Table of Contents

Biological Sciences

• Biochemistry

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    Creating ribosomes with an all-RNA 30S subunit P site

    Lee Hoang, Kurt Fredrick, and Harry F. Noller

    PNAS August 24, 2004 101 (34) 12439-12443; https://doi.org/10.1073/pnas.0405227101
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    Structural evidence for evolution of shark Ig new antigen receptor variable domain antibodies from a cell-surface receptor

    V. A. Streltsov, J. N. Varghese, J. A. Carmichael, R. A. Irving, P. J. Hudson, and S. D. Nuttall

    PNAS August 24, 2004 101 (34) 12444-12449; https://doi.org/10.1073/pnas.0403509101
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    An aminoacyl-tRNA synthetase that specifically activates pyrrolysine

    Carla Polycarpo, Alexandre Ambrogelly, Amélie Bérubé, SusAnn M. Winbush, James A. McCloskey, Pamela F. Crain, John L. Wood, and Dieter Söll

    PNAS August 24, 2004 101 (34) 12450-12454; https://doi.org/10.1073/pnas.0405362101
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    Structure of adeno-associated virus type 2 Rep40–ADP complex: Insight into nucleotide recognition and catalysis by superfamily 3 helicases

    J. Anson James, Aneel K. Aggarwal, R. Michael Linden, and Carlos R. Escalante

    PNAS August 24, 2004 101 (34) 12455-12460; https://doi.org/10.1073/pnas.0403454101
  • Open Access

    Discovery of an allosteric site in the caspases

    Jeanne A. Hardy, Joni Lam, Jack T. Nguyen, Tom O'Brien, and James A. Wells

    PNAS August 24, 2004 101 (34) 12461-12466; https://doi.org/10.1073/pnas.0404781101
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    Synthetic antibodies from a four-amino-acid code: A dominant role for tyrosine in antigen recognition

    Frederic A. Fellouse, Christian Wiesmann, and Sachdev S. Sidhu

    PNAS August 24, 2004 101 (34) 12467-12472; https://doi.org/10.1073/pnas.0401786101
  • Open Access

    Binding between the Niemann–Pick C1 protein and a photoactivatable cholesterol analog requires a functional sterol-sensing domain

    Nobutaka Ohgami, Dennis C. Ko, Matthew Thomas, Matthew P. Scott, Catherine C. Y. Chang, and Ta-Yuan Chang

    PNAS August 24, 2004 101 (34) 12473-12478; https://doi.org/10.1073/pnas.0405255101
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    A tagging-via-substrate technology for detection and proteomics of farnesylated proteins

    Yoonjung Kho, Sung Chan Kim, Chen Jiang, Deb Barma, Sung Won Kwon, Jinke Cheng, Janis Jaunbergs, Carolyn Weinbaum, Fuyuhiko Tamanoi, John Falck, and Yingming Zhao

    PNAS August 24, 2004 101 (34) 12479-12484; https://doi.org/10.1073/pnas.0403413101
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    Carbon dioxide mediates Mn(II)-catalyzed decomposition of hydrogen peroxide and peroxidation reactions

    Stefan I. Liochev and Irwin Fridovich

    PNAS August 24, 2004 101 (34) 12485-12490; https://doi.org/10.1073/pnas.0404911101

• Biophysics

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    Random-coil behavior and the dimensions of chemically unfolded proteins

    Jonathan E. Kohn, Ian S. Millett, Jaby Jacob, Bojan Zagrovic, Thomas M. Dillon, Nikolina Cingel, Robin S. Dothager, Soenke Seifert, P. Thiyagarajan, Tobin R. Sosnick, M. Zahid Hasan, Vijay S. Pande, Ingo Ruczinski, Sebastian Doniach, and Kevin W. Plaxco

    PNAS August 24, 2004 101 (34) 12491-12496; https://doi.org/10.1073/pnas.0403643101
  • Open Access

    Reassessing random-coil statistics in unfolded proteins

    Nicholas C. Fitzkee and George D. Rose

    PNAS August 24, 2004 101 (34) 12497-12502; https://doi.org/10.1073/pnas.0404236101
  • Open Access

    Single-molecule recognition imaging microscopy

    C. Stroh, H. Wang, R. Bash, B. Ashcroft, J. Nelson, H. Gruber, D. Lohr, S. M. Lindsay, and P. Hinterdorfer

    PNAS August 24, 2004 101 (34) 12503-12507; https://doi.org/10.1073/pnas.0403538101
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    Structural origins of constitutive activation in rhodopsin: Role of the K296/E113 salt bridge

    Jong-Myoung Kim, Christian Altenbach, Masahiro Kono, Daniel D. Oprian, Wayne L. Hubbell, and H. Gobind Khorana

    PNAS August 24, 2004 101 (34) 12508-12513; https://doi.org/10.1073/pnas.0404519101
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    Nonspecific hydrophobic interactions stabilize an equilibrium intermediate of apomyoglobin at a key position within the AGH region

    Angela M. Bertagna and Doug Barrick

    PNAS August 24, 2004 101 (34) 12514-12519; https://doi.org/10.1073/pnas.0404760101
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    Cell mechanosensitivity controls the anisotropy of focal adhesions

    Alice Nicolas, Benjamin Geiger, and Samuel A. Safran

    PNAS August 24, 2004 101 (34) 12520-12525; https://doi.org/10.1073/pnas.0403539101

• Cell Biology

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    Rho overexpression leads to mitosis-associated detachment of cells from epithelial sheets: A link to the mechanism of cancer dissemination

    • From the Cover

    J. M. Vasiliev, T. Omelchenko, I. M. Gelfand, H. H. Feder, and E. M. Bonder

    PNAS August 24, 2004 101 (34) 12526-12530; https://doi.org/10.1073/pnas.0404723101
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    Emi1-mediated M-phase arrest in Xenopus eggs is distinct from cytostatic factor arrest

    Keita Ohsumi, Ayako Koyanagi, Tomomi M. Yamamoto, Tetsuya Gotoh, and Takeo Kishimoto

    PNAS August 24, 2004 101 (34) 12531-12536; https://doi.org/10.1073/pnas.0405300101
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    Cotranslational integration and initial sorting at the endoplasmic reticulum translocon of proteins destined for the inner nuclear membrane

    Suraj Saksena, Yuanlong Shao, Sharon C. Braunagel, Max D. Summers, and Arthur E. Johnson

    PNAS August 24, 2004 101 (34) 12537-12542; https://doi.org/10.1073/pnas.0404934101

• Developmental Biology

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    Derivation of midbrain dopamine neurons from human embryonic stem cells

    • From the Cover

    Anselme L. Perrier, Viviane Tabar, Tiziano Barberi, Maria E. Rubio, Juan Bruses, Norbert Topf, Neil L. Harrison, and Lorenz Studer

    PNAS August 24, 2004 101 (34) 12543-12548; https://doi.org/10.1073/pnas.0404700101
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    The Caenorhabditis elegans F-box protein SEL-10 promotes female development and may target FEM-1 and FEM-3 for degradation by the proteasome

    Sibylle Jäger, Hillel T. Schwartz, H. Robert Horvitz, and Barbara Conradt

    PNAS August 24, 2004 101 (34) 12549-12554; https://doi.org/10.1073/pnas.0405087101
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    A gain-of-function mutation of Fgfr2c demonstrates the roles of this receptor variant in osteogenesis

    Veraragavan P. Eswarakumar, Mark C. Horowitz, Rachel Locklin, Gillian M. Morriss-Kay, and Peter Lonai

    PNAS August 24, 2004 101 (34) 12555-12560; https://doi.org/10.1073/pnas.0405031101
  • Open Access

    Inhibition of prostate cancer proliferation by interference with SONIC HEDGEHOG-GLI1 signaling

    Pilar Sanchez, Ana Maria Hernández, Barbara Stecca, Andrea J. Kahler, Amy M. DeGueme, Andrea Barrett, Mercedes Beyna, Milton W. Datta, Sumana Datta, and Ariel Ruiz i Altaba

    PNAS August 24, 2004 101 (34) 12561-12566; https://doi.org/10.1073/pnas.0404956101
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    A myocardin-related transcription factor regulates activity of serum response factor in Drosophila

    Zhe Han, Xiumin Li, Jiang Wu, and Eric N. Olson

    PNAS August 24, 2004 101 (34) 12567-12572; https://doi.org/10.1073/pnas.0405085101
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    GATA4 is essential for formation of the proepicardium and regulates cardiogenesis

    Alistair J. Watt, Michele A. Battle, Jixuan Li, and Stephen A. Duncan

    PNAS August 24, 2004 101 (34) 12573-12578; https://doi.org/10.1073/pnas.0400752101

• Ecology

  • Open Access

    Emissions pathways, climate change, and impacts on California

    Katharine Hayhoe, Daniel Cayan, Christopher B. Field, Peter C. Frumhoff, Edwin P. Maurer, Norman L. Miller, Susanne C. Moser, Stephen H. Schneider, Kimberly Nicholas Cahill, Elsa E. Cleland, Larry Dale, Ray Drapek, R. Michael Hanemann, Laurence S. Kalkstein, James Lenihan, Claire K. Lunch, Ronald P. Neilson, Scott C. Sheridan, and Julia H. Verville

    PNAS August 24, 2004 101 (34) 12422-12427; https://doi.org/10.1073/pnas.0404500101
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    Economic value of tropical forest to coffee production

    Taylor H. Ricketts, Gretchen C. Daily, Paul R. Ehrlich, and Charles D. Michener

    PNAS August 24, 2004 101 (34) 12579-12582; https://doi.org/10.1073/pnas.0405147101

• Environmental Sciences

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    Sulfur pollution suppression of the wetland methane source in the 20th and 21st centuries

    • From the Cover

    Vincent Gauci, Elaine Matthews, Nancy Dise, Bernadette Walter, Dorothy Koch, Gunnar Granberg, and Melanie Vile

    PNAS August 24, 2004 101 (34) 12583-12587; https://doi.org/10.1073/pnas.0404412101

• Evolution

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    Tissue-specific codon usage and the expression of human genes

    Joshua B. Plotkin, Harlan Robins, and Arnold J. Levine

    PNAS August 24, 2004 101 (34) 12588-12591; https://doi.org/10.1073/pnas.0404957101

• Genetics

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    Biography of Jeffrey L. Bennetzen

    • Inaugural Article

    Emma Hitt

    PNAS August 24, 2004 101 (34) 12402-12403; https://doi.org/10.1073/pnas.0405476101
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    Rapid recent growth and divergence of rice nuclear genomes

    • Inaugural Article

    Jianxin Ma and Jeffrey L. Bennetzen

    PNAS August 24, 2004 101 (34) 12404-12410; https://doi.org/10.1073/pnas.0403715101
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    A mechanical basis for chromosome function

    Nancy Kleckner, Denise Zickler, Gareth H. Jones, Job Dekker, Ruth Padmore, Jim Henle, and John Hutchinson

    PNAS August 24, 2004 101 (34) 12592-12597; https://doi.org/10.1073/pnas.0402724101
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    The RD1 virulence locus of Mycobacterium tuberculosis regulates DNA transfer in Mycobacterium smegmatis

    Jessica L. Flint, Joseph C. Kowalski, Pavan K. Karnati, and Keith M. Derbyshire

    PNAS August 24, 2004 101 (34) 12598-12603; https://doi.org/10.1073/pnas.0404892101
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    Variation in GRM3 affects cognition, prefrontal glutamate, and risk for schizophrenia

    Michael F. Egan, Richard E. Straub, Terry E. Goldberg, Imtiaz Yakub, Joseph H. Callicott, Ahmad R. Hariri, Venkata S. Mattay, Alessandro Bertolino, Thomas M. Hyde, Cynthia Shannon-Weickert, Mayada Akil, Jeremy Crook, Radha Krishna Vakkalanka, Rishi Balkissoon, Richard A. Gibbs, Joel E. Kleinman, and Daniel R. Weinberger

    PNAS August 24, 2004 101 (34) 12604-12609; https://doi.org/10.1073/pnas.0405077101
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    Multiple-stress analysis for isolation of Drosophila longevity genes

    Horng-Dar Wang, Parsa Kazemi-Esfarjani, and Seymour Benzer

    PNAS August 24, 2004 101 (34) 12610-12615; https://doi.org/10.1073/pnas.0404648101
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    Role of the yeast acetyltransferase Mpr1 in oxidative stress: Regulation of oxygen reactive species caused by a toxic proline catabolism intermediate

    Michiyo Nomura and Hiroshi Takagi

    PNAS August 24, 2004 101 (34) 12616-12621; https://doi.org/10.1073/pnas.0403349101

• Immunology

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    Evolutionarily conserved sequence elements that positively regulate IFN-γ expression in T cells

    Maria Shnyreva, William M. Weaver, Mathieu Blanchette, Scott L. Taylor, Martin Tompa, David R. Fitzpatrick, and Christopher B. Wilson

    PNAS August 24, 2004 101 (34) 12622-12627; https://doi.org/10.1073/pnas.0400849101
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    Aromatase-deficient mice spontaneously develop a lymphoproliferative autoimmune disease resembling Sjögren's syndrome

    Gil-Jin Shim, Margaret Warner, Hyun-Jin Kim, Sandra Andersson, Lining Liu, Jenny Ekman, Otabek Imamov, Margaret E. Jones, Evan R. Simpson, and Jan-Åke Gustafsson

    PNAS August 24, 2004 101 (34) 12628-12633; https://doi.org/10.1073/pnas.0405099101
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    Imaging inflammation of the pancreatic islets in type 1 diabetes

    Maria C. Denis, Umar Mahmood, Christophe Benoist, Diane Mathis, and Ralph Weissleder

    PNAS August 24, 2004 101 (34) 12634-12639; https://doi.org/10.1073/pnas.0404307101
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    Identification of 4Ig-B7-H3 as a neuroblastoma-associated molecule that exerts a protective role from an NK cell-mediated lysis

    Roberta Castriconi, Alessandra Dondero, Raffaella Augugliaro, Claudia Cantoni, Barbara Carnemolla, Angela Rita Sementa, Francesca Negri, Romana Conte, Maria Valeria Corrias, Lorenzo Moretta, Alessandro Moretta, and Cristina Bottino

    PNAS August 24, 2004 101 (34) 12640-12645; https://doi.org/10.1073/pnas.0405025101
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    Enhanced autoimmunity, arthritis, and encephalomyelitis in mice with a reduced oxidative burst due to a mutation in the Ncf1 gene

    Malin Hultqvist, Peter Olofsson, Jens Holmberg, B. Thomas Bäckström, Jesper Tordsson, and Rikard Holmdahl

    PNAS August 24, 2004 101 (34) 12646-12651; https://doi.org/10.1073/pnas.0403831101
  • Open Access

    Mycobacterium tuberculosis (Mtb) isocitrate dehydrogenases show strong B cell response and distinguish vaccinated controls from TB patients

    Sharmistha Banerjee, Ashok Nandyala, Raviprasad Podili, V. M. Katoch, K. J. R. Murthy, and Seyed E. Hasnain

    PNAS August 24, 2004 101 (34) 12652-12657; https://doi.org/10.1073/pnas.0404347101

• Medical Sciences

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    Developmentally regulated mannose 6-phosphate receptor-mediated transport of a lysosomal enzyme across the blood-brain barrier

    Akihiko Urayama, Jeffrey H. Grubb, William S. Sly, and William A. Banks

    PNAS August 24, 2004 101 (34) 12658-12663; https://doi.org/10.1073/pnas.0405042101
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    Mechanisms of embryonal tumor initiation: Distinct roles for MycN expression and MYCN amplification

    Loen M. Hansford, Wayne D. Thomas, Joanna M. Keating, Catherine A. Burkhart, Anne E. Peaston, Murray D. Norris, Michelle Haber, Patricia J. Armati, William A. Weiss, and Glenn M. Marshall

    PNAS August 24, 2004 101 (34) 12664-12669; https://doi.org/10.1073/pnas.0401083101
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    Insulin resistance in skeletal muscles of caveolin-3-null mice

    Jin Oshikawa, Koji Otsu, Yoshiyuki Toya, Takashi Tsunematsu, Raleigh Hankins, Jun-ichi Kawabe, Susumu Minamisawa, Satoshi Umemura, Yasuko Hagiwara, and Yoshihiro Ishikawa

    PNAS August 24, 2004 101 (34) 12670-12675; https://doi.org/10.1073/pnas.0402053101
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    Metabonomic investigations in mice infected with Schistosoma mansoni: An approach for biomarker identification

    Yulan Wang, Elaine Holmes, Jeremy K. Nicholson, Olivier Cloarec, Jacques Chollet, Marcel Tanner, Burton H. Singer, and Jürg Utzinger

    PNAS August 24, 2004 101 (34) 12676-12681; https://doi.org/10.1073/pnas.0404878101
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    A small molecule inhibitor of β-catenin/cyclic AMP response element-binding protein transcription

    Katayoon H. Emami, Cu Nguyen, Hong Ma, Dae Hoon Kim, Kwang Won Jeong, Masakatsu Eguchi, Randall T. Moon, Jia-Ling Teo, Se Wong Oh, Hak Yeop Kim, Sung Hwan Moon, Jong Ryul Ha, and Michael Kahn

    PNAS August 24, 2004 101 (34) 12682-12687; https://doi.org/10.1073/pnas.0404875101

• Microbiology

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    Biography of Patricia G. Spear

    • Inaugural Article

    Liza Q. Bundesen

    PNAS August 24, 2004 101 (34) 12411-12413; https://doi.org/10.1073/pnas.0405440101
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    Mutations in herpes simplex virus glycoprotein D that prevent cell entry via nectins and alter cell tropism

    • Inaugural Article

    Sharmila Manoj, Cheryl R. Jogger, Dawn Myscofski, Miri Yoon, and Patricia G. Spear

    PNAS August 24, 2004 101 (34) 12414-12421; https://doi.org/10.1073/pnas.0404211101
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    High-resolution structure of a picornaviral internal cis-acting RNA replication element (cre)

    Varatharasa Thiviyanathan, Yan Yang, Kumaralal Kaluarachchi, Rene Rijnbrand, David G. Gorenstein, and Stanley M. Lemon

    PNAS August 24, 2004 101 (34) 12688-12693; https://doi.org/10.1073/pnas.0403079101
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    Major genetic marker of nidoviruses encodes a replicative endoribonuclease

    Konstantin A. Ivanov, Tobias Hertzig, Mikhail Rozanov, Sonja Bayer, Volker Thiel, Alexander E. Gorbalenya, and John Ziebuhr

    PNAS August 24, 2004 101 (34) 12694-12699; https://doi.org/10.1073/pnas.0403127101

• Neuroscience

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    Regional glucose metabolism and glutamatergic neurotransmission in rat brain in vivo

    Robin A. de Graaf, Graeme F. Mason, Anant B. Patel, Douglas L. Rothman, and Kevin L. Behar

    PNAS August 24, 2004 101 (34) 12700-12705; https://doi.org/10.1073/pnas.0405065101
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    Nociceptor-specific gene deletion reveals a major role for Na_v1.7 (PN1) in acute and inflammatory pain

    Mohammed A. Nassar, L. Caroline Stirling, Greta Forlani, Mark D. Baker, Elizabeth A. Matthews, Anthony H. Dickenson, and John N. Wood

    PNAS August 24, 2004 101 (34) 12706-12711; https://doi.org/10.1073/pnas.0404915101
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    Correlates of transsaccadic integration in the primary visual cortex of the monkey

    Paul S. Khayat, Henk Spekreijse, and Pieter R. Roelfsema

    PNAS August 24, 2004 101 (34) 12712-12717; https://doi.org/10.1073/pnas.0301935101
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    Spatial patterns of gene expression in the olfactory bulb

    David M. Lin, Yee Hwa Yang, Jonathan A. Scolnick, Lisa J. Brunet, Heather Marsh, Vivian Peng, Yasushi Okazaki, Yoshihide Hayashizaki, Terence P. Speed, and John Ngai

    PNAS August 24, 2004 101 (34) 12718-12723; https://doi.org/10.1073/pnas.0404872101
  • Open Access

    Modality maps within primate somatosensory cortex

    Robert M. Friedman, Li Min Chen, and Anna Wang Roe

    PNAS August 24, 2004 101 (34) 12724-12729; https://doi.org/10.1073/pnas.0404884101
  • Open Access

    Granulocyte-macrophage colony-stimulating factor-induced arteriogenesis reduces energy failure in hemodynamic stroke

    Edda Schneeloch, Günter Mies, Hans-Jörg Busch, Ivo R. Buschmann, and Konstantin-Alexander Hossmann

    PNAS August 24, 2004 101 (34) 12730-12735; https://doi.org/10.1073/pnas.0404880101
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    Huntingtin-associated protein 1 regulates inhibitory synaptic transmission by modulating γ-aminobutyric acid type A receptor membrane trafficking

    Josef T. Kittler, Philip Thomas, Verena Tretter, Yuri D. Bogdanov, Volker Haucke, Trevor G. Smart, and Stephen J. Moss

    PNAS August 24, 2004 101 (34) 12736-12741; https://doi.org/10.1073/pnas.0401860101
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    Y1 receptors regulate aggressive behavior by modulating serotonin pathways

    Tim Karl, Shu Lin, Christoph Schwarzer, Amanda Sainsbury, Michelle Couzens, Walter Wittmann, Dana Boey, Stephan von Hörsten, and Herbert Herzog

    PNAS August 24, 2004 101 (34) 12742-12747; https://doi.org/10.1073/pnas.0404085101

• Physiology

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    Evidence for conformational coupling between two calcium channels

    C. Paolini, James D. Fessenden, Isaac N. Pessah, and C. Franzini-Armstrong

    PNAS August 24, 2004 101 (34) 12748-12752; https://doi.org/10.1073/pnas.0404836101

• Plant Biology

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    Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions

    • From the Cover

    Yukio Kurihara and Yuichiro Watanabe

    PNAS August 24, 2004 101 (34) 12753-12758; https://doi.org/10.1073/pnas.0403115101
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    Regulation of flowering time in Arabidopsis by K homology domain proteins

    Todd C. Mockler, Xuhong Yu, Dror Shalitin, Dhavan Parikh, Todd P. Michael, Jasmine Liou, Jie Huang, Zachery Smith, Jose M. Alonso, Joseph R. Ecker, Joanne Chory, and Chentao Lin

    PNAS August 24, 2004 101 (34) 12759-12764; https://doi.org/10.1073/pnas.0404552101
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    Mutations in ClpC2/Hsp100 suppress the requirement for FtsH in thylakoid membrane biogenesis

    Sungsoon Park and Steven R. Rodermel

    PNAS August 24, 2004 101 (34) 12765-12770; https://doi.org/10.1073/pnas.0402764101
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    Recessive-interfering mutations in the gibberellin signaling gene SLEEPY1 are rescued by overexpression of its homologue, SNEEZY

    Lucia C. Strader, Siân Ritchie, Jonathan D. Soule, Karen M. McGinnis, and Camille M. Steber

    PNAS August 24, 2004 101 (34) 12771-12776; https://doi.org/10.1073/pnas.0404287101