| | This journal provides immediate access to some articles. In This Issue Proc Natl Acad Sci U S A. 2005 April 5; 102(14): 4925–4926. doi: 10.1073/iti1405102.PMCID: PMC556012 Introduction Gene Regulatory Networks Special Feature: Gene regulatory networks Eric Davidson and Michael Levin PMCID: PMC556010 Commentaries A simple answer for a splicing conundrum Douglas L. Black PMCID: PMC555990 How ion channels sense membrane potential Richard Horn PMCID: PMC556002 Thrips and tospoviruses come of age: Mapping determinants of insect transmission Diane E. Ullman, Anna E. Whitfield, and Thomas L. German PMCID: PMC555985 Sigma cascades in prokaryotic regulatory networks Ferric C. Fang PMCID: PMC555993 Gene Regulatory Networks Special Feature Perspective Gene regulatory networks for development Michael Levine and Eric H. Davidson PMCID: PMC555974 Gene Regulatory Networks Special Feature: Xenopus as a model system to study transcriptional regulatory networks Tetsuya Koide, Tadayoshi Hayata, and Ken W. Y. Cho PMCID: PMC555977 Gene Regulatory Networks Special Feature: Contingent gene regulatory networks and B cell fate specification Harinder Singh, Kay L. Medina, and Jagan M. R. Pongubala PMCID: PMC555998 Gene Regulatory Networks Special Feature: Logic functions of the genomic cis-regulatory code Sorin Istrail and Eric H. Davidson PMCID: PMC555989 Gene Regulatory Networks Special Feature: The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila Amanda Ochoa-Espinosa, Gozde Yucel, Leah Kaplan, Adam Pare, Noel Pura, Adam Oberstein, Dmitri Papatsenko, and Stephen Small PMCID: PMC555997 Gene Regulatory Networks Special Feature: Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo Dmitri Papatsenko and Michael Levine PMCID: PMC555988 Gene Regulatory Networks Special Feature: Transcriptional network underlying Caenorhabditis elegans vulval development Takao Inoue, Minqin Wang, Ted O. Ririe, Jolene S. Fernandes, and Paul W. Sternberg PMCID: PMC555976 Physical Sciences Chemistry Detection of chiral sum frequency generation vibrational spectra of proteins and peptides at interfaces in situ Jie Wang, Xiaoyun Chen, Matthew L. Clarke, and Zhan Chen PMCID: PMC555967 Biological Sciences Biochemistry Structural origins of efficient proton abstraction from carbon by a catalytic antibody Erik W. Debler, Shuichiro Ito, Florian P. Seebeck, Andreas Heine, Donald Hilvert, and Ian A. Wilson PMCID: PMC555987 DNA precursor asymmetries in mammalian tissue mitochondria and possible contribution to mutagenesis through reduced replication fidelity Shiwei Song, Zachary F. Pursell, William C. Copeland, Matthew J. Longley, Thomas A. Kunkel, and Christopher K. Mathews PMCID: PMC555996 High-resolution functional proteomics by active-site peptide profiling Eric S. Okerberg, Jiangyue Wu, Baohong Zhang, Babak Samii, Kelly Blackford, David T. Winn, Kevin R. Shreder, Jonathan J. Burbaum, and Matthew P. Patricelli PMCID: PMC555687 From the Cover:
Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers El Chérif Ibrahim, Thomas D. Schaal, Klemens J. Hertel, Robin Reed, and Tom Maniatis PMCID: PMC555999 Temperature-sensitive protein–DNA dimerizers Karl E. Hauschild, Renee E. Metzler, Hans-Dieter Arndt, Rocco Moretti, Marni Raffaelle, Peter B. Dervan, and Aseem Z. Ansari PMCID: PMC555971 His6 tag-assisted chemical protein synthesis Duhee Bang and Stephen B. H. Kent PMCID: PMC555969 Biophysics S3b amino acid residues do not shuttle across the bilayer in voltage-dependent Shaker K+ channels Carlos Gonzalez, Francisco J. Morera, Eduardo Rosenmann, Osvaldo Alvarez, and Ramon Latorre PMCID: PMC554844 A protein folding pathway with multiple folding intermediates at atomic resolution Hanqiao Feng, Zheng Zhou, and Yawen Bai PMCID: PMC555603 Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis Dan McElheny, Jason R. Schnell, Jonathan C. Lansing, H. Jane Dyson, and Peter E. Wright PMCID: PMC556001 Ca2+-regulated structural changes in troponin Maia V. Vinogradova, Deborah B. Stone, Galina G. Malanina, Christina Karatzaferi, Roger Cooke, Robert A. Mendelson, and Robert J. Fletterick PMCID: PMC555973 Cell Biology Hydrogen peroxide generated extracellularly by receptor–ligand interaction facilitates cell signaling Garrett J. DeYulia, Jr., Juan M. Cárcamo, Oriana Bórquez-Ojeda, Christopher C. Shelton, and David W. Golde PMCID: PMC556007 A long-range attraction between aggregating 3T3 cells mediated by near-infrared light scattering Guenter Albrecht-Buehler PMCID: PMC555573 Phosphorylation of Hdmx mediates its Hdm2- and ATM-dependent degradation in response to DNA damage Yaron Pereg, Dganit Shkedy, Petra de Graaf, Erik Meulmeester, Marina Edelson-Averbukh, Mogjiborahman Salek, Sharon Biton, Amina F. A. S. Teunisse, Wolf D. Lehmann, Aart G. Jochemsen, and Yosef Shiloh PMCID: PMC555986 Developmental Biology Gene Regulatory Networks Special Feature: Xenopus as a model system to study transcriptional regulatory networks Tetsuya Koide, Tadayoshi Hayata, and Ken W. Y. Cho PMCID: PMC555977 Gene Regulatory Networks Special Feature: Contingent gene regulatory networks and B cell fate specification Harinder Singh, Kay L. Medina, and Jagan M. R. Pongubala PMCID: PMC555998 Gene Regulatory Networks Special Feature: Logic functions of the genomic cis-regulatory code Sorin Istrail and Eric H. Davidson PMCID: PMC555989 Gene Regulatory Networks Special Feature: The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila Amanda Ochoa-Espinosa, Gozde Yucel, Leah Kaplan, Adam Pare, Noel Pura, Adam Oberstein, Dmitri Papatsenko, and Stephen Small PMCID: PMC555997 Gene Regulatory Networks Special Feature: Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo Dmitri Papatsenko and Michael Levine PMCID: PMC555988 Gene Regulatory Networks Special Feature: Transcriptional network underlying Caenorhabditis elegans vulval development Takao Inoue, Minqin Wang, Ted O. Ririe, Jolene S. Fernandes, and Paul W. Sternberg PMCID: PMC555976 Bmpr1a and Bmpr1b have overlapping functions and are essential for chondrogenesis in vivo Byeong S. Yoon, Dmitry A. Ovchinnikov, Isaac Yoshii, Yuji Mishina, Richard R. Behringer, and Karen M. Lyons PMCID: PMC555995 Floral asymmetry involves an interplay between TCP and MYB transcription factors in Antirrhinum Susie B. Corley, Rosemary Carpenter, Lucy Copsey, and Enrico Coen PMCID: PMC555980 Ecology Diverse taxa of cyanobacteria produce β-N-methylamino-l-alanine, a neurotoxic amino acid Paul Alan Cox, Sandra Anne Banack, Susan J. Murch, Ulla Rasmussen, Georgia Tien, Robert Richard Bidigare, James S. Metcalf, Louise F. Morrison, Geoffrey A. Codd, and Birgitta Bergman PMCID: PMC555964 Global energy gradients and size in colonial organisms: Worker mass and worker number in ant colonies Michael Kaspari PMCID: PMC555972 Evolution Evolution of a large ribosomal RNA multigene family in filamentous fungi: Birth and death of a concerted evolution paradigm Alejandro P. Rooney and Todd J. Ward PMCID: PMC555991 Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates K. Praveen Karanth, Thomas Delefosse, Berthe Rakotosamimanana, Thomas J. Parsons, and Anne D. Yoder PMCID: PMC555979 Genetics A unique loop in T7 DNA polymerase mediates the binding of helicase-primase, DNA binding protein, and processivity factor Samir M. Hamdan, Boriana Marintcheva, Timothy Cook, Seung-Joo Lee, Stanley Tabor, and Charles C. Richardson PMCID: PMC556000 Regulation of hematopoietic stem cell aging in vivo by a distinct genetic element Hartmut Geiger, Gabriela Rennebeck, and Gary Van Zant PMCID: PMC555968 Immunology Estimating medium- and long-term trends in malaria transmission by using serological markers of malaria exposure C. J. Drakeley, P. H. Corran, P. G. Coleman, J. E. Tongren, S. L. R. McDonald, I. Carneiro, R. Malima, J. Lusingu, A. Manjurano, W. M. M. Nkya, M. M. Lemnge, J. Cox, H. Reyburn, and E. M. Riley PMCID: PMC555970 Commitment toward the natural T (iNKT) cell lineage occurs at the CD4+8+ stage of thymic ontogeny Jelena S. Bezbradica, Timothy Hill, Aleksandar K. Stanic, Luc Van Kaer, and Sebastian Joyce PMCID: PMC555981 Immunological role of neuronal receptor vanilloid receptor 1 expressed on dendritic cells Sreyashi Basu and Pramod Srivastava PMCID: PMC555601 Identifying Foxp3-expressing suppressor T cells with a bicistronic reporter Yisong Y. Wan and Richard A. Flavell PMCID: PMC556008 LPS induces the interaction of a transcription factor, LPS-induced TNF-α factor, and STAT6(B) with effects on multiple cytokines Xiaoren Tang, Deborah Levy Marciano, Susan E. Leeman, and Salomon Amar PMCID: PMC555602 Foxp3 interacts with nuclear factor of activated T cells and NF-κB to repress cytokine gene expression and effector functions of T helper cells Estelle Bettelli, Maryam Dastrange, and Mohamed Oukka PMCID: PMC555574 Varicelloviruses avoid T cell recognition by UL49.5-mediated inactivation of the transporter associated with antigen processing Danijela Koppers-Lalic, Eric A. J. Reits, Maaike E. Ressing, Andrea D. Lipinska, Rupert Abele, Joachim Koch, Marisa Marcondes Rezende, Pieter Admiraal, Daphne van Leeuwen, Krystyna Bienkowska-Szewczyk, Thomas C. Mettenleiter, Frans A. M. Rijsewijk, Robert Tampé, Jacques Neefjes, and Emmanuel J. H. J. Wiertz PMCID: PMC555605 Medical Sciences Leptin increase in multiple sclerosis associates with reduced number of CD4+CD25+ regulatory T cells Giuseppe Matarese, Pietro Biagio Carrieri, Antonio La Cava, Francesco Perna, Veronica Sanna, Veronica De Rosa, Daniela Aufiero, Silvia Fontana, and Serafino Zappacosta PMCID: PMC555982 Cyclin-dependent kinase 6 associates with the androgen receptor and enhances its transcriptional activity in prostate cancer cells Jin T. E. Lim, Mahesh Mansukhani, and I. Bernard Weinstein PMCID: PMC556011 Microbiology From the Cover:
Borrelia burgdorferi σ54 is required for mammalian infection and vector transmission but not for tick colonization Mark A. Fisher, Dorothee Grimm, Amy K. Henion, Abdallah F. Elias, Philip E. Stewart, Patricia A. Rosa, and Frank C. Gherardini PMCID: PMC555983 Viral genetic determinants for thrips transmission of Tomato spotted wilt virus Sang-Hoon Sin, Brian C. McNulty, George G. Kennedy, and James W. Moyer PMCID: PMC552972 The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages Tony Kwan, Jing Liu, Michael DuBow, Philippe Gros, and Jerry Pelletier PMCID: PMC556006 23S rRNA base pair 2057–2611 determines ketolide susceptibility and fitness cost of the macrolide resistance mutation 2058A→G Peter Pfister, Natascia Corti, Sven Hobbie, Christian Bruell, Raz Zarivach, Ada Yonath, and Erik C. Böttger PMCID: PMC555689 Intracellular Helicobacter pylori in gastric epithelial progenitors Jung D. Oh, Sherif M. Karam, and Jeffrey I. Gordon PMCID: PMC555607 Cytolysin-dependent evasion of lysosomal killing Anders Håkansson, Colette Cywes Bentley, Elizabeth A. Shakhnovic, and Michael R. Wessels PMCID: PMC555683 Neuroscience From the Cover:
The neurotrophin-3 receptor TrkC directly phosphorylates and activates the nucleotide exchange factor Dbs to enhance Schwann cell migration Junji Yamauchi, Jonah R. Chan, Yuki Miyamoto, Gozoh Tsujimoto, and Eric M. Shooter PMCID: PMC556009 Phosphatidylinositol phosphate kinase type Iγ regulates dynamics of large dense-core vesicle fusion Liang-Wei Gong, Gilbert Di Paolo, Ester Diaz, Gianluca Cestra, Maria-Elena Diaz, Manfred Lindau, Pietro De Camilli, and Derek Toomre PMCID: PMC555604 Three distinct kinetic groupings of the synaptotagmin family: Candidate sensors for rapid and delayed exocytosis Enfu Hui, Jihong Bai, Ping Wang, Mutsuyuki Sugimori, Rodolfo R. Llinas, and Edwin R. Chapman PMCID: PMC556003 Hypersensitivity of DJ-1-deficient mice to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrindine (MPTP) and oxidative stress Raymond H. Kim, Patrice D. Smith, Hossein Aleyasin, Shawn Hayley, Matthew P. Mount, Scott Pownall, Andrew Wakeham, Annick J. You-Ten, Suneil K. Kalia, Patrick Horne, David Westaway, Andres M. Lozano, Hymie Anisman, David S. Park, and Tak W. Mak PMCID: PMC555037 Defective N-acetylaspartate catabolism reduces brain acetate levels and myelin lipid synthesis in Canavan's disease Chikkathur N. Madhavarao, Peethambaran Arun, John R. Moffett, Sylvia Szucs, Sankar Surendran, Reuben Matalon, James Garbern, Diana Hristova, Anne Johnson, Wei Jiang, and M. A. Aryan Namboodiri PMCID: PMC555036 Adult human hematopoietic stem cells produce neurons efficiently in the regenerating chicken embryo spinal cord Olafur E. Sigurjonsson, Marie-Claude Perreault, Torstein Egeland, and Joel C. Glover PMCID: PMC556004 In vivo dynamics of retinal injury and repair in the rhodopsin mutant dog model of human retinitis pigmentosa Artur V. Cideciyan, Samuel G. Jacobson, Tomas S. Aleman, Danian Gu, Susan E. Pearce-Kelling, Alexander Sumaroka, Gregory M. Acland, and Gustavo D. Aguirre PMCID: PMC555975 Generalized Bienenstock–Cooper–Munro rule for spiking neurons that maximizes information transmission Taro Toyoizumi, Jean-Pascal Pfister, Kazuyuki Aihara, and Wulfram Gerstner PMCID: PMC555686 Mammalian motor neurons corelease glutamate and acetylcholine at central synapses Hiroshi Nishimaru, Carlos Ernesto Restrepo, Jesper Ryge, Yuchio Yanagawa, and Ole Kiehn PMCID: PMC555035 Visual working memory in decision making by honey bees Shaowu Zhang, Fiola Bock, Aung Si, Juergen Tautz, and Mandyam V. Srinivasan PMCID: PMC555688 Pharmacology Discovery of the ergothioneine transporter Dirk Gründemann, Stephanie Harlfinger, Stefan Golz, Andreas Geerts, Andreas Lazar, Reinhard Berkels, Norma Jung, Andrea Rubbert, and Edgar Schömig PMCID: PMC555966 Physiology Cortical, thalamic, and hypothalamic responses to cooling and warming the skin in awake humans: A positron-emission tomography study Gary F. Egan, John Johnson, Michael Farrell, Robin McAllen, Frank Zamarripa, Michael J. McKinley, Jack Lancaster, Derek Denton, and Peter T. Fox PMCID: PMC555992 From the Cover:
Relationship between follicle size at insemination and pregnancy success George A. Perry, Michael F. Smith, Matthew C. Lucy, Jonathan A. Green, Tina E. Parks, Michael D. MacNeil, Andrew J. Roberts, and Thomas W. Geary PMCID: PMC556005 Sites of proteolytic processing and noncovalent association of the distal C-terminal domain of CaV1.1 channels in skeletal muscle Joanne T. Hulme, Keiichi Konoki, Teddy W.-C. Lin, Marina A. Gritsenko, David G. Camp, II, Diana J. Bigelow, and William A. Catterall PMCID: PMC555994 Plant Biology An Arabidopsis transcription factor, AtbZIP60, regulates the endoplasmic reticulum stress response in a manner unique to plants Yuji Iwata and Nozomu Koizumi PMCID: PMC555978 Psychology Perceptual learning in clear displays optimizes perceptual expertise: Learning the limiting process Barbara Anne Dosher and Zhong-Lin Lu PMCID: PMC555685 Attention-driven discrete sampling of motion perception Rufin VanRullen, Leila Reddy, and Christof Koch PMCID: PMC555984 Plasticity of face processing in infancy O. Pascalis, L. S. Scott, D. J. Kelly, R. W. Shannon, E. Nicholson, M. Coleman, and C. A. Nelson PMCID: PMC555965 |
