    • In This Issue

      - Jul 22, 2008

• Biochemistry

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    Replication stalling at unstable inverted repeats: Interplay between DNA hairpins and fork stabilizing proteins

    Irina Voineagu, Vidhya Narayanan, Kirill S. Lobachev, and Sergei M. Mirkin

    PNAS July 22, 2008 105 (29) 9936-9941; https://doi.org/10.1073/pnas.0804510105
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    A βα-barrel built by the combination of fragments from different folds

    Tanmay A. M. Bharat, Simone Eisenbeis, Kornelius Zeth, and Birte Höcker

    PNAS July 22, 2008 105 (29) 9942-9947; https://doi.org/10.1073/pnas.0802202105
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    Flavin-dependent thymidylate synthase X limits chromosomal DNA replication

    Frédéric Escartin, Stéphane Skouloubris, Ursula Liebl, and Hannu Myllykallio

    PNAS July 22, 2008 105 (29) 9948-9952; https://doi.org/10.1073/pnas.0801356105
  • Open Access

    Host cell recognition by the henipaviruses: Crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3

    Kai Xu, Kanagalaghatta R. Rajashankar, Yee-Peng Chan, Juha P. Himanen, Christopher C. Broder, and Dimitar B. Nikolov

    PNAS July 22, 2008 105 (29) 9953-9958; https://doi.org/10.1073/pnas.0804797105
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    A modified cysteinyl-labeling assay reveals reversible oxidation of protein tyrosine phosphatases in angiomyolipoma cells

    Benoit Boivin, Sheng Zhang, Jack L. Arbiser, Zhong-Yin Zhang, and Nicholas K. Tonks

    PNAS July 22, 2008 105 (29) 9959-9964; https://doi.org/10.1073/pnas.0804336105
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    A protein from the salivary glands of the pea aphid, Acyrthosiphon pisum, is essential in feeding on a host plant

    Navdeep S. Mutti, Joe Louis, Loretta K. Pappan, Kirk Pappan, Khurshida Begum, Ming-Shun Chen, Yoonseong Park, Neal Dittmer, Jeremy Marshall, John C. Reese, and Gerald R. Reeck

    PNAS July 22, 2008 105 (29) 9965-9969; https://doi.org/10.1073/pnas.0708958105
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    The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1

    • From the Cover

    Zhicheng Dong, Meng-Hsuan Han, and Nina Fedoroff

    PNAS July 22, 2008 105 (29) 9970-9975; https://doi.org/10.1073/pnas.0803356105

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    • Reconstituting plant miRNA biogenesis

      - Jul 16, 2008
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    Structures of synthetic O-antigen fragments from serotype 2a Shigella flexneri in complex with a protective monoclonal antibody

    B. Vulliez-Le Normand, F. A. Saul, A. Phalipon, F. Bélot, C. Guerreiro, L. A. Mulard, and G. A. Bentley

    PNAS July 22, 2008 105 (29) 9976-9981; https://doi.org/10.1073/pnas.0801711105

• Biophysics

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    Shifting transition states in the unfolding of a large ankyrin repeat protein

    • From the Cover

    Nicolas D. Werbeck, Pamela J. E. Rowling, Vasuki R. Chellamuthu, and Laura S. Itzhaki

    PNAS July 22, 2008 105 (29) 9982-9987; https://doi.org/10.1073/pnas.0705300105

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    • The capillarity picture and the kinetics of one-dimensional protein folding

      - Jul 16, 2008
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    Distinct conformational changes in β-arrestin report biased agonism at seven-transmembrane receptors

    Arun K. Shukla, Jonathan D. Violin, Erin J. Whalen, Diane Gesty-Palmer, Sudha K. Shenoy, and Robert J. Lefkowitz

    PNAS July 22, 2008 105 (29) 9988-9993; https://doi.org/10.1073/pnas.0804246105
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    A synthetic mammalian gene circuit reveals antituberculosis compounds

    Wilfried Weber, Ronald Schoenmakers, Bettina Keller, Marc Gitzinger, Thomas Grau, Marie Daoud-El Baba, Peter Sander, and Martin Fussenegger

    PNAS July 22, 2008 105 (29) 9994-9998; https://doi.org/10.1073/pnas.0800663105
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    Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

    Arash Zarrine-Afsar, Stefan Wallin, A. Mirela Neculai, Philipp Neudecker, P. Lynne Howell, Alan R. Davidson, and Hue Sun Chan

    PNAS July 22, 2008 105 (29) 9999-10004; https://doi.org/10.1073/pnas.0801874105

• Cell Biology

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    Plasma membranes are poised for activation of raft phase coalescence at physiological temperature

    Daniel Lingwood, Jonas Ries, Petra Schwille, and Kai Simons

    PNAS July 22, 2008 105 (29) 10005-10010; https://doi.org/10.1073/pnas.0804374105
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    The role of microtubule movement in bidirectional organelle transport

    Igor M. Kulić, André E. X. Brown, Hwajin Kim, Comert Kural, Benjamin Blehm, Paul R. Selvin, Philip C. Nelson, and Vladimir I. Gelfand

    PNAS July 22, 2008 105 (29) 10011-10016; https://doi.org/10.1073/pnas.0800031105

• Developmental Biology

  • Open Access

    Circulating blood cells function as a surveillance system for damaged tissue in Drosophila larvae

    Daniel T. Babcock, Amanda R. Brock, Greg S. Fish, Yan Wang, Laurent Perrin, Mark A. Krasnow, and Michael J. Galko

    PNAS July 22, 2008 105 (29) 10017-10022; https://doi.org/10.1073/pnas.0709951105

• Ecology

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    Life-history change in disease-ravaged Tasmanian devil populations

    Menna E. Jones, Andrew Cockburn, Rodrigo Hamede, Clare Hawkins, Heather Hesterman, Shelly Lachish, Diana Mann, Hamish McCallum, and David Pemberton

    PNAS July 22, 2008 105 (29) 10023-10027; https://doi.org/10.1073/pnas.0711236105
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    Long-term resistance to simulated climate change in an infertile grassland

    J. Philip Grime, Jason D. Fridley, Andrew P. Askew, Ken Thompson, John G. Hodgson, and Chris R. Bennett

    PNAS July 22, 2008 105 (29) 10028-10032; https://doi.org/10.1073/pnas.0711567105
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    Male-derived butterfly anti-aphrodisiac mediates induced indirect plant defense

    • From the Cover

    Nina E. Fatouros, Colette Broekgaarden, Gabriella Bukovinszkine'Kiss, Joop J. A. van Loon, Roland Mumm, Martinus E. Huigens, Marcel Dicke, and Monika Hilker

    PNAS July 22, 2008 105 (29) 10033-10038; https://doi.org/10.1073/pnas.0707809105

• Evolution

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    Conservation and topology of protein interaction networks under duplication-divergence evolution

    Kirill Evlampiev and Hervé Isambert

    PNAS July 22, 2008 105 (29) 9863-9868; https://doi.org/10.1073/pnas.0804119105
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    Sterols in a unicellular relative of the metazoans

    Robin B. Kodner, Roger E. Summons, Ann Pearson, Nicole King, and Andrew H. Knoll

    PNAS July 22, 2008 105 (29) 9897-9902; https://doi.org/10.1073/pnas.0803975105
  • Open Access

    Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

    Tal Dagan, Yael Artzy-Randrup, and William Martin

    PNAS July 22, 2008 105 (29) 10039-10044; https://doi.org/10.1073/pnas.0800679105
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    Evolution of an RNP assembly system: A minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster

    Matthias Kroiss, Jörg Schultz, Julia Wiesner, Ashwin Chari, Albert Sickmann, and Utz Fischer

    PNAS July 22, 2008 105 (29) 10045-10050; https://doi.org/10.1073/pnas.0802287105
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    Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence

    Rob J. Kulathinal, Sarah M. Bennett, Courtney L. Fitzpatrick, and Mohamed A. F. Noor

    PNAS July 22, 2008 105 (29) 10051-10056; https://doi.org/10.1073/pnas.0801848105
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    Phylogenetic escalation and decline of plant defense strategies

    Anurag A. Agrawal and Mark Fishbein

    PNAS July 22, 2008 105 (29) 10057-10060; https://doi.org/10.1073/pnas.0802368105
  • Open Access

    The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts

    Sujith Puthiyaveetil, T. Anthony Kavanagh, Peter Cain, James A. Sullivan, Christine A. Newell, John C. Gray, Colin Robinson, Mark van der Giezen, Matthew B. Rogers, and John F. Allen

    PNAS July 22, 2008 105 (29) 10061-10066; https://doi.org/10.1073/pnas.0803928105

• Genetics

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    Hidden copy number variation in the HapMap population

    John C. Marioni, Michael White, Simon Tavaré, and Andrew G. Lynch

    PNAS July 22, 2008 105 (29) 10067-10072; https://doi.org/10.1073/pnas.0711252105

    See companion article:

    • In This Issue

      - Jul 22, 2008
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    The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis

    Bin Yu, Liu Bi, Binglian Zheng, Lijuan Ji, David Chevalier, Manu Agarwal, Vanitharani Ramachandran, Wanxiang Li, Thierry Lagrange, John C. Walker, and Xuemei Chen

    PNAS July 22, 2008 105 (29) 10073-10078; https://doi.org/10.1073/pnas.0804218105
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    uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs

    Ivaylo P. Ivanov, Gary Loughran, and John F. Atkins

    PNAS July 22, 2008 105 (29) 10079-10084; https://doi.org/10.1073/pnas.0801590105
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    The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon

    Marcé D. Lorenzen, Andreas Gnirke, Jonathan Margolis, Jeffrey Garnes, Margie Campbell, Jeffrey J. Stuart, Rajat Aggarwal, Stephen Richards, Yoonseong Park, and Richard W. Beeman

    PNAS July 22, 2008 105 (29) 10085-10089; https://doi.org/10.1073/pnas.0800444105

• Immunology

  • Open Access

    Conserved T cell receptor α-chain induces insulin autoantibodies

    Masakazu Kobayashi, Jean Jasinski, Edwin Liu, Marcella Li, Dongmei Miao, Li Zhang, Liping Yu, Maki Nakayama, and George S. Eisenbarth

    PNAS July 22, 2008 105 (29) 10090-10094; https://doi.org/10.1073/pnas.0801648105
  • Open Access

    Structure of UL18, a peptide-binding viral MHC mimic, bound to a host inhibitory receptor

    Zhiru Yang and Pamela J. Bjorkman

    PNAS July 22, 2008 105 (29) 10095-10100; https://doi.org/10.1073/pnas.0804551105
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    CXCR4–CCR5: A couple modulating T cell functions

    Rita Lucia Contento, Barbara Molon, Cedric Boularan, Tullio Pozzan, Santos Manes, Stefano Marullo, and Antonella Viola

    PNAS July 22, 2008 105 (29) 10101-10106; https://doi.org/10.1073/pnas.0804286105
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    Genomic expression profiling of TNF-α-treated BDC2.5 diabetogenic CD4⁺ T cells

    Li-Fen Lee, Chih-Jian Lih, Chao-Jen Huang, Thai Cao, Stanley N. Cohen, and Hugh O. McDevitt

    PNAS July 22, 2008 105 (29) 10107-10112; https://doi.org/10.1073/pnas.0803336105
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    Foxp3⁺ natural regulatory T cells preferentially form aggregates on dendritic cells in vitro and actively inhibit their maturation

    Yasushi Onishi, Zoltan Fehervari, Tomoyuki Yamaguchi, and Shimon Sakaguchi

    PNAS July 22, 2008 105 (29) 10113-10118; https://doi.org/10.1073/pnas.0711106105
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    Preprocalcitonin signal peptide generates a cytotoxic T lymphocyte-defined tumor epitope processed by a proteasome-independent pathway

    Faten El Hage, Vincent Stroobant, Isabelle Vergnon, Jean-François Baurain, Hamid Echchakir, Vladimir Lazar, Salem Chouaib, Pierre G. Coulie, and Fathia Mami-Chouaib

    PNAS July 22, 2008 105 (29) 10119-10124; https://doi.org/10.1073/pnas.0802753105

• Medical Sciences

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    Quantification of the infectious dose of Leishmania major transmitted to the skin by single sand flies

    Nicola Kimblin, Nathan Peters, Alain Debrabant, Nagila Secundino, Jackson Egen, Phillip Lawyer, Michael P. Fay, Shaden Kamhawi, and David Sacks

    PNAS July 22, 2008 105 (29) 10125-10130; https://doi.org/10.1073/pnas.0802331105

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    • In This Issue

      - Jul 22, 2008
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    Plant-produced idiotype vaccines for the treatment of non-Hodgkin's lymphoma: Safety and immunogenicity in a phase I clinical study

    A. A. McCormick, S. Reddy, S. J. Reinl, T. I. Cameron, D. K. Czerwinkski, F. Vojdani, K. M. Hanley, S. J. Garger, E. L. White, J. Novak, J. Barrett, R. B. Holtz, D. Tusé, and R. Levy

    PNAS July 22, 2008 105 (29) 10131-10136; https://doi.org/10.1073/pnas.0803636105
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    A Cre-loxP-based mouse model for conditional somatic gene expression and knockdown in vivo by using avian retroviral vectors

    Barbara Seidler, Annegret Schmidt, Ulrich Mayr, Hassan Nakhai, Roland M. Schmid, Günter Schneider, and Dieter Saur

    PNAS July 22, 2008 105 (29) 10137-10142; https://doi.org/10.1073/pnas.0800487105
  • Open Access

    A germ-line-selective advantage rather than an increased mutation rate can explain some unexpectedly common human disease mutations

    Soo-Kyung Choi, Song-Ro Yoon, Peter Calabrese, and Norman Arnheim

    PNAS July 22, 2008 105 (29) 10143-10148; https://doi.org/10.1073/pnas.0801267105
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    Microsatellites as EWS/FLI response elements in Ewing's sarcoma

    Kunal Gangwal, Savita Sankar, Peter C. Hollenhorst, Michelle Kinsey, Stephen C. Haroldsen, Atul A. Shah, Kenneth M. Boucher, W. Scott Watkins, Lynn B. Jorde, Barbara J. Graves, and Stephen L. Lessnick

    PNAS July 22, 2008 105 (29) 10149-10154; https://doi.org/10.1073/pnas.0801073105
  • Open Access

    Genomic markers for malignant progression in pulmonary adenocarcinoma with bronchioloalveolar features

    Sarit Aviel-Ronen, Bradley P. Coe, Suzanne K. Lau, Gilda da Cunha Santos, Chang-Qi Zhu, Dan Strumpf, Igor Jurisica, Wan L. Lam, and Ming-Sound Tsao

    PNAS July 22, 2008 105 (29) 10155-10160; https://doi.org/10.1073/pnas.0709618105
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    Glucose controls CREB activity in islet cells via regulated phosphorylation of TORC2

    Deidre Jansson, Andy Cheuk-Him Ng, Accalia Fu, Chantal Depatie, Mufida Al Azzabi, and Robert A. Screaton

    PNAS July 22, 2008 105 (29) 10161-10166; https://doi.org/10.1073/pnas.0800796105
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    FOXC2 controls Ang-2 expression and modulates angiogenesis, vascular patterning, remodeling, and functions in adipose tissue

    Yuan Xue, Renhai Cao, Daniel Nilsson, Shaohua Chen, Rickard Westergren, Eva-Maria Hedlund, Cecile Martijn, Lena Rondahl, Per Krauli, Erik Walum, Sven Enerbäck, and Yihai Cao

    PNAS July 22, 2008 105 (29) 10167-10172; https://doi.org/10.1073/pnas.0802486105
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    A pathogenic dyskerin mutation impairs proliferation and activates a DNA damage response independent of telomere length in mice

    Bai-Wei Gu, Monica Bessler, and Philip J. Mason

    PNAS July 22, 2008 105 (29) 10173-10178; https://doi.org/10.1073/pnas.0803559105
  • Open Access

    Fc receptor engagement mediates differentiation of cardiac fibroblast precursor cells

    Sandra B. Haudek, JoAnn Trial, Ying Xia, Damon Gupta, Darrell Pilling, and Mark L. Entman

    PNAS July 22, 2008 105 (29) 10179-10184; https://doi.org/10.1073/pnas.0804910105
  • Open Access

    Soluble receptor-mediated selective inhibition of VEGFR and PDGFRβ signaling during physiologic and tumor angiogenesis

    Frank Kuhnert, Betty Y. Y. Tam, Barbara Sennino, John T. Gray, Jenny Yuan, Angeline Jocson, Nihar R. Nayak, Richard C. Mulligan, Donald M. McDonald, and Calvin J. Kuo

    PNAS July 22, 2008 105 (29) 10185-10190; https://doi.org/10.1073/pnas.0803194105

• Microbiology

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    Listeria monocytogenes multidrug resistance transporters activate a cytosolic surveillance pathway of innate immunity

    Gregory T. Crimmins, Anat A. Herskovits, Kai Rehder, Kelsey E. Sivick, Peter Lauer, Thomas W. Dubensky Jr., and Daniel A. Portnoy

    PNAS July 22, 2008 105 (29) 10191-10196; https://doi.org/10.1073/pnas.0804170105
  • Open Access

    The relationship between dNTP pool levels and mutagenesis in an Escherichia coli NDP kinase mutant

    Jared Nordman and Andrew Wright

    PNAS July 22, 2008 105 (29) 10197-10202; https://doi.org/10.1073/pnas.0802816105
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    Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2

    Mohamed Baani and Werner Liesack

    PNAS July 22, 2008 105 (29) 10203-10208; https://doi.org/10.1073/pnas.0702643105
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    Respiratory syncytial virus uses a Vps4-independent budding mechanism controlled by Rab11-FIP2

    Thomas J. Utley, Nicole A. Ducharme, Vasundhara Varthakavi, Bryan E. Shepherd, Philip J. Santangelo, Michael E. Lindquist, James R. Goldenring, and James E. Crowe Jr.

    PNAS July 22, 2008 105 (29) 10209-10214; https://doi.org/10.1073/pnas.0712144105
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    Amide bonds assemble pili on the surface of bacilli

    Jonathan M. Budzik, Luciano A. Marraffini, Puneet Souda, Julian P. Whitelegge, Kym F. Faull, and Olaf Schneewind

    PNAS July 22, 2008 105 (29) 10215-10220; https://doi.org/10.1073/pnas.0803565105
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    In silico identified CCR4 antagonists target regulatory T cells and exert adjuvant activity in vaccination

    Jagadeesh Bayry, Elma Z. Tchilian, Matthew N. Davies, Emily K. Forbes, Simon J. Draper, Srini V. Kaveri, Adrian V. S. Hill, Michel D. Kazatchkine, Peter C. L. Beverley, Darren R. Flower, and David F. Tough

    PNAS July 22, 2008 105 (29) 10221-10226; https://doi.org/10.1073/pnas.0803453105

• Neuroscience

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    Identification of a population of sleep-active cerebral cortex neurons

    Dmitry Gerashchenko, Jonathan P. Wisor, Deirdre Burns, Rebecca K. Reh, Priyattam J. Shiromani, Takeshi Sakurai, Horacio O. de la Iglesia, and Thomas S. Kilduff

    PNAS July 22, 2008 105 (29) 10227-10232; https://doi.org/10.1073/pnas.0803125105
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    Widespread spatial integration in primary somatosensory cortex

    Jamie L. Reed, Pierre Pouget, Hui-Xin Qi, Zhiyi Zhou, Melanie R. Bernard, Mark J. Burish, John Haitas, A. B. Bonds, and Jon H. Kaas

    PNAS July 22, 2008 105 (29) 10233-10237; https://doi.org/10.1073/pnas.0803800105
  • Open Access

    Single treatment with RNAi against prion protein rescues early neuronal dysfunction and prolongs survival in mice with prion disease

    Melanie D. White, Michael Farmer, Ilaria Mirabile, Sebastian Brandner, John Collinge, and Giovanna R. Mallucci

    PNAS July 22, 2008 105 (29) 10238-10243; https://doi.org/10.1073/pnas.0802759105
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    RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways

    Marcel P. van der Brug, Jeff Blackinton, Jayanth Chandran, Ling-Yang Hao, Ashish Lal, Krystyna Mazan-Mamczarz, Jennifer Martindale, Chengsong Xie, Rili Ahmad, Kelly J. Thomas, Alexandra Beilina, J. Raphael Gibbs, Jinhui Ding, Amanda J. Myers, Ming Zhan, Huaibin Cai, Nancy M. Bonini, Myriam Gorospe, and Mark R. Cookson

    PNAS July 22, 2008 105 (29) 10244-10249; https://doi.org/10.1073/pnas.0708518105
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    Interneuron activity controls endocannabinoid-mediated presynaptic plasticity through calcineurin

    Boris D. Heifets, Vivien Chevaleyre, and Pablo E. Castillo

    PNAS July 22, 2008 105 (29) 10250-10255; https://doi.org/10.1073/pnas.0711880105

• Physiology

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    Nitrite reductase activity of myoglobin regulates respiration and cellular viability in myocardial ischemia-reperfusion injury

    Ulrike B. Hendgen-Cotta, Marc W. Merx, Sruti Shiva, Joel Schmitz, Stefanie Becher, Johann P. Klare, Heinz-Jürgen Steinhoff, Axel Goedecke, Jürgen Schrader, Mark T. Gladwin, Malte Kelm, and Tienush Rassaf

    PNAS July 22, 2008 105 (29) 10256-10261; https://doi.org/10.1073/pnas.0801336105

• Plant Biology

  • Open Access

    Proteome-wide characterization of sugarbeet seed vigor and its tissue specific expression

    Julie Catusse, Jean-Marc Strub, Claudette Job, Alain Van Dorsselaer, and Dominique Job

    PNAS July 22, 2008 105 (29) 10262-10267; https://doi.org/10.1073/pnas.0800585105