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At least 145 records · Page 8Linked to original sources
PubMed1990

Conditions required for the bactericidal activity of 4-quinolones against Serratia marcescens.

The conditions required to kill Serratia marcescens with nalidixic acid, ciprofloxacin, norfloxacin or ofloxacin were determined in nutrient broth and in phosphate-buffered saline. They were found to be similar to the conditions required for these 4-quinolones to kill Escherichia coli. Bacterial RNA synthesis and bacterial cell division were essential for the bactericidal activity of nalidixic acid but all three fluoroquinolones were bactericidal against non-dividing S. marcescens. However, as with E. coli, bacterial RNA synthesis was essential for the bactericidal activity of norfloxacin though this was not required to kill S. marcescens with ciprofloxacin or ofloxacin.

Anti-Bacterial Agents↗
PubMed2005

Intermediate states of ribonuclease III in complex with double-stranded RNA.

Bacterial ribonuclease III (RNase III) can affect RNA structure and gene expression in either of two ways: as a processing enzyme that cleaves double-stranded (ds) RNA, or as a binding protein that binds but does not cleave dsRNA. We previously proposed a model of the catalytic complex of RNase III with dsRNA based on three crystal structures, including the endonuclease domain of RNase III with and without bound metal ions and a dsRNA binding protein complexed with dsRNA. We also reported a noncatalytic assembly observed in the crystal structure of an RNase III mutant, which binds but does not cleave dsRNA, complexed with dsRNA. We hypothesize that the RNase III*dsRNA complex can exist in two functional forms, a catalytic complex and a noncatalytic assembly, and that in between the two forms there may be intermediate states. Here, we present four crystal structures of RNase III complexed with dsRNA, representing possible intermediates.

Base Sequence↗
PubMed1993

The use of a chemiluminescence-linked universal bacterial ribosomal RNA gene probe and blood gas analysis for the rapid detection of bacterial contamination in white cell-reduced and nonreduced platelets.

Because of the rising incidence of bacterial growth and septic platelet transfusions in aging units, platelet storage is currently limited in the United States to 5 days. This approved shelf life of platelets might be altered if methods were devised to rapidly detect infected units and/or to decrease the incidence of bacterially contaminated platelets. An investigation was conducted on the effect of a prototype blood collection system with an in-line filter for the production of white cell-reduced platelet-rich plasma on the growth of bacteria in platelets prepared from whole blood that had been inoculated with Staphylococcus epidermidis. Additional studies were conducted with a chemiluminescence-linked ribosomal RNA (rRNA) gene probe and with blood gas analysis to identify possible methods for the rapid detection of bacterial contamination. All units were followed for 9 days of storage. The filtration of the platelet-rich plasma resulted in an approximate 2 log10 reduction in white cells with an average loss of 6.7 percent of platelets. Filtration did not appear to alter bacterial growth. In all platelet units that supported growth, pO2 dropped to negligible values and pCO2 rose relative to culture-negative units. The changes were most sensitive and specific beyond 5 days of storage. The universal bacterial rRNA probe assay was able to detect S. epidermidis in concentrations as low as 1 x 10(3) colony-forming units per mL in some cases and reliably detected all units contaminated at a concentration of 1 x 10(4) colony-forming units per mL.(ABSTRACT TRUNCATED AT 250 WORDS)

Blood Gas Analysis↗
PubMed2006

Association between the presence of bacterial 16S RNA in prostate specimens taken during transurethral resection of prostate and subsequent risk of prostate cancer (Sweden).

OBJECTIVE: To study bacterial 16S RNA in archival prostate samples from 352 patients with benign prostate hyperplasia (BPH) and evaluate whether the presence of bacterial DNA was different in those who later developed prostate cancer (n = 171) and in the matched controls that did not progress to cancer (n = 181). METHODS: 16S DNA PCR followed by cloning and sequencing the positive samples. RESULTS: In 96/352 (27%) of the prostate tissue specimens 16S RNA were detected. Sequence analysis revealed Propionibacterium acnes as the predominant microorganism (23% of 16S RNA positive patients). The second most frequent isolate-Escherichia coli was found in 12 (12%) patients. The other isolates included Pseudomonas sp. (3 patients), Actinomyces sp. (2), Streptococcus mutans (1), Corynebacterium sp. (2), Nocardioides sp. (1), Rhodococcus sp. (1) Veillonella sp. (2). In P. acnes positive samples 62% exhibited severe histological inflammation versus 50% in the bacteria-negative group (p = 0.602). The presence of P. acnes in the prostate was associated with prostate cancer development (OR 2.17, 95% CI 0.77-6.95). CONCLUSIONS: This study has revealed P. acnes as the most common bacteria in the prostate in BPH. Further studies are needed to clarify its role in contributing to the development of prostatic inflammation and prostate cancer.

Aged↗
PubMed2004

Cutting edge: innate immune system discriminates between RNA containing bacterial versus eukaryotic structural features that prime for high-level IL-12 secretion by dendritic cells.

RNA derived from bacterial but not eukaryotic sources, when transfected into human monocyte-derived dendritic cell precursors, induces high-level IL-12 secretion in conjunction with dendritic cell maturation stimuli. In vitro-transcribed mRNA that mimics the structure of bacterial mRNA in the lack of a long 3'-poly(A) tail likewise induces IL-12 secretion, but this property is lost upon efficient enzymatic 3'-polyadenylation. Among other tested RNAs, only polyuridylic acid induced IL-12 p70. This RNA response phenomenon appears biologically distinct from the classically defined response to dsRNA. RNA-transfected APC also polarize T cells in an IL-12-dependent manner toward the IFN-gamma(high)IL-5 (low) Th1 phenotype, suggesting a link between the detection of appropriately structured RNA and the skewing of immune responses toward those best suited for controlling intracellular microbes. RNA structured to emulate bacterial patterns constitutes a novel vaccine strategy to engender polarized Th1-type immune responses.

3' Untranslated Regions↗
PubMed2002

Adaptive evolution after gene duplication.

One of the two ribonuclease genes in a leaf-eating monkey has adapted to a role in the digestion of bacterial RNA. Following duplication of the ancestral ribonuclease gene, adaptation occurred through a series of changes in the amino acid sequence of the protein it encodes. This example is a good illustration of how specialization of protein function after gene duplication can be as source of novel protein functions.

Adaptation, Biological↗
PubMedDate not supplied

Properties of RNase A immobilized on magnetic Poly(2-hydroxyethyl methacrylate) microspheres.

Magnetic hydrogel microspheres 1.5 microm in size were prepared by dispersion copolymerization of 2-hydroxyethyl methacrylate and ethylene dimethacrylate in the presence of magnetite, which formed the core of the particles. RNase A was coupled to the particles by the cyanuric chloride method. Gel electrophoresis of plasmid DNA pUC 19 (contaminated by bacterial RNA) confirmed RNA degradation with the immobilized enzyme. The effect of temperature and pH on the relative activity of immobilized RNase A was estimated after incubation of the samples at different temperatures (30-80 degrees C) and pH (4.0-8.0). Maximum relative activity was observed at 70 degrees C and pH 6.5. The matrices based on magnetic poly(HEMA) had a low tendency to adsorb RNA.

Biotechnology↗
PubMed1977

Transformation in Naegleria gruberi: patterns of RNA synthesis examined by polyacrylamide gel electrophoresis.

Naegleria gruberi were grown on bacteria and methods were devised to free the cellular RNA from bacterial RNA contamination. Use of actinomycin D and cycloheximide showed that the transformation of Naegleria from amoeba to flagellate required RNA synthesis for 30 min and protein synthesis for 40 min after the initial stimulus of distilled water. Comparison of the patterns of RNA synthesized during transformation with those during growth indicated a considerable amount of new RNA produced during the phenotypic change. Most marked was the increase in RNA co-migrating on polyacrylamide gels with the small ribosomal sub-unit RNA, together with RNAs between the latter and transfer RNA. These results were compared with other published results using axenically-grown cells cells and sucrose density gradient centrifugation. Cells placed in 80 mM NaCl instead of distilled water fail to transform but the pattern of newly-synthesized RNAs was not significantly different from that seen in transforming cells. This suggested that high salt concentrations inhibit transformation by inhibiting synthesis and/or assembly of certain proteins rather than RNA synthesis. Eluted material from various regions of polyacrylamide gels containing RNA extracted from transforming cells was used in a cell-free system. Incorporation of 3H-glutamic acid but not 3H-tryptophan was stimulated by material extracted from the 18S regions of the gels.

Amoeba↗
PubMed1989

Rapid determination of bacterial ribosomal RNA sequences by direct sequencing of enzymatically amplified DNA.

Ribosomal RNA sequences are an appealing target for bacterial classification as well as for development of group- or species-specific DNA probes. Using the polymerase chain reaction and synthetic primers, the feasibility of this gene amplification technique for rapid sequence determination of the major 16S ribosomal RNA domains from small amounts of input DNA is demonstrated. Information useful for phylogenetic classification as well as for construction of specific DNA probes may be obtained by comparison with known sequences.

Bacteria↗
PubMed1994

Platelet bacterial contamination and the use of a chemiluminescence-linked universal bacterial ribosomal RNA gene probe.

BACKGROUND: Currently, the maximum outdate for platelets is 5 days, because of the increasing chance of bacterial growth over time. Various methods for rapid detection of bacterial contamination of blood components have been described, with mixed results and no general acceptance. A recently described, molecular biologic approach for the detection of bacterial contamination involves a chemiluminescence-linked universal DNA bacterial probe to a highly conserved bacterial region of ribosomal RNA (rRNA). STUDY DESIGN AND METHODS: A multicenter trial of a chemiluminescence-linked universal bacterial rRNA probe for the detection of bacterial contamination in platelet concentrates is described. At each of five sites, platelet concentrates (no older than 1 day from date of phlebotomy) were inoculated in triplicate with isolates of four bacterial species (Pseudomonas aeruginosa, Bacillus cereus, Staphylococcus epidermidis, and Staphylococcus aureus) to a final concentration of 10 to 50 colony-forming units (CFUs) per mL and in triplicate to a final concentration of 1000 CFUs per mL. At one site, an additional 6 platelet concentrates were inoculated with sterile saline to serve as controls. Inoculated units were then subjected periodically to quantitative cultures and probe analyses. A total of 126 platelet concentrates were studied over a period of 7 days (120 inoculated with bacteria and 6 with sterile saline). RESULTS: This assay was, in some cases, able to detect S. aureus bacterial contamination in the range of 100 to 1000 CFUs per mL; the majority of samples (B. cereus, P. aeruginosa, S. aureus, and S. epidermidis) with contamination exceeding 10(4) CFUs per mL; and all samples with contamination of 2.1 x 10(5) CFUs per mL or greater. Increasing the sample size from the recommended 0.4 mL to 1.0 mL resulted in an unacceptable loss of specificity (83.3%). CONCLUSION: The routine use of this assay would be expected to result in a decreased risk of septic platelet transfusion reactions and could lead to a lengthening of the current 5 day storage period for platelets. Further, the pooling of random-donor platelet concentrates before storage instead of immediately before transfusion may be possible if this rRNA probe is employed to detect bacteria in the pool.

Bacillus cereus↗
PubMed1991

A gene required for RNase P activity in Candida (Torulopsis) glabrata mitochondria codes for a 227-nucleotide RNA with homology to bacterial RNase P RNA.

We have mapped a gene in the mitochondrial DNA of Candida (Torulopsis) glabrata and shown that it is required for 5' end maturation of mitochondrial tRNAs. It is located between the tRNAfMet and tRNAPro genes, the same tRNA genes that flank the mitochondrial RNase P RNA gene in the yeast Saccharomyces cerevisiae. The gene is extremely AT rich and codes for AU-rich RNAs that display some sequence homology with the mitochondrial RNase P RNA from S. cerevisiae, including two regions of striking sequence homology between the mitochondrial RNAs and the bacterial RNase P RNAs. RNase P activity that is sensitive to micrococcal nuclease has been detected in mitochondrial extracts of C. glabrata. An RNA of 227 nucleotides that is one of the RNAs encoded by the gene that we mapped cofractionated with this mitochondrial RNase P activity on glycerol gradients. The nuclease sensitivity of the activity, the cofractionation of the RNA with activity, and the homology of the RNA with known RNase P RNAs lead us to propose that the 227-nucleotide RNA is the RNA subunit of the C. glabrata mitochondrial RNase P enzyme.

Base Sequence↗
PubMed1966

The effect of high ionic strength on the sedimentation properties of the biologically active component of bacterial ribonucleic acid.

1. The sedimentation properties of the fraction of bacterial RNA which stimulates the incorporation of amino acids into acid-insoluble material in vitro depend on the ionic strength of the sedimentation medium. 2. The different distributions of stimulatory activity found in centrifuged linear sucrose gradients loaded with bacterial RNA and containing 0.1m- or 0.6m-sodium chloride resemble closely the different sedimentation profiles of rapidly labelled RNA observed under the same conditions. 3. These findings agree with those of previous work of a similar nature (Willson & Gros, 1964) and demonstrate that the component of bacterial RNA preparations which stimulates the incorporation of amino acids into acid-insoluble peptides in vitro is contained in their rapidly labelled fraction.

Carbon Isotopes↗
PubMed1995

Lack of detection of enteroviral RNA or bacterial DNA in magnetic resonance imaging-directed muscle biopsies from twenty children with active untreated juvenile dermatomyositis.

OBJECTIVE: To investigate for the presence of increased titers of circulating antibody to putative infectious agents and for detectable viral RNA or bacterial DNA in children with active recent-onset juvenile dermatomyositis (DM). METHODS: Magnetic resonance imaging-directed muscle biopsies were performed in 20 children with active, untreated, recent-onset juvenile DM and in age-matched children with neurologic disease. Sera were tested for complement-fixing antibody to Coxsackievirus B (CVB), influenza A and B, parainfluenza 1 and 3, Mycoplasma pneumoniae, mumps, respiratory syncytial virus, and Reovirus; and by immunofluorescence for IgG antibody to Toxoplasma gondii cytomegalovirus and IgM antibody to Epstein-Barr virus. Muscle from juvenile DM patients and control children, CD-1 Swiss mice with and without CVB1 infection, and viral stock positive for CVB1-6 were tested using reverse-transcriptase polymerase chain reaction with 5 primer sets, 4 probes (1 Coxsackievirus, 3 Enterovirus), and universal primers for DNA. RESULTS: No increased antibody, viral RNA, or bacterial DNA was present in the juvenile DM patients or the control children. CONCLUSION: Juvenile DM may be triggered by unidentified agent(s) in the genetically susceptible host.

Adolescent↗
PubMed2005

Inhibition of RNA polymerase by streptolydigin: no cycling allowed.

Bacterial RNA polymerase is a common target for many antibiotics. In two recent papers in Cell and Molecular Cell, and describe a structural basis for inhibition of bacterial RNA polymerase by the antibiotic streptolydigin. Streptolydigin may prevent distortion of a "bridge" alpha helix postulated to occur during the nucleotide addition cycle of RNA polymerase or may block a small movement of the bridge helix that helps load nucleotide triphosphates into the active site.

Aminoglycosides↗