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PubMedDate not supplied

Direct immunologic activities of CpG DNA and implications for gene therapy.

Vertebrate immune systems have evolved the ability to detect and be activated by most microbial and viral DNAs by virtue of their content of unmethylated 'CpG motifs', which are selectively suppressed in vertebrate DNA. Because their CpGs are also unmethylated, the DNA in gene therapy vectors routinely induces direct immune stimulation through activating this host defense mechanism. Administration of such 'CpG DNA' by injection or inhalation triggers rapid activation of B cells, monocytes, macrophages, dendritic cells, and natural killer cells, along with the release of pro-inflammatory cytokines. These immune stimulatory effects can be prevented by chloroquine and other drugs that interfere with endosomal maturation or by the presence of certain neutralizing DNA sequences, which block the immune stimulatory CpG motifs. Aside from serving as the genetic code, DNA can have direct immune activities. Vertebrate immune systems have evolved a defense mechanism that is able to broadly detect most microbial and viral DNAs because of differences in the frequency and methylation of CpG dinucleotides in particular base contexts. B cells, monocytes, macrophages, and dendritic cells spontaneously take up DNA of any type. If the DNA contains these immune stimulatory 'CpG-S motifs', the cells become activated within minutes and begin producing pro-inflammatory cytokines such as IL-6 and IL-12 and upregulate expression of co-stimulatory molecules. This results in the activation of both innate and acquired immune responses. The pro-inflammatory effects of CpG-S motifs are opposed by CpG dinucleotides in certain distinct base contexts, termed neutralizing or CpG-N motifs. Increasing the ratio of CpG-S to CpG-N motifs enhances the immune stimulatory effects of DNA, even if the total level of CpGs in the DNA is not altered. While this is useful in generating enhanced genetic vaccines, the opposite strategy is likely to become useful for the generation of gene therapy vectors with reduced inflammatory effects.

Adjuvants, Immunologic↗

PubMed1990

[Studies of intestinal microbial flora in the post-BMT (bone marrow transplantation) patients under a protected environment].

The changes of microbial burdens of six patients with leukemia (four patients with acute leukemia; two patients with chronic leukemia) were studied before and after bone marrow transplantation (BMT) under protected isolation. Oral nonabsorbable and topical antibodies were administered prophylactically to all patients. Under a protected environment, genus and species number of intestinal microbial flora were not so decreased in all patients who were treated with antibiotics, but no episodes of severe septicemia were detected due to intestinal microbial flora. From many previous reports, the same pathogen was isolated from both blood culture and stool in the patients with septicemia, however, no septicemia developed in our cases in spite of residue of many intestinal bacteria. These data have demonstrated a significant advantage of treatment with protected isolation and intensive antibiotic prophylaxis through oral, topical and intravenous administration for severe infection prevention.

Adolescent↗

PubMed2006

On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer.

BACKGROUND: The origin of microbial ORFans, ORFs having no detectable homology to other ORFs in the databases, is one of the unexplained puzzles of the post-genomic era. Several hypothesis on the origin of ORFans have been suggested in the last few years, most of which based on selected, relatively small, subsets of ORFans. One of the hypotheses for the origin of ORFans is that they have been acquired thru lateral transfer from viruses. Here we carry out a comprehensive, genome-wide study on the origins of ORFans to quantify the strength of current evidence supporting this hypothesis. RESULTS: We performed similarity searches by querying all current ORFans against the public virus protein database. Surprisingly, we found that only 2.8% of all microbial ORFans have detectable homologs in viruses, while the percentage of non-ORFans with detectable homologs in viruses is 7.9%, a significantly higher figure. This suggests that the current evidence for the origin of ORFans from lateral transfer from viruses is at best weak. However, an analysis of individual genomes revealed a number of organisms with much higher percentages, many of them belonging to the Firmicutes and Gamma-proteobacteria. We provide evidence suggesting that the current virus database may be biased towards those viruses attacking Firmicutes and Gamma-proteobacteria. CONCLUSION: We conclude that as more viral genomes are sequenced, more microbial ORFans will find homologs in viruses, but this trend may vary much for individual genomes. Thus, lateral transfer from viruses alone is unlikely to explain the origin of the majority of ORFans in the majority of prokaryotes and consequently, other, not necessarily exclusive, mechanisms are likely to better explain the origin of the increasing number of ORFans.

Bacteria↗

PubMed2005

Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction.

Real-time polymerase chain reaction (PCR) is a highly sensitive method that can be used for the detection and quantification of microbial populations without cultivating them in anaerobic processes and environmental samples. This work was conducted to design primer and probe sets for the detection of methanogens using a real-time PCR with the TaqMan system. Six group-specific methanogenic primer and probe sets were designed. These sets separately detect four orders (Methanococcales, Methanobacteriales, Methanomicrobiales, and Methanosarcinales) along with two families (Methanosarcinaceae and Methanosaetaceae) of the order Methanosarcinales. We also designed the universal primer and probe sets that specifically detect the 16S rDNA of prokaryotes and of the domain Bacteria and Archaea, and which are fully compatible with the TaqMan real-time PCR system. Target-group specificity of each primer and probe set was empirically verified by testing DNA isolated from 28 archaeal cultures and by analyzing potential false results. In general, each primer and probe set was very specific to the target group. The primer and probe sets designed in this study can be used to detect and quantify the order-level (family-level in the case of Methanosarcinales) methanogenic groups in anaerobic biological processes and various environments.

DNA Primers↗

PubMed1988

[Microbial contamination of water by pipe and hose material. 1. Detection of colony count changes].

Materials may produce a growth of microorganisms by contact with water. Pipes and hoses with a narrow diameter have not yet been tested on their influence on the microbial colonization of the water. A harmful change has been discussed especially in dental treatment units. Pipes and hoses were tested in their influence on the microbial growth for half a year. Glass, high grade steel, copper and PTFE showed no increase in microorganisms or only a little in the beginning. The other tested materials, PVC, PE, PA, silicon and rubber, produced an intensive microbial growth.

Bacteria↗

PubMed2006

Microbial imprinted polypyrrole/poly(3-methylthiophene) composite films for the detection of Bacillus endospores.

The fabrication of Bacillus subtilis endospore imprinted conducting polymer films and subsequent electrochemical detection of bound spores is reported. Imprinted films were prepared by absorbing spores on the surface of glassy carbon electrodes upon which a polypyrrole, followed by a poly(3-methylthiophene), layer were electrochemically deposited. Spore template release was achieved through soaking the modified electrode in DMSO. Binding of endospores to imprinted films could be detected via impedance spectroscopy by monitoring changes in Y'' (susceptance) using Mn(II)Cl2 (0.5M pH 3) as the supporting electrolyte. Here, the change in Y'' could be correlated to spore densities between 10(4) and 10(7)cfu/ml. More sensitive detection of absorbed spores was achieved by following endospore germination via changes in film charge as measured using cyclic voltammetry. Here, imprinted films were submerged in spore suspensions to permit absorption, heat activated at 70 degrees C for 10 min prior to transferring to an electrochemical cell containing germination activators. By using the assay format it was possible to detect 10(2)cfu/ml. The observed changes in film charge could be attributed to the interaction of the supporting conducting polymer with dipicolinic acid (DPA) and other constituents released from the core in the course of germination. In all cases, it was not possible to regenerate the imprinted films without losing electrode response. In summary, the study has provided proof-of-concept for fabricating microbial imprinted films using conducting polymers.

Bacillus subtilis↗

PubMedDate not supplied

Characterization of microbial communities from coastal waters using microarrays.

Molecular methods, including DNA probes, were used to identify and enumerate pathogenic Vibrio species in the Chesapeake Bay; our data indicated that Vibrio vulnificus exhibits seasonal fluctuations in number. Our work included a characterization of total microbial communities from the Bay; development of microarrays that identify and quantify the diversity of those communities; and observation of temporal changes in those communities. To identify members of the microbial community, we amplified the 16S rDNA gene from community DNA isolated from a biofilm sample collected from the Chesapeake Bay in February, 2000. The resultant 75 sequences were 95% or more similar to 7 species including two recently described Shewanella species, baltica and frigidimarina, that have not been previously isolated from the Chesapeake. When the genera of bacteria from biofilm after culturing are compared to those detected by subcloning amplified 16S fragments from community DNA, the cultured sample exhibited a strong bias. In oysters collected in February, the most common bacteria were previously unknown. Based on our 16S findings, we are developing microarrays to detect these and other microbial species in these estuarine communities. The microarrays will detect each species using four distinct loci, with the multiple loci serving as an internal control. The accuracy of the microarray will be measured using sentinel species such as Aeromonas species, Escherichia coli, and Vibrio vulnificus. Using microarrays, it should be possible to determine the annual fluctuations of bacterial species (culturable and non-culturable, pathogenic and non-pathogenic). The data may be applied to understanding patterns of environmental change; assessing the "health" of the Bay; and evaluating the risk of human illness associated with exposure to and ingestion of water and shellfish.

Animals↗

PubMed2005

Direct microbial reduction and subsequent preservation of uranium in natural near-surface sediment.

The fate of uranium in natural systems is of great environmental importance. X-ray absorption near-edge spectroscopy (XANES) revealed that U(VI) was reduced to U(IV) in shallow freshwater sediment at an open pit in an inactive uranium mine. Geochemical characterization of the sediment showed that nitrate, Fe(III), and sulfate had also been reduced in the sediment. Observations of the sediment particles and microbial cells by scanning and transmission electron microscopy, coupled with elemental analysis by energy dispersive spectroscopy, revealed that uranium was concentrated at microbial cell surfaces. U(IV) was not associated with framboidal pyrite or nanometer-scale iron sulfides, which are presumed to be of microbial origin. Uranium concentrations were not detected in association with algal cells. Phylogenetic analyses of microbial populations in the sediment by the use of 16S rRNA and dissimilatory sulfite reductase gene sequences detected organisms belonging to the families Geobacteraceae and Desulfovibrionaceae. Cultivated members of these lineages reduce U(VI) and precipitate iron sulfides. The association of uranium with cells, but not with sulfide surfaces, suggests that U(VI) is reduced by the enzymatic activities of microorganisms. Uranium was highly enriched (760 ppm) in a subsurface black layer in unsaturated sediment sampled from a pit which was exposed to seasonal fluctuations in the pond level. XANES analysis showed that the majority of uranium in this layer was U(IV), indicating that uranium is preserved in its reduced form after burial.

DNA, Bacterial↗

PubMed2002

Quantification of microcystin-producing cyanobacteria and E. coli in water by 5'-nuclease PCR.

AIMS: 5'-Nuclease (real-time, quantitative) PCR methodologies were developed and applied as diagnostic tools for the detection of microcystin-producing cyanobacteria and Escherichia coli in water. METHODS AND RESULTS: PCR was used to detect regions of the lacZ gene in E. coli, and the microcystin synthetase gene in microcystin-producing cyanobacteria. In environmental water samples, natural inhibitors to PCR were effectively removed with a prefiltration step and an EDTA wash. A lower detection limit of 10 cells ml(-1) was obtained with endpoint PCR detection. 5'-Nuclease PCR was used for microbial quantification of 1 ml inoculated water samples. We were able to detect down to three copies of our target genes per sample within about 2 h (post-DNA isolation) for both E. coli and microcystin-producing cyanobacteria. CONCLUSIONS: 5'-Nuclease PCR offers a rapid and sensitive method of bacterial quantification in water samples. SIGNIFICANCE AND IMPACT OF THE STUDY: 5'-Nuclease PCR can be adopted as an effective diagnostic tool for monitoring microbiological water quality, through coliform quantification, and detection of other waterborne microbial pathogens.

Cyanobacteria↗

PubMed2000

New genus-specific primers for the PCR identification of members of the genus Saccharomonospora and evaluation of the microbial diversity of wild-type isolates of Saccharomonospora detected from soil DNAs.

Members of the genus Saccharomonospora are isolated infrequently, probably due to the low occurrence of these actinomycetes in the environment. Although members of this genus can easily be identified by micromorphological criteria, the extensive chemotaxonomic characterization of each new isolate is a time-consuming task which cannot always be undertaken when handling large numbers of strains as is the case in natural products screening programmes. In this work, the design of one set of genus-specific oligonucleotides which allows rapid detection of members of the genus Saccharomonospora by means of PCR-specific amplification is presented. The genus specificity of these primers was validated on a wide range of collection and wild-type strains, and subsequently applied to evaluate the presence of representatives of this taxon directly from soil DNAs. Partial 16S rDNA sequencing of representative wild-type strains was used to validate their genus assignment. Further analyses of PCR fingerprinting patterns and 16S-23S internal transcribed spacer sequences were used to determine the diversity of wild-type isolates obtained from soils. This study shows the usefulness of the application of these primers for the direct identification of members of this genus and in assessment of its occurrence within natural microbial habitats.

Actinomycetales↗

PubMed2003

Comparison of real-time PCR with SYBR Green I or 5'-nuclease assays and dot-blot hybridization with rDNA-targeted oligonucleotide probes in quantification of selected faecal bacteria.

PCR primers and hybridization probes were designed for the 16S rRNA genes of six bacterial species or groups typically present in human faeces or used in the dairy industry. The primers and probes were applied for quantification of the target bacterial genomes added in artificial DNA mixtures or faecal DNA preparations, using dot-blot hybridization and real-time PCR with SYBR Green I and TaqMan chemistries. Dot-blot hybridization with (33)P-labelled oligonucleotide probes was shown to detect a 10 % target DNA fraction present in mixed DNA samples. Applicability of the rDNA-targeted oligonucleotide probes without pre-enrichment of the 16S gene pool by PCR was thus limited to the detection of the predominant microbial groups. Real-time PCR was performed using a 96-well format and was therefore feasible for straightforward analysis of large sample amounts. Both chemistries tested could detect and quantify a subpopulation of 0.01 % from the estimated number of total bacterial genomes present in a population sample. The linear range of amplification varied between three and five orders of magnitude for the specific target genome while the efficiency of amplification for the individual PCR assays was between 88.3 and 104 %. Use of a thermally activated polymerase was required with the SYBR Green I chemistry to obtain a similar sensitivity level to the TaqMan chemistry. In comparison to dot-blot hybridization, real-time PCR was easier and faster to perform and also proved to have a superior sensitivity. The results suggest that real-time PCR has a great potential for analysis of the faecal microflora.

Bacteria↗

PubMed1999

Salivary lactoferrin and low-Mr mucin MG2 in Actinobacillus actinomycetemcomitans-associated periodontitis.

Concentrations and output of lactoferrin and of low-Mr mucin MG2 were determined in saliva of subjects suffering from Actinobacillus actinomycetemcomitans-associated periodontal disease and healthy subjects. Periodontal patients were clinically examined and a microbiological sample was taken from the deepest bleeding pockets in each quadrant. The number of viable A. actinomycetemcomitans was determined in the sampled sites of each patient. The MG2 output in the diseased subjects (13.6 microg protein/min) was decreased at least by a factor three compared to periodontal healthy subjects (44.3 microg protein/min). On the other hand, output of lactoferrin was not significantly different in healthy (9.5 microg/min) and diseased subjects (7.6 microg/min). Western analyses demonstrated a higher iron-saturation of lactoferrin in diseased subjects in comparison with the healthy subjects. Lactoferrin degrading enzymes, probably derived from microbial sources, could be detected in saliva of the periodontally diseased subjects, but not in saliva of healthy subjects. The combination of iron-saturation and degradation of lactoferrin suggests that anti-microbial properties of lactoferrin are diminished in periodontitis patients. Moreover, the low concentration of mucin MG2 suggests a decline in mucin defence and consequently a higher susceptibility for oral infection. A negative correlation (r= -0.4, p < 0.05) between the number of subgingival A. actinomycetemcomitans and lactoferrin in saliva suggested that low concentrations of lactoferrin favour the growth of the bacterium. These data indicate that a decline in the salivary defence system might increase the risk for oral infection by A. actinomycetemcomitans.

Actinobacillus Infections↗

PubMed2006

The efficacy of an antiseptic and microbial anti-adhesive ear cleanser in dogs with otitis externa.

A new antimicrobial ear cleanser was evaluated for the treatment of bacterial and yeast ear infection in dogs. Forty-five dogs with erythemato-ceruminous or purulent otitis externa were randomly allocated to two treatment groups: reference ear cleanser (Epiotic, Virbac) or test ear cleanser (Epiotic Advanced, Virbac). Ear cleansing was performed twice daily for 2 weeks, and no other treatment was allowed. By week 2, clinical (exudate quantity, erythema, stenosis, excoriation, and odor) and discomfort (pain, ear scratching, and head shaking) scores were significantly decreased (P < .0001 for all) and no microbial overgrowth could be detected in 25 (64.1%) and 32 (68.1%) ears treated with Epiotic and Epiotic Advanced, respectively. The new pH-balanced, propylene glycol-free test ear cleanser, which incorporates microbial adhesin-blocking carbohydrates, proved as effective as the reference acidic formula.

Administration, Topical↗

PubMed1986

Growth of four microorganisms in polyethylene glycol-electrolyte lavage solution.

The growth of Staphylococcus epidermidis, Serratia marcescens, Pseudomonas aeruginosa, and Candida albicans in reconstituted polyethylene glycol-electrolyte lavage solution (PEG-ELS) stored under refrigeration and at room temperature was studied. A standard inoculum of each organism was added to one of four 4-L containers (one organism per container). From each container 28 aliquots of 25-mL each were removed and stored under refrigeration or at room temperature. One container was not inoculated and served as a control. Duplicate aliquots of the inoculated and the control solutions were filtered and incubated for quantification of organisms on days 0, 1, 2, 4, 8, 16, and 30. Solutions stored at room temperature supported the growth of S. marcescens and Ps. aeruginosa. The counts of these organisms increased to approximately 10(6) colony-forming units (CFU)/mL over 16 days. The counts of Staph. epidermidis in solutions stored at room temperature increased slightly over the first 24 hours and declined steadily to zero after day 4. C. albicans reached a maximum colony count of 5.84 cfu/mL on day 16 and steadily declined to 0.92 cfu/mL on day 30. Solutions stored under refrigeration did not support the growth of any microorganisms. Microbial growth was not detected in any of the control solutions over the 30-day study period. The polyethylene glycol-electrolyte lavage solution studied here should be refrigerated after reconstitution to minimize microbial growth. This solution may be used for up to 30 days after reconstitution when it is stored under refrigeration.

Bacteria↗

PubMed2005

Confirmatory and quantitative analysis of beta-lactam antibiotics in bovine kidney tissue by dispersive solid-phase extraction and liquid chromatography-tandem mass spectrometry.

A simple, rapid, rugged, sensitive, and specific method for the confirmation and quantitation of 10 beta-lactam antibiotics in fortified and incurred bovine kidney tissue has been developed. The method uses a simple solvent extraction, dispersive solid-phase extraction (dispersive-SPE) cleanup, and liquid chromatography-tandem mass spectrometry (LC/MS/MS) for confirmation and quantitation. Dispersive-SPE greatly simplifies and accelerates sample cleanup and improves overall recoveries compared with conventional SPE cleanup. The beta-lactam antibiotics tested were as follows: deacetylcephapirin (an antimicrobial metabolite of cephapirin), amoxicillin, desfuroylceftiofur cysteine disulfide (DCCD, an antimicrobial metabolite of ceftiofur), ampicillin, cefazolin, penicillin G, oxacillin, cloxacillin, naficillin, and dicloxacillin. Average recoveries of fortified samples were 70% or better for all beta-lactams except DCCD, which had an average recovery of 58%. The LC/MS/MS method was able to demonstrate quantitative recoveries at established tolerance levels and provide confirmatory data for unambiguous analyte identification. The method was also tested on 30 incurred bovine kidney samples obtained from the USDA Food Safety and Inspection Service, which had previously tested the samples using the approved semiquantitative microbial assay. The results from the quantitative LC/MS/MS analysis were in general agreement with the microbial assay for 23 samples although the LC/MS/MS method was superior in that it could specifically identify which beta-lactam was present and quantitate its concentration, whereas the microbial assay could only identify the type of beta-lactam present and report a concentration with respect to the microbial inhibition of a penicillin G standard. In addition, for 6 of the 23 samples, LC/MS/MS analysis detected a penicillin and a cephalosporin beta-lactam, whereas the microbial assay detected only a penicillin beta-lactam. For samples that do not fall into the "general agreement" category, the most serious discrepancy involves two samples where the LC/MS/MS method detected a violative level of a cephalosporin beta-lactam (deacetylcephapirin) in the first sample and a possibly violative level of desfuroylceftiofur in the second, whereas the microbial assay identified the two samples as having only violative levels of a penicillin beta-lactam.

Animals↗

PubMed1980

Fluorometric determination of adenosine nucleotide derivatives as measures of the microfouling, detrital, and sedimentary microbial biomass and physiological status.

Adenosine, adenine, cyclic adenosine monophosphate (AMP), AMP, nicotinamide adenine dinucleotide, adenosine diphosphate, and adenosine triphosphate (ATP) were recovered quantitatively from aqueous portions of lipid extracts of microfouling, detrital, and sedimentary microbial communities. These could be detected quantitatively in the picomolar range by forming their 1-N-etheno derivatives and analyzing by high-pressure liquid chromatography with fluorescence detection. Lipid extraction and subsequent analysis allowed the simultaneous measurement of the microbial community structure, total microbial biomass with the quantitative recovery of the adenine-containing cellular components, which were protected from enzymatic destruction. This extraction and fluorescent derivatization method showed equivalency with the luciferin-luciferase method for bacterial ATP measurements. Quick-freezing samples in the field with dry ice-acetone preserved the ATP and energy charge (a ratio of adenosine nucleotides) for analysis at remote laboratories. The metabolic lability of ATP in estuarine detrital and microfouling communities, as well as bacterial monocultures of constant biomass, showed ATP to be a precarious measure of biomass under some conditions. Combinations of adenosine and adenine nucleotides gave better correlations with microbial biomass measured as extractable lipid phosphate in the detrital and microfouling microbial communities than did ATP alone. Stresses such as anoxia or filtration are reflected in the rapid accumulation of intracellular adenosine and the excretion of adenosine and AMP into the surrounding milieu. Increases in AMP and adenosine may prove to be more sensitive indicators of metabolic status than the energy charge.

Journal Article↗

PubMed1998

Identification of bacterial species on or in crevicular epithelial cells from healthy and periodontally diseased patients using DNA-DNA hybridization.

The purpose of this investigation was to identify bacterial species present on or in crevicular epithelial cells in healthy and diseased sites using DNA probes. In order to achieve this aim, further improvements were made in the separation of unattached bacteria from those adherent to epithelial cells isolated from the human gingival crevice or periodontal pocket. Then the DNA probes were used to determine the prevalence of detectable DNA from 15 microbial species on or in crevicular epithelial cells. One sample was taken from a single subgingival site in each of 51 individuals ranging in age from 19 to 45 years. Samples were taken from 27 sites of clinically healthy subjects and 24 samples were taken from subjects having periodontally diseased sites. DNA-DNA hybridization indicated that a majority of epithelial cells from healthy sites (63%) were in contact with or harbored Streptococcus oralis. On the other hand, species such as Bacteroides forsythus, Prevotella intermedia, Capnocytophaga ochracea and Campylobacter rectus were more frequently detected in elevated numbers in periodontally diseased sites. Cluster analysis of the microbial profiles generally aggregated subjects with and without periodontitis into separate cluster groups. The cluster patterns suggest the possibility that microbial complexes will be, in part, determined by the receptors available on the epithelial cells.

Adult↗

PubMed2000

Toll signaling pathways in the innate immune response.

The Toll signaling pathway, which is required for the establishment of the dorsal-ventral axis in Drosophila embryos, plays an important role in the response of larval and adult Drosophila to microbial infections. Recent genetic evidence has shown that a mammalian Toll-like receptor, mouse Tlr4, is the signal transducing receptor activated by bacterial lipopolysaccharide. Thus, Toll-like receptors appear to detect a variety of microbial components and to trigger a defensive reaction in both Drosophila and mammals. Genetic data from both Drosophila and mice have defined components required for activation of Toll-like receptors and for the downstream pathways activated by the Toll-like receptors.

Animals↗