Table of Contents

Biological Sciences

• Applied Biological Sciences

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    Kinase requirements in human cells: I. Comparing kinase requirements across various cell types

    Dorre A. Grueneberg, Sebastien Degot, Joseph Pearlberg, Wenliang Li, Joan E. Davies, Amy Baldwin, Wilson Endege, John Doench, Jacqueline Sawyer, Yanhui Hu, Frederick Boyce, Jun Xian, Karl Munger, and Ed Harlow

    PNAS October 28, 2008 105 (43) 16472-16477; https://doi.org/10.1073/pnas.0808019105
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    Kinase requirements in human cells: II. Genetic interaction screens identify kinase requirements following HPV16 E7 expression in cancer cells

    Amy Baldwin, Wenliang Li, Miranda Grace, Joseph Pearlberg, Ed Harlow, Karl Münger, and Dorre A. Grueneberg

    PNAS October 28, 2008 105 (43) 16478-16483; https://doi.org/10.1073/pnas.0806195105
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    Kinase requirements in human cells: III. Altered kinase requirements in VHL−/− cancer cells detected in a pilot synthetic lethal screen

    Archana Bommi-Reddy, Ingrid Almeciga, Jacqueline Sawyer, Christoph Geisen, Wenliang Li, Ed Harlow, William G. Kaelin Jr, and Dorre A. Grueneberg

    PNAS October 28, 2008 105 (43) 16484-16489; https://doi.org/10.1073/pnas.0806574105
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    Kinase requirements in human cells: IV. Differential kinase requirements in cervical and renal human tumor cell lines

    Dorre A. Grueneberg, Wenliang Li, Joan E. Davies, Jacqueline Sawyer, Joseph Pearlberg, and Ed Harlow

    PNAS October 28, 2008 105 (43) 16490-16495; https://doi.org/10.1073/pnas.0806578105

• Biochemistry

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    Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria

    • From the Cover

    Aline Bender, Parvana Hajieva, and Bernd Moosmann

    PNAS October 28, 2008 105 (43) 16496-16501; https://doi.org/10.1073/pnas.0802779105
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    Quality control despite mistranslation caused by an ambiguous genetic code

    Benfang Ruan, Sotiria Palioura, Jeffrey Sabina, Laure Marvin-Guy, Sunil Kochhar, Robert A. LaRossa, and Dieter Söll

    PNAS October 28, 2008 105 (43) 16502-16507; https://doi.org/10.1073/pnas.0809179105
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    Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions

    Aarthy C. Vallur and Nancy Maizels

    PNAS October 28, 2008 105 (43) 16508-16512; https://doi.org/10.1073/pnas.0805327105
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    Transport of LDL-derived cholesterol from the NPC1 compartment to the ER involves the trans-Golgi network and the SNARE protein complex

    Yasuomi Urano, Hiroshi Watanabe, Stephanie R. Murphy, Yohei Shibuya, Yong Geng, Andrew A. Peden, Catherine C. Y. Chang, and Ta Yuan Chang

    PNAS October 28, 2008 105 (43) 16513-16518; https://doi.org/10.1073/pnas.0807450105
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    Insights into the structural dynamics of the Hsp110–Hsp70 interaction reveal the mechanism for nucleotide exchange activity

    Claes Andréasson, Jocelyne Fiaux, Heike Rampelt, Silke Druffel-Augustin, and Bernd Bukau

    PNAS October 28, 2008 105 (43) 16519-16524; https://doi.org/10.1073/pnas.0804187105
  • Open Access

    Prolonged signaling at the parathyroid hormone receptor by peptide ligands targeted to a specific receptor conformation

    Makoto Okazaki, Sebastien Ferrandon, Jean-Pierre Vilardaga, Mary L. Bouxsein, John T. Potts Jr, and Thomas J. Gardella

    PNAS October 28, 2008 105 (43) 16525-16530; https://doi.org/10.1073/pnas.0808750105
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    Dynamic stabilization of actin filaments

    Hao Yuan Kueh, William M. Brieher, and Timothy J. Mitchison

    PNAS October 28, 2008 105 (43) 16531-16536; https://doi.org/10.1073/pnas.0807394105

• Biophysics

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    Stability and structural recovery of the tetramerization domain of p53-R337H mutant induced by a designed templating ligand

    Susana Gordo, Vera Martos, Eva Santos, Margarita Menéndez, Carles Bo, Ernest Giralt, and Javier de Mendoza

    PNAS October 28, 2008 105 (43) 16426-16431; https://doi.org/10.1073/pnas.0805658105
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    Dynamics of shear-induced ATP release from red blood cells

    Jiandi Wan, William D. Ristenpart, and Howard A. Stone

    PNAS October 28, 2008 105 (43) 16432-16437; https://doi.org/10.1073/pnas.0805779105
  • Open Access

    NMR studies of a channel protein without membranes: Structure and dynamics of water-solubilized KcsA

    Dejian Ma, Tommy S. Tillman, Pei Tang, Eva Meirovitch, Roderic Eckenhoff, Anna Carnini, and Yan Xu

    PNAS October 28, 2008 105 (43) 16537-16542; https://doi.org/10.1073/pnas.0805501105
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    Atomic detail of chemical transformation at the transition state of an enzymatic reaction

    Suwipa Saen-oon, Sara Quaytman-Machleder, Vern L. Schramm, and Steven D. Schwartz

    PNAS October 28, 2008 105 (43) 16543-16548; https://doi.org/10.1073/pnas.0808413105
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    Side-chain recognition and gating in the ribosome exit tunnel

    Paula M. Petrone, Christopher D. Snow, Del Lucent, and Vijay S. Pande

    PNAS October 28, 2008 105 (43) 16549-16554; https://doi.org/10.1073/pnas.0801795105
  • Open Access

    Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptors

    Cezar M. Khursigara, Xiongwu Wu, Peijun Zhang, Jonathan Lefman, and Sriram Subramaniam

    PNAS October 28, 2008 105 (43) 16555-16560; https://doi.org/10.1073/pnas.0806401105
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    Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore

    Hartmut Luecke, Brigitte Schobert, Jason Stagno, Eleonora S. Imasheva, Jennifer M. Wang, Sergei P. Balashov, and Janos K. Lanyi

    PNAS October 28, 2008 105 (43) 16561-16565; https://doi.org/10.1073/pnas.0807162105
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    Using diastereopeptides to control metal ion coordination in proteins

    Anna F. A. Peacock, Lars Hemmingsen, and Vincent L. Pecoraro

    PNAS October 28, 2008 105 (43) 16566-16571; https://doi.org/10.1073/pnas.0806792105

• Cell Biology

  • Open Access

    Different polycomb group CBX family proteins associate with distinct regions of chromatin using nonhomologous protein sequences

    Claudius Vincenz and Tom K. Kerppola

    PNAS October 28, 2008 105 (43) 16572-16577; https://doi.org/10.1073/pnas.0805317105
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    Human DNA polymerase η activity and translocation is regulated by phosphorylation

    Yih-wen Chen, James E. Cleaver, Zafer Hatahet, Richard E. Honkanen, Jang-Yang Chang, Yun Yen, and Kai-ming Chou

    PNAS October 28, 2008 105 (43) 16578-16583; https://doi.org/10.1073/pnas.0808589105
  • Open Access

    Nuclear Akt interacts with B23/NPM and protects it from proteolytic cleavage, enhancing cell survival

    Sang Bae Lee, Truong L. Xuan Nguyen, Joung Woo Choi, Kyung-Hoon Lee, Sung-Woo Cho, Zhixue Liu, Keqiang Ye, Sun Sik Bae, and Jee-Yin Ahn

    PNAS October 28, 2008 105 (43) 16584-16589; https://doi.org/10.1073/pnas.0807668105
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    Acid phosphatase 5 is responsible for removing the mannose 6-phosphate recognition marker from lysosomal proteins

    Pengling Sun, David E. Sleat, Michèle Lecocq, Alison R. Hayman, Michel Jadot, and Peter Lobel

    PNAS October 28, 2008 105 (43) 16590-16595; https://doi.org/10.1073/pnas.0807472105
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    Specificity of the J-protein Sis1 in the propagation of 3 yeast prions

    Takashi Higurashi, Justin K. Hines, Chandan Sahi, Rebecca Aron, and Elizabeth A. Craig

    PNAS October 28, 2008 105 (43) 16596-16601; https://doi.org/10.1073/pnas.0808934105
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    A bacterial control circuit integrates polar localization and proteolysis of key regulatory proteins with a phospho-signaling cascade

    Antonio A. Iniesta and Lucy Shapiro

    PNAS October 28, 2008 105 (43) 16602-16607; https://doi.org/10.1073/pnas.0808807105

• Developmental Biology

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    Modulation of potassium channel function confers a hyperproliferative invasive phenotype on embryonic stem cells

    Junji Morokuma, Douglas Blackiston, Dany S. Adams, Guiscard Seebohm, Barry Trimmer, and Michael Levin

    PNAS October 28, 2008 105 (43) 16608-16613; https://doi.org/10.1073/pnas.0808328105
  • Open Access

    Ancestral Notch-mediated segmentation revealed in the cockroach Periplaneta americana

    • From the Cover

    J. I. Pueyo, R. Lanfear, and J. P. Couso

    PNAS October 28, 2008 105 (43) 16614-16619; https://doi.org/10.1073/pnas.0804093105
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    Loss of ephrin-A5 function disrupts lens fiber cell packing and leads to cataract

    Margaret A. Cooper, Alexander I. Son, Daniel Komlos, Yuhai Sun, Norman J. Kleiman, and Renping Zhou

    PNAS October 28, 2008 105 (43) 16620-16625; https://doi.org/10.1073/pnas.0808987105
  • Open Access

    Mesothelium contributes to vascular smooth muscle and mesenchyme during lung development

    Jianwen Que, Bettina Wilm, Hiroshi Hasegawa, Fan Wang, David Bader, and Brigid L. M. Hogan

    PNAS October 28, 2008 105 (43) 16626-16630; https://doi.org/10.1073/pnas.0808649105

• Ecology

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    Asymmetric disassembly and robustness in declining networks

    • From the Cover

    Serguei Saavedra, Felix Reed-Tsochas, and Brian Uzzi

    PNAS October 28, 2008 105 (43) 16466-16471; https://doi.org/10.1073/pnas.0804740105
  • Open Access

    Building trophic modules into a persistent food web

    Michio Kondoh

    PNAS October 28, 2008 105 (43) 16631-16635; https://doi.org/10.1073/pnas.0805870105

• Evolution

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    Hindwings are unnecessary for flight but essential for execution of normal evasive flight in Lepidoptera

    Benjamin Jantzen and Thomas Eisner

    PNAS October 28, 2008 105 (43) 16636-16640; https://doi.org/10.1073/pnas.0807223105
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    Molecular phylogeny of choanoflagellates, the sister group to Metazoa

    M. Carr, B. S. C. Leadbeater, R. Hassan, M. Nelson, and S. L. Baldauf

    PNAS October 28, 2008 105 (43) 16641-16646; https://doi.org/10.1073/pnas.0801667105
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    Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers

    Sabyasachi Das, Nikolas Nikolaidis, Jan Klein, and Masatoshi Nei

    PNAS October 28, 2008 105 (43) 16647-16652; https://doi.org/10.1073/pnas.0808800105

• Genetics

  • Open Access

    Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes

    Scott J. Dixon, Yaroslav Fedyshyn, Judice L. Y. Koh, T. S. Keshava Prasad, Charly Chahwan, Gordon Chua, Kiana Toufighi, Anastasija Baryshnikova, Jacqueline Hayles, Kwang-Lae Hoe, Dong-Uk Kim, Han-Oh Park, Chad L. Myers, Akhilesh Pandey, Daniel Durocher, Brenda J. Andrews, and Charles Boone

    PNAS October 28, 2008 105 (43) 16653-16658; https://doi.org/10.1073/pnas.0806261105
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    Small-scale copy number variation and large-scale changes in gene expression

    Yuriy Mileyko, Richard I. Joh, and Joshua S. Weitz

    PNAS October 28, 2008 105 (43) 16659-16664; https://doi.org/10.1073/pnas.0806239105
  • Open Access

    Genes involved in pre-mRNA 3′-end formation and transcription termination revealed by a lin-15 operon Muv suppressor screen

    Mingxue Cui, Mary Ann Allen, Alison Larsen, Margaret MacMorris, Min Han, and Tom Blumenthal

    PNAS October 28, 2008 105 (43) 16665-16670; https://doi.org/10.1073/pnas.0807104105

• Immunology

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    How the thymus designs antigen-specific and self-tolerant T cell receptor sequences

    Andrej Košmrlj, Abhishek K. Jha, Eric S. Huseby, Mehran Kardar, and Arup K. Chakraborty

    PNAS October 28, 2008 105 (43) 16671-16676; https://doi.org/10.1073/pnas.0808081105
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    FADD and caspase-8 control the outcome of autophagic signaling in proliferating T cells

    Bryan D. Bell, Sabrina Leverrier, Brian M. Weist, Ryan H. Newton, Adrian F. Arechiga, Keith A. Luhrs, Naomi S. Morrissette, and Craig M. Walsh

    PNAS October 28, 2008 105 (43) 16677-16682; https://doi.org/10.1073/pnas.0808597105
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    Adjuvants targeting innate and adaptive immunity synergize to enhance tumor immunotherapy

    Grégory Verdeil, Kristi Marquardt, Charles D. Surh, and Linda A. Sherman

    PNAS October 28, 2008 105 (43) 16683-16688; https://doi.org/10.1073/pnas.0805054105
  • Open Access

    Exploring regulatory mechanisms of CD8⁺ T cell contraction

    Martin Prlic and Michael J. Bevan

    PNAS October 28, 2008 105 (43) 16689-16694; https://doi.org/10.1073/pnas.0808997105
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    Functional recognition of a distinct receptor preferential for leukotriene E₄ in mice lacking the cysteinyl leukotriene 1 and 2 receptors

    Akiko Maekawa, Yoshihide Kanaoka, Wei Xing, and K. Frank Austen

    PNAS October 28, 2008 105 (43) 16695-16700; https://doi.org/10.1073/pnas.0808993105

• Medical Sciences

  • Open Access

    Increased substrate oxidation and mitochondrial uncoupling in skeletal muscle of endurance-trained individuals

    Douglas E. Befroy, Kitt Falk Petersen, Sylvie Dufour, Graeme F. Mason, Douglas L. Rothman, and Gerald I. Shulman

    PNAS October 28, 2008 105 (43) 16701-16706; https://doi.org/10.1073/pnas.0808889105
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    Striatal progenitors derived from human ES cells mature into DARPP32 neurons in vitro and in quinolinic acid-lesioned rats

    Laetitia Aubry, Aurore Bugi, Nathalie Lefort, France Rousseau, Marc Peschanski, and Anselme L. Perrier

    PNAS October 28, 2008 105 (43) 16707-16712; https://doi.org/10.1073/pnas.0808488105
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    The ubiquitin ligase Siah2 regulates tumorigenesis and metastasis by HIF-dependent and -independent pathways

    Jianfei Qi, Koh Nakayama, Supriya Gaitonde, James S. Goydos, Stan Krajewski, Alexey Eroshkin, Dafna Bar-Sagi, David Bowtell, and Ze'ev Ronai

    PNAS October 28, 2008 105 (43) 16713-16718; https://doi.org/10.1073/pnas.0804063105
  • Open Access

    Hec1 overexpression hyperactivates the mitotic checkpoint and induces tumor formation in vivo

    Elena Diaz-Rodríguez, Rocio Sotillo, Juan-Manuel Schvartzman, and Robert Benezra

    PNAS October 28, 2008 105 (43) 16719-16724; https://doi.org/10.1073/pnas.0803504105

• Microbiology

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    HIV rebounds from latently infected cells, rather than from continuing low-level replication

    Beda Joos, Marek Fischer, Herbert Kuster, Satish K. Pillai, Joseph K. Wong, Jürg Böni, Bernard Hirschel, Rainer Weber, Alexandra Trkola, Huldrych F. Günthard, and The Swiss HIV Cohort Study2

    PNAS October 28, 2008 105 (43) 16725-16730; https://doi.org/10.1073/pnas.0804192105
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    Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

    • From the Cover

    Harry Sokol, Bénédicte Pigneur, Laurie Watterlot, Omar Lakhdari, Luis G. Bermúdez-Humarán, Jean-Jacques Gratadoux, Sébastien Blugeon, Chantal Bridonneau, Jean-Pierre Furet, Gérard Corthier, Corinne Grangette, Nadia Vasquez, Philippe Pochart, Germain Trugnan, Ginette Thomas, Hervé M. Blottière, Joël Doré, Philippe Marteau, Philippe Seksik, and Philippe Langella

    PNAS October 28, 2008 105 (43) 16731-16736; https://doi.org/10.1073/pnas.0804812105
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    Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius

    Iain G. Duggin, Simon A. McCallum, and Stephen D. Bell

    PNAS October 28, 2008 105 (43) 16737-16742; https://doi.org/10.1073/pnas.0806414105
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    Roles of RIG-I N-terminal tandem CARD and splice variant in TRIM25-mediated antiviral signal transduction

    Michaela U. Gack, Axel Kirchhofer, Young C. Shin, Kyung-Soo Inn, Chengyu Liang, Sheng Cui, Sua Myong, Taekjip Ha, Karl-Peter Hopfner, and Jae U. Jung

    PNAS October 28, 2008 105 (43) 16743-16748; https://doi.org/10.1073/pnas.0804947105
  • Open Access

    A host dicer is required for defective viral RNA production and recombinant virus vector RNA instability for a positive sense RNA virus

    Xuemin Zhang and Donald L. Nuss

    PNAS October 28, 2008 105 (43) 16749-16754; https://doi.org/10.1073/pnas.0807225105
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    Induction of group A Streptococcus virulence by a human antimicrobial peptide

    Ioannis Gryllos, Hien J. Tran-Winkler, Ming-Fang Cheng, Hachung Chung, Robert Bolcome III, Wuyuan Lu, Robert I. Lehrer, and Michael R. Wessels

    PNAS October 28, 2008 105 (43) 16755-16760; https://doi.org/10.1073/pnas.0803815105
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    The potential of desferrioxamine-gallium as an anti-Pseudomonas therapeutic agent

    Ehud Banin, Alina Lozinski, Keith M. Brady, Eduard Berenshtein, Phillip W. Butterfield, Maya Moshe, Mordechai Chevion, Everett Peter Greenberg, and Eyal Banin

    PNAS October 28, 2008 105 (43) 16761-16766; https://doi.org/10.1073/pnas.0808608105
  • Open Access

    Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41

    Buck S. Samuel, Abdullah Shaito, Toshiyuki Motoike, Federico E. Rey, Fredrik Backhed, Jill K. Manchester, Robert E. Hammer, S. Clay Williams, Jan Crowley, Masashi Yanagisawa, and Jeffrey I. Gordon

    PNAS October 28, 2008 105 (43) 16767-16772; https://doi.org/10.1073/pnas.0808567105

• Neuroscience

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    Activation of P2X7 receptors in glial satellite cells reduces pain through downregulation of P2X3 receptors in nociceptive neurons

    Yong Chen, Xiaofei Zhang, Congying Wang, GuangWen Li, Yanping Gu, and Li-Yen Mae Huang

    PNAS October 28, 2008 105 (43) 16773-16778; https://doi.org/10.1073/pnas.0801793105
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    Vulnerability of white matter towards antenatal hypoxia is linked to a species-dependent regulation of glutamate receptor subunits

    Romain H. Fontaine, Paul Olivier, Véronique Massonneau, Philippe Leroux, Vincent Degos, Sophie Lebon, Vincent El Ghouzzi, Vincent Lelièvre, Pierre Gressens, and Olivier Baud

    PNAS October 28, 2008 105 (43) 16779-16784; https://doi.org/10.1073/pnas.0803004105
  • Open Access

    Procedure for recording the simultaneous activity of single neurons distributed across cortical areas during sensory discrimination

    Adrián Hernández, Verónica Nácher, Rogelio Luna, Manuel Alvarez, Antonio Zainos, Silvia Cordero, Liliana Camarillo, Yuriria Vázquez, Luis Lemus, and Ranulfo Romo

    PNAS October 28, 2008 105 (43) 16785-16790; https://doi.org/10.1073/pnas.0808702105
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    A specialized NMDA receptor function in layer 5 recurrent microcircuitry of the adult rat prefrontal cortex

    Huaixing Wang, George G. Stradtman III, Xiao-Jing Wang, and Wen-Jun Gao

    PNAS October 28, 2008 105 (43) 16791-16796; https://doi.org/10.1073/pnas.0804318105
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    Delayed plasticity of inhibitory neurons in developing visual cortex

    Sunil P. Gandhi, Yuchio Yanagawa, and Michael P. Stryker

    PNAS October 28, 2008 105 (43) 16797-16802; https://doi.org/10.1073/pnas.0806159105
  • Open Access

    Sequential development of synapses in dendritic domains during adult neurogenesis

    Wolfgang Kelsch, Chia-Wei Lin, and Carlos Lois

    PNAS October 28, 2008 105 (43) 16803-16808; https://doi.org/10.1073/pnas.0807970105

• Pharmacology

  • Open Access

    Identification of a new JNK inhibitor targeting the JNK-JIP interaction site

    John L. Stebbins, Surya K. De, Thomas Machleidt, Barbara Becattini, Jesus Vazquez, Christian Kuntzen, Li-Hsing Chen, Jason F. Cellitti, Megan Riel-Mehan, Aras Emdadi, Giovanni Solinas, Michael Karin, and Maurizio Pellecchia

    PNAS October 28, 2008 105 (43) 16809-16813; https://doi.org/10.1073/pnas.0805677105

• Plant Biology

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    Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice

    Takeshi Fukao and Julia Bailey-Serres

    PNAS October 28, 2008 105 (43) 16814-16819; https://doi.org/10.1073/pnas.0807821105