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Related Strains (relate + strain)
Selected AbstractsDesign and testing of ,genome-proxy' microarrays to profile marine microbial communitiesENVIRONMENTAL MICROBIOLOGY, Issue 2 2008Virginia I. Rich Summary Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a ,genome-proxy' microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to 13 of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual open reading frame, and distributed along each ,40,160 kbp contiguous genomic region. The targeted organisms or clones, and close relatives, were hybridized to the array both as pure DNA mixtures and as additions of cells to a background of coastal seawater. This prototype array correctly identified the presence or absence of the target organisms and their relatives in laboratory mixes, with negligible cross-hybridization to organisms having , ,75% genomic identity. In addition, the array correctly identified target cells added to a background of environmental DNA, with a limit of detection of ,0.1% of the community, corresponding to ,103 cells ml,1 in these samples. Signal correlated to cell concentration with an R2 of 1.0 across six orders of magnitude. In addition, the array could track a related strain (at 86% genomic identity to that targeted) with a linearity of R2 = 0.9999 and a limit of detection of ,1% of the community. Closely related genotypes were distinguishable by differing hybridization patterns across each probe set. This array's multiple-probe, ,genome-proxy' approach and consequent ability to track both target genotypes and their close relatives is important for the array's environmental application given the recent discoveries of considerable intrapopulation diversity within marine microbial communities. [source] One-bond 13C,13C coupling constants in alkyl-substituted cyclopropenes: experimental and theoretical studies,MAGNETIC RESONANCE IN CHEMISTRY, Issue 10 2002Krystyna Kamie, ska-Trela Abstract Measurements of one-bond carbon,carbon coupling constants, 1J(C, C), were performed for two series of compounds, alkyl-substituted cyclopropenes and cyclopropanes. The experimental data were complemented by a set of DFT-calculated J couplings for the parent cyclopropene (1), its methyl and silyl derivatives and, additionally, for 1-methylcyclobutene (3), 1-methylcyclopentene (4) and 1-methylcyclohexene (5) and good agreement was observed between the experimental and the calculated data; all the trends are perfectly maintained, including a dramatic decrease in the couplings across endocyclic single bonds in cyclopropene and its derivatives, and a significant decrease in the corresponding couplings in cyclobutene. Using the data obtained, the s characters of the carbon hybrid orbitals involved in the formation of the cyclopropene were calculated. The results clearly show that the ring closure and the related strain exerted upon the cyclopropene molecule only slightly disturb the electron structure of the double bond. The s character of the corresponding carbon orbital is 0.314 in cyclopropene vs the theoretical value of 0.333 in ethene. This is at variance with the endo- and exocyclic single bonds, where the s characters of the orbitals forming the endocyclic single bonds are much smaller than those of the bonds in the open-chain compounds, i.e. 0.229 (C-1 and/or C-2) and 0.166 (C-3). The s values calculated for the exocyclic CH bonds are 0.334 for C-3 and 0.456 for C-1 and/or C-2. Copyright © 2002 John Wiley & Sons, Ltd. [source] Contributions of the effector gene hopQ1-1 to differences in host range between Pseudomonas syringae pv. phaseolicola and P. syringae pv. tabaciMOLECULAR PLANT PATHOLOGY, Issue 6 2009PATRIZIA FERRANTE SUMMARY To study the role of type III-secreted effectors in the host adaptation of the tobacco (Nicotiana sp.) pathogen Pseudomonas syringae pv. tabaci, a selection of seven strains was first characterized by multilocus sequence typing (MLST) to determine their phylogenetic affinity. MLST revealed that all strains represented a tight phylogenetic group and that the most closely related strain with a completely sequenced genome was the bean (Phaseolus vulgaris) pathogen P. syringae pv. phaseolicola 1448A. Using primers designed to 21 P. syringae pv. phaseolicola 1448A effector genes, it was determined that P. syringae pv. phaseolicola 1448A shared at least 10 effectors with all tested P. syringae pv. tabaci strains. Six of the 11 effectors that failed to amplify from P. syringae pv. tabaci strains were individually expressed in one P. syringae pv. tabaci strain. Although five effectors had no effect on phenotype, growth in planta and disease severity of the transgenic P. syringae pv. tabaci expressing hopQ1-1Pph1448A were significantly increased in bean, but reduced in tobacco. We conclude that hopQ1-1 has been retained in P. syringae pv. phaseolicola 1448A, as this effector suppresses immunity in bean, whereas hopQ1-1 is missing from P. syringae pv. tabaci strains because it triggers defences in Nicotiana spp. This provides evidence that fine-tuning effector repertoires during host adaptation lead to a concomitant reduction in virulence in non-host species. [source] First report of a ,Candidatus Phytoplasma asteris'-related strain associated with little leaf disease of Helianthus debilis in Florida, USAPLANT PATHOLOGY, Issue 4 2008N. A. Harrison No abstract is available for this article. [source] Identification of a ,Candidatus Phytoplasma asteris'-related strain associated with spike disease of sandal (Santalum album) in IndiaPLANT PATHOLOGY, Issue 4 2006J. A. Khan No abstract is available for this article. [source] A Novel Mycolactone Toxin Obtained by Biosynthetic EngineeringCHEMBIOCHEM, Issue 17 2007Hui Hong Dr. A novel structural variant of the mycobacterial polyketide toxin mycolactone has been obtained by cloning a P450 hydroxylase gene from a related strain. This technique increases the range of available mycolactones for studies on the mode of action of the toxin. [source] Ericoid mycorrhiza: a partnership that exploits harsh edaphic conditionsEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 4 2003J. W. G. Cairney Summary Plants that form ericoid mycorrhizal associations are widespread in harsh habitats. Ericoid mycorrhizal fungal endophytes are a genetically diverse group, and they appear to be able to alleviate certain environmental stresses and so facilitate the establishment and survival of Ericaceae. Some of the fungal taxa that form ericoid mycorrhizas, or at least closely related strains, also form associations with other plant hosts (trees and leafy liverworts). The functional significance of these associations and putative mycelial links between Ericaceae and other plant taxa, however, remain unclear. Evidence from environments that are contaminated by toxic metals indicates that ericoid mycorrhizal fungal endophytes, and in some instances their plant hosts, can evolve resistance to these metals. The apparent ability of these endophytes to develop resistance enables ericoid mycorrhizal plants to colonize polluted soil. This seems to be a major factor in the success of ericoid mycorrhizal taxa in a range of harsh environments. [source] The identity of the O-specific polysaccharide structure of Citrobacter strains from serogroups O2, O20 and O25 and immunochemical characterisation of C. youngae PCM 1507 (O2a,1b) and related strainsFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 1-2 2003gorzata Miesza Abstract Serological studies using SDS,PAGE and immunoblotting revealed that from five strains that are ascribed to Citrobacter serogroup O2, four strains, PCM 1494, PCM 1495, PCM 1496 and PCM 1507, are reactive with specific anti- Citrobacter O2 serum. In contrast, strain PCM 1573 did not react with anti- Citrobacter O2 serum and, hence, does not belong to serogroup O2. The LPS of Citrobacter youngae O2a,1b (strain PCM 1507) was degraded under mild acidic conditions and the O-specific polysaccharide (OPS) released was isolated by gel chromatography. Sugar and methylation analyses along with 1H- and 13C-NMR spectroscopy, including two-dimensional 1H,1H COSY, TOCSY, NOESY and 1H,13C HSQC experiments, showed that the repeating unit of the OPS has the following structure: NMR spectroscopic studies demonstrated that Citrobacter werkmanii O20 and C. youngae O25 have the same OPS structure as C. youngae O2. Sugar and methylation analyses of the core oligosaccharide fractions demonstrated structural differences in the lipopolysaccharide core regions of these strains, which may substantiate their classification in different serogroups. [source] Bacillus subtilis and B. mojavensis strains connected to food poisoning produce the heat stable toxin amylosinJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2009C. Apetroaie-Constantin Abstract Aim:, To screen and characterize toxic, heat-stable substances produced by food borne strains from Bacillus subtilis group. Methods and Results:, Using the boar sperm motility inhibition assay, six isolates from two outbreaks, out of the 94 isolates from 26 foods, were found to produce ethanol-soluble heat-stable substances that were toxic to sperm cells by depleting the mitochondrial membrane potentials. The toxic isolates were identified as Bacillus subtilis and B mojavensis. Colon carcinoma cells (Caco-2) were used to model the contact with the human digestive tract. The extract of B. subtilis F 2564/96 depolarized the mitochondria in intact Caco-2 cells similarly as in sperm cells. The substance responsible for these effects was purified using HPLC and identified by electron spray ionization ion trap mass spectrometry analysis as amylosin. The temperature requirement for amylosin production was 21,37°C for B. subtilis and 11,21°C for B. mojavensis. Both species produced amylosin in air as well as in 7,8% CO2 with 8,9% O2. Conclusions:, Food borne illness related strains of B. subtilis and B. mojavensis, produced the heat-stable toxin amylosin. Significance and Impact of the Study:, This is the first report that suggests a role for the heat-stable, ion-channel forming toxin amylosin, as a virulence factor in food borne Bacillus. [source] Wide variation in effectiveness of laboratory disinfectants against bacteriophagesLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2008D.E. Halfhide Abstract Aims:, The purpose of this study was to identify an effective disinfectant for the inactivation of the bacteriophages (phages) being used in our laboratory, as published studies on phage inactivation are far from unanimous in their conclusions. Methods and Results:, The phages studied were three closely related strains of Myoviridae and three strains of Siphoviridae. Three disinfectants which are used commonly in microbiology laboratories were evaluated: Virkon (1%), ethanol (75%) and sodium hypochlorite (2500 ppm available chlorine). The most effective of these was Virkon, which inactivated all six phages rapidly. Ethanol was effective against the Myoviridae but had little effect on the Siphoviridae. Sodium hypochlorite was the least effective of the disinfectants evaluated. Conclusions:, The findings of this study demonstrate a wide diversity in the effectiveness of disinfectants tested for inactivation of phages. Significance and Impact of the Study:, Of the disinfectants tested Virkon is the most suitable choice for those unable to carry out disinfection validation studies, or where a broad spectrum disinfectant against phages is required. All of the phages in this study showed resilience to inactivation by sodium hypochlorite, and therefore this disinfectant is an unwise choice for use against phage without first assessing its effectiveness. [source] The use of (GTG)5 oligonucleotide as an RAPD primer to type Campylobacter concisusLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2006M.I. Matsheka Abstract Aim:, DNA fingerprinting using (GTG)5 oligonucleotide as a primer in a random amplified polymorphic DNA (RAPD) assay was assessed by typing isolates of Campylobacter concisus strains, collected over a period of 8 years. Methods and Results:, RAPD analysis using the (GTG)5 oligonucleotide as a primer was used to type 100 isolates of C. concisus comprising mostly isolates from children with diarrhoea. Using this method, 86% of the isolates were found to be genotypically diverse. Of these heterogeneous isolates, 25 of the strains were also shown to be genetically distinct in a previous study using pulsed field gel electrophoresis. The remaining isolates (14) could be classified into five profile groups based on the DNA fingerprinting patterns. The assay successfully identified epidemiologically linked strains from the unrelated genetically diverse pool of strains. Conclusions:, Laboratory RADP typing using the (GTG)5 primer proved to be useful in distinguishing related strains of C. concisus from a large pool of unrelated strains of this organism. Significance and Impact of the Study:, RAPD typing using (GTG)5 is a simple method that could be used to investigate the epidemiology of C. concisus. The results suggest that homologous lineages of C. concisus may exist within an otherwise heterogeneous species complex. However, these data need to be confirmed using a more robust typing method. [source] Bacillus anthracis, a story of nature subverted by manLETTERS IN APPLIED MICROBIOLOGY, Issue 3 2005L.W.J. Baillie Summary Bacillus anthracis is a pathogen of animals which rarely infects humans. Its use as a bioweapon has stimulated efforts to develop genetic typing methods and therapeutics to respond to an attack. Of particular concern is the transfer of virulence genes from B. anthracis to other closely related strains of bacillus. [source] Molecular epidemiology of viral infections.APMIS, Issue 2 2000How sequence information helps us understand the evolution, dissemination of viruses Viruses evolve much faster than cellular organisms. Together with recent advances in nucleic acid sequencing and biocomputing, this allows us to distinguish between related strains of viruses, and to deduce the relationships between viruses from different outbreaks or individual patients. Databases of nucleotide sequences contain a large number of viral sequences with which novel sequences from local outbreaks can be compared. In this way the dissemination of viruses can be followed both locally and globally. We here review the biological and technological background to the use of virus nucleic acid sequences in epidemiological studies, and provide examples of how this information can be used to monitor human viruses. Molecular studies are particularly valuable for understanding the dissemination and evolution of viruses. The knowledge obtained is useful in epidemiological reconstructions, in real-time surveillance, and may even enable us to make predictions about the future developments of viral diseases. [source] Integrons as tools for epidemiological studiesCLINICAL MICROBIOLOGY AND INFECTION, Issue 2 2004P. Severino Abstract The integron content of Gram-negative strains implicated in three distinct episodes of suspected cross-infection among inpatients was investigated and compared with ribotyping. In the first episode, ribotyping identified a strain of Acinetobacter, isolated over a 3-month period, responsible for an outbreak associated with the use of mechanical ventilation in the intensive care unit (ICU). The second episode concerned simultaneous isolations of Pseudomonas aeruginosa and Serratia marcescens from 13 bronchoscopy patients. In these two episodes, results obtained by analysis of integron content and ribotyping were in agreement and correctly identified the epidemiologically related strains. In the third episode, isolates of Enterobacter cloacae were collected from patients in the neonatal ICU over a 3-month period. Although several isolates belonged to the same ribotype, cross-infection could not always be confirmed when the integron content was analysed. Integron detection can be considered a useful tool for studying molecular epidemiology in hospital environments, facilitating the quick detection of possible cross-infection cases, especially in critical wards such as the ICU. [source] | ||||||||||||||||||||||||||||