Table of Contents

Biological Sciences

• Biochemistry

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    Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs

    Maki Inada and Christine Guthrie

    PNAS January 13, 2004 101 (2) 434-439; https://doi.org/10.1073/pnas.0307425100
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    The second extracellular loop of the dopamine D₂ receptor lines the binding-site crevice

    Lei Shi and Jonathan A. Javitch

    PNAS January 13, 2004 101 (2) 440-445; https://doi.org/10.1073/pnas.2237265100
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    A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans

    Vitali Svetlitchnyi, Holger Dobbek, Wolfram Meyer-Klaucke, Thomas Meins, Bärbel Thiele, Piero Römer, Robert Huber, and Ortwin Meyer

    PNAS January 13, 2004 101 (2) 446-451; https://doi.org/10.1073/pnas.0304262101
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    Bacillus subtilis RecU protein cleaves Holliday junctions and anneals single-stranded DNA

    Silvia Ayora, Begoña Carrasco, Ernesto Doncel, Rudi Lurz, and Juan C. Alonso

    PNAS January 13, 2004 101 (2) 452-457; https://doi.org/10.1073/pnas.2533829100
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    Myc-interacting protein 1 target gene profile: A link to microtubules, extracellular signal-regulated kinase, and cell growth

    Joseph Ziegelbauer, Joyce Wei, and Robert Tjian

    PNAS January 13, 2004 101 (2) 458-463; https://doi.org/10.1073/pnas.0307562100
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    Physical and functional interaction of androgen receptor with calmodulin in prostate cancer cells

    Eugenia Cifuentes, Jennifer M. Mataraza, Barbara A. Yoshida, Mani Menon, David B. Sacks, Evelyn R. Barrack, and G. Prem-Veer Reddy

    PNAS January 13, 2004 101 (2) 464-469; https://doi.org/10.1073/pnas.0307161101
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    A proteomic approach for the analysis of instantly released wound and immune proteins in Drosophila melanogaster hemolymph

    • From the Cover

    Evy Vierstraete, Peter Verleyen, Geert Baggerman, Wannes D'Hertog, Gert Van den Bergh, Lutgarde Arckens, Arnold De Loof, and Liliane Schoofs

    PNAS January 13, 2004 101 (2) 470-475; https://doi.org/10.1073/pnas.0304567101
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    Context-dependent regulation of GATA-1 by friend of GATA-1

    Danielle L. Letting, Ying-Yu Chen, Carrie Rakowski, Sarah Reedy, and Gerd A. Blobel

    PNAS January 13, 2004 101 (2) 476-481; https://doi.org/10.1073/pnas.0306315101
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    Directed evolution of mammalian paraoxonases PON1 and PON3 for bacterial expression and catalytic specialization

    Amir Aharoni, Leonid Gaidukov, Shai Yagur, Lilly Toker, Israel Silman, and Dan S. Tawfik

    PNAS January 13, 2004 101 (2) 482-487; https://doi.org/10.1073/pnas.2536901100
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    Analysis of C5a-mediated chemotaxis by lentiviral delivery of small interfering RNA

    • From the Cover

    Jong-Ik Hwang, Iain D. C. Fraser, Sangdun Choi, Xiao-Feng Qin, and Melvin I. Simon

    PNAS January 13, 2004 101 (2) 488-493; https://doi.org/10.1073/pnas.0307549100
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    Availability of specific reductases controls the temporal activity of the cytochrome P450 complement of Streptomyces coelicolor A3(2)

    Li Lei, Michael R. Waterman, Armand J. Fulco, Steven L. Kelly, and David C. Lamb

    PNAS January 13, 2004 101 (2) 494-499; https://doi.org/10.1073/pnas.2435922100
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    Demonstration of mammalian protein O-mannosyltransferase activity: Coexpression of POMT1 and POMT2 required for enzymatic activity

    Hiroshi Manya, Atsuro Chiba, Aruto Yoshida, Xiaohui Wang, Yasunori Chiba, Yoshifumi Jigami, Richard U. Margolis, and Tamao Endo

    PNAS January 13, 2004 101 (2) 500-505; https://doi.org/10.1073/pnas.0307228101

• Biophysics

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    The origin of vibrational mode couplings in various secondary structural motifs of polypeptides

    Andrew Moran and Shaul Mukamel

    PNAS January 13, 2004 101 (2) 506-510; https://doi.org/10.1073/pnas.2533089100
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    Protein topology determines binding mechanism

    Yaakov Levy, Peter G. Wolynes, and José N. Onuchic

    PNAS January 13, 2004 101 (2) 511-516; https://doi.org/10.1073/pnas.2534828100
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    Entropic switch regulates myristate exposure in the HIV-1 matrix protein

    • From the Cover

    Chun Tang, Erin Loeliger, Paz Luncsford, Isaac Kinde, Dorothy Beckett, and Michael F. Summers

    PNAS January 13, 2004 101 (2) 517-522; https://doi.org/10.1073/pnas.0305665101

    See companion article:

    • A myristoyl switch regulates membrane binding of HIV-1 Gag

      - Jan 05, 2004
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    Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling

    Zoya Ignatova and Lila M. Gierasch

    PNAS January 13, 2004 101 (2) 523-528; https://doi.org/10.1073/pnas.0304533101
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    The catalytic cycle of cytochrome c oxidase is not the sum of its two halves

    Dmitry Bloch, Ilya Belevich, Audrius Jasaitis, Camilla Ribacka, Anne Puustinen, Michael I. Verkhovsky, and Mårten Wikström

    PNAS January 13, 2004 101 (2) 529-533; https://doi.org/10.1073/pnas.0306036101
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    Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme

    Zheng Xie, Narayanan Srividya, Tobin R. Sosnick, Tao Pan, and Norbert F. Scherer

    PNAS January 13, 2004 101 (2) 534-539; https://doi.org/10.1073/pnas.2636333100

• Cell Biology

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    Transcriptional signature of histone deacetylase inhibition in multiple myeloma: Biological and clinical implications

    Constantine S. Mitsiades, Nicholas S. Mitsiades, Ciaran J. McMullan, Vassiliki Poulaki, Reshma Shringarpure, Teru Hideshima, Masaharu Akiyama, Dharminder Chauhan, Nikhil Munshi, Xuesong Gu, Charles Bailey, Marie Joseph, Towia A. Libermann, Victoria M. Richon, Paul A. Marks, and Kenneth C. Anderson

    PNAS January 13, 2004 101 (2) 540-545; https://doi.org/10.1073/pnas.2536759100
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    Regulation of synaptojanin 1 by cyclin-dependent kinase 5 at synapses

    Sang Yoon Lee, Markus R. Wenk, Yong Kim, Angus C. Nairn, and Pietro De Camilli

    PNAS January 13, 2004 101 (2) 546-551; https://doi.org/10.1073/pnas.0307813100
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    Conditional targeting of E-cadherin in skin: Insights into hyperproliferative and degenerative responses

    Christopher L. Tinkle, Terry Lechler, H. Amalia Pasolli, and Elaine Fuchs

    PNAS January 13, 2004 101 (2) 552-557; https://doi.org/10.1073/pnas.0307437100

• Ecology

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    Hatching failure increases with severity of population bottlenecks in birds

    • From the Cover

    James V. Briskie and Myles Mackintosh

    PNAS January 13, 2004 101 (2) 558-561; https://doi.org/10.1073/pnas.0305103101
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    Response of C₃ and C₄ plants to middle-Holocene climatic variation near the prairie–forest ecotone of Minnesota

    David M. Nelson, Feng Sheng Hu, Jian Tian, Ivanka Stefanova, and Thomas A. Brown

    PNAS January 13, 2004 101 (2) 562-567; https://doi.org/10.1073/pnas.0307450100

• Evolution

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    Phylogenetic evidence for the early evolution of microcystin synthesis

    Anne Rantala, David P. Fewer, Michael Hisbergues, Leo Rouhiainen, Jaana Vaitomaa, Thomas Börner, and Kaarina Sivonen

    PNAS January 13, 2004 101 (2) 568-573; https://doi.org/10.1073/pnas.0304489101

• Genetics

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    Loss of CDX1 expression in colorectal carcinoma: Promoter methylation, mutation, and loss of heterozygosity analyses of 37 cell lines

    N. A. C. S. Wong, M. P. Britton, G. S. Choi, T. K. Stanton, D. C. Bicknell, J. L. Wilding, and W. F. Bodmer

    PNAS January 13, 2004 101 (2) 574-579; https://doi.org/10.1073/pnas.0307190101
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    Design of genetic networks with specified functions by evolution in silico

    Paul François and Vincent Hakim

    PNAS January 13, 2004 101 (2) 580-585; https://doi.org/10.1073/pnas.0304532101

• Immunology

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    IL-13 receptor α 2 down-modulates granulomatous inflammation and prolongs host survival in schistosomiasis

    Margaret M. Mentink-Kane, Allen W. Cheever, Robert W. Thompson, Danielle M. Hari, Narcis B. Kabatereine, Birgitte J. Vennervald, John H. Ouma, Joseph K. Mwatha, Frances M. Jones, Debra D. Donaldson, Michael J. Grusby, David W. Dunne, and Thomas A. Wynn

    PNAS January 13, 2004 101 (2) 586-590; https://doi.org/10.1073/pnas.0305064101

• Medical Sciences

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    Role of prostaglandin E₂-dependent angiogenic switch in cyclooxygenase 2-induced breast cancer progression

    • From the Cover

    Sung-Hee Chang, Catherine H. Liu, Rebecca Conway, David K. Han, Kasem Nithipatikom, Ovidiu C. Trifan, Timothy F. Lane, and Timothy Hla

    PNAS January 13, 2004 101 (2) 591-596; https://doi.org/10.1073/pnas.2535911100

    See companion article:

    • Cyclooxygenase 2-derived prostaglandin E₂ regulates the angiogenic switch

      - Jan 05, 2004
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    Somatic activation of oncogenic Kras in hematopoietic cells initiates a rapidly fatal myeloproliferative disorder

    Benjamin S. Braun, David A. Tuveson, Namie Kong, Doan T. Le, Scott C. Kogan, Jacob Rozmus, Michelle M. Le Beau, Tyler E. Jacks, and Kevin M. Shannon

    PNAS January 13, 2004 101 (2) 597-602; https://doi.org/10.1073/pnas.0307203101
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    Electrocardiographic and other cardiac anomalies in β-glucuronidase-null mice corrected by nonablative neonatal marrow transplantation

    A. J. T. Schuldt, T. J. Hampton, V. Chu, C. A. Vogler, N. Galvin, M. D. Lessard, and J. E. Barker

    PNAS January 13, 2004 101 (2) 603-608; https://doi.org/10.1073/pnas.0305284101
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    Defective lysosomal targeting of activated fibroblast growth factor receptor 3 in achondroplasia

    Jay Y. Cho, Changsheng Guo, Monica Torello, Gregory P. Lunstrum, Tomoko Iwata, Chuxia Deng, and William A. Horton

    PNAS January 13, 2004 101 (2) 609-614; https://doi.org/10.1073/pnas.2237184100
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    In silico dissection of cell-type-associated patterns of gene expression in prostate cancer

    Robert O. Stuart, William Wachsman, Charles C. Berry, Jessica Wang-Rodriguez, Linda Wasserman, Igor Klacansky, Dan Masys, Karen Arden, Steven Goodison, Michael McClelland, Yipeng Wang, Anne Sawyers, Iveta Kalcheva, David Tarin, and Dan Mercola

    PNAS January 13, 2004 101 (2) 615-620; https://doi.org/10.1073/pnas.2536479100
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    Binding of mouse VL30 retrotransposon RNA to PSF protein induces genes repressed by PSF: Effects on steroidogenesis and oncogenesis

    Xu Song, Aiwei Sui, and Alan Garen

    PNAS January 13, 2004 101 (2) 621-626; https://doi.org/10.1073/pnas.0307794100

• Microbiology

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    The chitinolytic cascade in Vibrios is regulated by chitin oligosaccharides and a two-component chitin catabolic sensor/kinase

    Xibing Li and Saul Roseman

    PNAS January 13, 2004 101 (2) 627-631; https://doi.org/10.1073/pnas.0307645100
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    Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways

    Que Dang, Jianbo Chen, Derya Unutmaz, John M. Coffin, Vinay K. Pathak, Douglas Powell, Vineet N. KewalRamani, Frank Maldarelli, and Wei-Shau Hu

    PNAS January 13, 2004 101 (2) 632-637; https://doi.org/10.1073/pnas.0307636100
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    Residual integrated viral DNA after hepadnavirus clearance by nucleoside analog therapy

    Jesse Summers and William S. Mason

    PNAS January 13, 2004 101 (2) 638-640; https://doi.org/10.1073/pnas.0307422100
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    Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis

    Katy C. Kao, Young-Lyeol Yang, Riccardo Boscolo, Chiara Sabatti, Vwani Roychowdhury, and James C. Liao

    PNAS January 13, 2004 101 (2) 641-646; https://doi.org/10.1073/pnas.0305287101

• Neuroscience

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    Identification of calcium- and nitric oxide-regulated genes by differential analysis of library expression (DAzLE)

    Huiwu Li, Xiujing Gu, Valina L. Dawson, and Ted M. Dawson

    PNAS January 13, 2004 101 (2) 647-652; https://doi.org/10.1073/pnas.0305145101
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    NADH augments blood flow in physiologically activated retina and visual cortex

    Yasuo Ido, Katherine Chang, and Joseph R. Williamson

    PNAS January 13, 2004 101 (2) 653-658; https://doi.org/10.1073/pnas.0307458100
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    Increased lactate/pyruvate ratio augments blood flow in physiologically activated human brain

    Mark A. Mintun, Andrei G. Vlassenko, Melissa M. Rundle, and Marcus E. Raichle

    PNAS January 13, 2004 101 (2) 659-664; https://doi.org/10.1073/pnas.0307457100
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    JNK-mediated induction of cyclooxygenase 2 is required for neurodegeneration in a mouse model of Parkinson's disease

    Stéphane Hunot, Miquel Vila, Peter Teismann, Roger J. Davis, Etienne C. Hirsch, Serge Przedborski, Pasko Rakic, and Richard A. Flavell

    PNAS January 13, 2004 101 (2) 665-670; https://doi.org/10.1073/pnas.0307453101
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    Association of β-catenin with the α-subunit of neuronal large-conductance Ca²⁺-activated K+ channels

    F. Lesage, H. Hibino, and A. J. Hudspeth

    PNAS January 13, 2004 101 (2) 671-675; https://doi.org/10.1073/pnas.0307681100
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    Protein phosphatase 2A inhibition induces cerebellar long-term depression and declustering of synaptic AMPA receptor

    T. Launey, S. Endo, R. Sakai, J. Harano, and M. Ito

    PNAS January 13, 2004 101 (2) 676-681; https://doi.org/10.1073/pnas.0302914101
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    Functional expression in frog oocytes of human ρ1 receptors produced in Saccharomyces cerevisiae

    Alejandro Martínez-Martínez, Jorge Mauricio Reyes-Ruiz, Ataúlfo Martínez-Torres, and Ricardo Miledi

    PNAS January 13, 2004 101 (2) 682-686; https://doi.org/10.1073/pnas.0307564100

• Plant Biology

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    RF2b, a rice bZIP transcription activator, interacts with RF2a and is involved in symptom development of rice tungro disease

    Shunhong Dai, Zhihong Zhang, Shouyi Chen, and Roger N. Beachy

    PNAS January 13, 2004 101 (2) 687-692; https://doi.org/10.1073/pnas.0307687100