Table of Contents

Biological Sciences

• Biochemistry

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    Active cytosine demethylation triggered by a nuclear receptor involves DNA strand breaks

    Clémence Kress, Hélène Thomassin, and Thierry Grange

    PNAS July 25, 2006 103 (30) 11112-11117; https://doi.org/10.1073/pnas.0601793103
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    Topoisomerase IIIα and Bloom’s helicase can resolve a mobile double Holliday junction substrate through convergent branch migration

    Jody L. Plank, Jianhong Wu, and Tao-shih Hsieh

    PNAS July 25, 2006 103 (30) 11118-11123; https://doi.org/10.1073/pnas.0604873103
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    The 2.7-Å crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase

    Yinyan Tang, Chu-Young Kim, Irimpan I. Mathews, David E. Cane, and Chaitan Khosla

    PNAS July 25, 2006 103 (30) 11124-11129; https://doi.org/10.1073/pnas.0601924103

• Biophysics

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    A two-dimensional view of the folding energy landscape of cytochrome c

    James H. Werner, Raymond Joggerst, R. Brian Dyer, and Peter M. Goodwin

    PNAS July 25, 2006 103 (30) 11130-11135; https://doi.org/10.1073/pnas.0604712103
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    Single-molecule dynamics of phytochrome-bound fluorophores probed by fluorescence correlation spectroscopy

    Abigail E. Miller, Amanda J. Fischer, Ted Laurence, Christopher W. Hollars, Richard J. Saykally, J. Clark Lagarias, and Thomas Huser

    PNAS July 25, 2006 103 (30) 11136-11141; https://doi.org/10.1073/pnas.0604724103

• Cell Biology

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    A global topology map of the Saccharomyces cerevisiae membrane proteome

    Hyun Kim, Karin Melén, Marie Österberg, and Gunnar von Heijne

    PNAS July 25, 2006 103 (30) 11142-11147; https://doi.org/10.1073/pnas.0604075103
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    Phenotypic effects of membrane protein overexpression in Saccharomyces cerevisiae

    Marie Österberg, Hyun Kim, Jonas Warringer, Karin Melén, Anders Blomberg, and Gunnar von Heijne

    PNAS July 25, 2006 103 (30) 11148-11153; https://doi.org/10.1073/pnas.0604078103
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    Ovarian cancer side population defines cells with stem cell-like characteristics and Mullerian Inhibiting Substance responsiveness

    Paul P. Szotek, Rafael Pieretti-Vanmarcke, Peter T. Masiakos, Daniela M. Dinulescu, Denise Connolly, Rosemary Foster, David Dombkowski, Frederic Preffer, David T. MacLaughlin, and Patricia K. Donahoe

    PNAS July 25, 2006 103 (30) 11154-11159; https://doi.org/10.1073/pnas.0603672103
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    MAGE-A tumor antigens target p53 transactivation function through histone deacetylase recruitment and confer resistance to chemotherapeutic agents

    Martin Monte, Marta Simonatto, Leticia Y. Peche, Debora R. Bublik, Stefania Gobessi, Marco A. Pierotti, Monica Rodolfo, and Claudio Schneider

    PNAS July 25, 2006 103 (30) 11160-11165; https://doi.org/10.1073/pnas.0510834103
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    Biophysical model of self-organized spindle formation patterns without centrosomes and kinetochores

    Stuart C. Schaffner and Jorge V. José

    PNAS July 25, 2006 103 (30) 11166-11171; https://doi.org/10.1073/pnas.0604721103
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    Alzheimer's disease β-amyloid peptides are released in association with exosomes

    Lawrence Rajendran, Masanori Honsho, Tobias R. Zahn, Patrick Keller, Kathrin D. Geiger, Paul Verkade, and Kai Simons

    PNAS July 25, 2006 103 (30) 11172-11177; https://doi.org/10.1073/pnas.0603838103
  • Open Access

    An amphipathic helix targets serum and glucocorticoid-induced kinase 1 to the endoplasmic reticulum-associated ubiquitin-conjugation machinery

    Maria Francisca Arteaga, Lin Wang, Tommer Ravid, Mark Hochstrasser, and Cecilia M. Canessa

    PNAS July 25, 2006 103 (30) 11178-11183; https://doi.org/10.1073/pnas.0604816103

• Developmental Biology

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    Influence of sex chromosome constitution on the genomic imprinting of germ cells

    Gabriela Durcova-Hills, Petra Hajkova, Stephen Sullivan, Sheila Barton, M. Azim Surani, and Anne McLaren

    PNAS July 25, 2006 103 (30) 11184-11188; https://doi.org/10.1073/pnas.0602621103
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    A threshold of GATA4 and GATA6 expression is required for cardiovascular development

    Mei Xin, Christopher A. Davis, Jeffery D. Molkentin, Ching-Ling Lien, Stephen A. Duncan, James A. Richardson, and Eric N. Olson

    PNAS July 25, 2006 103 (30) 11189-11194; https://doi.org/10.1073/pnas.0604604103
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    Molecular evidence for deep evolutionary roots of bilaterality in animal development

    • From the Cover

    David Q. Matus, Kevin Pang, Heather Marlow, Casey W. Dunn, Gerald H. Thomsen, and Mark Q. Martindale

    PNAS July 25, 2006 103 (30) 11195-11200; https://doi.org/10.1073/pnas.0601257103

    See companion article:

    • In This Issue

      - Jul 25, 2006

• Ecology

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    A stable isotope aridity index for terrestrial environments

    Naomi E. Levin, Thure E. Cerling, Benjamin H. Passey, John M. Harris, and James R. Ehleringer

    PNAS July 25, 2006 103 (30) 11201-11205; https://doi.org/10.1073/pnas.0604719103
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    Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels

    • From the Cover

    Jason Hill, Erik Nelson, David Tilman, Stephen Polasky, and Douglas Tiffany

    PNAS July 25, 2006 103 (30) 11206-11210; https://doi.org/10.1073/pnas.0604600103

    See companion article:

    • In This Issue

      - Jul 25, 2006
  • Open Access

    Parasites dominate food web links

    Kevin D. Lafferty, Andrew P. Dobson, and Armand M. Kuris

    PNAS July 25, 2006 103 (30) 11211-11216; https://doi.org/10.1073/pnas.0604755103

• Environmental Sciences

  • Open Access

    Extreme heat reduces and shifts United States premium wine production in the 21st century

    M. A. White, N. S. Diffenbaugh, G. V. Jones, J. S. Pal, and F. Giorgi

    PNAS July 25, 2006 103 (30) 11217-11222; https://doi.org/10.1073/pnas.0603230103

• Evolution

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    Rapid Asia–Europe–North America geographic dispersal of earliest Eocene primate Teilhardina during the Paleocene–Eocene Thermal Maximum

    Thierry Smith, Kenneth D. Rose, and Philip D. Gingerich

    PNAS July 25, 2006 103 (30) 11223-11227; https://doi.org/10.1073/pnas.0511296103
  • Open Access

    Adaptive evolution by mutations in the FLO11 gene

    Manuel Fidalgo, Ramon R. Barrales, Jose I. Ibeas, and Juan Jimenez

    PNAS July 25, 2006 103 (30) 11228-11233; https://doi.org/10.1073/pnas.0601713103

• Genetics

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    Mouse genomic representational oligonucleotide microarray analysis: Detection of copy number variations in normal and tumor specimens

    B. Lakshmi, Ira M. Hall, Christopher Egan, Joan Alexander, Anthony Leotta, John Healy, Lars Zender, Mona S. Spector, Wen Xue, Scott W. Lowe, Michael Wigler, and Robert Lucito

    PNAS July 25, 2006 103 (30) 11234-11239; https://doi.org/10.1073/pnas.0602984103
  • Open Access

    A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes

    Susanne M. D. Goldberg, Justin Johnson, Dana Busam, Tamara Feldblyum, Steve Ferriera, Robert Friedman, Aaron Halpern, Hoda Khouri, Saul A. Kravitz, Federico M. Lauro, Kelvin Li, Yu-Hui Rogers, Robert Strausberg, Granger Sutton, Luke Tallon, Torsten Thomas, Eli Venter, Marvin Frazier, and J. Craig Venter

    PNAS July 25, 2006 103 (30) 11240-11245; https://doi.org/10.1073/pnas.0604351103
  • Open Access

    Heritable and stable gene knockdown in rats

    Christina Tenenhaus Dann, Alma L. Alvarado, Robert E. Hammer, and David L. Garbers

    PNAS July 25, 2006 103 (30) 11246-11251; https://doi.org/10.1073/pnas.0604657103

• Immunology

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    Glycolipid α-C-galactosylceramide is a distinct inducer of dendritic cell function during innate and adaptive immune responses of mice

    Shin-ichiro Fujii, Kanako Shimizu, Hiroaki Hemmi, Mikiko Fukui, Anthony J. Bonito, Guangwu Chen, Richard W. Franck, Moriya Tsuji, and Ralph M. Steinman

    PNAS July 25, 2006 103 (30) 11252-11257; https://doi.org/10.1073/pnas.0604812103
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    Transfer of NKG2D and MICB at the cytotoxic NK cell immune synapse correlates with a reduction in NK cell cytotoxic function

    Pedro Roda-Navarro, Mar Vales-Gomez, Susan E. Chisholm, and Hugh T. Reyburn

    PNAS July 25, 2006 103 (30) 11258-11263; https://doi.org/10.1073/pnas.0600721103
  • Open Access

    Consequences of receptor editing at the λ locus: Multireactivity and light chain secretion

    Colleen M. Doyle, Jiong Han, Martin G. Weigert, and Eline T. Luning Prak

    PNAS July 25, 2006 103 (30) 11264-11269; https://doi.org/10.1073/pnas.0604053103

• Medical Sciences

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    Real-time metabolic imaging

    Klaes Golman, René in ‘t Zandt, and Mikkel Thaning

    PNAS July 25, 2006 103 (30) 11270-11275; https://doi.org/10.1073/pnas.0601319103
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    Transgenic mice rich in endogenous omega-3 fatty acids are protected from colitis

    Christian A. Hudert, Karsten H. Weylandt, Yan Lu, Jingdong Wang, Song Hong, Axel Dignass, Charles N. Serhan, and Jing X. Kang

    PNAS July 25, 2006 103 (30) 11276-11281; https://doi.org/10.1073/pnas.0601280103

    See companion article:

    • In This Issue

      - Jul 25, 2006
  • Open Access

    Drusen, choroidal neovascularization, and retinal pigment epithelium dysfunction in SOD1-deficient mice: A model of age-related macular degeneration

    Yutaka Imamura, Setsuko Noda, Kouhei Hashizume, Kei Shinoda, Mineko Yamaguchi, Satoshi Uchiyama, Takahiko Shimizu, Yutaka Mizushima, Takuji Shirasawa, and Kazuo Tsubota

    PNAS July 25, 2006 103 (30) 11282-11287; https://doi.org/10.1073/pnas.0602131103
  • Open Access

    A polymorphism within a conserved β₁-adrenergic receptor motif alters cardiac function and β-blocker response in human heart failure

    Stephen B. Liggett, Jeanne Mialet-Perez, Surai Thaneemit-Chen, Stewart A. Weber, Scott M. Greene, Danielle Hodne, Bradley Nelson, Jennifer Morrison, Michael J. Domanski, Lynne E. Wagoner, William T. Abraham, Jeffrey L. Anderson, John F. Carlquist, Heidi J. Krause-Steinrauf, Laura C. Lazzeroni, J. David Port, Philip W. Lavori, and Michael R. Bristow

    PNAS July 25, 2006 103 (30) 11288-11293; https://doi.org/10.1073/pnas.0509937103
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    Noninvasive imaging of islet grafts using positron-emission tomography

    Yuxin Lu, Hoa Dang, Blake Middleton, Zesong Zhang, Lorraine Washburn, David B. Stout, Martha Campbell-Thompson, Mark A. Atkinson, Michael Phelps, Sanjiv Sam Gambhir, Jide Tian, and Daniel L. Kaufman

    PNAS July 25, 2006 103 (30) 11294-11299; https://doi.org/10.1073/pnas.0603909103
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    Antioxidants reduce cone cell death in a model of retinitis pigmentosa

    Keiichi Komeima, Brian S. Rogers, Lili Lu, and Peter A. Campochiaro

    PNAS July 25, 2006 103 (30) 11300-11305; https://doi.org/10.1073/pnas.0604056103
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    Genes and pathways downstream of telomerase in melanoma metastasis

    Sepideh Bagheri, Mehdi Nosrati, Shang Li, Sylvia Fong, Sima Torabian, Javier Rangel, Dan H. Moore, Scot Federman, Rebecca R. LaPosa, Frederick L. Baehner, Richard W. Sagebiel, James E. Cleaver, Christopher Haqq, Robert J. Debs, Elizabeth H. Blackburn, and Mohammed Kashani-Sabet

    PNAS July 25, 2006 103 (30) 11306-11311; https://doi.org/10.1073/pnas.0510085103
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    Human prions and plasma lipoproteins

    Jiri G. Safar, Holger Wille, Michael D. Geschwind, Camille Deering, Diane Latawiec, Ana Serban, David J. King, Giuseppe Legname, Karl H. Weisgraber, Robert W. Mahley, Bruce L. Miller, Stephen J. DeArmond, and Stanley B. Prusiner

    PNAS July 25, 2006 103 (30) 11312-11317; https://doi.org/10.1073/pnas.0604021103
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    Hsp90 inhibition transiently activates Src kinase and promotes Src-dependent Akt and Erk activation

    Fumitaka Koga, Wanping Xu, Tatiana S. Karpova, James G. McNally, Roland Baron, and Len Neckers

    PNAS July 25, 2006 103 (30) 11318-11322; https://doi.org/10.1073/pnas.0604705103
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    Benefit of farnesoid X receptor inhibition in obstructive cholestasis

    Catherine Stedman, Christopher Liddle, Sally Coulter, Junichiro Sonoda, Jacqueline G. Alvarez, Ronald M. Evans, and Michael Downes

    PNAS July 25, 2006 103 (30) 11323-11328; https://doi.org/10.1073/pnas.0604772103
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    Utilization of host SR protein kinases and RNA-splicing machinery during viral replication

    Takeshi Fukuhara, Takamitsu Hosoya, Saki Shimizu, Kengo Sumi, Takako Oshiro, Yoshiyuki Yoshinaka, Masaaki Suzuki, Naoki Yamamoto, Leonore A. Herzenberg, Leonard A. Herzenberg, and Masatoshi Hagiwara

    PNAS July 25, 2006 103 (30) 11329-11333; https://doi.org/10.1073/pnas.0604616103

• Microbiology

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    Regulation of intracellular free calcium concentration during heterocyst differentiation by HetR and NtcA in Anabaena sp. PCC 7120

    Yunming Shi, Weixing Zhao, Wei Zhang, Zi Ye, and Jindong Zhao

    PNAS July 25, 2006 103 (30) 11334-11339; https://doi.org/10.1073/pnas.0602839103
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    Regulatory protein that inhibits both synthesis and use of the target protein controls flagellar phase variation in Salmonella enterica

    Phillip D. Aldridge, Cheng Wu, Joshua Gnerer, Joyce E. Karlinsey, Kelly T. Hughes, and Matthew S. Sachs

    PNAS July 25, 2006 103 (30) 11340-11345; https://doi.org/10.1073/pnas.0602127103
  • Open Access

    Dissecting virulence pathways of Mycobacterium tuberculosis through protein–protein association

    Amit Singh, Deborah Mai, Ashwani Kumar, and Adrie J. C. Steyn

    PNAS July 25, 2006 103 (30) 11346-11351; https://doi.org/10.1073/pnas.0602817103
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    Distinguishing features of δ-proteobacterial genomes

    Samuel Karlin, Luciano Brocchieri, Jan Mrázek, and Dale Kaiser

    PNAS July 25, 2006 103 (30) 11352-11357; https://doi.org/10.1073/pnas.0604311103
  • Open Access

    Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms

    Yuri A. Gorby, Svetlana Yanina, Jeffrey S. McLean, Kevin M. Rosso, Dianne Moyles, Alice Dohnalkova, Terry J. Beveridge, In Seop Chang, Byung Hong Kim, Kyung Shik Kim, David E. Culley, Samantha B. Reed, Margaret F. Romine, Daad A. Saffarini, Eric A. Hill, Liang Shi, Dwayne A. Elias, David W. Kennedy, Grigoriy Pinchuk, Kazuya Watanabe, Shun’ichi Ishii, Bruce Logan, Kenneth H. Nealson, and Jim K. Fredrickson

    PNAS July 25, 2006 103 (30) 11358-11363; https://doi.org/10.1073/pnas.0604517103
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    Structural basis for targeting HIV-1 Gag proteins to the plasma membrane for virus assembly

    • From the Cover

    Jamil S. Saad, Jaime Miller, Janet Tai, Andrew Kim, Ruba H. Ghanam, and Michael F. Summers

    PNAS July 25, 2006 103 (30) 11364-11369; https://doi.org/10.1073/pnas.0602818103

    See companion article:

    • In This Issue

      - Jul 25, 2006
    • HIV-1 Gag: Flipped out for PI(4,5)P₂

      - Jul 17, 2006

• Neuroscience

  • Open Access

    A form of motor cortical plasticity that correlates with recovery of function after brain injury

    Dhakshin Ramanathan, James M. Conner, and Mark H. Tuszynski

    PNAS July 25, 2006 103 (30) 11370-11375; https://doi.org/10.1073/pnas.0601065103
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    Acid-sensitive ionic channels in midbrain dopamine neurons are sensitive to ammonium, which may contribute to hyperammonemia damage

    Volodymyr I. Pidoplichko and John A. Dani

    PNAS July 25, 2006 103 (30) 11376-11380; https://doi.org/10.1073/pnas.0600768103
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    The influence of meaning on the perception of speech sounds

    Nina Kazanina, Colin Phillips, and William Idsardi

    PNAS July 25, 2006 103 (30) 11381-11386; https://doi.org/10.1073/pnas.0604821103
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    Cortical systems mediating visual attention to both objects and spatial locations

    Sarah Shomstein and Marlene Behrmann

    PNAS July 25, 2006 103 (30) 11387-11392; https://doi.org/10.1073/pnas.0601813103
  • Open Access

    The cannabinoid WIN 55,212-2 inhibits transient receptor potential vanilloid 1 (TRPV1) and evokes peripheral antihyperalgesia via calcineurin

    Amol M. Patwardhan, Nathaniel A. Jeske, Theodore J. Price, Nikita Gamper, Armen N. Akopian, and Kenneth M. Hargreaves

    PNAS July 25, 2006 103 (30) 11393-11398; https://doi.org/10.1073/pnas.0603861103
  • Open Access

    Factors regulating the abundance and localization of synaptobrevin in the plasma membrane

    Jeremy S. Dittman and Joshua M. Kaplan

    PNAS July 25, 2006 103 (30) 11399-11404; https://doi.org/10.1073/pnas.0600784103

• Physiology

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    Nonvascular VEGF receptor 3 expression by corneal epithelium maintains avascularity and vision

    Claus Cursiefen, Lu Chen, Magali Saint-Geniez, Pedram Hamrah, Yiping Jin, Saadia Rashid, Bronislaw Pytowski, Kris Persaud, Yan Wu, J. Wayne Streilein, and Reza Dana

    PNAS July 25, 2006 103 (30) 11405-11410; https://doi.org/10.1073/pnas.0506112103
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    Barttin modulates trafficking and function of ClC-K channels

    Ute Scholl, Simon Hebeisen, Audrey G. H. Janssen, Gerhard Müller-Newen, Alexi Alekov, and Christoph Fahlke

    PNAS July 25, 2006 103 (30) 11411-11416; https://doi.org/10.1073/pnas.0601631103

• Plant Biology

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    Development and application of a suite of polysaccharide-degrading enzymes for analyzing plant cell walls

    • From the Cover

    Stefan Bauer, Prasanna Vasu, Staffan Persson, Andrew J. Mort, and Chris R. Somerville

    PNAS July 25, 2006 103 (30) 11417-11422; https://doi.org/10.1073/pnas.0604632103

    See companion article:

    • In This Issue

      - Jul 25, 2006

• Population Biology

  • Open Access

    Globalization and the population structure of Toxoplasma gondii

    • From the Cover

    Tovi Lehmann, Paula L. Marcet, Doug H. Graham, Erica R. Dahl, and J. P. Dubey

    PNAS July 25, 2006 103 (30) 11423-11428; https://doi.org/10.1073/pnas.0601438103