Table of Contents

Biological Sciences

• Applied Biological Sciences

  • Open Access

    Counting individual DNA molecules by the stochastic attachment of diverse labels

    Glenn K. Fu, Jing Hu, Pei-Hua Wang, and Stephen P. A. Fodor

    PNAS May 31, 2011 108 (22) 9026-9031; https://doi.org/10.1073/pnas.1017621108
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    In vivo fluorescence imaging of exogenous enzyme activity in the gastrointestinal tract

    Gregor Fuhrmann and Jean-Christophe Leroux

    PNAS May 31, 2011 108 (22) 9032-9037; https://doi.org/10.1073/pnas.1100285108

• Biochemistry

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    Soluble epoxide hydrolase deficiency alters pancreatic islet size and improves glucose homeostasis in a model of insulin resistance

    Ayala Luria, Ahmed Bettaieb, Yannan Xi, Guang-Jong Shieh, Hsin-Chen Liu, Hiromi Inoue, Hsing-Ju Tsai, John D. Imig, Fawaz G. Haj, and Bruce D. Hammock

    PNAS May 31, 2011 108 (22) 9038-9043; https://doi.org/10.1073/pnas.1103482108
  • Open Access

    Regulation of human EGF receptor by lipids

    Ünal Coskun, Michał Grzybek, David Drechsel, and Kai Simons

    PNAS May 31, 2011 108 (22) 9044-9048; https://doi.org/10.1073/pnas.1105666108
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    Peptide surfactants for cell-free production of functional G protein-coupled receptors

    Xiaoqiang Wang, Karolina Corin, Philipp Baaske, Christoph J. Wienken, Moran Jerabek-Willemsen, Stefan Duhr, Dieter Braun, and Shuguang Zhang

    PNAS May 31, 2011 108 (22) 9049-9054; https://doi.org/10.1073/pnas.1018185108
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    Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1)

    • From the Cover

    Kohei Takeshita, Isao Suetake, Eiki Yamashita, Michihiro Suga, Hirotaka Narita, Atsushi Nakagawa, and Shoji Tajima

    PNAS May 31, 2011 108 (22) 9055-9059; https://doi.org/10.1073/pnas.1019629108

    See companion article:

    • Twists and turns of DNA methylation

      - May 18, 2011
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    Optimized clinical performance of growth hormone with an expanded genetic code

    Ho Cho, Tom Daniel, Ying Ji Buechler, David C. Litzinger, Zhenwei Maio, Anna-Maria Hays Putnam, Vadim S. Kraynov, Bee-Cheng Sim, Stuart Bussell, Tsotne Javahishvili, Sami Kaphle, Guillermo Viramontes, Mike Ong, Stephanie Chu, Becky GC, Ricky Lieu, Nick Knudsen, Paola Castiglioni, Thea C. Norman, Douglas W. Axelrod, Andrew R. Hoffman, Peter G. Schultz, Richard D. DiMarchi, and Bruce E. Kimmel

    PNAS May 31, 2011 108 (22) 9060-9065; https://doi.org/10.1073/pnas.1100387108
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    Agonist trapped in ATP-binding sites of the P2X2 receptor

    Ruotian Jiang, Damien Lemoine, Adeline Martz, Antoine Taly, Sophie Gonin, Lia Prado de Carvalho, Alexandre Specht, and Thomas Grutter

    PNAS May 31, 2011 108 (22) 9066-9071; https://doi.org/10.1073/pnas.1102170108
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    Inhibition of autoprocessing of natural variants and multidrug resistant mutant precursors of HIV-1 protease by clinical inhibitors

    John M. Louis, Annie Aniana, Irene T. Weber, and Jane M. Sayer

    PNAS May 31, 2011 108 (22) 9072-9077; https://doi.org/10.1073/pnas.1102278108

• Biophysics and Computational Biology

  • Open Access

    Two-phase dynamics of p53 in the DNA damage response

    Xiao-Peng Zhang, Feng Liu, and Wei Wang

    PNAS May 31, 2011 108 (22) 8990-8995; https://doi.org/10.1073/pnas.1100600108
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    Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion

    Derrick W. Meinhold and Peter E. Wright

    PNAS May 31, 2011 108 (22) 9078-9083; https://doi.org/10.1073/pnas.1105682108
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    Mechanics of surface area regulation in cells examined with confined lipid membranes

    Margarita Staykova, Douglas P. Holmes, Clarke Read, and Howard A. Stone

    PNAS May 31, 2011 108 (22) 9084-9088; https://doi.org/10.1073/pnas.1102358108
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    T-cell triggering thresholds are modulated by the number of antigen within individual T-cell receptor clusters

    Boryana N. Manz, Bryan L. Jackson, Rebecca S. Petit, Michael L. Dustin, and Jay Groves

    PNAS May 31, 2011 108 (22) 9089-9094; https://doi.org/10.1073/pnas.1018771108
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    KCNE1 enhances phosphatidylinositol 4,5-bisphosphate (PIP₂) sensitivity of I_Ks to modulate channel activity

    Yang Li, Mark A. Zaydman, Dick Wu, Jingyi Shi, Michael Guan, Brett Virgin-Downey, and Jianmin Cui

    PNAS May 31, 2011 108 (22) 9095-9100; https://doi.org/10.1073/pnas.1100872108
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    Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method

    Raffaello Verardi, Lei Shi, Nathaniel J. Traaseth, Naomi Walsh, and Gianluigi Veglia

    PNAS May 31, 2011 108 (22) 9101-9106; https://doi.org/10.1073/pnas.1016535108

• Cell Biology

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    Integrin adhesion drives the emergent polarization of active cytoskeletal stresses to pattern cell delamination

    C. Meghana, Nisha Ramdas, Feroz Meeran Hameed, Madan Rao, G. V. Shivashankar, and Maithreyi Narasimha

    PNAS May 31, 2011 108 (22) 9107-9112; https://doi.org/10.1073/pnas.1018652108
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    Cell-free sorting of peroxisomal membrane proteins from the endoplasmic reticulum

    Gaurav Agrawal, Saurabh Joshi, and Suresh Subramani

    PNAS May 31, 2011 108 (22) 9113-9118; https://doi.org/10.1073/pnas.1018749108
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    Ubiquitin-recognition protein Ufd1 couples the endoplasmic reticulum (ER) stress response to cell cycle control

    Meifan Chen, Gustavo J. Gutierrez, and Ze'ev A. Ronai

    PNAS May 31, 2011 108 (22) 9119-9124; https://doi.org/10.1073/pnas.1100028108

• Developmental Biology

  • Open Access

    Phosphorylation state of a Tob/BTG protein, FOG-3, regulates initiation and maintenance of the Caenorhabditis elegans sperm fate program

    Myon-Hee Lee, Kyung Won Kim, Clinton T. Morgan, Dyan E. Morgan, and Judith Kimble

    PNAS May 31, 2011 108 (22) 9125-9130; https://doi.org/10.1073/pnas.1106027108
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    Doublesex and mab-3–related transcription factor 5 promotes midbrain dopaminergic identity in pluripotent stem cells by enforcing a ventral-medial progenitor fate

    Nicole Gennet, Emily Gale, Xinsheng Nan, Emma Farley, Katalin Takacs, Barbara Oberwallner, David Chambers, and Meng Li

    PNAS May 31, 2011 108 (22) 9131-9136; https://doi.org/10.1073/pnas.1016679108
  • Open Access

    Autoregulatory and repressive inputs localize Hydra Wnt3 to the head organizer

    Yukio Nakamura, Charisios D. Tsiairis, Suat Özbek, and Thomas W. Holstein

    PNAS May 31, 2011 108 (22) 9137-9142; https://doi.org/10.1073/pnas.1018109108
  • Open Access

    Direct development of neurons within foregut endoderm of sea urchin embryos

    Zheng Wei, Robert C. Angerer, and Lynne M. Angerer

    PNAS May 31, 2011 108 (22) 9143-9147; https://doi.org/10.1073/pnas.1018513108

• Ecology

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    Impacts of a recent storm surge on an Arctic delta ecosystem examined in the context of the last millennium

    Michael F. J. Pisaric, Joshua R. Thienpont, Steven V. Kokelj, Holly Nesbitt, Trevor C. Lantz, Steven Solomon, and John P. Smol

    PNAS May 31, 2011 108 (22) 8960-8965; https://doi.org/10.1073/pnas.1018527108
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    Hyperspectral imaging of cuttlefish camouflage indicates good color match in the eyes of fish predators

    Chuan-Chin Chiao, J. Kenneth Wickiser, Justine J. Allen, Brock Genter, and Roger T. Hanlon

    PNAS May 31, 2011 108 (22) 9148-9153; https://doi.org/10.1073/pnas.1019090108

• Evolution

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    Climatically driven biogeographic provinces of Late Triassic tropical Pangea

    Jessica H. Whiteside, Danielle S. Grogan, Paul E. Olsen, and Dennis V. Kent

    PNAS May 31, 2011 108 (22) 8972-8977; https://doi.org/10.1073/pnas.1102473108
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    Evolution of sodium channels predates the origin of nervous systems in animals

    Benjamin J. Liebeskind, David M. Hillis, and Harold H. Zakon

    PNAS May 31, 2011 108 (22) 9154-9159; https://doi.org/10.1073/pnas.1106363108
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    Amphioxus FGF signaling predicts the acquisition of vertebrate morphological traits

    Stephanie Bertrand, Alain Camasses, Ildiko Somorjai, Mohamed R. Belgacem, Olivier Chabrol, Marie-Line Escande, Pierre Pontarotti, and Hector Escriva

    PNAS May 31, 2011 108 (22) 9160-9165; https://doi.org/10.1073/pnas.1014235108

• Genetics

  • Open Access

    Obligate biotrophy features unraveled by the genomic analysis of rust fungi

    • From the Cover

    Sébastien Duplessis, Christina A. Cuomo, Yao-Cheng Lin, Andrea Aerts, Emilie Tisserant, Claire Veneault-Fourrey, David L. Joly, Stéphane Hacquard, Joëlle Amselem, Brandi L. Cantarel, Readman Chiu, Pedro M. Coutinho, Nicolas Feau, Matthew Field, Pascal Frey, Eric Gelhaye, Jonathan Goldberg, Manfred G. Grabherr, Chinnappa D. Kodira, Annegret Kohler, Ursula Kües, Erika A. Lindquist, Susan M. Lucas, Rohit Mago, Evan Mauceli, Emmanuelle Morin, Claude Murat, Jasmyn L. Pangilinan, Robert Park, Matthew Pearson, Hadi Quesneville, Nicolas Rouhier, Sharadha Sakthikumar, Asaf A. Salamov, Jeremy Schmutz, Benjamin Selles, Harris Shapiro, Philippe Tanguay, Gerald A. Tuskan, Bernard Henrissat, Yves Van de Peer, Pierre Rouzé, Jeffrey G. Ellis, Peter N. Dodds, Jacqueline E. Schein, Shaobin Zhong, Richard C. Hamelin, Igor V. Grigoriev, Les J. Szabo, and Francis Martin

    PNAS May 31, 2011 108 (22) 9166-9171; https://doi.org/10.1073/pnas.1019315108

    See companion article:

    • Genomes of obligate plant pathogens reveal adaptations for obligate parasitism

      - May 16, 2011
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    Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing

    Kalpana Kannan, Liguo Wang, Jianghua Wang, Michael M. Ittmann, Wei Li, and Laising Yen

    PNAS May 31, 2011 108 (22) 9172-9177; https://doi.org/10.1073/pnas.1100489108

• Immunology

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    Systematic identification of immunodominant CD8⁺ T-cell responses to influenza A virus in HLA-A2 individuals

    Chao Wu, Damien Zanker, Sophie Valkenburg, Bee Tan, Katherine Kedzierska, Quan Ming Zou, Peter C. Doherty, and Weisan Chen

    PNAS May 31, 2011 108 (22) 9178-9183; https://doi.org/10.1073/pnas.1105624108
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    NF-κB dysregulation in microRNA-146a–deficient mice drives the development of myeloid malignancies

    Jimmy L. Zhao, Dinesh S. Rao, Mark P. Boldin, Konstantin D. Taganov, Ryan M. O'Connell, and David Baltimore

    PNAS May 31, 2011 108 (22) 9184-9189; https://doi.org/10.1073/pnas.1105398108
  • Open Access

    Immune surveillance by mast cells during dengue infection promotes natural killer (NK) and NKT-cell recruitment and viral clearance

    Ashley L. St. John, Abhay P. S. Rathore, Han Yap, Mah-Lee Ng, Dean D. Metcalfe, Subhash G. Vasudevan, and Soman N. Abraham

    PNAS May 31, 2011 108 (22) 9190-9195; https://doi.org/10.1073/pnas.1105079108
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    Control of Toxoplasma reactivation by rescue of dysfunctional CD8⁺ T-cell response via PD-1–PDL-1 blockade

    Rajarshi Bhadra, Jason P. Gigley, Louis M. Weiss, and Imtiaz A. Khan

    PNAS May 31, 2011 108 (22) 9196-9201; https://doi.org/10.1073/pnas.1015298108

• Medical Sciences

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    Role of low-frequency HIV-1 variants in failure of nevirapine-containing antiviral therapy in women previously exposed to single-dose nevirapine

    Valerie F. Boltz, Yu Zheng, Shahin Lockman, Feiyu Hong, Elias K. Halvas, James McIntyre, Judith S. Currier, Margret C. Chibowa, Cecelia Kanyama, Apsara Nair, Willis Owino-Ong'or, Michael Hughes, John M. Coffin, and John W. Mellors

    PNAS May 31, 2011 108 (22) 9202-9207; https://doi.org/10.1073/pnas.1105688108
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    Thermodynamic stability of small hairpin RNAs highly influences the loading process of different mammalian Argonautes

    Shuo Gu, Lan Jin, Feijie Zhang, Yong Huang, Dirk Grimm, John J. Rossi, and Mark A. Kay

    PNAS May 31, 2011 108 (22) 9208-9213; https://doi.org/10.1073/pnas.1018023108
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    Decellularized tissue-engineered blood vessel as an arterial conduit

    Clay Quint, Yuka Kondo, Roberto J. Manson, Jeffrey H. Lawson, Alan Dardik, and Laura E. Niklason

    PNAS May 31, 2011 108 (22) 9214-9219; https://doi.org/10.1073/pnas.1019506108
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    Regulation of type 17 helper T-cell function by nitric oxide during inflammation

    Wanda Niedbala, Jose C. Alves-Filho, Sandra Y. Fukada, Silvio Manfredo Vieira, Akio Mitani, Fabiane Sonego, Ananda Mirchandani, Daniele C. Nascimento, Fernando Q. Cunha, and Foo Y. Liew

    PNAS May 31, 2011 108 (22) 9220-9225; https://doi.org/10.1073/pnas.1100667108
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    Repair of injured proximal tubule does not involve specialized progenitors

    Benjamin D. Humphreys, Suzanne Czerniak, Derek P. DiRocco, Wirasat Hasnain, Rabia Cheema, and Joseph V. Bonventre

    PNAS May 31, 2011 108 (22) 9226-9231; https://doi.org/10.1073/pnas.1100629108
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    miR-33a/b contribute to the regulation of fatty acid metabolism and insulin signaling

    Alberto Dávalos, Leigh Goedeke, Peter Smibert, Cristina M. Ramírez, Nikhil P. Warrier, Ursula Andreo, Daniel Cirera-Salinas, Katey Rayner, Uthra Suresh, José Carlos Pastor-Pareja, Enric Esplugues, Edward A. Fisher, Luiz O. F. Penalva, Kathryn J. Moore, Yajaira Suárez, Eric C. Lai, and Carlos Fernández-Hernando

    PNAS May 31, 2011 108 (22) 9232-9237; https://doi.org/10.1073/pnas.1102281108

• Microbiology

  • Open Access

    Helicobacter pylori cytotoxin-associated gene A (CagA) subverts the apoptosis-stimulating protein of p53 (ASPP2) tumor suppressor pathway of the host

    Ludovico Buti, Eric Spooner, Annemarthe G. Van der Veen, Rino Rappuoli, Antonello Covacci, and Hidde L. Ploegh

    PNAS May 31, 2011 108 (22) 9238-9243; https://doi.org/10.1073/pnas.1106200108
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    HIV DNA is heavily uracilated, which protects it from autointegration

    Nan Yan, Elizabeth O'Day, Lee Adam Wheeler, Alan Engelman, and Judy Lieberman

    PNAS May 31, 2011 108 (22) 9244-9249; https://doi.org/10.1073/pnas.1102943108
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    Wolbachia uses host microRNAs to manipulate host gene expression and facilitate colonization of the dengue vector Aedes aegypti

    Mazhar Hussain, Francesca D. Frentiu, Luciano A. Moreira, Scott L. O'Neill, and Sassan Asgari

    PNAS May 31, 2011 108 (22) 9250-9255; https://doi.org/10.1073/pnas.1105469108

• Neuroscience

  • Open Access

    Minimally invasive molecular delivery into the brain using optical modulation of vascular permeability

    Myunghwan Choi, Taeyun Ku, Kyuha Chong, Jonghee Yoon, and Chulhee Choi

    PNAS May 31, 2011 108 (22) 9256-9261; https://doi.org/10.1073/pnas.1018790108
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    Antidepressant effects of selective serotonin reuptake inhibitors (SSRIs) are attenuated by antiinflammatory drugs in mice and humans

    • From the Cover

    Jennifer L. Warner-Schmidt, Kimberly E. Vanover, Emily Y. Chen, John J. Marshall, and Paul Greengard

    PNAS May 31, 2011 108 (22) 9262-9267; https://doi.org/10.1073/pnas.1104836108

    See companion article:

    • Serotonin, cytokines, p11, and depression

      - May 18, 2011
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    Human Mu Opioid Receptor (OPRM1 A118G) polymorphism is associated with brain mu-opioid receptor binding potential in smokers

    Riju Ray, Kosha Ruparel, Andrew Newberg, E. Paul Wileyto, James W. Loughead, Chaitanya Divgi, Julie A. Blendy, Jean Logan, Jon-Kar Zubieta, and Caryn Lerman

    PNAS May 31, 2011 108 (22) 9268-9273; https://doi.org/10.1073/pnas.1018699108
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    Genetic analysis of age-dependent defects of the Caenorhabditis elegans touch receptor neurons

    Chun-Liang Pan, Chiu-Ying Peng, Chun-Hao Chen, and Steven McIntire

    PNAS May 31, 2011 108 (22) 9274-9279; https://doi.org/10.1073/pnas.1011711108
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    Changes in striatal procedural memory coding correlate with learning deficits in a mouse model of Huntington disease

    Sebastien Cayzac, Sebastien Delcasso, Vietminh Paz, Yannick Jeantet, and Yoon H. Cho

    PNAS May 31, 2011 108 (22) 9280-9285; https://doi.org/10.1073/pnas.1016190108

• Plant Biology

  • Open Access

    The Arabidopsis flagellin receptor FLS2 mediates the perception of Xanthomonas Ax21 secreted peptides

    Cristian H. Danna, Yves A. Millet, Teresa Koller, Sang-Wook Han, Andrew F. Bent, Pamela C. Ronald, and Frederick M. Ausubel

    PNAS May 31, 2011 108 (22) 9286-9291; https://doi.org/10.1073/pnas.1106366108
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    Circadian oscillation of gibberellin signaling in Arabidopsis

    María Verónica Arana, Nora Marín-de la Rosa, Julin N. Maloof, Miguel A. Blázquez, and David Alabadí

    PNAS May 31, 2011 108 (22) 9292-9297; https://doi.org/10.1073/pnas.1101050108
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    Cytochrome P450 CYP94B3 mediates catabolism and inactivation of the plant hormone jasmonoyl-L-isoleucine

    Abraham J. K. Koo, Thomas F. Cooke, and Gregg A. Howe

    PNAS May 31, 2011 108 (22) 9298-9303; https://doi.org/10.1073/pnas.1103542108

• Psychological and Cognitive Sciences

  • Open Access

    How social influence can undermine the wisdom of crowd effect

    Jan Lorenz, Heiko Rauhut, Frank Schweitzer, and Dirk Helbing

    PNAS May 31, 2011 108 (22) 9020-9025; https://doi.org/10.1073/pnas.1008636108

• Sustainability Science

  • Open Access

    Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection

    Harry Noyes, Andy Brass, Isaiah Obara, Susan Anderson, Alan L. Archibald, Dan G. Bradley, Paul Fisher, Abigail Freeman, John Gibson, Michael Gicheru, Laurence Hall, Olivier Hanotte, Helen Hulme, Declan McKeever, Caitriona Murray, Sung Jung Oh, Catriona Tate, Ken Smith, Miika Tapio, John Wambugu, Diana J. Williams, Morris Agaba, and Stephen J. Kemp

    PNAS May 31, 2011 108 (22) 9304-9309; https://doi.org/10.1073/pnas.1013486108

• Systems Biology

  • Open Access

    Continuous polo-like kinase 1 activity regulates diffusion to maintain centrosome self-organization during mitosis

    Robert Mahen, Anand D. Jeyasekharan, Nicholas P. Barry, and Ashok R. Venkitaraman

    PNAS May 31, 2011 108 (22) 9310-9315; https://doi.org/10.1073/pnas.1101112108