| | This journal provides immediate access to some articles. In This Issue Proc Natl Acad Sci U S A. 2005 March 22; 102(12): 4217–4218. doi: 10.1073/iti1205102.PMCID: PMC555510 Commentary Understanding biology by reverse engineering the control Claire J. Tomlin and Jeffrey D. Axelrod PMCID: PMC555517 Physical Sciences Applied Mathematics From the Cover:
Subnets of scale-free networks are not scale-free: Sampling properties of networks Michael P. H. Stumpf, Carsten Wiuf, and Robert M. May PMCID: PMC555505 Physics Reversible self-assembly and directed assembly of DNA-linked micrometer-sized colloids Marie-Pierre Valignat, Olivier Theodoly, John C. Crocker, William B. Russel, and Paul M. Chaikin PMCID: PMC553286 Simulation of dynamical properties of normal and superfluid helium Akira Nakayama and Nancy Makri PMCID: PMC555495 Statistics On the utility of pooling biological samples in microarray experiments C. Kendziorski, R. A. Irizarry, K.-S. Chen, J. D. Haag, and M. N. Gould PMCID: PMC552978 Biological Sciences Biochemistry Biosynthesis of a D-amino acid in peptide linkage by an enzyme from frog skin secretions Alexander Jilek, Christa Mollay, Christa Tippelt, Jacques Grassi, Giuseppina Mignogna, Johannes Müllegger, Veronika Sander, Christine Fehrer, Donatella Barra, and Günther Kreil PMCID: PMC555527 The 1.51-Å structure of the poxvirus L1 protein, a target of potent neutralizing antibodies Hua-Poo Su, Scott C. Garman, Timothy J. Allison, Christiana Fogg, Bernard Moss, and David N. Garboczi PMCID: PMC555483 Target-directed proteolysis at the ribosome Tanja Henrichs, Natasha Mikhaleva, Charlotte Conz, Elke Deuerling, Dana Boyd, Adrian Zelazny, Eitan Bibi, Nenad Ban, and Michael Ehrmann PMCID: PMC555484 On the utility of pooling biological samples in microarray experiments C. Kendziorski, R. A. Irizarry, K.-S. Chen, J. D. Haag, and M. N. Gould PMCID: PMC552978 Cap-binding protein 1-mediated and eukaryotic translation initiation factor 4E-mediated pioneer rounds of translation in yeast Qinshan Gao, Biswadip Das, Fred Sherman, and Lynne E. Maquat PMCID: PMC555522 From cyclohydrolase to oxidoreductase: Discovery of nitrile reductase activity in a common fold Steven G. Van Lanen, John S. Reader, Manal A. Swairjo, Valérie de Crécy-Lagard, Bobby Lee, and Dirk Iwata-Reuyl PMCID: PMC555470 Lack of heme synthesis in a free-living eukaryote Anita U. Rao, Lynn K. Carta, Emmanuel Lesuisse, and Iqbal Hamza PMCID: PMC555530 Intramolecular interaction between phosphorylated tyrosine-783 and the C-terminal Src homology 2 domain activates phospholipase C-γ1 Benoit Poulin, Fujio Sekiya, and Sue Goo Rhee PMCID: PMC555506 Biophysics Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins Steven T. Whitten, Bertrand García-Moreno E., and Vincent J. Hilser PMCID: PMC555489 Activation of pausing F1 motor by external force Yoko Hirono-Hara, Koji Ishizuka, Kazuhiko Kinosita, Jr., Masasuke Yoshida, and Hiroyuki Noji PMCID: PMC555477 Structural characterization of copper(II) binding to α-synuclein: Insights into the bioinorganic chemistry of Parkinson's disease Rodolfo M. Rasia, Carlos W. Bertoncini, Derek Marsh, Wolfgang Hoyer, Dmitry Cherny, Markus Zweckstetter, Christian Griesinger, Thomas M. Jovin, and Claudio O. Fernández PMCID: PMC555498 Cell Biology FRET measurements of cell-traction forces and nano-scale clustering of adhesion ligands varied by substrate stiffness Hyun Joon Kong, Thomas R. Polte, Eben Alsberg, and David J. Mooney PMCID: PMC555469 ROMK1 channel activity is regulated by monoubiquitination Dao-Hong Lin, Hyacinth Sterling, Zhijian Wang, Elisa Babilonia, Baofeng Yang, Ke Dong, Steven C. Hebert, Gerhard Giebisch, and Wen-Hui Wang PMCID: PMC555508 PTEN as an effector in the signaling of antimigratory G protein-coupled receptor Teresa Sanchez, Shobha Thangada, Ming-Tao Wu, Christopher D. Kontos, Dianqing Wu, Hong Wu, and Timothy Hla PMCID: PMC555509 A role for the anaphase-promoting complex inhibitor Emi2/XErp1, a homolog of early mitotic inhibitor 1, in cytostatic factor arrest of Xenopus eggs Jeffrey J. Tung, David V. Hansen, Kenneth H. Ban, Alexander V. Loktev, Matthew K. Summers, John R. Adler, III, and Peter K. Jackson PMCID: PMC552977 MET and MYC cooperate in mammary tumorigenesis Alana L. Welm, Suwon Kim, Bryan E. Welm, and J. Michael Bishop PMCID: PMC552784 The polyglutamine neurodegenerative protein ataxin 3 regulates aggresome formation Barrington G. Burnett and Randall N. Pittman PMCID: PMC555481 A small-molecule inhibitor of isoprenylcysteine carboxyl methyltransferase with antitumor activity in cancer cells Ann M. Winter-Vann, Rudi A. Baron, Waihay Wong, June dela Cruz, John D. York, David M. Gooden, Martin O. Bergo, Stephen G. Young, Eric J. Toone, and Patrick J. Casey PMCID: PMC555472 Disease-associated mutations cause premature oligomerization of myelin proteolipid protein in the endoplasmic reticulum Eileithyia Swanton, Andrew Holland, Stephen High, and Philip Woodman PMCID: PMC555485 Engineering of vault nanocapsules with enzymatic and fluorescent properties Valerie A. Kickhoefer, Yvette Garcia, Yeshi Mikyas, Erik Johansson, Jing C. Zhou, Sujna Raval-Fernandes, Payam Minoofar, Jeffrey I. Zink, Bruce Dunn, Phoebe L. Stewart, and Leonard H. Rome PMCID: PMC555531 From the Cover:
Force production by depolymerizing microtubules: A theoretical study M. I. Molodtsov, E. L. Grishchuk, A. K. Efremov, J. R. McIntosh, and F. I. Ataullakhanov PMCID: PMC555502 From the Cover:
Syne proteins anchor muscle nuclei at the neuromuscular junction R. Mark Grady, Daniel A. Starr, Gail L. Ackerman, Joshua R. Sanes, and Min Han PMCID: PMC555524 Colonic tumorigenesis in BubR1+/–ApcMin/+ compound mutant mice is linked to premature separation of sister chromatids and enhanced genomic instability Chinthalapally V. Rao, Yang-Ming Yang, Malisetty V. Swamy, Tongyi Liu, Yuqiang Fang, Radma Mahmood, Meena Jhanwar-Uniyal, and Wei Dai PMCID: PMC555497 Developmental Biology Tbx2b is essential for neuronal differentiation along the dorsal/ventral axis of the zebrafish retina Jeffrey M. Gross and John E. Dowling PMCID: PMC555474 The basic helix–loop–helix olig3 establishes the neural plate boundary of the trunk and is necessary for development of the dorsal spinal cord Alida Filippi, Natascia Tiso, Gianluca Deflorian, Elisabetta Zecchin, Marino Bortolussi, and Francesco Argenton PMCID: PMC549604 Ecology From the Cover:
Remote analysis of biological invasion and biogeochemical change Gregory P. Asner and Peter M. Vitousek PMCID: PMC554001 Functional- and abundance-based mechanisms explain diversity loss due to N fertilization Katharine N. Suding, Scott L. Collins, Laura Gough, Christopher Clark, Elsa E. Cleland, Katherine L. Gross, Daniel G. Milchunas, and Steven Pennings PMCID: PMC555488 Phytoplankton species richness scales consistently from laboratory microcosms to the world's oceans Val H. Smith, Bryan L. Foster, James P. Grover, Robert D. Holt, Mathew A. Leibold, and Frank deNoyelles, Jr. PMCID: PMC555514 Environmental Sciences Climate-driven regime shifts in the biological communities of arctic lakes John P. Smol, Alexander P. Wolfe, H. John B. Birks, Marianne S. V. Douglas, Vivienne J. Jones, Atte Korhola, Reinhard Pienitz, Kathleen Rühland, Sanna Sorvari, Dermot Antoniades, Stephen J. Brooks, Marie-Andrée Fallu, Mike Hughes, Bronwyn E. Keatley, Tamsin E. Laing, Neal Michelutti, Larisa Nazarova, Marjut Nyman, Andrew M. Paterson, Bianca Perren, Roberto Quinlan, Milla Rautio, Émilie Saulnier-Talbot, Susanna Siitonen, Nadia Solovieva, and Jan Weckström PMCID: PMC555516 Evolution Resolution of a deep animal divergence by the pattern of intron conservation Scott William Roy and Walter Gilbert PMCID: PMC555513 From the Cover:
Osteocalcin protein sequences of Neanderthals and modern primates Christina M. Nielsen-Marsh, Michael P. Richards, Peter V. Hauschka, Jane E. Thomas-Oates, Erik Trinkaus, Paul B. Pettitt, Ivor Karavanić, Hendrik Poinar, and Matthew J. Collins PMCID: PMC555519 Mate choice decisions of stickleback females predictably modified by MHC peptide ligands Manfred Milinski, Siân Griffiths, K. Mathias Wegner, Thorsten B. H. Reusch, Annette Haas-Assenbaum, and Thomas Boehm PMCID: PMC555479 Integrons in Xanthomonas: A source of species genome diversity Michael R. Gillings, Marita P. Holley, H. W. Stokes, and Andrew J. Holmes PMCID: PMC555480 Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups Stéphane Hué, Deenan Pillay, Jonathan P. Clewley, and Oliver G. Pybus PMCID: PMC555492 Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis Štěpánka Vaňáčová, Weihong Yan, Jane M. Carlton, and Patricia J. Johnson PMCID: PMC554003 Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data Tae-Kun Seo, Hirohisa Kishino, and Jeffrey L. Thorne PMCID: PMC555482 A mechanism for the association of amino acids with their codons and the origin of the genetic code Shelley D. Copley, Eric Smith, and Harold J. Morowitz PMCID: PMC555468 Suppression of viral infectivity through lethal defection Ana Grande-Pérez, Ester Lázaro, Pedro Lowenstein, Esteban Domingo, and Susanna C. Manrubia PMCID: PMC555496 Genetics Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays Viktor Stolc, Manoj Pratim Samanta, Waraporn Tongprasit, Himanshu Sethi, Shoudan Liang, David C. Nelson, Adrian Hegeman, Clark Nelson, David Rancour, Sebastian Bednarek, Eldon L. Ulrich, Qin Zhao, Russell L. Wrobel, Craig S. Newman, Brian G. Fox, George N. Phillips, Jr., John L. Markley, and Michael R. Sussman PMCID: PMC555476 Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues Xinmin Zhang, Duncan T. Odom, Seung-Hoi Koo, Michael D. Conkright, Gianluca Canettieri, Jennifer Best, Huaming Chen, Richard Jenner, Elizabeth Herbolsheimer, Elizabeth Jacobsen, Shilpa Kadam, Joseph R. Ecker, Beverly Emerson, John B. Hogenesch, Terry Unterman, Richard A. Young, and Marc Montminy PMCID: PMC555478 On the role of Cro in λ prophage induction Sine L. Svenningsen, Nina Costantino, Donald L. Court, and Sankar Adhya PMCID: PMC555511 Quantitative kinetic analysis of the bacteriophage λ genetic network Oren Kobiler, Assaf Rokney, Nir Friedman, Donald L. Court, Joel Stavans, and Amos B. Oppenheim PMCID: PMC549295 Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae James H. Thomas, Joanna L. Kelley, Hugh M. Robertson, Kim Ly, and Willie J. Swanson PMCID: PMC555475 Juxtaposition of C(2)M and the transverse filament protein C(3)G within the central region of Drosophila synaptonemal complex Lorinda K. Anderson, Suzanne M. Royer, Scott L. Page, Kim S. McKim, Ann Lai, Mary A. Lilly, and R. Scott Hawley PMCID: PMC555515 The interaction between σ70 and the β-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation Bryce E. Nickels, Sean J. Garrity, Vladimir Mekler, Leonid Minakhin, Konstantin Severinov, Richard H. Ebright, and Ann Hochschild PMCID: PMC555512 JNK regulates lifespan in Caenorhabditis elegans by modulating nuclear translocation of forkhead transcription factor/DAF-16 Seung Wook Oh, Arnab Mukhopadhyay, Nenad Svrzikapa, Feng Jiang, Roger J. Davis, and Heidi A. Tissenbaum PMCID: PMC555525 Segmental trisomy of chromosome 17: A mouse model of human aneuploidy syndromes Tomáš Vacík, Michael Ort, Soňa Gregorová, Petr Strnad, Radek Blatný, Nathalie Conte, Allan Bradley, Jan Bureš, and Jiří Forejt PMCID: PMC552979 Immunology A target selection of somatic hypermutations is regulated similarly between T and B cells upon activation-induced cytidine deaminase expression Ai Kotani, Il-mi Okazaki, Masamichi Muramatsu, Kazuo Kinoshita, Nasim A. Begum, Toshiharu Nakajima, Hirohisa Saito, and Tasuku Honjo PMCID: PMC555529 Characterization of functional and phenotypic changes in anti-Gag vaccine-induced T cell responses and their role in protection after HIV-1 infection Michael R. Betts, Barbara Exley, David A. Price, Anju Bansal, Zenaido Tres Camacho, Vanessa Teaberry, Sadie M. West, David R. Ambrozak, Georgia Tomaras, Mario Roederer, J. Michael Kilby, Jim Tartaglia, Robert Belshe, Feng Gao, Daniel C. Douek, Kent J. Weinhold, Richard A. Koup, Paul Goepfert, and Guido Ferrari PMCID: PMC552973 Long-term in vivo provision of antigen-specific T cell immunity by programming hematopoietic stem cells Lili Yang and David Baltimore PMCID: PMC553287 STAT3 regulates Nemo-like kinase by mediating its interaction with IL-6-stimulated TGFβ-activated kinase 1 for STAT3 Ser-727 phosphorylation Hirotada Kojima, Takanori Sasaki, Tohru Ishitani, Shun-ichiro Iemura, Hong Zhao, Shuhei Kaneko, Hiroyuki Kunimoto, Tohru Natsume, Kunihiro Matsumoto, and Koichi Nakajima PMCID: PMC555521 Multiple mechanisms allow Mycobacterium tuberculosis to continuously inhibit MHC class II-mediated antigen presentation by macrophages Stewart T. Chang, Jennifer J. Linderman, and Denise E. Kirschner PMCID: PMC555518 A proinflammatory chemokine, CCL3, sensitizes the heat- and capsaicin-gated ion channel TRPV1 Ning Zhang, Sadeet Inan, Alan Cowan, Ronghua Sun, Ji Ming Wang, Thomas J. Rogers, Michael Caterina, and Joost J. Oppenheim PMCID: PMC555471 Medical Sciences A survey of homozygous deletions in human cancer genomes Charles Cox, Graham Bignell, Chris Greenman, Arne Stabenau, William Warren, Philip Stephens, Helen Davies, Stephen Watt, Jon Teague, Sara Edkins, Ewan Birney, Douglas F. Easton, Richard Wooster, P. Andrew Futreal, and Michael R. Stratton PMCID: PMC555487 Inhibitors of type II NADH:menaquinone oxidoreductase represent a class of antitubercular drugs Edward A. Weinstein, Takahiro Yano, Lin-Sheng Li, David Avarbock, Andrew Avarbock, Douglas Helm, Andrew A. McColm, Ken Duncan, John T. Lonsdale, and Harvey Rubin PMCID: PMC555520 Neutral sphingomyelinase 2 (smpd3) in the control of postnatal growth and development Wilhelm Stoffel, Britta Jenke, Barbara Blöck, Markus Zumbansen, and Jürgen Koebke PMCID: PMC555473 Evidence for cross-genotype neutralization of hepatitis C virus pseudo-particles and enhancement of infectivity by apolipoprotein C1 Jean-Christophe Meunier, Ronald E. Engle, Kristina Faulk, Ming Zhao, Birke Bartosch, Harvey Alter, Suzanne U. Emerson, Francois-Loic Cosset, Robert H. Purcell, and Jens Bukh PMCID: PMC555507 High-dose radiation with bone marrow transfer prevents neurodegeneration in an inherited glaucoma Michael G. Anderson, Richard T. Libby, Douglas B. Gould, Richard S. Smith, and Simon W. M. John PMCID: PMC555465 Core 3 synthase is down-regulated in colon carcinoma and profoundly suppresses the metastatic potential of carcinoma cells Toshie Iwai, Takashi Kudo, Risa Kawamoto, Tomomi Kubota, Akira Togayachi, Toru Hiruma, Tomoko Okada, Toru Kawamoto, Kyoei Morozumi, and Hisashi Narimatsu PMCID: PMC555466 Effects of titanium particle size on osteoblast functions in vitro and in vivo Moon G. Choi, Hae S. Koh, Daniel Kluess, Daniel O'Connor, Anshu Mathur, George A. Truskey, Janet Rubin, David X. F. Zhou, and K.-L. Paul Sung PMCID: PMC555523 Extremely potent triterpenoid inducers of the phase 2 response: Correlations of protection against oxidant and inflammatory stress Albena T. Dinkova-Kostova, Karen T. Liby, Katherine K. Stephenson, W. David Holtzclaw, Xiangqun Gao, Nanjoo Suh, Charlotte Williams, Renee Risingsong, Tadashi Honda, Gordon W. Gribble, Michael B. Sporn, and Paul Talalay PMCID: PMC555528 Microbiology Viable adenovirus vaccine prototypes: High-level production of a papillomavirus capsid antigen from the major late transcriptional unit Michael Berg, Julie DiFatta, Egbert Hoiczyk, Richard Schlegel, and Gary Ketner PMCID: PMC554749 Structures of two core subunits of the bacterial type IV secretion system, VirB8 from Brucella suis and ComB10 from Helicobacter pylori Laurent Terradot, Richard Bayliss, Clasien Oomen, Gordon A. Leonard, Christian Baron, and Gabriel Waksman PMCID: PMC555499 Neuroscience Coding for spatial goals in the prelimbic/infralimbic area of the rat frontal cortex V. Hok, E. Save, P. P. Lenck-Santini, and B. Poucet PMCID: PMC555486 A previously uncharacterized role for estrogen receptor β: Defeminization of male brain and behavior Andrea E. Kudwa, Cristian Bodo, Jan-Åke Gustafsson, and Emilie F. Rissman PMCID: PMC555526 Cross GTPase-activating protein (CrossGAP)/Vilse links the Roundabout receptor to Rac to regulate midline repulsion Hailan Hu, Ming Li, Juan-Pablo Labrador, Jason McEwen, Eric C. Lai, Corey S. Goodman, and Greg J. Bashaw PMCID: PMC555501 Genotype–environment interactions in mouse behavior: A way out of the problem Neri Kafkafi, Yoav Benjamini, Anat Sakov, Greg I. Elmer, and Ilan Golani PMCID: PMC555503 The RNA-binding protein HuD regulates neuronal cell identity and maturation Wado Akamatsu, Hiroaki Fujihara, Takayuki Mitsuhashi, Masato Yano, Shinsuke Shibata, Yoshika Hayakawa, Hirotaka James Okano, Shin-ichi Sakakibara, Hiroshi Takano, Toshiya Takano, Takao Takahashi, Tetsuo Noda, and Hideyuki Okano PMCID: PMC555491 Activity-dependent maintenance and growth of dendrites in adult cortex Chris Tailby, Layne L. Wright, Andrew B. Metha, and Mike B. Calford PMCID: PMC555467 Pharmacology Role of Toll-like receptors 2 and 4 in the induction of cyclooxygenase-2 in vascular smooth muscle Rosario Jimenez, Elizabeth Belcher, Shiranee Sriskandan, Ruth Lucas, Shaun McMaster, Ivana Vojnovic, Timothy D. Warner, and Jane A. Mitchell PMCID: PMC555494 Physiology Receptor-induced depletion of phosphatidylinositol 4,5-bisphosphate inhibits inwardly rectifying K+ channels in a receptor-specific manner Hana Cho, Doyun Lee, Suk Ho Lee, and Won-Kyung Ho PMCID: PMC555493 Plant Biology Evidence that CRABS CLAW and TOUSLED have conserved their roles in carpel development since the ancestor of the extant angiosperms Chloé Fourquin, Marion Vinauger-Douard, Bruno Fogliani, Christian Dumas, and Charles P. Scutt PMCID: PMC555504 Corrections Proc Natl Acad Sci U S A. 2005 March 22; 102(12): 4655. doi: 10.1073/pnas.0501116102.PMCID: PMC555490 Corrects: Yi Yang, et al. S-nitrosoprotein formation and localization in endothelial cells. Proc Natl Acad Sci U S A. 2005 January 4; 102(1): 117–122. Proc Natl Acad Sci U S A. 2005 March 22; 102(12): 4655. doi: 10.1073/pnas.0501139102.PMCID: PMC555500 Corrects: Eric Bonnet, et al. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci U S A. 2004 August 3; 101(31): 11511–11516. |
