| | Molecular Biology Proteomic analysis of the U1 snRNP of Schizosaccharomyces pombe reveals three essential organism-specific proteins Alain N. S. Newo, Martin Lützelberger, Claudia A. Bottner, Jürgen Wehland, Josef Wissing, Lothar Jänsch, and Norbert F. Käufer PMCID: PMC1865046 Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques S. Semprini, T.J. Troup, N. Kotelevtseva, K. King, J.R.E. Davis, L.J. Mullins, K.E. Chapman, D.R. Dunbar, and J.J. Mullins PMCID: PMC1865043 Interplay between CRP-cAMP and PII-Ntr systems forms novel regulatory network between carbon metabolism and nitrogen assimilation in Escherichia coli Xian-Jun Mao, Yi-Xin Huo, Martin Buck, Annie Kolb, and Yi-Ping Wang PMCID: PMC1865078 Translational repression of mouse mu opioid receptor expression via leaky scanning Kyu Young Song, Cheol Kyu Hwang, Chun Sung Kim, Hack Sun Choi, Ping-Yee Law, Li-Na Wei, and Horace H. Loh PMCID: PMC1865057 Rabies virus matrix protein interplay with eIF3, new insights into rabies virus pathogenesis Anastassia V. Komarova, Eléonore Real, Andrew M. Borman, Michèle Brocard, Patrick England, Noël Tordo, John W.B. Hershey, Katherine M. Kean, and Yves Jacob PMCID: PMC1865048 Quantitative and mechanism-based investigation of post-nuclear delivery events between adenovirus and lipoplex Susumu Hama, Hidetaka Akita, Shinya Iida, Hiroyuki Mizuguchi, and Hideyoshi Harashima PMCID: PMC1865055 Human base excision repair complex is physically associated to DNA replication and cell cycle regulatory proteins Eleonora Parlanti, Giada Locatelli, Giovanni Maga, and Eugenia Dogliotti PMCID: PMC1865045 Interaction between trichosanthin, a ribosome-inactivating protein, and the ribosomal stalk protein P2 by chemical shift perturbation and mutagenesis analyses Denise S.B. Chan, Lai-On Chu, Ka-Ming Lee, Priscilla H.M. Too, Kit-Wan Ma, Kong-Hung Sze, Guang Zhu, Pang-Chui Shaw, and Kam-Bo Wong PMCID: PMC1865052 Ubiquitin-interaction motifs of RAP80 are critical in its regulation of estrogen receptor α Jun Yan, Yong-Sik Kim, Xiao-Ping Yang, Michael Albers, Manfred Koegl, and Anton M. Jetten PMCID: PMC1865050 Ovol1 represses its own transcription by competing with transcription activator c-Myb and by recruiting histone deacetylase activity Mahalakshmi Nair, Virginia Bilanchone, Kori Ortt, Satrajit Sinha, and Xing Dai PMCID: PMC1865076 RNA Eukaryotic ribosomal protein RPS25 interacts with the conserved loop region in a dicistroviral intergenic internal ribosome entry site Takashi Nishiyama, Hiroshi Yamamoto, Toshio Uchiumi, and Nobuhiko Nakashima PMCID: PMC1865070 Small ncRNA transcriptome analysis from kinetoplast mitochondria of Leishmania tarentolae Monika J. Madej, Juan D. Alfonzo, and Alexander Hüttenhofer PMCID: PMC1865066 Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism Nasslie Choonee, Sergine Even, Lena Zig, and Harald Putzer PMCID: PMC1865079 Group II intron in Bacillus cereus has an unusual 3′ extension and splices 56 nucleotides downstream of the predicted site Fredrik B. Stabell, Nicolas J. Tourasse, Solveig Ravnum, and Anne-Brit Kolstø PMCID: PMC1865049 The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation Marcel Ooms, Daniel Cupac, Truus E. M. Abbink, Hendrik Huthoff, and Ben Berkhout PMCID: PMC1865047 Structural Biology Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation Marzanna Deniziak, Claude Sauter, Hubert Dominique Becker, Caroline Alexandra Paulus, Richard Giegé, and Daniel Kern PMCID: PMC1865053 Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context Fabián A. Rodríguez, Yuqin Cai, Chin Lin, Yijin Tang, Alexander Kolbanovskiy, Shantu Amin, Dinshaw J. Patel, Suse Broyde, and Nicholas E. Geacintov PMCID: PMC1865068 Insights into Fanconi Anaemia from the structure of human FANCE Ravi K. Nookala, Shobbir Hussain, and Luca Pellegrini PMCID: PMC1865054 Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing–duplex structural transition Xiaoyan Sun, Qi Zhang, and Hashim M. Al-Hashimi PMCID: PMC1865058 Modeling RNA tertiary structure motifs by graph-grammars Karine St-Onge, Philippe Thibault, Sylvie Hamel, and François Major PMCID: PMC1865062 Interactions of Kid–Kis toxin–antitoxin complexes with the parD operator-promoter region of plasmid R1 are piloted by the Kis antitoxin and tuned by the stoichiometry of Kid–Kis oligomers Maria C. Monti, Ana M. Hernández-Arriaga, Monique B. Kamphuis, Juan López-Villarejo, Albert J. R. Heck, Rolf Boelens, Ramón Díaz-Orejas, and Robert H. H. van den Heuvel PMCID: PMC1865072 Survey and Summary The structure and function of small nucleolar ribonucleoproteins Steve L. Reichow, Tomoko Hamma, Adrian R. Ferré-D'Amaré, and Gabriele Varani PMCID: PMC1865073 Genomics Transgenerational changes in the genome stability and methylation in pathogen-infected plants: (Virus-induced plant genome instability) Alexander Boyko, Palak Kathiria, Franz J. Zemp, Youli Yao, Igor Pogribny, and Igor Kovalchuk PMCID: PMC1865051 Chemistry 2′-Fluoro-4′-thioarabino-modified oligonucleotides: conformational switches linked to siRNA activity Jonathan K. Watts, Niloufar Choubdar, Kashinath Sadalapure, Francis Robert, Alexander S. Wahba, Jerry Pelletier, B. Mario Pinto, and Masad J. Damha PMCID: PMC1865065 Methods Online A new method for accurate assessment of DNA quality after bisulfite treatment Mathias Ehrich, Scott Zoll, Sudipto Sur, and Dirk van den Boom PMCID: PMC1865059 Novel DNA probes with low background and high hybridization-triggered fluorescence Eugeny A. Lukhtanov, Sergey G. Lokhov, Vladimir V. Gorn, Mikhail A. Podyminogin, and Walt Mahoney PMCID: PMC1865069 Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method Zhongfa Liu, Shujun Liu, Zhiliang Xie, William Blum, Danilo Perrotti, Peter Paschka, Rebecca Klisovic, John Byrd, Kenneth K. Chan, and Guido Marcucci PMCID: PMC1865075 Combinatorial expression vector engineering for tuning of recombinant protein production in Escherichia coli Nina Bandmann and Per-Åke Nygren PMCID: PMC1865067 Alternating-electric-field-enhanced reversible switching of DNA nanocontainers with pH Youdong Mao, Dongsheng Liu, Shutao Wang, Songnian Luo, Wenxing Wang, Yanlian Yang, Qi Ouyang, and Lei Jiang PMCID: PMC1865044 Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells Lili Milani, Manu Gupta, Malin Andersen, Sumeer Dhar, Mårten Fryknäs, Anders Isaksson, Rolf Larsson, and Ann-Christine Syvänen PMCID: PMC1865061 Exploiting noise in array CGH data to improve detection of DNA copy number change Jing Hu, Jian-Bo Gao, Yinhe Cao, Erwin Bottinger, and Weijia Zhang PMCID: PMC1994778 An optimized method for detecting gamma-H2AX in blood cells reveals a significant interindividual variation in the gamma-H2AX response among humans Ismail Hassan Ismail, Tabasum Imran Wadhra, and Ola Hammarsten PMCID: PMC1865071 Computational Biology DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces Harianto Tjong and Huan-Xiang Zhou PMCID: PMC1865077 Localizing hotspots of antisense transcription Giacomo Finocchiaro, Maria Stella Carro, Stephanie Francois, Paola Parise, Valentina DiNinni, and Heiko Muller PMCID: PMC1865042 Nucleic Acid Enzymes Biochemical and genetic analysis of RNA cap guanine-N2 methyltransferases from Giardia lamblia and Schizosaccharomyces pombe Stéphane Hausmann, Alejandro Ramirez, Susanne Schneider, Beate Schwer, and Stewart Shuman PMCID: PMC1865056 A rapid reaction analysis of uracil DNA glycosylase indicates an active mechanism of base flipping Stuart R.W. Bellamy, Kuakarun Krusong, and Geoff S. Baldwin PMCID: PMC1865060 Homing endonuclease I-TevIII: dimerization as a means to a double-strand break Justin B. Robbins, Michelle Stapleton, Matthew J. Stanger, Dorie Smith, John T. Dansereau, Victoria Derbyshire, and Marlene Belfort PMCID: PMC1865063 Rapid determination of the active fraction of DNA repair glycosylases: a novel fluorescence assay for trapped intermediates Jeffrey O. Blaisdell and Susan S. Wallace PMCID: PMC1865064 The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase Sangeetha Vijayakumar, Brian R. Chapados, Kristina H. Schmidt, Richard D. Kolodner, John A. Tainer, and Alan E. Tomkinson PMCID: PMC1865074 |
