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Table of Contents
December 04, 2007; vol. 104 no. 49
This Week in PNAS
Physical Sciences
Applied Mathematics
- Open AccessA mathematical tool for exploring the dynamics of biological networks
- Inaugural Article
Paolo E. Barbano, Marina Spivak, Marc Flajolet, Angus C. Nairn, Paul Greengard, and Leslie Greengard - You have accessSubnetwork analysis reveals dynamic features of complex (bio)chemical networksCarsten Conradi, Dietrich Flockerzi, Jörg Raisch, and Jörg Stelling
Chemistry
- You have accessAxial ligand tuning of a nonheme iron(IV)–oxo unit for hydrogen atom abstractionChivukula V. Sastri, Jimin Lee, Kyungeun Oh, Yoon Jin Lee, Junghyun Lee, Timothy A. Jackson, Kallol Ray, Hajime Hirao, Woonsup Shin, Jason A. Halfen, Jinheung Kim, Lawrence Que Jr, Sason Shaik, and Wonwoo Nam
Physics
- You have accessSymmetry, shape, and orderAntonio Trovato, Trinh Xuan Hoang, Jayanth R. Banavar, and Amos Maritan
Statistics
- Open AccessA forest-based approach to identifying gene and gene–gene interactionsXiang Chen, Ching-Ti Liu, Meizhuo Zhang, and Heping Zhang
Social Sciences
Psychology
- You have accessThe blinking spotlight of attentionRufin VanRullen, Thomas Carlson, and Patrick Cavanagh
Biological Sciences
Anthropology
- You have accessSavanna chimpanzees use tools to harvest the underground storage organs of plants
- Cozzarelli Prize Winner
- From the Cover
R. Adriana Hernandez-Aguilar, Jim Moore, and Travis Rayne PickeringSee companion article:
- Savanna chimpanzees dig for food- Nov 28, 2007
- In This Issue- Dec 04, 2007
- Open AccessGlobal climate change, war, and population decline in recent human historyDavid D. Zhang, Peter Brecke, Harry F. Lee, Yuan-Qing He, and Jane Zhang
- You have accessA new Late Miocene great ape from Kenya and its implications for the origins of African great apes and humansYutaka Kunimatsu, Masato Nakatsukasa, Yoshihiro Sawada, Tetsuya Sakai, Masayuki Hyodo, Hironobu Hyodo, Tetsumaru Itaya, Hideo Nakaya, Haruo Saegusa, Arnaud Mazurier, Mototaka Saneyoshi, Hiroshi Tsujikawa, Ayumi Yamamoto, and Emma Mbua
See companion article:
- In This Issue- Dec 04, 2007
- New apes fill the gap- Dec 05, 2007
Biochemistry
- Open AccessA mathematical tool for exploring the dynamics of biological networks
- Inaugural Article
Paolo E. Barbano, Marina Spivak, Marc Flajolet, Angus C. Nairn, Paul Greengard, and Leslie Greengard - You have accessJARID1B is a histone H3 lysine 4 demethylase up-regulated in prostate cancerYang Xiang, Ziqi Zhu, Gang Han, Xiaolei Ye, Bo Xu, Zhouchun Peng, Yuanjun Ma, Yi Yu, Hanqing Lin, Adele Pin Chen, and Charlie Degui Chen
- You have accessDirected selection of a conformational antibody domain that prevents mature amyloid fibril formation by stabilizing Aβ protofibrilsGernot Habicht, Christian Haupt, Ralf P. Friedrich, Peter Hortschansky, Carsten Sachse, Jessica Meinhardt, Karin Wieligmann, Gerald P. Gellermann, Michael Brodhun, Jürgen Götz, Karl-Jürgen Halbhuber, Christoph Röcken, Uwe Horn, and Marcus Fändrich
- You have accessEpidermal growth factor receptor juxtamembrane region regulates allosteric tyrosine kinase activationKristina W. Thiel and Graham Carpenter
- You have accessAntiinflammatory glucocorticoid receptor ligand with reduced side effects exhibits an altered protein–protein interaction profileJeffrey N. Miner, Bob Ardecky, Khalid Benbatoul, Kimberly Griffiths, Christopher J. Larson, Dale E. Mais, Keith Marschke, Jon Rosen, Eric Vajda, Lin Zhi, and Andres Negro-Vilar
- You have accessMitochondrial origin-binding protein UMSBP mediates DNA replication and segregation in trypanosomesNeta Milman, Shawn A. Motyka, Paul T. Englund, Derrick Robinson, and Joseph Shlomai
- You have accessProtein–protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 Nef proteinStéphane Betzi, Audrey Restouin, Sandrine Opi, Stefan T. Arold, Isabelle Parrot, Françoise Guerlesquin, Xavier Morelli, and Yves Collette
- You have accessLaforin is a glycogen phosphatase, deficiency of which leads to elevated phosphorylation of glycogen in vivoVincent S. Tagliabracci, Julie Turnbull, Wei Wang, Jean-Marie Girard, Xiaochu Zhao, Alexander V. Skurat, Antonio V. Delgado-Escueta, Berge A. Minassian, Anna A. DePaoli-Roach, and Peter J. Roach
- You have accessA novel polydnavirus protein inhibits the insect prophenoloxidase activation pathwayMarkus H. Beck and Michael R. Strand
- You have accessThe all-trans-retinal dimer series of lipofuscin pigments in retinal pigment epithelial cells in a recessive Stargardt disease modelSo R. Kim, Young P. Jang, Steffen Jockusch, Nathan E. Fishkin, Nicholas J. Turro, and Janet R. Sparrow
- You have accessStructure of the Nitrosomonas europaea Rh proteinXin Li, Sanjay Jayachandran, Hiep-Hoa T. Nguyen, and Michael K. Chan
- You have accessRegulation of hypothalamic malonyl-CoA by central glucose and leptinMichael J. Wolfgang, Seung Hun Cha, Aniket Sidhaye, Shigeru Chohnan, Gary Cline, Gerald I. Shulman, and M. Daniel Lane
- Open AccessA biochemical approach to identifying microRNA targetsFedor V. Karginov, Cecilia Conaco, Zhenyu Xuan, Bryan H. Schmidt, Joel S. Parker, Gail Mandel, and Gregory J. Hannon
Biophysics
- You have accessConstruction of effective free energy landscape from single-molecule time seriesAkinori Baba and Tamiki Komatsuzaki
- You have accessThe 1.3-Å resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteinsDomenico Lupo, Xiao-Dan Li, Anne Durand, Takashi Tomizaki, Baya Cherif-Zahar, Giorgio Matassi, Mike Merrick, and Fritz K. Winkler
- You have accessDisulfide bond influence on protein structural dynamics probed with 2D-IR vibrational echo spectroscopyHaruto Ishikawa, Seongheun Kim, Kyungwon Kwak, Keisuke Wakasugi, and Michael D. Fayer
- You have accessCryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteinsManjuli R. Sharma, Daniel N. Wilson, Partha P. Datta, Chandana Barat, Frank Schluenzen, Paola Fucini, and Rajendra K. Agrawal
- You have accessMechanoenzymes under superstall and large assisting loads reveal structural featuresDenis Tsygankov and Michael E. Fisher
Cell Biology
- You have accessSubnetwork analysis reveals dynamic features of complex (bio)chemical networksCarsten Conradi, Dietrich Flockerzi, Jörg Raisch, and Jörg Stelling
- You have accessMatrix metalloproteinase 7 controls pancreatic acinar cell transdifferentiation by activating the Notch signaling pathwayEric T. Sawey, Johnny A. Johnson, and Howard C. Crawford
- Open AccessEssential role of Epac2/Rap1 signaling in regulation of insulin granule dynamics by cAMPTadao Shibasaki, Harumi Takahashi, Takashi Miki, Yasuhiro Sunaga, Kimio Matsumura, Mami Yamanaka, Changliang Zhang, Atsuko Tamamoto, Takaya Satoh, Jun-ichi Miyazaki, and Susumu Seino
- You have accessStructural differentiation of skeletal muscle fibers in the absence of innervation in humansSimona Boncompagni, Helmut Kern, Katia Rossini, Christian Hofer, Winfried Mayr, Ugo Carraro, and Feliciano Protasi
- You have accessBeyond aerobic glycolysis: Transformed cells can engage in glutamine metabolism that exceeds the requirement for protein and nucleotide synthesisRalph J. DeBerardinis, Anthony Mancuso, Evgueni Daikhin, Ilana Nissim, Marc Yudkoff, Suzanne Wehrli, and Craig B. Thompson
Developmental Biology
- You have accessDNA methylation, insulin resistance, and blood pressure in offspring determined by maternal periconceptional B vitamin and methionine statusKevin D. Sinclair, Cinzia Allegrucci, Ravinder Singh, David S. Gardner, Sonia Sebastian, Jayson Bispham, Alexandra Thurston, John F. Huntley, William D. Rees, Christopher A. Maloney, Richard G. Lea, Jim Craigon, Tom G. McEvoy, and Lorraine E. Young
- You have accessBlocking LIF action in the uterus by using a PEGylated antagonist prevents implantation: A nonhormonal contraceptive strategy
- From the Cover
Christine A. White, Jian-Guo Zhang, Lois A. Salamonsen, Manuel Baca, W. Douglas Fairlie, Donald Metcalf, Nicos A. Nicola, Lorraine Robb, and Evdokia Dimitriadis
Evolution
- Open AccessUsing plastid genome-scale data to resolve enigmatic relationships among basal angiospermsMichael J. Moore, Charles D. Bell, Pamela S. Soltis, and Douglas E. Soltis
- You have accessAnalysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patternsRobert K. Jansen, Zhengqiu Cai, Linda A. Raubeson, Henry Daniell, Claude W. dePamphilis, James Leebens-Mack, Kai F. Müller, Mary Guisinger-Bellian, Rosemarie C. Haberle, Anne K. Hansen, Timothy W. Chumley, Seung-Bum Lee, Rhiannon Peery, Joel R. McNeal, Jennifer V. Kuehl, and Jeffrey L. Boore
- You have accessLong-term evolution of transposable elementsArnaud Le Rouzic, Thibaud S. Boutin, and Pierre Capy
- Open AccessThe signal environment is more important than diet or chemical specialization in the evolution of warning coloration
- From the Cover
Kathleen L. Prudic, Jeffrey C. Oliver, and Felix A. H. Sperling - You have accessGenetic variation in the cysteine biosynthesis pathway causes sensitivity to pharmacological compoundsHyun Seok Kim and Justin C. Fay
- You have accessParallel genomic evolution and metabolic interdependence in an ancient symbiosisJohn P. McCutcheon and Nancy A. Moran
See companion article:
- In This Issue- Dec 04, 2007
- You have accessExtensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classificationDavid M. Spooner, Jorge Núñez, Guillermo Trujillo, María del Rosario Herrera, Frank Guzmán, and Marc Ghislain
- You have accessEvolutionary plasticity of developmental gene regulatory network architectureVeronica F. Hinman and Eric H. Davidson
Genetics
- Open AccessA forest-based approach to identifying gene and gene–gene interactionsXiang Chen, Ching-Ti Liu, Meizhuo Zhang, and Heping Zhang
- You have accessPseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation terminationMorten Ejby, Michael A. Sørensen, and Steen Pedersen
- You have accessIntegrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genesDag H. Yasui, Sailaja Peddada, Mark C. Bieda, Roxanne O. Vallero, Amber Hogart, Raman P. Nagarajan, Karen N. Thatcher, Peggy J. Farnham, and Janine M. LaSalle
- Open AccessA knockin mouse model of the Bardet–Biedl syndrome 1 M390R mutation has cilia defects, ventriculomegaly, retinopathy, and obesityRoger E. Davis, Ruth E. Swiderski, Kamal Rahmouni, Darryl Y. Nishimura, Robert F. Mullins, Khristofor Agassandian, Alisdair R. Philp, Charles C. Searby, Michael P. Andrews, Stewart Thompson, Christopher J. Berry, Daniel R. Thedens, Baoli Yang, Robert M. Weiss, Martin D. Cassell, Edwin M. Stone, and Val C. Sheffield
- You have accessDistinguishing protein-coding and noncoding genes in the human genome
- From the Cover
Michele Clamp, Ben Fry, Mike Kamal, Xiaohui Xie, James Cuff, Michael F. Lin, Manolis Kellis, Kerstin Lindblad-Toh, and Eric S. LanderSee companion article:
- In This Issue- Dec 04, 2007
Immunology
- You have accessHistamine is stored in mast cells of most evolutionarily advanced fish and regulates the fish inflammatory responseIván Mulero, M. Pilar Sepulcre, José Meseguer, Alfonsa García-Ayala, and Victoriano Mulero
- You have accessChronic stimulation of Nod2 mediates tolerance to bacterial productsMatija Hedl, Jing Li, Judy H. Cho, and Clara Abraham
- You have accessCD4+CD25+Foxp3+ regulatory T cells induce alternative activation of human monocytes/macrophagesMachteld M. Tiemessen, Ann L. Jagger, Hayley G. Evans, Martijn J. C. van Herwijnen, Susan John, and Leonie S. Taams
- You have accessAssembly and structural properties of glucocorticoid-induced TNF receptor ligand: Implications for functionKausik Chattopadhyay, Udupi A. Ramagopal, Arunika Mukhopadhaya, Vladimir N. Malashkevich, Teresa P. DiLorenzo, Michael Brenowitz, Stanley G. Nathenson, and Steven C. Almo
- You have accessB7-H3 and B7x are highly expressed in human prostate cancer and associated with disease spread and poor outcomeXingxing Zang, R. Houston Thompson, Hikmat A. Al-Ahmadie, Angel M. Serio, Victor E. Reuter, James A. Eastham, Peter T. Scardino, Padmanee Sharma, and James P. Allison
Medical Sciences
- You have accessSyndecan-3 is a dendritic cell-specific attachment receptor for HIV-1Lot de Witte, Michael Bobardt, Udayan Chatterji, Gisèle Degeest, Guido David, Teunis B. H. Geijtenbeek, and Philippe Gallay
- You have accessDynamic interplay between nitration and phosphorylation of tubulin cofactor B in the control of microtubule dynamicsSuresh K. Rayala, Emil Martin, Iraida G. Sharina, Poonam R. Molli, Xiaoping Wang, Raymond Jacobson, Ferid Murad, and Rakesh Kumar
- Open AccessSilencing of OB-RGRP in mouse hypothalamic arcuate nucleus increases leptin receptor signaling and prevents diet-induced obesityCyril Couturier, Chamsy Sarkis, Karin Séron, Sandrine Belouzard, Patty Chen, Aude Lenain, Laetitia Corset, Julie Dam, Virginie Vauthier, Anne Dubart, Jacques Mallet, Philippe Froguel, Yves Rouillé, and Ralf Jockers
- You have accessHDAC inhibitor PCI-24781 decreases RAD51 expression and inhibits homologous recombinationShanthi Adimoolam, Mint Sirisawad, Jun Chen, Patti Thiemann, James M. Ford, and Joseph J. Buggy
- You have accessTumor cell-selective regulation of NOXA by c-MYC in response to proteasome inhibitionMikhail A. Nikiforov, MaryBeth Riblett, Wen-Hua Tang, Vladimir Gratchouck, Dazhong Zhuang, Yolanda Fernandez, Monique Verhaegen, Sooryanarayana Varambally, Arul M. Chinnaiyan, Andrzej J. Jakubowiak, and Maria S. Soengas
- You have accessIn vivo multiphoton microscopy of NADH and FAD redox states, fluorescence lifetimes, and cellular morphology in precancerous epitheliaMelissa C. Skala, Kristin M. Riching, Annette Gendron-Fitzpatrick, Jens Eickhoff, Kevin W. Eliceiri, John G. White, and Nirmala Ramanujam
- You have accessNIX is required for programmed mitochondrial clearance during reticulocyte maturationRachel L. Schweers, Ji Zhang, Mindy S. Randall, Melanie R. Loyd, Weimin Li, Frank C. Dorsey, Mondira Kundu, Joseph T. Opferman, John L. Cleveland, Jeffery L. Miller, and Paul A. Ney
- You have accessID genes mediate tumor reinitiation during breast cancer lung metastasisGaorav P. Gupta, Jonathan Perk, Swarnali Acharyya, Paola de Candia, Vivek Mittal, Katia Todorova-Manova, William L. Gerald, Edi Brogi, Robert Benezra, and Joan Massagué
- Open AccessSmall molecule obatoclax (GX15-070) antagonizes MCL-1 and overcomes MCL-1-mediated resistance to apoptosisMai Nguyen, Richard C. Marcellus, Anne Roulston, Mark Watson, Lucile Serfass, S. R. Murthy Madiraju, Daniel Goulet, Jean Viallet, Laurent Bélec, Xavier Billot, Stephane Acoca, Enrico Purisima, Adrian Wiegmans, Leonie Cluse, Ricky W. Johnstone, Pierre Beauparlant, and Gordon C. Shore
Microbiology
- Open AccessCytoskeletal “jellyfish” structure of Mycoplasma mobileDaisuke Nakane and Makoto Miyata
- Open AccessRapid magnetosome formation shown by real-time x-ray magnetic circular dichroismSarah Staniland, Bruce Ward, Andrew Harrison, Gerrit van der Laan, and Neil Telling
- You have accessSubstrate binding by a bacterial ABC transporter involved in polysaccharide exportLeslie Cuthbertson, Matthew S. Kimber, and Chris Whitfield
- You have accessCrystal structure of measles virus hemagglutinin provides insight into effective vaccinesTakao Hashiguchi, Mizuho Kajikawa, Nobuo Maita, Makoto Takeda, Kimiko Kuroki, Kaori Sasaki, Daisuke Kohda, Yusuke Yanagi, and Katsumi Maenaka
See companion article:
- You have accessHuman papillomaviruses activate caspases upon epithelial differentiation to induce viral genome amplificationCary A. Moody, Amelie Fradet-Turcotte, Jacques Archambault, and Laimonis A. Laimins
- Open AccessThe P2 capsid protein of the nonenveloped rice dwarf phytoreovirus induces membrane fusion in insect host cellsFeng Zhou, Yingying Pu, Taiyun Wei, Huijun Liu, Wulan Deng, Chunhong Wei, Biao Ding, Toshihiro Omura, and Yi Li
Neuroscience
- You have accessThe blinking spotlight of attentionRufin VanRullen, Thomas Carlson, and Patrick Cavanagh
- You have accessRegulation of spine morphology and spine density by NMDA receptor signaling in vivoSila K. Ultanir, Ji-Eun Kim, Benjamin J. Hall, Thomas Deerinck, Mark Ellisman, and Anirvan Ghosh
- You have accessModulation of metabolic brain networks after subthalamic gene therapy for Parkinson's diseaseAndrew Feigin, Michael G. Kaplitt, Chengke Tang, Tanya Lin, Paul Mattis, Vijay Dhawan, Matthew J. During, and David Eidelberg
- You have accessRedundant and unique roles of retinol dehydrogenases in the mouse retinaAkiko Maeda, Tadao Maeda, Wenyu Sun, Houbin Zhang, Wolfgang Baehr, and Krzysztof Palczewski
- You have accessA structural basis for enhancement of long-term associative memory in single dendritic spines regulated by PKCJarin Hongpaisan and Daniel L. Alkon
- You have accessSpecific subgroups of FruM neurons control sexually dimorphic patterns of aggression in Drosophila melanogasterYick-Bun Chan and Edward A. Kravitz
- You have accessA helix-breaking mutation in TRPML3 leads to constitutive activity underlying deafness in the varitint-waddler mouseChristian Grimm, Math P. Cuajungco, Alexander F. J. van Aken, Michael Schnee, Simone Jörs, Corné J. Kros, Anthony J. Ricci, and Stefan Heller
Pharmacology
- Open AccessIdentification of retinoic acid as an inhibitor of transcription factor Nrf2 through activation of retinoic acid receptor alphaXiu Jun Wang, John D. Hayes, Colin J. Henderson, and C. Roland Wolf
- You have accessAcute-phase protein α-1-acid glycoprotein mediates neutrophil migration failure in sepsis by a nitric oxide-dependent mechanismF. L. A. C. Mestriner, F. Spiller, H. J. Laure, F. O. Souto, B. M. Tavares-Murta, J. C. Rosa, A. Basile-Filho, S. H. Ferreira, L. J. Greene, and F. Q. Cunha
Physiology
- You have accessβ cell-specific deficiency of the stimulatory G protein α-subunit Gsα leads to reduced β cell mass and insulin-deficient diabetesTao Xie, Min Chen, Qing-Hong Zhang, Zheng Ma, and Lee S. Weinstein
- You have accessYeast gain-of-function mutations reveal structure–function relationships conserved among different subfamilies of transient receptor potential channelsZhenwei Su, Xinliang Zhou, W. John Haynes, Stephen H. Loukin, Andriy Anishkin, Yoshiro Saimi, and Ching Kung
Plant Biology
- You have accessCERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in ArabidopsisAyako Miya, Premkumar Albert, Tomonori Shinya, Yoshitake Desaki, Kazuya Ichimura, Ken Shirasu, Yoshihiro Narusaka, Naoto Kawakami, Hanae Kaku, and Naoto Shibuya
- You have accessPhloem loading in Verbascum phoeniceum L. depends on the synthesis of raffinose-family oligosaccharidesAshlee McCaskill and Robert Turgeon
- You have accessAUREOCHROME, a photoreceptor required for photomorphogenesis in stramenopilesFumio Takahashi, Daisuke Yamagata, Mié Ishikawa, Yosuke Fukamatsu, Yasunobu Ogura, Masahiro Kasahara, Tomohiro Kiyosue, Munehiro Kikuyama, Masamitsu Wada, and Hironao Kataoka
See companion article:
- Shedding (blue) light on algal gene expression- Jan 02, 2008
- You have accessDelayed leaf senescence induces extreme drought tolerance in a flowering plantRosa M. Rivero, Mikiko Kojima, Amira Gepstein, Hitoshi Sakakibara, Ron Mittler, Shimon Gepstein, and Eduardo Blumwald
- You have accessVitamin B1 biosynthesis in plants requires the essential iron–sulfur cluster protein, THICMaja Raschke, Lukas Bürkle, Nadine Müller, Adriano Nunes-Nesi, Alisdair R. Fernie, Duilio Arigoni, Nikolaus Amrhein, and Teresa B. Fitzpatrick
Psychology
- You have accessTask-specific change of unconscious neural priming in the cerebral language networkKimihiro Nakamura, Stanislas Dehaene, Antoinette Jobert, Denis Le Bihan, and Sid Kouider
- You have accessAttention-deficit/hyperactivity disorder is characterized by a delay in cortical maturation
- From the Cover
P. Shaw, K. Eckstrand, W. Sharp, J. Blumenthal, J. P. Lerch, D. Greenstein, L. Clasen, A. Evans, J. Giedd, and J. L. RapoportSee companion article:
- In This Issue- Dec 04, 2007
Commentaries
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