| | Molecular Biology Mutation analysis of a recombinant NS replicon shows that influenza virus NS1 protein blocks the splicing and nucleo-cytoplasmic transport of its own viral mRNA Urtzi Garaigorta and Juan Ortín PMCID: PMC1950557 Delta–Notch—and then? Protein interactions and proposed modes of repression by Hes and Hey bHLH factors Andreas Fischer and Manfred Gessler PMCID: PMC1950541 Alternatively spliced isoforms of the human elk-1 mRNA within the 5′ UTR: implications for ELK-1 expression Tanguy Araud, Raphael Genolet, Pascale Jaquier-Gubler, and Joseph Curran PMCID: PMC1950554 Widely variable endogenous retroviral methylation levels in human placenta Daphne Reiss, Ying Zhang, and Dixie L. Mager PMCID: PMC1950553 Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon Irina Saraiva Franco, Luís Jaime Mota, Cláudio Manuel Soares, and Isabel de Sá-Nogueira PMCID: PMC1950556 Cap-independent translation through the p27 5′-UTR Hong Jiang, Jennifer Coleman, Robin Miskimins, Rekha Srinivasan, and W. Keith Miskimins PMCID: PMC1950543 Generalized substitution of isoencoding codons shortens the duration of papillomavirus L1 protein expression in transiently gene-transfected keratinocytes due to cell differentiation Wenyi Gu, Jianmin Ding, Xiao Wang, Rachel L. de Kluyver, Nicholas A. Saunders, Ian H. Frazer, and Kong-Nan Zhao PMCID: PMC1950544 Elk1 and SRF transcription factors convey basal transcription and mediate glucose response via their binding sites in the human LXRB gene promoter Maria Nilsson, Karin Dahlman-Wright, Charlotta Karelmo, Jan-Åke Gustafsson, and Knut R. Steffensen PMCID: PMC1950530 Zinc fingers 1 and 7 of yeast TFIIIA are essential for assembly of a functional transcription complex on the 5  S RNA gene Karen Rothfels, Owen Rowland, and Jacqueline Segall PMCID: PMC1950542 Real-time monitoring of functional interactions between upstream and core promoter sequences in living cells of sea urchin embryos Akiko Kobayashi, Youko Watanabe, Koji Akasaka, and Tetsuro Kokubo PMCID: PMC1950538 RNA Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis Xiaowei (Sylvia) Chen, Timofey S. Rozhdestvensky, Lesley J. Collins, Jürgen Schmitz, and David Penny PMCID: PMC1950533 A search for structurally similar cellular internal ribosome entry sites Stephen D. Baird, Stephen M. Lewis, Marcel Turcotte, and Martin Holcik PMCID: PMC1950536 GW body disassembly triggered by siRNAs independently of their silencing activity A. Serman, F. Le Roy, C. Aigueperse, M. Kress, F. Dautry, and D. Weil PMCID: PMC1950551 Site-specific modification of Shigella flexneri virF mRNA by tRNA-guanine transglycosylase in vitro Julie K. Hurt, Sureyya Olgen, and George A. Garcia PMCID: PMC1950534 Structural Biology The crystal structure of the Thermus aquaticus DnaB helicase monomer Scott Bailey, William K. Eliason, and Thomas A. Steitz PMCID: PMC1950529 Adaptation of the base-paired double-helix molecular architecture to extreme pressure Eric Girard, Thierry Prangé, Anne-Claire Dhaussy, Evelyne Migianu-Griffoni, Marc Lecouvey, Jean-Claude Chervin, Mohamed Mezouar, Richard Kahn, and Roger Fourme PMCID: PMC1950552 Determinants for DNA target structure selectivity of the human LINE-1 retrotransposon endonuclease Kostas Repanas, Nora Zingler, Liliana E. Layer, Gerald G. Schumann, Anastassis Perrakis, and Oliver Weichenrieder PMCID: PMC1950540 Genomics Detecting laterally transferred genes: use of entropic clustering methods and genome position Rajeev K. Azad and Jeffrey G. Lawrence PMCID: PMC1950545 iGentifier: indexing and large-scale profiling of unknown transcriptomes Achim Fischer, Alistair Lenhard, Heike Tronecker, Yvonne Lorat, Marcel Kraenzle, Oliver Sorgenfrei, Tim Zeppenfeld, Michael Haushalter, Gerhard Vogt, Ulrich Gruene, Annette Meyer, Ulrich Handlbichler, Patrick Schweizer, and Leo Gaelweiler PMCID: PMC1950539 Intron length distributions and gene prediction Scott William Roy and David Penny PMCID: PMC1950532 Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline Zasha Weinberg, Jeffrey E. Barrick, Zizhen Yao, Adam Roth, Jane N. Kim, Jeremy Gore, Joy Xin Wang, Elaine R. Lee, Kirsten F. Block, Narasimhan Sudarsan, Shane Neph, Martin Tompa, Walter L. Ruzzo, and Ronald R. Breaker PMCID: PMC1950547 Chemistry Quantification of oxidative single-base and intrastrand cross-link lesions in unmethylated and CpG-methylated DNA induced by Fenton-type reagents Huachuan Cao and Yinsheng Wang PMCID: PMC1976268 Computational Biology The identification of complete domains within protein sequences using accurate E-values for semi-global alignment Maricel G. Kann, Sergey L. Sheetlin, Yonil Park, Stephen H. Bryant, and John L. Spouge PMCID: PMC1950549 Reconstructing the evolution of the mitochondrial ribosomal proteome Paulien Smits, Jan A. M. Smeitink, Lambert P. van den Heuvel, Martijn A. Huynen, and Thijs J. G. Ettema PMCID: PMC1950548 A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing Debopriya Das, Tyson A. Clark, Anthony Schweitzer, Miki Yamamoto, Henry Marr, Josh Arribere, Simon Minovitsky, Alexander Poliakov, Inna Dubchak, John E. Blume, and John G. Conboy PMCID: PMC1950531 Nucleic Acid Enzymes Novel activity of eukaryotic translocase, eEF2: dissociation of the 80S ribosome into subunits with ATP but not with GTP Natalia Demeshkina, Go Hirokawa, Akira Kaji, and Hideko Kaji PMCID: PMC1950535 Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI Shuang-Yong Xu, Zhenyu Zhu, Penghua Zhang, Siu-Hong Chan, James C. Samuelson, Jianping Xiao, Debra Ingalls, and Geoffrey G. Wilson PMCID: PMC1950550 Parallel dimerization of a PrrC-anticodon nuclease region implicated in tRNALys recognition Daniel Klaiman, Michal Amitsur, Shani Blanga-Kanfi, Michal Chai, Darrell R. Davis, and Gabriel Kaufmann PMCID: PMC1950546 Binding parameters and thermodynamics of the interaction of the human cytomegalovirus DNA polymerase accessory protein, UL44, with DNA: implications for the processivity mechanism Arianna Loregian, Elisa Sinigalia, Beatrice Mercorelli, Giorgio Palù, and Donald M. Coen PMCID: PMC1950537 Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence Gintautas Tamulaitis, Mindaugas Zaremba, Roman H. Szczepanowski, Matthias Bochtler, and Virginijus Siksnys PMCID: PMC1950555 Enantioselectivity of human AMP, dTMP and UMP-CMP kinases Julie A.C. Alexandre, Béatrice Roy, Dimitri Topalis, Sylvie Pochet, Christian Périgaud, and Dominique Deville-Bonne PMCID: PMC1950558 |
