Table of Contents

Biological Sciences

• Applied Biological Sciences

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    An algorithm for assembly of ordered restriction maps from single DNA molecules

    Anton Valouev, David C. Schwartz, Shiguo Zhou, and Michael S. Waterman

    PNAS October 24, 2006 103 (43) 15770-15775; https://doi.org/10.1073/pnas.0604040103

• Applied Mathematics

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    An algorithm for assembly of ordered restriction maps from single DNA molecules

    Anton Valouev, David C. Schwartz, Shiguo Zhou, and Michael S. Waterman

    PNAS October 24, 2006 103 (43) 15770-15775; https://doi.org/10.1073/pnas.0604040103

• Biochemistry

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    Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase

    Lin Wang, Nina M. Goodey, Stephen J. Benkovic, and Amnon Kohen

    PNAS October 24, 2006 103 (43) 15753-15758; https://doi.org/10.1073/pnas.0606976103
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    Human DNA polymerase κ forms nonproductive complexes with matched primer termini but not with mismatched primer termini

    Karissa D. Carlson, Robert E. Johnson, Louise Prakash, Satya Prakash, and M. Todd Washington

    PNAS October 24, 2006 103 (43) 15776-15781; https://doi.org/10.1073/pnas.0605785103
  • Open Access

    The genomic landscape of histone modifications in human T cells

    Tae-Young Roh, Suresh Cuddapah, Kairong Cui, and Keji Zhao

    PNAS October 24, 2006 103 (43) 15782-15787; https://doi.org/10.1073/pnas.0607617103
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    The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II

    Hans Elmlund, Vera Baraznenok, Martin Lindahl, Camilla O. Samuelsen, Philip J. B. Koeck, Steen Holmberg, Hans Hebert, and Claes M. Gustafsson

    PNAS October 24, 2006 103 (43) 15788-15793; https://doi.org/10.1073/pnas.0607483103
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    Vitamin K-dependent proteins in Ciona intestinalis, a basal chordate lacking a blood coagulation cascade

    John D. Kulman, Jeff E. Harris, Noriko Nakazawa, Michio Ogasawara, Masanobu Satake, and Earl W. Davie

    PNAS October 24, 2006 103 (43) 15794-15799; https://doi.org/10.1073/pnas.0607543103
  • Open Access

    Global aggregation of newly translated proteins in an Escherichia coli strain deficient of the chaperonin GroEL

    Eli Chapman, George W. Farr, Renata Usaite, Krystyna Furtak, Wayne A. Fenton, Tapan K. Chaudhuri, Elise R. Hondorp, Rowena G. Matthews, Sharon G. Wolf, John R. Yates, Marc Pypaert, and Arthur L. Horwich

    PNAS October 24, 2006 103 (43) 15800-15805; https://doi.org/10.1073/pnas.0607534103

• Biophysics

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    Recent progress in understanding hydrophobic interactions

    • Inaugural Article

    Emily E. Meyer, Kenneth J. Rosenberg, and Jacob Israelachvili

    PNAS October 24, 2006 103 (43) 15739-15746; https://doi.org/10.1073/pnas.0606422103
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    Characterization of the nanoscale properties of individual amyloid fibrils

    Jeffrey F. Smith, Tuomas P. J. Knowles, Christopher M. Dobson, Cait E. MacPhee, and Mark E. Welland

    PNAS October 24, 2006 103 (43) 15806-15811; https://doi.org/10.1073/pnas.0604035103
  • Open Access

    The distance that kinesin-1 holds its cargo from the microtubule surface measured by fluorescence interference contrast microscopy

    Jacob Kerssemakers, Jonathon Howard, Henry Hess, and Stefan Diez

    PNAS October 24, 2006 103 (43) 15812-15817; https://doi.org/10.1073/pnas.0510400103
  • Open Access

    Cell-free formation of misfolded prion protein with authentic prion infectivity

    Petra Weber, Armin Giese, Niklas Piening, Gerda Mitteregger, Achim Thomzig, Michael Beekes, and Hans A. Kretzschmar

    PNAS October 24, 2006 103 (43) 15818-15823; https://doi.org/10.1073/pnas.0605608103
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    Generic hydrophobic residues are sufficient to promote aggregation of the Alzheimer's Aβ42 peptide

    Woojin Kim and Michael H. Hecht

    PNAS October 24, 2006 103 (43) 15824-15829; https://doi.org/10.1073/pnas.0605629103
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    Structural basis for mRNA and tRNA positioning on the ribosome

    Veysel Berk, Wen Zhang, Raj D. Pai, and Jamie H. D. Cate

    PNAS October 24, 2006 103 (43) 15830-15834; https://doi.org/10.1073/pnas.0607541103
  • Open Access

    Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination

    Masoud Vedadi, Frank H. Niesen, Abdellah Allali-Hassani, Oleg Y. Fedorov, Patrick J. Finerty Jr., Gregory A. Wasney, Ron Yeung, Cheryl Arrowsmith, Linda J. Ball, Helena Berglund, Raymond Hui, Brian D. Marsden, Pär Nordlund, Michael Sundstrom, Johan Weigelt, and Aled M. Edwards

    PNAS October 24, 2006 103 (43) 15835-15840; https://doi.org/10.1073/pnas.0605224103
  • Open Access

    Time scales of membrane fusion revealed by direct imaging of vesicle fusion with high temporal resolution

    • From the Cover

    Christopher K. Haluska, Karin A. Riske, Valérie Marchi-Artzner, Jean-Marie Lehn, Reinhard Lipowsky, and Rumiana Dimova

    PNAS October 24, 2006 103 (43) 15841-15846; https://doi.org/10.1073/pnas.0602766103
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    Unusual mechanical stability of a minimal RNA kissing complex

    Pan T. X. Li, Carlos Bustamante, and Ignacio Tinoco Jr.

    PNAS October 24, 2006 103 (43) 15847-15852; https://doi.org/10.1073/pnas.0607202103
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    Pressure-driven transport of confined DNA polymers in fluidic channels

    Derek Stein, Frank H. J. van der Heyden, Wiepke J. A. Koopmans, and Cees Dekker

    PNAS October 24, 2006 103 (43) 15853-15858; https://doi.org/10.1073/pnas.0605900103
  • Open Access

    Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

    J. Juraszek and P. G. Bolhuis

    PNAS October 24, 2006 103 (43) 15859-15864; https://doi.org/10.1073/pnas.0606692103
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    Distance measurements reveal a common topology of prokaryotic voltage-gated ion channels in the lipid bilayer

    Jessica Richardson, Rikard Blunck, Pinghua Ge, Paul R. Selvin, Francisco Bezanilla, Diane M. Papazian, and Ana M. Correa

    PNAS October 24, 2006 103 (43) 15865-15870; https://doi.org/10.1073/pnas.0607532103
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    Effect of force on mononucleosomal dynamics

    Shirley Mihardja, Andrew J. Spakowitz, Yongli Zhang, and Carlos Bustamante

    PNAS October 24, 2006 103 (43) 15871-15876; https://doi.org/10.1073/pnas.0607526103

• Cell Biology

  • Open Access

    UV irradiation induces a postreplication DNA damage checkpoint

    • From the Cover

    A. John Callegari and Thomas J. Kelly

    PNAS October 24, 2006 103 (43) 15877-15882; https://doi.org/10.1073/pnas.0607343103
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    An intramolecular folding sensor for imaging estrogen receptor–ligand interactions

    Ramasamy Paulmurugan and Sanjiv S. Gambhir

    PNAS October 24, 2006 103 (43) 15883-15888; https://doi.org/10.1073/pnas.0607385103
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    erbB2 is required for G protein-coupled receptor signaling in the heart

    Alejandra Negro, Bhawanjit K. Brar, Yusu Gu, Kirk L. Peterson, Wylie Vale, and Kuo-Fen Lee

    PNAS October 24, 2006 103 (43) 15889-15893; https://doi.org/10.1073/pnas.0607499103

• Developmental Biology

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    Tdrd1/Mtr-1, a tudor-related gene, is essential for male germ-cell differentiation and nuage/germinal granule formation in mice

    Shinichiro Chuma, Mihoko Hosokawa, Kouichi Kitamura, Shinya Kasai, Makio Fujioka, Masateru Hiyoshi, Kazufumi Takamune, Toshiaki Noce, and Norio Nakatsuji

    PNAS October 24, 2006 103 (43) 15894-15899; https://doi.org/10.1073/pnas.0601878103
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    Diversin regulates heart formation and gastrulation movements in development

    Heinz Moeller, Andreas Jenny, Hans-Joerg Schaeffer, Thomas Schwarz-Romond, Marek Mlodzik, Matthias Hammerschmidt, and Walter Birchmeier

    PNAS October 24, 2006 103 (43) 15900-15905; https://doi.org/10.1073/pnas.0603808103

• Ecology

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    A tunable algorithm for collective decision-making

    Stephen C. Pratt and David J. T. Sumpter

    PNAS October 24, 2006 103 (43) 15906-15910; https://doi.org/10.1073/pnas.0604801103

• Evolution

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    Natural variation in Drosophila melanogaster diapause due to the insulin-regulated PI3-kinase

    Karen D. Williams, Macarena Busto, Maximiliano L. Suster, Anthony K.-C. So, Yehuda Ben-Shahar, Sally J. Leevers, and Marla B. Sokolowski

    PNAS October 24, 2006 103 (43) 15911-15915; https://doi.org/10.1073/pnas.0604592103
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    Microsporidian mitosomes retain elements of the general mitochondrial targeting system

    Lena Burri, Bryony A. P. Williams, Dejan Bursac, Trevor Lithgow, and Patrick J. Keeling

    PNAS October 24, 2006 103 (43) 15916-15920; https://doi.org/10.1073/pnas.0604109103
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    Hereditary family signature of facial expression

    • From the Cover

    Gili Peleg, Gadi Katzir, Ofer Peleg, Michal Kamara, Leonid Brodsky, Hagit Hel-Or, Daniel Keren, and Eviatar Nevo

    PNAS October 24, 2006 103 (43) 15921-15926; https://doi.org/10.1073/pnas.0607551103

• Genetics

  • Open Access

    Knockout of Slc25a19 causes mitochondrial thiamine pyrophosphate depletion, embryonic lethality, CNS malformations, and anemia

    Marjorie J. Lindhurst, Giuseppe Fiermonte, Shiwei Song, Eduard Struys, Francesco De Leonardis, Pamela L. Schwartzberg, Amy Chen, Alessandra Castegna, Nanda Verhoeven, Christopher K. Mathews, Ferdinando Palmieri, and Leslie G. Biesecker

    PNAS October 24, 2006 103 (43) 15927-15932; https://doi.org/10.1073/pnas.0607661103
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    Isolation, characterization, and genetic complementation of a cellular mutant resistant to retroviral infection

    Sumit Agarwal, Josephine Harada, Jeffrey Schreifels, Patrycja Lech, Bryan Nikolai, Tomoyuki Yamaguchi, Sumit K. Chanda, and Nikunj V. Somia

    PNAS October 24, 2006 103 (43) 15933-15938; https://doi.org/10.1073/pnas.0602674103
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    Differential sensitivities of transcription factor target genes underlie cell type-specific gene expression profiles

    Kirby D. Johnson, Shin-Il Kim, and Emery H. Bresnick

    PNAS October 24, 2006 103 (43) 15939-15944; https://doi.org/10.1073/pnas.0604041103

• Immunology

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    Recruitment of CD63 to Cryptococcus neoformans phagosomes requires acidification

    Katerina Artavanis-Tsakonas, J. Christopher Love, Hidde L. Ploegh, and Jatin M. Vyas

    PNAS October 24, 2006 103 (43) 15945-15950; https://doi.org/10.1073/pnas.0607528103
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    Disseminated and sustained HIV infection in CD34⁺ cord blood cell-transplanted Rag2^−/−γ_c^−/− mice

    Stefan Baenziger, Roxane Tussiwand, Erika Schlaepfer, Luca Mazzucchelli, Mathias Heikenwalder, Michael O. Kurrer, Silvia Behnke, Joachim Frey, Annette Oxenius, Helen Joller, Adriano Aguzzi, Markus G. Manz, and Roberto F. Speck

    PNAS October 24, 2006 103 (43) 15951-15956; https://doi.org/10.1073/pnas.0604493103
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    GATA factors participate in tissue-specific immune responses in Drosophila larvae

    Kate Senger, Kristina Harris, and Mike Levine

    PNAS October 24, 2006 103 (43) 15957-15962; https://doi.org/10.1073/pnas.0607608103
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    Differences in potential for amino acid change after mutation reveals distinct strategies for κ and λ light-chain variation

    Uri Hershberg and Mark J. Shlomchik

    PNAS October 24, 2006 103 (43) 15963-15968; https://doi.org/10.1073/pnas.0607581103

• Medical Sciences

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    Androgen receptor phosphorylation and stabilization in prostate cancer by cyclin-dependent kinase 1

    Shaoyong Chen, Youyuan Xu, Xin Yuan, Glenn J. Bubley, and Steven P. Balk

    PNAS October 24, 2006 103 (43) 15969-15974; https://doi.org/10.1073/pnas.0604193103
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    Galectin-1 is essential in tumor angiogenesis and is a target for antiangiogenesis therapy

    Victor L. J. L. Thijssen, Ruben Postel, Ricardo J. M. G. E. Brandwijk, Ruud P. M. Dings, Irina Nesmelova, Sietske Satijn, Nicole Verhofstad, Yusaku Nakabeppu, Linda G. Baum, Jeroen Bakkers, Kevin H. Mayo, Françoise Poirier, and Arjan W. Griffioen

    PNAS October 24, 2006 103 (43) 15975-15980; https://doi.org/10.1073/pnas.0603883103
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    An inherent role of microtubule network in the action of nuclear receptor

    Bramanandam Manavathi, Filippo Acconcia, Suresh K. Rayala, and Rakesh Kumar

    PNAS October 24, 2006 103 (43) 15981-15986; https://doi.org/10.1073/pnas.0607445103
  • Open Access

    Protective immunity to lethal challenge of the 1918 pandemic influenza virus by vaccination

    Wing-pui Kong, Chantelle Hood, Zhi-yong Yang, Chih-Jen Wei, Ling Xu, Adolfo García-Sastre, Terrence M. Tumpey, and Gary J. Nabel

    PNAS October 24, 2006 103 (43) 15987-15991; https://doi.org/10.1073/pnas.0607564103
  • Open Access

    Detection of inflamed atherosclerotic lesions with diadenosine-5′,5‴-P¹,P⁴-tetraphosphate (Ap₄A) and positron-emission tomography

    D. R. Elmaleh, A. J. Fischman, A. Tawakol, A. Zhu, T. M. Shoup, U. Hoffmann, A.-L. Brownell, and P. C. Zamecnik

    PNAS October 24, 2006 103 (43) 15992-15996; https://doi.org/10.1073/pnas.0607246103
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    Ultrashort antibacterial and antifungal lipopeptides

    Arik Makovitzki, Dorit Avrahami, and Yechiel Shai

    PNAS October 24, 2006 103 (43) 15997-16002; https://doi.org/10.1073/pnas.0606129103
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    PGC-1α controls hepatitis B virus through nutritional signals

    Amir Shlomai, Nir Paran, and Yosef Shaul

    PNAS October 24, 2006 103 (43) 16003-16008; https://doi.org/10.1073/pnas.0607837103

• Microbiology

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    Emergence of a bacterial clone with enhanced virulence by acquisition of a phage encoding a secreted phospholipase A₂

    Izabela Sitkiewicz, Michal J. Nagiec, Paul Sumby, Stephanie D. Butler, Colette Cywes-Bentley, and James M. Musser

    PNAS October 24, 2006 103 (43) 16009-16014; https://doi.org/10.1073/pnas.0607669103

• Neuroscience

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    Direct magnetic resonance detection of neuronal electrical activity

    Natalia Petridou, Dietmar Plenz, Afonso C. Silva, Murray Loew, Jerzy Bodurka, and Peter A. Bandettini

    PNAS October 24, 2006 103 (43) 16015-16020; https://doi.org/10.1073/pnas.0603219103
  • Open Access

    Wild-type microglia extend survival in PU.1 knockout mice with familial amyotrophic lateral sclerosis

    David R. Beers, Jenny S. Henkel, Qin Xiao, Weihua Zhao, Jinghong Wang, Albert A. Yen, Laszlo Siklos, Scott R. McKercher, and Stanley H. Appel

    PNAS October 24, 2006 103 (43) 16021-16026; https://doi.org/10.1073/pnas.0607423103
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    A role for adrenomedullin as a pain-related peptide in the rat

    Weiya Ma, Jean-Guy Chabot, and Remi Quirion

    PNAS October 24, 2006 103 (43) 16027-16032; https://doi.org/10.1073/pnas.0602488103
  • Open Access

    Neural correlates of epigenesis

    Turhan Canli, Maolin Qiu, Kazufumi Omura, Eliza Congdon, Brian W. Haas, Zenab Amin, Martin J. Herrmann, R. Todd Constable, and Klaus Peter Lesch

    PNAS October 24, 2006 103 (43) 16033-16038; https://doi.org/10.1073/pnas.0601674103

• Physiology

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    IL-1 resets glucose homeostasis at central levels

    Adriana del Rey, Eduardo Roggero, Anke Randolf, Carolina Mahuad, Samuel McCann, Valeria Rettori, and Hugo O. Besedovsky

    PNAS October 24, 2006 103 (43) 16039-16044; https://doi.org/10.1073/pnas.0607076103
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    Renal cortical cyclooxygenase 2 expression is differentially regulated by angiotensin II AT₁ and AT₂ receptors

    Ming-Zhi Zhang, Bing Yao, Hui-Fang Cheng, Su-Wan Wang, Tadashi Inagami, and Raymond C. Harris

    PNAS October 24, 2006 103 (43) 16045-16050; https://doi.org/10.1073/pnas.0602176103

• Plant Biology

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    Calcium regulation of chloroplast protein translocation is mediated by calmodulin binding to Tic32

    Fatima Chigri, Friederike Hörmann, Anna Stamp, David K. Stammers, Bettina Bölter, Jürgen Soll, and Ute C. Vothknecht

    PNAS October 24, 2006 103 (43) 16051-16056; https://doi.org/10.1073/pnas.0607150103