| | This journal provides immediate access to some articles. From the Academy Colloquium Papers: Characterization and prediction of protein–protein interactions within and between complexes Einat Sprinzak, Yael Altuvia, and Hanah Margalit PMCID: PMC1595418 Colloquium Papers: Genomic analysis of the hierarchical structure of regulatory networks Haiyuan Yu and Mark Gerstein PMCID: PMC1595419 This Week in PNAS Proc Natl Acad Sci U S A. 2006 October 3; 103(40): 14643–14644. doi: 10.1073/iti4006103.PMCID: PMC1595402 Commentaries Monoclonal antibodies from plants: A new speed record Andrew Hiatt and Michael Pauly PMCID: PMC1595403 Encapsulation of a reactive core in neuromelanin Shosuke Ito PMCID: PMC1595404 Tumors reveal their secrets to cytotoxic T cells Nicholas A. Williamson, Jamie Rossjohn, and Anthony W. Purcell PMCID: PMC1595405 Imatinib spells BAD news for Bcr/abl-positive leukemias Scott H. Kaufmann PMCID: PMC1595406 Perspective Reconstruction of New Orleans after Hurricane Katrina: A research perspective R. W. Kates, C. E. Colten, S. Laska, and S. P. Leatherman PMCID: PMC1595407 Profile Profile of Daniel J. Cosgrove Tinsley H. Davis PMCID: PMC1595408 Physical Sciences Applied Physical Sciences Prediction of protein orientation upon immobilization on biological and nonbiological surfaces AmirAli H. Talasaz, Mohsen Nemat-Gorgani, Yang Liu, Patrik Ståhl, Robert W. Dutton, Mostafa Ronaghi, and Ronald W. Davis PMCID: PMC1576295 Chemistry Templated biomineralization on self-assembled protein fibers K. Subburaman, N. Pernodet, S. Y. Kwak, E. DiMasi, S. Ge, V. Zaitsev, X. Ba, N. L. Yang, and M. Rafailovich PMCID: PMC1595410 A Trojan horse transition state analogue generated by MgF3− formation in an enzyme active site Nicola J. Baxter, Luis F. Olguin, Marko Goličnik, Guoqiang Feng, Andrea M. Hounslow, Wolfgang Bermel, G. Michael Blackburn, Florian Hollfelder, Jonathan P. Waltho, and Nicholas H. Williams PMCID: PMC1595420 From the Cover:
Identification of class I MHC-associated phosphopeptides as targets for cancer immunotherapy Angela L. Zarling, Joy M. Polefrone, Anne M. Evans, Leann M. Mikesh, Jeffrey Shabanowitz, Sarah T. Lewis, Victor H. Engelhard, and Donald F. Hunt PMCID: PMC1595446 Engineering A hypothesis for vulnerable plaque rupture due to stress-induced debonding around cellular microcalcifications in thin fibrous caps Yuliya Vengrenyuk, Stéphane Carlier, Savvas Xanthos, Luis Cardoso, Peter Ganatos, Renu Virmani, Shmuel Einav, Lane Gilchrist, and Sheldon Weinbaum PMCID: PMC1595411 Geology Biological formation of ethane and propane in the deep marine subsurface Kai-Uwe Hinrichs, John M. Hayes, Wolfgang Bach, Arthur J. Spivack, Laura R. Hmelo, Nils G. Holm, Carl G. Johnson, and Sean P. Sylva PMCID: PMC1595412 Geophysics From the Cover:
A theory for the atmospheric energy spectrum: Depth-limited temperature anomalies at the tropopause R. Tulloch and K. S. Smith PMCID: PMC1595413 Physics The ferroelectric and cubic phases in BaTiO3 ferroelectrics are also antiferroelectric Qingsong Zhang, Tahir Cagin, and William A. Goddard, III PMCID: PMC1595414 Deterministic hydrodynamics: Taking blood apart John A. Davis, David W. Inglis, Keith J. Morton, David A. Lawrence, Lotien R. Huang, Stephen Y. Chou, James C. Sturm, and Robert H. Austin PMCID: PMC1595428 Biological Sciences Applied Biological Sciences From the Cover:
Rapid high-yield expression of full-size IgG antibodies in plants coinfected with noncompeting viral vectors Anatoli Giritch, Sylvestre Marillonnet, Carola Engler, Gerben van Eldik, Johan Botterman, Victor Klimyuk, and Yuri Gleba PMCID: PMC1566189 Calcium-sensitive MRI contrast agents based on superparamagnetic iron oxide nanoparticles and calmodulin Tatjana Atanasijevic, Maxim Shusteff, Peter Fam, and Alan Jasanoff PMCID: PMC1595416 Culling and cattle controls influence tuberculosis risk for badgers Rosie Woodroffe, Christl A. Donnelly, Helen E. Jenkins, W. Thomas Johnston, David R. Cox, F. John Bourne, Chris L. Cheeseman, Richard J. Delahay, Richard S. Clifton-Hadley, George Gettinby, Peter Gilks, R. Glyn Hewinson, John P. McInerney, and W. Ivan Morrison PMCID: PMC1586183 Biochemistry Colloquium Papers: Characterization and prediction of protein–protein interactions within and between complexes Einat Sprinzak, Yael Altuvia, and Hanah Margalit PMCID: PMC1595418 Colloquium Papers: Genomic analysis of the hierarchical structure of regulatory networks Haiyuan Yu and Mark Gerstein PMCID: PMC1595419 A Trojan horse transition state analogue generated by MgF3− formation in an enzyme active site Nicola J. Baxter, Luis F. Olguin, Marko Goličnik, Guoqiang Feng, Andrea M. Hounslow, Wolfgang Bermel, G. Michael Blackburn, Florian Hollfelder, Jonathan P. Waltho, and Nicholas H. Williams PMCID: PMC1595420 Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a prolyl-4-hydroxylase Lee M. Hoffart, Eric W. Barr, Robert B. Guyer, J. Martin Bollinger, Jr., and Carsten Krebs PMCID: PMC1578498 Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase Hiroshi M. Sasaki, Shun-ichi Sekine, Toru Sengoku, Ryuya Fukunaga, Motoyuki Hattori, Yukiko Utsunomiya, Chizu Kuroishi, Seiki Kuramitsu, Mikako Shirouzu, and Shigeyuki Yokoyama PMCID: PMC1595422 Detoxification of superoxide without production of H2O2: Antioxidant activity of superoxide reductase complexed with ferrocyanide Fernando P. Molina-Heredia, Chantal Houée-Levin, Catherine Berthomieu, Danièle Touati, Emilie Tremey, Vincent Favaudon, Virgile Adam, and Vincent Nivière PMCID: PMC1595423 Preferential transfer of the complete glycan is determined by the oligosaccharyltransferase complex and not by the catalytic subunit Olga Castro, Federico Movsichoff, and Armando J. Parodi PMCID: PMC1595424 Asymmetric phospholipid distribution drives in vitro reconstituted SNARE-dependent membrane fusion Jérôme Vicogne, Daniel Vollenweider, Jeffery R. Smith, Ping Huang, Michael A. Frohman, and Jeffrey E. Pessin PMCID: PMC1595425 Posttranslational hydroxylation of ankyrin repeats in IκB proteins by the hypoxia-inducible factor (HIF) asparaginyl hydroxylase, factor inhibiting HIF (FIH) Matthew E. Cockman, David E. Lancaster, Ineke P. Stolze, Kirsty S. Hewitson, Michael A. McDonough, Mathew L. Coleman, Charlotte H. Coles, Xiaohong Yu, Ronald T. Hay, Steven C. Ley, Christopher W. Pugh, Neil J. Oldham, Norma Masson, Christopher J. Schofield, and Peter J. Ratcliffe PMCID: PMC1578504 Biophysics Prediction of protein orientation upon immobilization on biological and nonbiological surfaces AmirAli H. Talasaz, Mohsen Nemat-Gorgani, Yang Liu, Patrik Ståhl, Robert W. Dutton, Mostafa Ronaghi, and Ronald W. Davis PMCID: PMC1576295 Deterministic hydrodynamics: Taking blood apart John A. Davis, David W. Inglis, Keith J. Morton, David A. Lawrence, Lotien R. Huang, Stephen Y. Chou, James C. Sturm, and Robert H. Austin PMCID: PMC1595428 From the Cover:
The surface oxidation potential of human neuromelanin reveals a spherical architecture with a pheomelanin core and a eumelanin surface William D. Bush, Jacob Garguilo, Fabio A. Zucca, Alberto Albertini, Luigi Zecca, Glenn S. Edwards, Robert J. Nemanich, and John D. Simon PMCID: PMC1595429 Measurement of the mechanical properties of isolated tectorial membrane using atomic force microscopy Rachel Gueta, David Barlam, Roni Z. Shneck, and Itay Rousso PMCID: PMC1595430 Two ligand-binding sites in the O2-sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling Eftychia Pinakoulaki, Hideaki Yoshimura, Vangelis Daskalakis, Shiro Yoshioka, Shigetoshi Aono, and Constantinos Varotsis PMCID: PMC1595431 Cell Biology FLASH is an essential component of Cajal bodies D. Barcaroli, D. Dinsdale, M. H. Neale, L. Bongiorno-Borbone, M. Ranalli, E. Munarriz, A. E. Sayan, J. M. McWilliam, T. M. Smith, E. Fava, R. A. Knight, G. Melino, and V. De Laurenzi PMCID: PMC1578500 FLASH is required for histone transcription and S-phase progression D. Barcaroli, L. Bongiorno-Borbone, A. Terrinoni, T. G. Hofmann, M. Rossi, R. A. Knight, A. G. Matera, G. Melino, and V. De Laurenzi PMCID: PMC1578501 Transaldolase is essential for maintenance of the mitochondrial transmembrane potential and fertility of spermatozoa Andras Perl, Yueming Qian, Kazim R. Chohan, Cynthia R. Shirley, Wendy Amidon, Sanjay Banerjee, Frank A. Middleton, Karina L. Conkrite, Maureen Barcza, Nick Gonchoroff, Susan S. Suarez, and Katalin Banki PMCID: PMC1595434 Genome-wide functional analysis of human cell-cycle regulators Mridul Mukherji, Russell Bell, Lubica Supekova, Yan Wang, Anthony P. Orth, Serge Batalov, Loren Miraglia, Dieter Huesken, Joerg Lange, Christopher Martin, Sudhir Sahasrabudhe, Mischa Reinhardt, Francois Natt, Jonathan Hall, Craig Mickanin, Mark Labow, Sumit K. Chanda, Charles Y. Cho, and Peter G. Schultz PMCID: PMC1595435 S100A4 accelerates tumorigenesis and invasion of human prostate cancer through the transcriptional regulation of matrix metalloproteinase 9 Mohammad Saleem, Mee-Hyang Kweon, Jeremy James Johnson, Vaqar Mustafa Adhami, Irina Elcheva, Naghma Khan, Bilal Bin Hafeez, Kumar M. R. Bhat, Sami Sarfaraz, Shannon Reagan-Shaw, Vladimir S. Spiegelman, Vijayasaradhi Setaluri, and Hasan Mukhtar PMCID: PMC1595436 Aging may be a conditional strategic choice and not an inevitable outcome for bacteria Milind Watve, Sweta Parab, Prajakta Jogdand, and Sarita Keni PMCID: PMC1595437 Deactivation of phosphatidylinositol 3,4,5-trisphosphate/Akt signaling mediates neutrophil spontaneous death Daocheng Zhu, Hidenori Hattori, Hakryul Jo, Yonghui Jia, Kulandayan K. Subramanian, Fabien Loison, Jian You, Yi Le, Marek Honczarenko, Leslie Silberstein, and Hongbo R. Luo PMCID: PMC1595438 Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation Julie B. Sneddon, Hanson H. Zhen, Kelli Montgomery, Matt van de Rijn, Aaron D. Tward, Robert West, Hayes Gladstone, Howard Y. Chang, Greg S. Morganroth, Anthony E. Oro, and Patrick O. Brown PMCID: PMC1578503 Developmental Biology The role of Pax-6 in lens regeneration Mayur Madhavan, Tracy L. Haynes, Nicholas C. Frisch, Mindy K. Call, Craig M. Minich, Panagiotis A. Tsonis, and Katia Del Rio-Tsonis PMCID: PMC1595439 Poly(ADP-ribose) polymerase-2 contributes to the fidelity of male meiosis I and spermiogenesis Françoise Dantzer, Manuel Mark, Delphine Quenet, Harry Scherthan, Aline Huber, Bodo Liebe, Lucia Monaco, Alexandra Chicheportiche, Paolo Sassone-Corsi, Gilbert de Murcia, and Josiane Ménissier-de Murcia PMCID: PMC1595440 Environmental Sciences Biological formation of ethane and propane in the deep marine subsurface Kai-Uwe Hinrichs, John M. Hayes, Wolfgang Bach, Arthur J. Spivack, Laura R. Hmelo, Nils G. Holm, Carl G. Johnson, and Sean P. Sylva PMCID: PMC1595412 Evolution A northern glacial refugium for bank voles (Clethrionomys glareolus) Petr Kotlík, Valérie Deffontaine, Silvia Mascheretti, Jan Zima, Johan R. Michaux, and Jeremy B. Searle PMCID: PMC1595441 Genetics Predicting interpretability of metabolome models based on behavior, putative identity, and biological relevance of explanatory signals David P. Enot, Manfred Beckmann, David Overy, and John Draper PMCID: PMC1595442 Nonhomologous chromosomal integration of foreign DNA is completely dependent on MUS-53 (human Lig4 homolog) in Neurospora Kazuma Ishibashi, Keiichiro Suzuki, Yoshinori Ando, Chihiro Takakura, and Hirokazu Inoue PMCID: PMC1595443 Formation of functional centromeric chromatin is specified epigenetically in Candida albicans Mary Baum, Kaustuv Sanyal, Prashant K. Mishra, Nathaniel Thaler, and John Carbon PMCID: PMC1595444 Immunology Recruitment of dynein to the Jurkat immunological synapse Jeffrey Combs, Soo Jin Kim, Sarah Tan, Lee A. Ligon, Erika L. F. Holzbaur, Jeffrey Kuhn, and Martin Poenie PMCID: PMC1595445 From the Cover:
Identification of class I MHC-associated phosphopeptides as targets for cancer immunotherapy Angela L. Zarling, Joy M. Polefrone, Anne M. Evans, Leann M. Mikesh, Jeffrey Shabanowitz, Sarah T. Lewis, Victor H. Engelhard, and Donald F. Hunt PMCID: PMC1595446 Cationic amino acid transporter 2 regulates inflammatory homeostasis in the lung Marc E. Rothenberg, Matthew P. Doepker, Ian P. Lewkowich, Monica G. Chiaramonte, Keith F. Stringer, Fred D. Finkelman, Carol L. MacLeod, Lesley G. Ellies, and Nives Zimmermann PMCID: PMC1595447 Medical Sciences A class of iron chelators with a wide spectrum of potent antitumor activity that overcomes resistance to chemotherapeutics Megan Whitnall, Jonathan Howard, Prem Ponka, and Des R. Richardson PMCID: PMC1595448 Bim and Bad mediate imatinib-induced killing of Bcr/Abl+ leukemic cells, and resistance due to their loss is overcome by a BH3 mimetic Junya Kuroda, Hamsa Puthalakath, Mark S. Cragg, Priscilla N. Kelly, Philippe Bouillet, David C. S. Huang, Shinya Kimura, Oliver G. Ottmann, Brian J. Druker, Andreas Villunger, Andrew W. Roberts, and Andreas Strasser PMCID: PMC1595449 Hormonal activity of AIMP1/p43 for glucose homeostasis Sang Gyu Park, Young Sun Kang, Jin Young Kim, Chang Seok Lee, Young Gyu Ko, Woo Je Lee, Ki-Up Lee, Young Il Yeom, and Sunghoon Kim PMCID: PMC1595450 Role of the Menkes copper-transporting ATPase in NMDA receptor-mediated neuronal toxicity Michelle L. Schlief, Tim West, Ann Marie Craig, David M. Holtzman, and Jonathan D. Gitlin PMCID: PMC1578502 Follicle-stimulating hormone stimulates TNF production from immune cells to enhance osteoblast and osteoclast formation Jameel Iqbal, Li Sun, T. Rajendra Kumar, Harry C. Blair, and Mone Zaidi PMCID: PMC1595452 The age incidence of chronic myeloid leukemia can be explained by a one-mutation model Franziska Michor, Yoh Iwasa, and Martin A. Nowak PMCID: PMC1595453 Microbiology Three restricted forms of Epstein–Barr virus latency counteracting apoptosis in c-myc-expressing Burkitt lymphoma cells Gemma L. Kelly, Anne E. Milner, Gouri S. Baldwin, Andrew I. Bell, and Alan B. Rickinson PMCID: PMC1595454 An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination Toru Tobe, Scott A. Beatson, Hisaaki Taniguchi, Hiroyuki Abe, Christopher M. Bailey, Amanda Fivian, Rasha Younis, Sophie Matthews, Olivier Marches, Gad Frankel, Tetsuya Hayashi, and Mark J. Pallen PMCID: PMC1595455 Tail-interacting protein TIP47 is a connector between Gag and Env and is required for Env incorporation into HIV-1 virions Sandra Lopez-Vergès, Grégory Camus, Guillaume Blot, Roxane Beauvoir, Richard Benarous, and Clarisse Berlioz-Torrent PMCID: PMC1595456 Neuroscience When motion appears stopped: Stereo motion standstill Chia-huei Tseng, Joetta L. Gobell, Zhong-Lin Lu, and George Sperling PMCID: PMC1595457 Plant Biology INAUGURAL ARTICLE by a Recently Elected Academy Member: Crystal structure and activities of EXPB1 (Zea m 1), a β-expansin and group-1 pollen allergen from maize Neela H. Yennawar, Lian-Chao Li, David M. Dudzinski, Akira Tabuchi, and Daniel J. Cosgrove PMCID: PMC1595409 Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes Steven B. Cannon, Lieven Sterck, Stephane Rombauts, Shusei Sato, Foo Cheung, Jérôme Gouzy, Xiaohong Wang, Joann Mudge, Jayprakash Vasdewani, Thomas Schiex, Manuel Spannagl, Erin Monaghan, Christine Nicholson, Sean J. Humphray, Heiko Schoof, Klaus F. X. Mayer, Jane Rogers, Francis Quétier, Giles E. Oldroyd, Frédéric Debellé, Douglas R. Cook, Ernest F. Retzel, Bruce A. Roe, Christopher D. Town, Satoshi Tabata, Yves Van de Peer, and Nevin D. Young PMCID: PMC1578499 Quorum signal molecules as biosurfactants affecting swarming in Rhizobium etli Ruth Daniels, Sven Reynaert, Hans Hoekstra, Christel Verreth, Joost Janssens, Kristien Braeken, Maarten Fauvart, Serge Beullens, Christophe Heusdens, Ivo Lambrichts, Dirk E. De Vos, Jos Vanderleyden, Jan Vermant, and Jan Michiels PMCID: PMC1595459 Psychology Increased sensitivity after repeated stimulation of residual spatial channels in blindsight Arash Sahraie, Ceri T. Trevethan, Mary Joan MacLeod, Alison D. Murray, John A. Olson, and Lawrence Weiskrantz PMCID: PMC1595460 Social Sciences Psychology When motion appears stopped: Stereo motion standstill Chia-huei Tseng, Joetta L. Gobell, Zhong-Lin Lu, and George Sperling PMCID: PMC1595457 Corrections Correction for Leung et al., Estrogen receptor (ER)-β isoforms: A key to understanding ER-β signaling PMCID: PMC1595461 Corrects: Yuet-Kin Leung, et al. Estrogen receptor (ER)-β isoforms: A key to understanding ER-β signaling. Proc Natl Acad Sci U S A. 2006 August 29; 103(35): 13162–13167. Correction for Zigman, In search of an effective obesity treatment: A shot in the dark or a shot in the arm? PMCID: PMC1595462 Corrects: Jeffrey M. Zigman, et al. In search of an effective obesity treatment: A shot in the dark or a shot in the arm? Proc Natl Acad Sci U S A. 2006 August 29; 103(35): 12961–12962. Correction for Stiller et al., Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA PMCID: PMC1595463 Corrects: M. Stiller, et al. INAUGURAL ARTICLE by a Recently Elected Academy Member: Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc Natl Acad Sci U S A. 2006 September 12; 103(37): 13578–13584. Correction for Meulener et al., Mutational analysis of DJ-1 in Drosophila implicates functional inactivation by oxidative damage and aging PMCID: PMC1595464 Corrects: Marc C. Meulener, et al. Mutational analysis of DJ-1 in Drosophila implicates functional inactivation by oxidative damage and aging. Proc Natl Acad Sci U S A. 2006 August 15; 103(33): 12517–12522. Correction for Swanson et al., Anxiolytic- and antidepressant-like profiles of the galanin-3 receptor (Gal3) antagonists SNAP 37889 and SNAP 398299 PMCID: PMC1595465 Corrects: Chad J. Swanson, et al. From the Cover:
Anxiolytic- and antidepressant-like profiles of the galanin-3 receptor (Gal3) antagonists SNAP 37889 and SNAP 398299. Proc Natl Acad Sci U S A. 2005 November 29; 102(48): 17489–17494. |
