PubMed Central (PMC3 - NLM DTD)
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Archive of life sciences journal literature at the U.S. National Institutes of Health (NIH), developed and managed by NIH's National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM).
Mostrando recursos 121 - 140 de 141,942
121.
A Novel Bacterium Associated with Lymphadenitis in a Patient with Chronic Granulomatous Disease - Greenberg, David E; Ding, Li; Zelazny, Adrian M; Stock, Frida; Wong, Alexandra; Anderson, Victoria L; Miller, Georgina; Kleiner, David E; Tenorio, Allan R; Brinster, Lauren; Dorward, David W; Murray, Patrick R; Holland, Steven M
Chronic granulomatous disease (CGD) is a rare inherited disease of the phagocyte NADPH oxidase system causing defective production of toxic oxygen metabolites, impaired bacterial and fungal killing, and recurrent life-threatening infections. We identified a novel gram-negative rod in excised lymph nodes from a patient with CGD. Gram-negative rods grew on charcoal-yeast extract, but conventional tests could not identify it. The best 50 matches of the 16S rRNA (using BLAST) were all members of the family Acetobacteraceae, with the closest match being Gluconobacter sacchari. Patient serum showed specific band recognition in whole lysate immunoblot. We used mouse models of CGD to...
122.
New Perspectives on Host-Parasite Interplay by Comparative Transcriptomic and Proteomic Analyses of Schistosoma japonicum - Liu, Feng; Lu, Jiong; Hu, Wei; Wang, Sheng-Yue; Cui, Shu-Jian; Chi, Ming; Yan, Qing; Wang, Xin-Rong; Song, Huai-Dong; Xu, Xue-Nian; Wang, Ju-Jun; Zhang, Xiang-Lin; Zhang, Xin; Wang, Zhi-Qin; Xue, Chun-Liang; Brindley, Paul J; McManus, Donald P; Yang, Peng-Yuan; Feng, Zheng; Chen, Zhu; Han, Ze-Guang
Schistosomiasis remains a serious public health problem with an estimated 200 million people infected in 76 countries. Here we isolated ~ 8,400 potential protein-encoding cDNA contigs from Schistosoma japonicum after sequencing circa 84,000 expressed sequence tags. In tandem, we undertook a high-throughput proteomics approach to characterize the protein expression profiles of a number of developmental stages (cercariae, hepatic schistosomula, female and male adults, eggs, and miracidia) and tissues at the host-parasite interface (eggshell and tegument) by interrogating the protein database deduced from the contigs. Comparative analysis of these transcriptomic and proteomic data, the latter including 3,260 proteins with putative identities,...
123.
The MogR Transcriptional Repressor Regulates Nonhierarchal Expression of Flagellar Motility Genes and Virulence in Listeria monocytogenes - Shen, Aimee; Higgins, Darren E
Flagella are surface structures critical for motility and virulence of many bacterial species. In Listeria monocytogenes, MogR tightly represses expression of flagellin (FlaA) during extracellular growth at 37 °C and during intracellular infection. MogR is also required for full virulence in a murine model of infection. Using in vitro and in vivo infection models, we determined that the severe virulence defect of MogR-negative bacteria is due to overexpression of FlaA. Specifically, overproduction of FlaA in MogR-negative bacteria caused pleiotropic defects in bacterial division (chaining phenotype), intracellular spread, and virulence in mice. DNA binding and microarray analyses revealed that MogR represses...
125.
Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation - Hallier, Marc; Desreac, Jessie; Felden, Brice
During trans-translation, stalled bacterial ribosomes are rescued by small protein B (SmpB) and by transfer-messenger RNA (tmRNA). Stalled ribosomes switch translation from the defective messages to a short internal reading frame on tmRNA that tags the nascent peptide chain for degradation and recycles the ribosomes. We present evidences that SmpB binds the large and small ribosomal subunits in vivo and in vitro. The binding between SmpB and the ribosomal subunits is very tight, with a dissociation constant of 1.7 × 10?10 M, similar to its KD for the 70S ribosome or for tmRNA. tmRNA displaces SmpB from its 50S binding...
135.
An antibody-based microarray assay for small RNA detection - Hu, Zonglin; Zhang, Aixia; Storz, Gisela; Gottesman, Susan; Leppla, Stephen H.
Detection of RNAs on microarrays is rapidly becoming a standard approach for molecular biologists. However, current methods frequently discriminate against structured and/or small RNA species. Here we present an approach that bypasses these problems. Unmodified RNA is hybridized directly to DNA microarrays and detected with the high-affinity, nucleotide sequence-independent, DNA/RNA hybrid-specific mouse monoclonal antibody S9.6. Subsequent reactions with a fluorescently-labeled anti-mouse IgG antibody or biotin-labeled anti-mouse IgG together with fluorescently labeled streptavidin produces a signal that can be measured in a standard microarray scanner. The antibody-based method was able to detect low abundance small RNAs of Escherichia coli much more...
136.
Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups - Wels, Michiel; Francke, Christof; Kerkhoven, Robert; Kleerebezem, Michiel; Siezen, Roland J.
Cis-acting elements in Lactobacillus plantarum were predicted by comparative analysis of the upstream regions of conserved genes and predicted transcriptional units (TUs) in different bacterial genomes. TUs were predicted for two species sets, with different evolutionary distances to L.plantarum. TUs were designated cluster of orthologous transcriptional units (COT) when >50% of the genes were orthologous in different species. Conserved DNA sequences were detected in the upstream regions of different COTs. Subsequently, conserved motifs were used to scan upstream regions of all TUs. This method revealed 18 regulatory motifs only present in lactic acid bacteria (LAB). The 18 LAB-specific candidate regulatory...
137.
Computer simulation of chaperone effects of Archaeal C/D box sRNA binding on rRNA folding - Schoemaker, Ruud J. W.; Gultyaev, Alexander P.
Archaeal C/D box small RNAs (sRNAs) are homologues of eukaryotic C/D box small nucleolar RNAs (snoRNAs). Their main function is guiding 2?-O-ribose methylation of nucleotides in rRNAs. The methylation requires the pairing of an sRNA antisense element to an rRNA target site with formation of an RNARNA duplex. The temporary formation of such a duplex during rRNA maturation is expected to influence rRNA folding in a chaperone-like way, in particular in thermophilic Archaea, where multiple sRNAs with two binding sites are found. Here we investigate possible mechanisms of chaperone function of Archaeoglobus fulgidus and Pyrococcus abyssi C/D box sRNAs using...
138.
Aspects of large-scale chromatin structures in mouse liver nuclei can be predicted from the DNA sequence - Cioffi, Alfred; Fleury, Tomara J.; Stein, Arnold
The large amount of non-coding DNA present in mammalian genomes suggests that some of it may play a structural or functional role. We provide evidence that it is possible to predict computationally, from the DNA sequence, loci in mouse liver nuclei that possess distinctive nucleosome arrays. We tested the hypothesis that a 100 kb region of DNA possessing a strong, in-phase, dinucleosome period oscillation in the motif period-10 non-T, A/T, G, should generate a nucleosome array with a nucleosome repeat that is one-half of the dinucleosome oscillation period value, as computed by Fourier analysis of the sequence. Ten loci with...
139.
Structural model for the multisubunit Type IC restrictionmodification DNA methyltransferase M.EcoR124I in complex with DNA - Obarska, Agnieszka; Blundell, Alex; Feder, Marcin; Vejsadová, t?pánka; iáková, Eva; Weiserová, Marie; Bujnicki, Janusz M.; Firman, Keith
Recent publication of crystal structures for the putative DNA-binding subunits (HsdS) of the functionally uncharacterized Type I restrictionmodification (R-M) enzymes MjaXIP and MgeORF438 have provided a convenient structural template for analysis of the more extensively characterized members of this interesting family of multisubunit molecular motors. Here, we present a structural model of the Type IC M.EcoR124I DNA methyltransferase (MTase), comprising the HsdS subunit, two HsdM subunits, the cofactor AdoMet and the substrate DNA molecule. The structure was obtained by docking models of individual subunits generated by fold-recognition and comparative modelling, followed by optimization of inter-subunit contacts by energy minimization. The...
140.
NMR solution structures of LNA (locked nucleic acid) modified quadruplexes - Nielsen, Jakob T.; Arar, Khalil; Petersen, Michael
We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of the LNA nucleotides. However, local structural alterations are observed owing to the locked LNA sugars. In particular, a distinct change in the sugarphosphate backbone is observed at the G2pL3 and L2pL3 base steps and sequence dependent changes in the twist between tetrads are also seen. Both the LNA modified quadruplexes have raised thermostability as...
121.
