Table of Contents

Biological Sciences

• Applied Biological Sciences

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    Vascularized organoid engineered by modular assembly enables blood perfusion

    Alison P. McGuigan and Michael V. Sefton

    PNAS August 1, 2006 103 (31) 11461-11466; https://doi.org/10.1073/pnas.0602740103
  • Open Access

    Quantitative high-throughput screening: A titration-based approach that efficiently identifies biological activities in large chemical libraries

    James Inglese, Douglas S. Auld, Ajit Jadhav, Ronald L. Johnson, Anton Simeonov, Adam Yasgar, Wei Zheng, and Christopher P. Austin

    PNAS August 1, 2006 103 (31) 11473-11478; https://doi.org/10.1073/pnas.0604348103
  • Open Access

    Targeting lentiviral vectors to specific cell types in vivo

    Lili Yang, Leslie Bailey, David Baltimore, and Pin Wang

    PNAS August 1, 2006 103 (31) 11479-11484; https://doi.org/10.1073/pnas.0604993103

    See companion article:

    • In This Issue

      - Aug 01, 2006

• Biochemistry

  • Open Access

    MPS1-dependent mitotic BLM phosphorylation is important for chromosome stability

    Mei Leng, Doug W. Chan, Hao Luo, Cihui Zhu, Jun Qin, and Yi Wang

    PNAS August 1, 2006 103 (31) 11485-11490; https://doi.org/10.1073/pnas.0601828103
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    Structural basis for the design of potent and species-specific inhibitors of 3-hydroxy-3-methylglutaryl CoA synthases

    Florence Pojer, Jean-Luc Ferrer, Stéphane B. Richard, Dinesh A. Nagegowda, Mee-Len Chye, Thomas J. Bach, and Joseph P. Noel

    PNAS August 1, 2006 103 (31) 11491-11496; https://doi.org/10.1073/pnas.0604935103
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    DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA·TTC repeats in Friedreich's ataxia

    Ryan Burnett, Christian Melander, James W. Puckett, Leslie S. Son, Robert D. Wells, Peter B. Dervan, and Joel M. Gottesfeld

    PNAS August 1, 2006 103 (31) 11497-11502; https://doi.org/10.1073/pnas.0604939103
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    Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease

    Stephanie X. Wang, Kailash C. Pandey, John R. Somoza, Puran S. Sijwali, Tanja Kortemme, Linda S. Brinen, Robert J. Fletterick, Philip J. Rosenthal, and James H. McKerrow

    PNAS August 1, 2006 103 (31) 11503-11508; https://doi.org/10.1073/pnas.0600489103
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    Nanodiscs separate chemoreceptor oligomeric states and reveal their signaling properties

    Thomas Boldog, Stephen Grimme, Mingshan Li, Stephen G. Sligar, and Gerald L. Hazelbauer

    PNAS August 1, 2006 103 (31) 11509-11514; https://doi.org/10.1073/pnas.0604988103
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    Regulation of neddylation and deneddylation of cullin1 in SCF^Skp2 ubiquitin ligase by F-box protein and substrate

    Gil Bornstein, Dvora Ganoth, and Avram Hershko

    PNAS August 1, 2006 103 (31) 11515-11520; https://doi.org/10.1073/pnas.0603921103
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    CDC7 kinase phosphorylates serine residues adjacent to acidic amino acids in the minichromosome maintenance 2 protein

    Won-Ho Cho, Young-Joo Lee, Soo-Im Kong, Jerard Hurwitz, and Joon-Kyu Lee

    PNAS August 1, 2006 103 (31) 11521-11526; https://doi.org/10.1073/pnas.0604990103

• Biophysics

  • Open Access

    Macromolecular-scale resolution in biological fluorescence microscopy

    • Cozzarelli Prize Winner

    Gerald Donnert, Jan Keller, Rebecca Medda, M. Alexandra Andrei, Silvio O. Rizzoli, Reinhard Lührmann, Reinhard Jahn, Christian Eggeling, and Stefan W. Hell

    PNAS August 1, 2006 103 (31) 11440-11445; https://doi.org/10.1073/pnas.0604965103
  • Open Access

    Molecular transport through channels and pores: Effects of in-channel interactions and blocking

    • From the Cover

    Wolfgang R. Bauer and Walter Nadler

    PNAS August 1, 2006 103 (31) 11446-11451; https://doi.org/10.1073/pnas.0601769103

    See companion article:

    • Enhancing molecular flux through nanopores by means of attractive interactions

      - Aug 01, 2006
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    Free-energy distribution of binary protein–protein binding suggests cross-species interactome differences

    Yi Y. Shi, Gerald A. Miller, Hong Qian, and Karol Bomsztyk

    PNAS August 1, 2006 103 (31) 11527-11532; https://doi.org/10.1073/pnas.0604316103
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    Molecular dynamics analyses of cross-β-spine steric zipper models: β-Sheet twisting and aggregation

    Luciana Esposito, Carlo Pedone, and Luigi Vitagliano

    PNAS August 1, 2006 103 (31) 11533-11538; https://doi.org/10.1073/pnas.0602345103

    See companion article:

    • In This Issue

      - Aug 01, 2006
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    Coil–globule transition in the denatured state of a small protein

    Eilon Sherman and Gilad Haran

    PNAS August 1, 2006 103 (31) 11539-11543; https://doi.org/10.1073/pnas.0601395103
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    Direct observation of DNA rotation during branch migration of Holliday junction DNA by Escherichia coli RuvA–RuvB protein complex

    Yong-Woon Han, Tomomi Tani, Masahito Hayashi, Takashi Hishida, Hiroshi Iwasaki, Hideo Shinagawa, and Yoshie Harada

    PNAS August 1, 2006 103 (31) 11544-11548; https://doi.org/10.1073/pnas.0600753103
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    Cellular asymmetry and individuality in directional sensing

    Azadeh Samadani, Jerome Mettetal, and Alexander van Oudenaarden

    PNAS August 1, 2006 103 (31) 11549-11554; https://doi.org/10.1073/pnas.0601909103
  • Open Access

    Tension-dependent DNA cleavage by restriction endonucleases: Two-site enzymes are “switched off” at low force

    Gregory J. Gemmen, Rachel Millin, and Douglas E. Smith

    PNAS August 1, 2006 103 (31) 11555-11560; https://doi.org/10.1073/pnas.0604463103
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    Single-molecule detection of structural changes during Per-Arnt-Sim (PAS) domain activation

    Jason Ming Zhao, Haeshin Lee, Rene A. Nome, Sophia Majid, Norbert F. Scherer, and Wouter D. Hoff

    PNAS August 1, 2006 103 (31) 11561-11566; https://doi.org/10.1073/pnas.0601567103

• Cell Biology

  • Open Access

    Cyclin D1 repression of nuclear respiratory factor 1 integrates nuclear DNA synthesis and mitochondrial function

    Chenguang Wang, Zhiping Li, Yinan Lu, Runlei Du, Sanjay Katiyar, Jianguo Yang, Maofu Fu, Jennifer E. Leader, Andrew Quong, Phyllis M. Novikoff, and Richard G. Pestell

    PNAS August 1, 2006 103 (31) 11567-11572; https://doi.org/10.1073/pnas.0603363103
  • Open Access

    Different mitochondrial intermembrane space proteins are released during apoptosis in a manner that is coordinately initiated but can vary in duration

    Cristina Muñoz-Pinedo, Ana Guío-Carrión, Joshua C. Goldstein, Patrick Fitzgerald, Donald D. Newmeyer, and Douglas R. Green

    PNAS August 1, 2006 103 (31) 11573-11578; https://doi.org/10.1073/pnas.0603007103
  • Open Access

    N-Myc and the cyclin-dependent kinase inhibitors p18^Ink4c and p27^Kip1 coordinately regulate cerebellar development

    Frederique Zindy, Paul S. Knoepfler, Suqing Xie, Charles J. Sherr, Robert N. Eisenman, and Martine F. Roussel

    PNAS August 1, 2006 103 (31) 11579-11583; https://doi.org/10.1073/pnas.0604727103
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    A Drosophila model of Barth syndrome

    Yang Xu, Morgan Condell, Heide Plesken, Irit Edelman-Novemsky, Jinping Ma, Mindong Ren, and Michael Schlame

    PNAS August 1, 2006 103 (31) 11584-11588; https://doi.org/10.1073/pnas.0603242103
  • Open Access

    E2-25K mediates US11-triggered retro-translocation of MHC class I heavy chains in a permeabilized cell system

    Dennis Flierman, Catherine S. Coleman, Cecile M. Pickart, Tom A. Rapoport, and Vincent Chau

    PNAS August 1, 2006 103 (31) 11589-11594; https://doi.org/10.1073/pnas.0605215103

• Developmental Biology

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    Liprin-α has LAR-independent functions in R7 photoreceptor axon targeting

    Kerstin Hofmeyer, Corinne Maurel-Zaffran, Helen Sink, and Jessica E. Treisman

    PNAS August 1, 2006 103 (31) 11595-11600; https://doi.org/10.1073/pnas.0604766103
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    Liprin-α is required for photoreceptor target selection in Drosophila

    Kwang-Min Choe, Saurabh Prakash, Ali Bright, and Thomas R. Clandinin

    PNAS August 1, 2006 103 (31) 11601-11606; https://doi.org/10.1073/pnas.0601185103
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    An early role for Sonic hedgehog from foregut endoderm in jaw development: Ensuring neural crest cell survival

    José M. Brito, Marie-Aimée Teillet, and Nicole M. Le Douarin

    PNAS August 1, 2006 103 (31) 11607-11612; https://doi.org/10.1073/pnas.0604751103
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    Robust, bistable patterning of the dorsal surface of the Drosophila embryo

    David M. Umulis, Mihaela Serpe, Michael B. O’Connor, and Hans G. Othmer

    PNAS August 1, 2006 103 (31) 11613-11618; https://doi.org/10.1073/pnas.0510398103

• Evolution

  • Open Access

    Sympatric speciation under incompatibility selection

    Yael Artzy-Randrup and Alexey S. Kondrashov

    PNAS August 1, 2006 103 (31) 11619-11624; https://doi.org/10.1073/pnas.0602339103
  • Open Access

    Solution structure of Urm1 and its implications for the origin of protein modifiers

    Junjie Xu, Jiahai Zhang, Li Wang, Jie Zhou, Hongda Huang, Jihui Wu, Yang Zhong, and Yunyu Shi

    PNAS August 1, 2006 103 (31) 11625-11630; https://doi.org/10.1073/pnas.0604876103
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    The role of the proline-rich domain of Ssdp1 in the modular architecture of the vertebrate head organizer

    Badam Enkhmandakh, Alexandr V. Makeyev, and Dashzeveg Bayarsaihan

    PNAS August 1, 2006 103 (31) 11631-11636; https://doi.org/10.1073/pnas.0605209103
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    Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes

    Todd H. Oakley, Bjørn Østman, and Asa C. V. Wilson

    PNAS August 1, 2006 103 (31) 11637-11641; https://doi.org/10.1073/pnas.0600750103

• Genetics

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    Carcinogens induce genome-wide loss of heterozygosity in normal stem cells without persistent chromosomal instability

    Sarah L. Donahue, Qing Lin, Shang Cao, and H. Earl Ruley

    PNAS August 1, 2006 103 (31) 11642-11646; https://doi.org/10.1073/pnas.0510741103
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    Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

    • From the Cover

    Evelyne Derelle, Conchita Ferraz, Stephane Rombauts, Pierre Rouzé, Alexandra Z. Worden, Steven Robbens, Frédéric Partensky, Sven Degroeve, Sophie Echeynié, Richard Cooke, Yvan Saeys, Jan Wuyts, Kamel Jabbari, Chris Bowler, Olivier Panaud, Benoît Piégu, Steven G. Ball, Jean-Philippe Ral, François-Yves Bouget, Gwenael Piganeau, Bernard De Baets, André Picard, Michel Delseny, Jacques Demaille, Yves Van de Peer, and Hervé Moreau

    PNAS August 1, 2006 103 (31) 11647-11652; https://doi.org/10.1073/pnas.0604795103

    See companion article:

    • In This Issue

      - Aug 01, 2006
    • Genome complexity in a lean, mean photosynthetic machine

      - Aug 01, 2006
  • Open Access

    The regulatory utilization of genetic redundancy through responsive backup circuits

    Ran Kafri, Melissa Levy, and Yitzhak Pilpel

    PNAS August 1, 2006 103 (31) 11653-11658; https://doi.org/10.1073/pnas.0604883103
  • Open Access

    A family of conserved noncoding elements derived from an ancient transposable element

    Xiaohui Xie, Michael Kamal, and Eric S. Lander

    PNAS August 1, 2006 103 (31) 11659-11664; https://doi.org/10.1073/pnas.0604768103

• Immunology

  • Open Access

    The Ets factor Spi-B is a direct critical target of the coactivator OBF-1

    Boris Bartholdy, Camille Du Roure, Alain Bordon, Dianne Emslie, Lynn M. Corcoran, and Patrick Matthias

    PNAS August 1, 2006 103 (31) 11665-11670; https://doi.org/10.1073/pnas.0509430103
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    Direct stimulation of T cells by membrane vesicles from antigen-presenting cells

    Marek Kovar, Onur Boyman, Xuefei Shen, Inkyu Hwang, Rachel Kohler, and Jonathan Sprent

    PNAS August 1, 2006 103 (31) 11671-11676; https://doi.org/10.1073/pnas.0603466103
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    Essential role of TAK1 in thymocyte development and activation

    Hong-Hsing Liu, Min Xie, Michael D. Schneider, and Zhijian J. Chen

    PNAS August 1, 2006 103 (31) 11677-11682; https://doi.org/10.1073/pnas.0603089103
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    DRB1*0401-restricted human T cell clone specific for the major proinsulin73-90 epitope expresses a down-regulatory T helper 2 phenotype

    Ivana Durinovic-Belló, Silke Rosinger, Jennifer A. Olson, Mauro Congia, Regina C. Ahmad, Mathias Rickert, Johannes Hampl, Hubert Kalbacher, Jan W. Drijfhout, Elizabeth D. Mellins, Sascha Al Dahouk, Thomas Kamradt, Markus J. Maeurer, Carol Nhan, Bart O. Roep, Bernhard O. Boehm, Constantin Polychronakos, Gerald T. Nepom, Wolfram Karges, Hugh O. McDevitt, and Grete Sønderstrup

    PNAS August 1, 2006 103 (31) 11683-11688; https://doi.org/10.1073/pnas.0603682103
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    Nitric oxide inhibits exocytosis of cytolytic granules from lymphokine-activated killer cells

    Marcella Ferlito, Kaikobad Irani, Nauder Faraday, and Charles J. Lowenstein

    PNAS August 1, 2006 103 (31) 11689-11694; https://doi.org/10.1073/pnas.0600275103
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    Regulation of T cell activation and tolerance by PDL2

    Yongliang Zhang, Yeonseok Chung, Caroline Bishop, Betsy Daugherty, Hilary Chute, Paige Holst, Carole Kurahara, Fred Lott, Ning Sun, Andrew A. Welcher, and Chen Dong

    PNAS August 1, 2006 103 (31) 11695-11700; https://doi.org/10.1073/pnas.0601347103

• Medical Sciences

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    Differential HIV-1 replication in neonatal and adult blood mononuclear cells is influenced at the level of HIV-1 gene expression

    Vasudha Sundaravaradan, Shailendra K. Saxena, Rajesh Ramakrishnan, Venkat R. K. Yedavalli, David T. Harris, and Nafees Ahmad

    PNAS August 1, 2006 103 (31) 11701-11706; https://doi.org/10.1073/pnas.0602185103
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    Inhibition of aldehyde dehydrogenase and retinoid signaling induces the expansion of human hematopoietic stem cells

    John P. Chute, Garrett G. Muramoto, John Whitesides, Michael Colvin, Rachid Safi, Nelson J. Chao, and Donald P. McDonnell

    PNAS August 1, 2006 103 (31) 11707-11712; https://doi.org/10.1073/pnas.0603806103
  • Open Access

    B cell receptors in TCL1 transgenic mice resemble those of aggressive, treatment-resistant human chronic lymphocytic leukemia

    Xiao-jie Yan, Emilia Albesiano, Nicola Zanesi, Sophia Yancopoulos, Alan Sawyer, Egidio Romano, Aleksandar Petlickovski, Dimitar G. Efremov, Carlo M. Croce, and Nicholas Chiorazzi

    PNAS August 1, 2006 103 (31) 11713-11718; https://doi.org/10.1073/pnas.0604564103
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    Noninvasive localized delivery of Herceptin to the mouse brain by MRI-guided focused ultrasound-induced blood–brain barrier disruption

    Manabu Kinoshita, Nathan McDannold, Ferenc A. Jolesz, and Kullervo Hynynen

    PNAS August 1, 2006 103 (31) 11719-11723; https://doi.org/10.1073/pnas.0604318103
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    Identification and characterization of a lysophosphatidylcholine acyltransferase in alveolar type II cells

    Xueni Chen, Brian A. Hyatt, Michael L. Mucenski, Robert J. Mason, and John M. Shannon

    PNAS August 1, 2006 103 (31) 11724-11729; https://doi.org/10.1073/pnas.0604946103
  • Open Access

    Unique risk factors for insertional mutagenesis in a mouse model of XSCID gene therapy

    Yan Shou, Zhijun Ma, Taihe Lu, and Brian P. Sorrentino

    PNAS August 1, 2006 103 (31) 11730-11735; https://doi.org/10.1073/pnas.0603635103
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    Topical vitamin D3 and low-calcemic analogs induce thymic stromal lymphopoietin in mouse keratinocytes and trigger an atopic dermatitis

    Mei Li, Pierre Hener, Zhikun Zhang, Shigeaki Kato, Daniel Metzger, and Pierre Chambon

    PNAS August 1, 2006 103 (31) 11736-11741; https://doi.org/10.1073/pnas.0604575103
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    T lineage differentiation from human embryonic stem cells

    • From the Cover

    Zoran Galić, Scott G. Kitchen, Amelia Kacena, Aparna Subramanian, Bryan Burke, Ruth Cortado, and Jerome A. Zack

    PNAS August 1, 2006 103 (31) 11742-11747; https://doi.org/10.1073/pnas.0604244103

    See companion article:

    • In This Issue

      - Aug 01, 2006
    • Embryonic stem cells make human T cells

      - Aug 15, 2006
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    Reversal of RNA missplicing and myotonia after muscleblind overexpression in a mouse poly(CUG) model for myotonic dystrophy

    Rahul N. Kanadia, Jihae Shin, Yuan Yuan, Stuart G. Beattie, Thurman M. Wheeler, Charles A. Thornton, and Maurice S. Swanson

    PNAS August 1, 2006 103 (31) 11748-11753; https://doi.org/10.1073/pnas.0604970103

• Microbiology

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    Identification of a protein complex that assembles lipopolysaccharide in the outer membrane of Escherichia coli

    Tao Wu, Andrew C. McCandlish, Luisa S. Gronenberg, Shu-Sin Chng, Thomas J. Silhavy, and Daniel Kahne

    PNAS August 1, 2006 103 (31) 11754-11759; https://doi.org/10.1073/pnas.0604744103
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    Characterization of mycobacterial virulence genes through genetic interaction mapping

    Swati M. Joshi, Amit K. Pandey, Nicole Capite, Sarah M. Fortune, Eric J. Rubin, and Christopher M. Sassetti

    PNAS August 1, 2006 103 (31) 11760-11765; https://doi.org/10.1073/pnas.0603179103
  • Open Access

    Adaptive response of Yersinia pestis to extracellular effectors of innate immunity during bubonic plague

    Florent Sebbane, Nadine Lemaître, Daniel E. Sturdevant, Roberto Rebeil, Kimmo Virtaneva, Stephen F. Porcella, and B. Joseph Hinnebusch

    PNAS August 1, 2006 103 (31) 11766-11771; https://doi.org/10.1073/pnas.0601182103
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    A nutrient uptake role for bacterial cell envelope extensions

    • From the Cover

    Jennifer K. Wagner, Sima Setayeshgar, Laura A. Sharon, James P. Reilly, and Yves V. Brun

    PNAS August 1, 2006 103 (31) 11772-11777; https://doi.org/10.1073/pnas.0602047103

    See companion article:

    • In This Issue

      - Aug 01, 2006
    • Bacterial stalks are nutrient-scavenging antennas

      - Aug 01, 2006

• Neuroscience

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    Modulation of competing memory systems by distraction

    Karin Foerde, Barbara J. Knowlton, and Russell A. Poldrack

    PNAS August 1, 2006 103 (31) 11778-11783; https://doi.org/10.1073/pnas.0602659103
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    Glatiramer acetate fights against Alzheimer’s disease by inducing dendritic-like microglia expressing insulin-like growth factor 1

    • From the Cover

    Oleg Butovsky, Maya Koronyo-Hamaoui, Gilad Kunis, Eran Ophir, Gennady Landa, Hagit Cohen, and Michal Schwartz

    PNAS August 1, 2006 103 (31) 11784-11789; https://doi.org/10.1073/pnas.0604681103
  • Open Access

    Microsomal prostaglandin E synthase-1 is a critical factor of stroke-reperfusion injury

    Yuri Ikeda-Matsuo, Azusa Ota, Tetsuya Fukada, Satoshi Uematsu, Shizuo Akira, and Yasuharu Sasaki

    PNAS August 1, 2006 103 (31) 11790-11795; https://doi.org/10.1073/pnas.0604400103

• Plant Biology

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    Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation

    Fernanda Agius, Avnish Kapoor, and Jian-Kang Zhu

    PNAS August 1, 2006 103 (31) 11796-11801; https://doi.org/10.1073/pnas.0603563103

• Population Biology

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    Ecological and immunological determinants of dengue epidemics

    Helen J. Wearing and Pejman Rohani

    PNAS August 1, 2006 103 (31) 11802-11807; https://doi.org/10.1073/pnas.0602960103

• Psychology

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    Spatial remapping of touch: Confusion of perceived stimulus order across hand and foot

    Tobias Schicke and Brigitte Röder

    PNAS August 1, 2006 103 (31) 11808-11813; https://doi.org/10.1073/pnas.0601486103