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Sample records for analysis establishes mycobacterium

  1. Polyphasic taxonomic analysis establishes Mycobacterium indicus pranii as a distinct species.

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    Vikram Saini

    necessitated further analysis of MIP with more sensitive and segregating parameters to ascertain its precise taxonomic position as a new species. The analysis of MIP and its comparison with other mycobacterial reference strains based on cellular and biochemical features, growth characteristics and chemotaxonomic studies like FAME profiling confirmed that MIP is uniquely endowed with diverse metabolic attributes that effectively distinguishes it from all the closely related mycobacteria including M. intracellulare and M. chimaera. CONCLUSION: The results presented in this study coupled with the non-pathogenic nature and different biochemical and immunomodulatory properties of MIP affirm it as a distinct species belonging to M. avium complex (MAC. It is further proposed to use an earlier suggested name Mycobacterium indicus pranii for this newly established mycobacterial species. This study also exemplifies the growing need for a uniform, consensus based broader polyphasic frame work for the purpose of taxonomy and speciation, particularly in the genus Mycobacterium.

  2. MycoCAP - Mycobacterium Comparative Analysis Platform.

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    Choo, Siew Woh; Ang, Mia Yang; Dutta, Avirup; Tan, Shi Yang; Siow, Cheuk Chuen; Heydari, Hamed; Mutha, Naresh V R; Wee, Wei Yee; Wong, Guat Jah

    2015-12-15

    Mycobacterium spp. are renowned for being the causative agent of diseases like leprosy, Buruli ulcer and tuberculosis in human beings. With more and more mycobacterial genomes being sequenced, any knowledge generated from comparative genomic analysis would provide better insights into the biology, evolution, phylogeny and pathogenicity of this genus, thus helping in better management of diseases caused by Mycobacterium spp.With this motivation, we constructed MycoCAP, a new comparative analysis platform dedicated to the important genus Mycobacterium. This platform currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive web-based tools have been integrated in MycoCAP particularly for comparative analysis including the PGC tool for comparison between two genomes, PathoProT for comparing the virulence genes among the Mycobacterium strains and the SuperClassification tool for the phylogenic classification of the Mycobacterium strains and a specialized classification system for strains of Mycobacterium abscessus. We hope the broad range of functions and easy-to-use tools provided in MycoCAP makes it an invaluable analysis platform to speed up the research discovery on mycobacteria for researchers. Database URL: http://mycobacterium.um.edu.my.

  3. Variable-Number Tandem-Repeat Analysis of Respiratory and Household Water Biofilm Isolates of “Mycobacterium avium subsp. hominissuis” with Establishment of a PCR Database

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    Iakhiaeva, Elena; Howard, Susan T.; Brown Elliott, Barbara A.; McNulty, Steven; Newman, Kristopher L.; Falkinham, Joseph O.; Williams, Myra; Kwait, Rebecca; Lande, Leah; Vasireddy, Ravikiran; Turenne, Christine

    2016-01-01

    Mycobacterium avium subsp. hominissuis” is an important cause of pulmonary disease. It is acquired from environmental sources, but there is no methodology for large population studies. We evaluated the potential of variable-number tandem-repeat (VNTR) analysis. Clinical and household biofilm M. avium isolates underwent molecular identification. Testing for IS901 was done to separate M. avium subsp. avium from M. avium subsp. hominissuis. VNTR types were defined using VNTR loci, and subtyping was performed using 3′ hsp65 and internal transcribed spacer (ITS) sequencing. Forty-nine VNTR types and eight subtypes of M. avium subsp. hominissuis (IS901 negative) were identified among 416 isolates of M. avium from 121 patients and 80 biofilm sites. Of those types, 67% were found only among patient isolates, 11% only among household water isolates, and 23% among both. Of 13 VNTR types that included ≥4 patients, the majority (61.5%) represented geographic clustering (same city). Most VNTR types with multiple patients belonged to the same 3′ hsp65 sequence code (sequevar). A total of 44 isolates belonging to four M. avium subsp. hominissuis VNTR types (8%), including three with the rare Mav-F ITS sequence and 0/8 subspecies, produced amplicons with IS901 PCR primers. By sequencing, all 44 amplicons were not IS901 but ISMav6, which was recently observed in Japan but had not been previously described among U.S. isolates. VNTR analysis of M. avium subsp. hominissuis isolates is easier and faster than pulsed-field gel electrophoresis. Seven VNTR loci separated 417 isolates into 49 types. No isolates of M. avium subsp. avium were identified. The distributions of the VNTR copy numbers, the allelic diversity, and the low prevalence of ISMav6 differed from the findings for respiratory isolates reported from Japan. PMID:26739155

  4. Whole genome sequence analysis of Mycobacterium suricattae

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    Dippenaar, Anzaan

    2015-10-21

    Tuberculosis occurs in various mammalian hosts and is caused by a range of different lineages of the Mycobacterium tuberculosis complex (MTBC). A recently described member, Mycobacterium suricattae, causes tuberculosis in meerkats (Suricata suricatta) in Southern Africa and preliminary genetic analysis showed this organism to be closely related to an MTBC pathogen of rock hyraxes (Procavia capensis), the dassie bacillus. Here we make use of whole genome sequencing to describe the evolution of the genome of M. suricattae, including known and novel regions of difference, SNPs and IS6110 insertion sites. We used genome-wide phylogenetic analysis to show that M. suricattae clusters with the chimpanzee bacillus, previously isolated from a chimpanzee (Pan troglodytes) in West Africa. We propose an evolutionary scenario for the Mycobacterium africanum lineage 6 complex, showing the evolutionary relationship of M. africanum and chimpanzee bacillus, and the closely related members M. suricattae, dassie bacillus and Mycobacterium mungi.

  5. Potential of Mycobacterium vanbaalenii as a model organism to study drug transporters of Mycobacterium tuberculosis, Mycobacterium marinum and Mycobacterium ulcerans: homology analysis of M. tuberculosis drug transporters among mycobacterial species.

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    Gupta, Anuj Kumar; Katoch, V M; Chauhan, D S; Lavania, Mallika

    2012-06-01

    Drug efflux pumps have been one of the important mechanisms of drug resistance in Mycobacterium tuberculosis. There is a prerequisite to study the behavior and mechanisms of these drug efflux pumps in detail for being considered in future anti-TB drug designing. The need of a rapid grower non-pathogenic mycobacterium with significant genomic homology for such type of studies is often being felt. During microarray and Real-Time PCR analysis of drug efflux pump genes of M. tuberculosis, we found 10 genes to be over-expressed during stress induced by common anti-TB drugs. In the present study homology analysis of these genes was done in order to know its phylogenetic relationship among other bacteria/mycobacteria. It was found that amino acid sequences of 7 out of 10 genes were significantly (>40%) identical to a non-pathogenic rapid grower environmental mycobacterium, Mycobacterium vanbaalenii. The protein sequences of M. vanbaalenii share important sequence motifs with M. tuberculosis useful for drug efflux mechanism based study across species. Like Mycobacterium smegmatis, it can be used as a model organism to study drug efflux pumps of M. tuberculosis and also other pathogenic mycobacteria such as Mycobacterium ulcerans and Mycobacterium marinum. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Local and regional re-establishment of cellular immunity during curative antibiotherapy of murine Mycobacterium ulcerans infection.

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    Teresa G Martins

    Full Text Available BACKGROUND: Buruli ulcer (BU is a neglected necrotizing disease of the skin, subcutaneous tissue and bone, caused by Mycobacterium ulcerans. BU pathogenesis is associated with mycolactone, a lipidic exotoxin with cytotoxic and immunosuppressive properties. Since 2004, the World Health Organization recommends the treatment of BU with a combination of rifampicin and streptomycin (RS. Histological analysis of human tissue samples suggests that such antibiotic treatment reverses the mycolactone-induced local immunosuppression, leading to increased inflammatory infiltrations and phagocytosis of bacilli. METHODOLOGY/PRINCIPAL FINDINGS: We used a mouse model of M. ulcerans footpad infection, followed by combined RS treatment. Time-lapsed analyses of macroscopic lesions, bacterial burdens, histology and immunohistochemistry were performed in footpads. We also performed CFU counts, histology and immunohistochemistry in the popliteal draining lymph nodes (DLN. We observed a shift in the cellular infiltrates from a predominantly neutrophilic/macrophagic to a lymphocytic/macrophagic profile in the infected footpads of antibiotic-treated mice. This shift occurred before the elimination of viable M. ulcerans organisms, which were ultimately eradicated as demonstrated by the administration of dexamethasone. This reduction of bacillary loads was accompanied by an increased expression of inducible nitric oxide synthase (NOS2 or iNOS. Predominantly mononuclear infiltrates persisted in the footpads during and after treatment, coincident with the long persistence of non-viable poorly stained acid-fast bacilli (AFB. We additionally observed that antibiotherapy prevented DLN destruction and lymphocyte depletion, which occurs during untreated experimental infections. CONCLUSIONS/SIGNIFICANCE: Early RS treatment of M. ulcerans mouse footpad infections results in the rapid elimination of viable bacilli with pathogen eradication. However, non-viable AFB persisted for

  7. High throughput phenotypic analysis of Mycobacterium tuberculosis and Mycobacterium bovis strains' metabolism using biolog phenotype microarrays.

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    Bhagwati Khatri

    Full Text Available Tuberculosis is a major human and animal disease of major importance worldwide. Genetically, the closely related strains within the Mycobacterium tuberculosis complex which cause disease are well-characterized but there is an urgent need better to understand their phenotypes. To search rapidly for metabolic differences, a working method using Biolog Phenotype MicroArray analysis was developed. Of 380 substrates surveyed, 71 permitted tetrazolium dye reduction, the readout over 7 days in the method. By looking for ≥5-fold differences in dye reduction, 12 substrates differentiated M. tuberculosis H37Rv and Mycobacterium bovis AF2122/97. H37Rv and a Beijing strain of M. tuberculosis could also be distinguished in this way, as could field strains of M. bovis; even pairs of strains within one spoligotype could be distinguished by 2 to 3 substrates. Cluster analysis gave three clear groups: H37Rv, Beijing, and all the M. bovis strains. The substrates used agreed well with prior knowledge, though an unexpected finding that AF2122/97 gave greater dye reduction than H37Rv with hexoses was investigated further, in culture flasks, revealing that hexoses and Tween 80 were synergistic for growth and used simultaneously rather than in a diauxic fashion. Potential new substrates for growth media were revealed, too, most promisingly N-acetyl glucosamine. Osmotic and pH arrays divided the mycobacteria into two groups with different salt tolerance, though in contrast to the substrate arrays the groups did not entirely correlate with taxonomic differences. More interestingly, these arrays suggested differences between the amines used by the M. tuberculosis complex and enteric bacteria in acid tolerance, with some hydrophobic amino acids being highly effective. In contrast, γ-aminobutyrate, used in the enteric bacteria, had no effect in the mycobacteria. This study proved principle that Phenotype MicroArrays can be used with slow-growing pathogenic mycobacteria

  8. Mycobacterium tuberculosis Universal Stress Protein Rv2623 Regulates Bacillary Growth by ATP Binding: Requirement for Establishing Chronic Persistent Infection

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    Drumm, J.; Mi, K; Bilder, P; Sun, M; Lim, J; Bielefeldt-Ohmann, H; Basaraba, R; So, M; Zhu, G; et. al.

    2009-01-01

    Tuberculous latency and reactivation play a significant role in the pathogenesis of tuberculosis, yet the mechanisms that regulate these processes remain unclear. The Mycobacterium tuberculosisuniversal stress protein (USP) homolog, rv2623, is among the most highly induced genes when the tubercle bacillus is subjected to hypoxia and nitrosative stress, conditions thought to promote latency. Induction of rv2623 also occurs when M. tuberculosis encounters conditions associated with growth arrest, such as the intracellular milieu of macrophages and in the lungs of mice with chronic tuberculosis. Therefore, we tested the hypothesis that Rv2623 regulates tuberculosis latency. We observed that an Rv2623-deficient mutant fails to establish chronic tuberculous infection in guinea pigs and mice, exhibiting a hypervirulence phenotype associated with increased bacterial burden and mortality. Consistent with this in vivo growth-regulatory role, constitutive overexpression of rv2623 attenuates mycobacterial growth in vitro. Biochemical analysis of purified Rv2623 suggested that this mycobacterial USP binds ATP, and the 2.9-A-resolution crystal structure revealed that Rv2623 engages ATP in a novel nucleotide-binding pocket. Structure-guided mutagenesis yielded Rv2623 mutants with reduced ATP-binding capacity. Analysis of mycobacteria overexpressing these mutants revealed that the in vitro growth-inhibitory property of Rv2623 correlates with its ability to bind ATP. Together, the results indicate that i M. tuberculosis Rv2623 regulates mycobacterial growth in vitro and in vivo, and ii Rv2623 is required for the entry of the tubercle bacillus into the chronic phase of infection in the host; in addition, iii Rv2623 binds ATP; and iv the growth-regulatory attribute of this USP is dependent on its ATP-binding activity. We propose that Rv2623 may function as an ATP-dependent signaling intermediate in a pathway that promotes persistent infection.

  9. Insights on the Emergence of Mycobacterium tuberculosis from the Analysis of Mycobacterium kansasii

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    Wang, Joyce; McIntosh, Fiona; Radomski, Nicolas; Dewar, Ken; Simeone, Roxane; Enninga, Jost; Brosch, Roland; Rocha, Eduardo P.; Veyrier, Frédéric J.; Behr, Marcel A.

    2015-01-01

    By phylogenetic analysis, Mycobacterium kansasii is closely related to Mycobacterium tuberculosis. Yet, although both organisms cause pulmonary disease, M. tuberculosis is a global health menace, whereas M. kansasii is an opportunistic pathogen. To illuminate the differences between these organisms, we have sequenced the genome of M. kansasii ATCC 12478 and its plasmid (pMK12478) and conducted side-by-side in vitro and in vivo investigations of these two organisms. The M. kansasii genome is 6,432,277 bp, more than 2 Mb longer than that of M. tuberculosis H37Rv, and the plasmid contains 144,951 bp. Pairwise comparisons reveal conserved and discordant genes and genomic regions. A notable example of genomic conservation is the virulence locus ESX-1, which is intact and functional in the low-virulence M. kansasii, potentially mediating phagosomal disruption. Differences between these organisms include a decreased predicted metabolic capacity, an increased proportion of toxin–antitoxin genes, and the acquisition of M. tuberculosis-specific genes in the pathogen since their common ancestor. Consistent with their distinct epidemiologic profiles, following infection of C57BL/6 mice, M. kansasii counts increased by less than 10-fold over 6 weeks, whereas M. tuberculosis counts increased by over 10,000-fold in just 3 weeks. Together, these data suggest that M. kansasii can serve as an image of the environmental ancestor of M. tuberculosis before its emergence as a professional pathogen, and can be used as a model organism to study the switch from an environmental opportunistic pathogen to a professional host-restricted pathogen. PMID:25716827

  10. hsp65 PCR-restriction analysis (PRA) with capillary electrophoresis for species identification and differentiation of Mycobacterium kansasii and Mycobacterium chelonae-Mycobacterium abscessus group.

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    Sajduda, Anna; Martin, Anandi; Portaels, Françoise; Palomino, Juan Carlos

    2012-03-01

    The aim of the present study was to identify and differentiate Mycobacterium kansasii and Mycobacterium chelonae-Mycobacterium abscessus group strains isolated from clinical and environmental sources in different countries. PCR-restriction analysis of the hsp65 gene (PRA) with automated capillary electrophoresis was applied to the isolates previously identified by conventional biochemical testing and the molecular INNO-LiPA MYCOBACTERIA assay. PRA performed very well in comparison with the two other methods (96.4% concordance). Among 27 M. kansasii isolates, this method detected five genetic types, of which type 1 represented the most common clinical isolate, as it is worldwide. PRA differentiated 29 M. chelonae-M. abscessus group isolates into Mycobacterium immunogenum type 2 (n=13), M. chelonae (n=12), and M. abscessus types 1 (n=1) and 2 (n=1). M. immunogenum was the most frequent (69%) isolate from humans, but only one of 11 cases was clinically significant. M. chelonae was the most commonly (83%) recovered from water. PRA also identified two isolates with hsp65 alleles representing previously unreported patterns. PRA based on automated capillary electrophoresis is a rapid, simple, and reliable method for the identification and differentiation of both clinically relevant and environmental isolates of M. kansasii and M. chelonae-M. abscessus group. Copyright © 2012 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  11. Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

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    McGuire Abigail

    2012-03-01

    Full Text Available Abstract Background The sequence of the pathogen Mycobacterium tuberculosis (Mtb strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of Mtb pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org, including 8 strains of Mtb and M. bovis, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes, and Bifidobacterium longum. Results Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four. Conclusions Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of Mtb in a comparative context, and are available online and through TBDB.org.

  12. Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.

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    McGuire, Abigail Manson; Weiner, Brian; Park, Sang Tae; Wapinski, Ilan; Raman, Sahadevan; Dolganov, Gregory; Peterson, Matthew; Riley, Robert; Zucker, Jeremy; Abeel, Thomas; White, Jared; Sisk, Peter; Stolte, Christian; Koehrsen, Mike; Yamamoto, Robert T; Iacobelli-Martinez, Milena; Kidd, Matthew J; Maer, Andreia M; Schoolnik, Gary K; Regev, Aviv; Galagan, James

    2012-03-28

    The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of Mtb pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org), including 8 strains of Mtb and M. bovis, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes, and Bifidobacterium longum. Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four. Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of Mtb in a comparative context, and are available online and through TBDB.org.

  13. Proteomic analysis of extracellular vesicles derived from Mycobacterium tuberculosis.

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    Lee, Jaewook; Kim, Si-Hyun; Choi, Dong-Sic; Lee, Jong Seok; Kim, Dae-Kyum; Go, Gyeongyun; Park, Seon-Min; Kim, Si Hyun; Shin, Jeong Hwan; Chang, Chulhun L; Gho, Yong Song

    2015-10-01

    The release of extracellular vesicles, also known as outer membrane vesicles, membrane vesicles, exosomes, and microvesicles, is an evolutionarily conserved phenomenon from bacteria to eukaryotes. It has been reported that Mycobacterium tuberculosis releases extracellular vesicles harboring immunologically active molecules, and these extracellular vesicles have been suggested to be applicable in vaccine development and biomarker discovery. However, the comprehensive proteomic analysis has not been performed for M. tuberculosis extracellular vesicles. In this study, we identified a total of 287 vesicular proteins by four LC-MS/MS analyses with high confidence. In addition, we identified several vesicular proteins associated with the virulence of M. tuberculosis. This comprehensive proteome profile will help elucidate the pathogenic mechanism of M. tuberculosis. The data have been deposited to the ProteomeXchange with identifier PXD001160 (http://proteomecentral.proteomexchange.org/dataset/PXD001160). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Proteomic analysis of protein purified derivative of Mycobacterium bovis.

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    Roperto, Sante; Varano, Mariaconcetta; Russo, Valeria; Lucà, Roberta; Cagiola, Monica; Gaspari, Marco; Ceccarelli, Dora Maria; Cuda, Giovanni; Roperto, Franco

    2017-04-03

    Tuberculin skin test based on in vivo intradermal inoculation of purified protein derivative from Mycobacterium bovis (bPPD) is the diagnostic test for the control and surveillance of bovine tuberculosis (bTB). Proteomic analysis was performed on different bPPD preparations from M. bovis, strain AN5. Proteins were precipitated from bPPD solutions by TCA precipitation. The proteome of bPPD preparations was investigated by bottom-up proteomics, which consisted in protein digestion and nano-LC-MS/MS analysis. Mass spectrometry analysis was performed on a Q-exactive hybrid quadrupole-Orbitrap mass spectrometer coupled online to an Easy nano-LC1000 system. Three hundred and fifty-six proteins were identified and quantified by at least 2 peptides (99% confidence per peptide). One hundred and ninety-eight proteins, which had not been previously described, were detected; furthermore, the proteomic profile shared 80 proteins with previous proteomes from bPPDs from the United Kingdom and Brazil and 139 protein components from bPPD from Korea. Locus name of M. bovis (Mb) with orthologs from M. tuberculosis H37Rv, comparative gene and protein length, molecular mass, functional categories, gene name and function of each protein were reported. Ninety-two T cell mycobacterial antigens responsible for delayed-type hypersensitivity were detected, fifty-two of which were not previously reported in any bPPD proteome. Data are available via ProteomeXchange with identifier PXD005920. This study represents the highest proteome coverage of bPPD preparations to date. Since proteins perform cellular functions essential to health and/or disease, obtaining knowledge of their presence and variance is of great importance in understanding disease states and for advancing translational studies. Therefore, to better understand Mycobacterium tuberculosis complex biology during infection, survival, and persistence, the reproducible evaluation of the proteins that catalyze and control these

  15. [Usefulness of the variable numbers of tandem repeats (VNTR) analysis for complex infections of Mycobacterium avium and Mycobacterium intracellulare].

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    Tsunematsu, Noriko; Goto, Mieko; Saiki, Yumiko; Baba, Michiko; Udagawa, Tadashi; Kazumi, Yuko

    2008-09-01

    The bacilli which were isolated from a patient suspected of the mixed infections with Mycobacterium avium and Mycobacterium intracellulare, were analyzed. The genotypes of M. avium in the sedimented fractions of treated sputum and in some colonies isolated from Ogawa medium were compared by the Variable Numbers of Tandem Repeats (VNTR). A woman, aged 57. Mycobacterial species isolated from some colonies by culture in 2004 and 2006 and from the treated sputum in 2006, were determined by DNA sequencing analysis of the 16S rRNA gene. Also, by using VNTR, the genotype of mycobacteria was analyzed. [Results] (1) The colony isolated from Ogawa medium in 2004 was monoclonal M. avium. (2) By VNTR analyses of specimens in 2006, multiple acid-fast bacteria were found in the sputum sediment and in isolated bacteria from Ogawa medium. (3) By analyses of 16S rRNA DNA sequence, M. avium and M. intracellulare were found in the colonies isolated from the sputum sediment and the Ogawa medium in 2006. (4) The same VNTR patterns were obtained in M. avium in 2004 and 2006 when single colony was analyzed. (5) From the showerhead and culvert of the bathroom in the patient's house, M. avium was not detected. By VNTR analyses, it was considered that the mixed infections of M. avium and M. intracellulare had been generated during treatment in this case. Therefore, in the case of suspected complex infection, VNTR analysis would be a useful genotyping method in M. avium complex infection.

  16. Mycobacterial Interspersed Repetitive-Unit–Variable-Number Tandem-Repeat (MIRU-VNTR) Genotyping of Mycobacterium intracellulare for Strain Comparison with Establishment of a PCR-Based Database

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    Iakhiaeva, Elena; McNulty, Steven; Brown Elliott, Barbara A.; Falkinham, Joseph O.; Williams, Myra D.; Vasireddy, Ravikiran; Wilson, Rebecca W.; Turenne, Christine

    2013-01-01

    Strain comparison is important to population genetics and to evaluate relapses in patients with Mycobacterium avium complex (MAC) lung disease, but the “gold standard” of pulsed-field gel electrophoresis (PFGE) is time-consuming and complex. We used variable-number tandem repeats (VNTR) for fingerprinting of respiratory isolates of M. intracellulare from patients with underlying bronchiectasis, to establish a nonsequence-based database for population analysis. Different genotypes identified by PFGE underwent species identification using a 16S rRNA gene multiplex PCR. Genotypes of M. intracellulare were confirmed by internal transcribed spacer 1 (ITS1) sequencing and characterized using seven VNTR primers. The pattern of VNTR amplicon sizes and repeat number defined each specific VNTR type. Forty-two VNTR types were identified among 84 genotypes. PFGE revealed most isolates with the same VNTR type to be clonal or exhibit similar grouping of bands. Repetitive sequence-based PCR (rep-PCR) showed minimal pattern diversity between VNTR types compared to PFGE. Fingerprinting of relapse isolates from 31 treated patients using VNTR combined with 16S multiplex PCR unambiguously and reliably distinguished different genotypes from the same patient, with results comparable to those of PFGE. VNTR for strain comparison is easier and faster than PFGE, is as accurate as PFGE, and does not require sequencing. Starting with a collection of 167 M. intracellulare isolates, VNTR distinguished M. intracellulare into 42 clonal groups. Comparison of isolates from different geographic areas, habitats, and clinical settings is now possible. PMID:23175249

  17. Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping of mycobacterium intracellulare for strain comparison with establishment of a PCR-based database.

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    Iakhiaeva, Elena; McNulty, Steven; Brown Elliott, Barbara A; Falkinham, Joseph O; Williams, Myra D; Vasireddy, Ravikiran; Wilson, Rebecca W; Turenne, Christine; Wallace, Richard J

    2013-02-01

    Strain comparison is important to population genetics and to evaluate relapses in patients with Mycobacterium avium complex (MAC) lung disease, but the "gold standard" of pulsed-field gel electrophoresis (PFGE) is time-consuming and complex. We used variable-number tandem repeats (VNTR) for fingerprinting of respiratory isolates of M. intracellulare from patients with underlying bronchiectasis, to establish a nonsequence-based database for population analysis. Different genotypes identified by PFGE underwent species identification using a 16S rRNA gene multiplex PCR. Genotypes of M. intracellulare were confirmed by internal transcribed spacer 1 (ITS1) sequencing and characterized using seven VNTR primers. The pattern of VNTR amplicon sizes and repeat number defined each specific VNTR type. Forty-two VNTR types were identified among 84 genotypes. PFGE revealed most isolates with the same VNTR type to be clonal or exhibit similar grouping of bands. Repetitive sequence-based PCR (rep-PCR) showed minimal pattern diversity between VNTR types compared to PFGE. Fingerprinting of relapse isolates from 31 treated patients using VNTR combined with 16S multiplex PCR unambiguously and reliably distinguished different genotypes from the same patient, with results comparable to those of PFGE. VNTR for strain comparison is easier and faster than PFGE, is as accurate as PFGE, and does not require sequencing. Starting with a collection of 167 M. intracellulare isolates, VNTR distinguished M. intracellulare into 42 clonal groups. Comparison of isolates from different geographic areas, habitats, and clinical settings is now possible.

  18. Comparative Genomics and Transcriptomic Analysis of Mycobacterium Kansasii

    KAUST Repository

    Alzahid, Yara

    2014-04-01

    The group of Mycobacteria is one of the most intensively studied bacterial taxa, as they cause the two historical and worldwide known diseases: leprosy and tuberculosis. Mycobacteria not identified as tuberculosis or leprosy complex, have been referred to by ‘environmental mycobacteria’ or ‘Nontuberculous mycobacteria (NTM). Mycobacterium kansasii (M. kansasii) is one of the most frequent NTM pathogens, as it causes pulmonary disease in immuno-competent patients and pulmonary, and disseminated disease in patients with various immuno-deficiencies. There have been five documented subtypes of this bacterium, by different molecular typing methods, showing that type I causes tuberculosis-like disease in healthy individuals, and type II in immune-compromised individuals. The remaining types are said to be environmental, thereby, not causing any diseases. The aim of this project was to conduct a comparative genomic study of M. kansasii types I-V and investigating the gene expression level of those types. From various comparative genomics analysis, provided genomics evidence on why M. kansasii type I is considered pathogenic, by focusing on three key elements that are involved in virulence of Mycobacteria: ESX secretion system, Phospholipase c (plcb) and Mammalian cell entry (Mce) operons. The results showed the lack of the espA operon in types II-V, which renders the ESX- 1 operon dysfunctional, as espA is one of the key factors that control this secretion system. However, gene expression analysis showed this operon to be deleted in types II, III and IV. Furthermore, plcB was found to be truncated in types III and IV. Analysis of Mce operons (1-4) show that mce-1 operon is duplicated, mce-2 is absent and mce-3 and mce-4 is present in one copy in M. kansasii types I-V. Gene expression profiles of type I-IV, showed that the secreted proteins of ESX-1 were slightly upregulated in types II-IV when compared to type I and the secreted forms of ESX-5 were highly down

  19. Molecular analysis of clinical isolates previously diagnosed as Mycobacterium intracellulare reveals incidental findings of "Mycobacterium indicus pranii" genotypes in human lung infection.

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    Kim, Su-Young; Park, Hye Yun; Jeong, Byeong-Ho; Jeon, Kyeongman; Huh, Hee Jae; Ki, Chang-Seok; Lee, Nam Yong; Han, Seung-Jung; Shin, Sung Jae; Koh, Won-Jung

    2015-09-30

    Mycobacterium intracellulare is a major cause of Mycobacterium avium complex lung disease in many countries. Molecular studies have revealed several new Mycobacteria species that are closely related to M. intracellulare. The aim of this study was to re-identify and characterize clinical isolates from patients previously diagnosed with M. intracellulare lung disease at the molecular level. Mycobacterial isolates from 77 patients, initially diagnosed with M. intracellulare lung disease were re-analyzed by multi-locus sequencing and pattern of insertion sequences. Among the 77 isolates, 74 (96 %) isolates were designated as M. intracellulare based on multigene sequence-based analysis. Interestingly, the three remaining strains (4 %) were re-identified as "Mycobacterium indicus pranii" according to distinct molecular phylogenetic positions in rpoB and hsp65 sequence-based typing. In hsp65 sequevar analysis, code 13 was found in the majority of cases and three unreported codes were identified. In 16S-23S rRNA internal transcribed spacer (ITS) sequevar analysis, all isolates of both species were classified within the Min-A ITS sequevar. Interestingly, four of the M. intracellulare isolates harbored IS1311, a M. avium-specific element. Two of three patients infected with "M. indicus pranii" had persistent positive sputum cultures after antibiotic therapy, indicating the clinical relevance of this study. This analysis highlights the importance of precise identification of clinical isolates genetically close to Mycobacterium species, and suggests that greater attention should be paid to nontuberculous mycobacteria lung disease caused by "M. indicus pranii".

  20. Typing Method for the QUB11a Locus of Mycobacterium tuberculosis: IS6110 Insertions and Tandem Repeat Analysis

    Directory of Open Access Journals (Sweden)

    Eriko Maeda-Mitani

    2016-01-01

    Full Text Available QUB11a is used as a locus for variable number of tandem repeats (VNTR analysis of Mycobacterium tuberculosis Beijing lineage. However, amplification of QUB11a occasionally produces large fragments (>1,400 bp that are not easily measured by capillary electrophoresis because of a lack of the typical stutter peak patterns that are used for counting repeat numbers. IS6110 insertion may complicate VNTR analysis of large QUB11a fragments in M. tuberculosis. We established a method for determining both tandem repeat numbers and IS6110 insertion in the QUB11a locus of M. tuberculosis using capillary electrophoresis analysis and BsmBI digestion. All 29 large QUB11a fragments (>1,200 bp investigated contained IS6110 insertions and varied in the number of repeats (18 patterns and location of IS6110 insertions. This method allows VNTR analysis with high discrimination.

  1. Phylogenetic analysis of vitamin B12-related metabolism in Mycobacterium tuberculosis

    OpenAIRE

    Young, Douglas B.; Comas, I?aki; de Carvalho, Luiz P. S.

    2015-01-01

    Comparison of genome sequences from clinical isolates of Mycobacterium tuberculosis with phylogenetically-related pathogens Mycobacterium marinum, Mycobacterium kansasii, and Mycobacterium leprae reveals diversity amongst genes associated with vitamin B12-related metabolism. Diversity is generated by gene deletion events, differential acquisition of genes by horizontal transfer, and single nucleotide polymorphisms (SNPs) with predicted impact on protein function and transcriptional regulation...

  2. Characterization and transcriptome analysis of Mycobacterium tuberculosis persisters.

    Science.gov (United States)

    Keren, Iris; Minami, Shoko; Rubin, Eric; Lewis, Kim

    2011-01-01

    Tuberculosis continues to be a major public health problem in many parts of the world. Significant obstacles in controlling the epidemic are the length of treatment and the large reservoir of latently infected people. Bacteria form dormant, drug-tolerant persister cells, which may be responsible for the difficulty in treating both acute and latent infections. We find that in Mycobacterium tuberculosis, low numbers of drug-tolerant persisters are present in lag and early exponential phases, increasing sharply at late exponential and stationary phases to make up ~1% of the population. This suggests that persister formation is governed by both stochastic and deterministic mechanisms. In order to isolate persisters, an exponentially growing population was treated with d-cycloserine, and cells surviving lysis were collected by centrifugation. A transcriptome of persisters was obtained by using hybridization to an Affymetrix array. The transcriptome shows downregulation of metabolic and biosynthetic pathways, consistent with a certain degree of dormancy. A set of genes was upregulated in persisters, and these are likely involved in persister formation and maintenance. A comparison of the persister transcriptome with transcriptomes obtained for several in vitro dormancy models identified a small number of genes upregulated in all cases, which may represent a core dormancy response. © 2011 Keren et al.

  3. Analysis of isoniazid, streptomycin and ethambutol resistance in Mycobacterium tuberculosis isolates from Morocco.

    Science.gov (United States)

    Chaoui, Imane; Sabouni, Radia; Kourout, Moussa; Jordaan, Annemie M; Lahlou, Ouafae; Elouad, Rajae; Akrim, Mohammed; Victor, Thomas C; El Mzibri, Mohammed

    2009-05-01

    Drug-resistant tuberculosis is a major problem worldwide. Based on the knowledge of specific mutations occurring in Mycobacterium tuberculosis genome, drug resistance can be detected earlier. The aim of this study was to determine the prevalence of the most common mutations associated with resistance to Isoniazid (INH), Streptomycin (SM) and Ethambutol (EMB) in Mycobacterium tuberculosis isolates from Morocco in order to select target mutations to develop tests for rapid detection of drug-resistant Mycobacterium tuberculosis Moroccan isolates. A total of 199 M. tuberculosis isolates collected from the National Tuberculosis Reference Laboratory in Morocco were subject to katG, inhA, rrs, rpsL and emb mutation analysis by PCR probe-based assay. The genotypic results were then compared to drug susceptibility testing results for the corresponding drugs. Among 66 phenotypically INH resistant isolates, 80.3% (53/66) were found to be genotypically INH resistant from which 77.3% (51/66) and 3% (2/66) had respective mutations in katG315 and inhp-15 codons. Of the 58 phenotypically SM resistant isolates, genotypic SM resistance was confirmed in 17.2% (10/58) cases. Nucleotide mutations at codons 43 and 88 of rpsL gene and at codon 512 of rrs gene were found respectively in 12.1% (7/58); 1.7% (1/58) and 3.4% (2/58) of the phenotypically SM resistant Mycobacterium tuberculosis isolates. Finally, mutations at codon 306 of embB gene were identified in 42.3% (11/26) of Mycobacterium tuberculosis isolates phenotypically EMB resistant. This study showed that a large proportion of Mycobacterium tuberculosis resistant isolates from Morocco carry a large number of mutations in different codons (especially katG315, embB306 and rpsL43) of the corresponding genes associated with drug resistance. Thus, molecular analysis based on the identification of such mutations is useful but not fully sufficient to predict all drug resistance cases. Based on these results, rapid drug resistance

  4. Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

    Directory of Open Access Journals (Sweden)

    Niyaz Ahmed

    Full Text Available BACKGROUND: Evolutionary dynamics plays a central role in facilitating the mechanisms of species divergence among pathogenic and saprophytic mycobacteria. The ability of mycobacteria to colonize hosts, to proliferate and to cause diseases has evolved due to its predisposition to various evolutionary forces acting over a period of time. Mycobacterium indicus pranii (MIP, a taxonomically unknown 'generalist' mycobacterium, acts as an immunotherapeutic against leprosy and is approved for use as a vaccine against it. The large-scale field trials of this MIP based leprosy vaccine coupled with its demonstrated immunomodulatory and adjuvant property has led to human clinical evaluations of MIP in interventions against HIV-AIDS, psoriasis and bladder cancer. MIP, commercially available as 'Immuvac', is currently the focus of advanced phase III clinical trials for its antituberculosis efficacy. Thus a comprehensive analysis of MIP vis-à-vis evolutionary path, underpinning its immanent immunomodulating properties is of the highest desiderata. PRINCIPAL FINDINGS: Genome wide comparisons together with molecular phylogenetic analyses by fluorescent amplified fragment length polymorphism (FAFLP, enterobacterial repetitive intergenic consensus (ERIC based genotyping and candidate orthologues sequencing revealed that MIP has been the predecessor of highly pathogenic Mycobacterium avium intracellulare complex (MAIC that did not resort to parasitic adaptation by reductional gene evolution and therefore, preferred a free living life-style. Further analysis suggested a shared aquatic phase of MAIC bacilli with the early pathogenic forms of Mycobacterium, well before the latter diverged as 'specialists'. CONCLUSIONS/SIGNIFICANCE: This evolutionary paradigm possibly affirms to marshall our understanding about the acquisition and optimization of virulence in mycobacteria and determinants of boundaries therein.

  5. Gluconeogenic carbon flow of tricarboxylic acid cycle intermediates is critical for Mycobacterium tuberculosis to establish and maintain infection.

    Science.gov (United States)

    Marrero, Joeli; Rhee, Kyu Y; Schnappinger, Dirk; Pethe, Kevin; Ehrt, Sabine

    2010-05-25

    Metabolic adaptation to the host niche is a defining feature of the pathogenicity of Mycobacterium tuberculosis (Mtb). In vitro, Mtb is able to grow on a variety of carbon sources, but mounting evidence has implicated fatty acids as the major source of carbon and energy for Mtb during infection. When bacterial metabolism is primarily fueled by fatty acids, biosynthesis of sugars from intermediates of the tricarboxylic acid cycle is essential for growth. The role of gluconeogenesis in the pathogenesis of Mtb however remains unaddressed. Phosphoenolpyruvate carboxykinase (PEPCK) catalyzes the first committed step of gluconeogenesis. We applied genetic analyses and (13)C carbon tracing to confirm that PEPCK is essential for growth of Mtb on fatty acids and catalyzes carbon flow from tricarboxylic acid cycle-derived metabolites to gluconeogenic intermediates. We further show that PEPCK is required for growth of Mtb in isolated bone marrow-derived murine macrophages and in mice. Importantly, Mtb lacking PEPCK not only failed to replicate in mouse lungs but also failed to survive, and PEPCK depletion during the chronic phase of infection resulted in mycobacterial clearance. Mtb thus relies on gluconeogenesis throughout the infection. PEPCK depletion also attenuated Mtb in IFNgamma-deficient mice, suggesting that this enzyme represents an attractive target for chemotherapy.

  6. Metabolite analysis of Mycobacterium species under aerobic and hypoxic conditions reveals common metabolic traits.

    Science.gov (United States)

    Drapal, Margit; Wheeler, Paul R; Fraser, Paul D

    2016-08-01

    A metabolite profiling approach has been implemented to elucidate metabolic adaptation at set culture conditions in five Mycobacterium species (two fast- and three slow-growing) with the potential to act as model organisms for Mycobacterium tuberculosis (Mtb). Analysis has been performed over designated growth phases and under representative environments (nutrient and oxygen depletion) experienced by Mtb during infection. The procedure was useful in determining a range of metabolites (60-120 compounds) covering nucleotides, amino acids, organic acids, saccharides, fatty acids, glycerols, -esters, -phosphates and isoprenoids. Among these classes of compounds, key biomarker metabolites, which can act as indicators of pathway/process activity, were identified. In numerous cases, common metabolite traits were observed for all five species across the experimental conditions (e.g. uracil indicating DNA repair). Amino acid content, especially glutamic acid, highlighted the different properties between the fast- and slow-growing mycobacteria studied (e.g. nitrogen assimilation). The greatest similarities in metabolite composition between fast- and slow-growing mycobacteria were apparent under hypoxic conditions. A comparison to previously reported transcriptomic data revealed a strong correlation between changes in transcription and metabolite content. Collectively, these data validate the changes in the transcription at the metabolite level, suggesting transcription exists as one of the predominant modes of cellular regulation in Mycobacterium. Sectors with restricted correlation between metabolites and transcription (e.g. hypoxic cultivation) warrant further study to elucidate and exploit post-transcriptional modes of regulation. The strong correlation between the laboratory conditions used and data derived from in vivo conditions, indicate that the approach applied is a valuable addition to our understanding of cell regulation in these Mycobacterium species.

  7. Streptomycin induced protein expression analysis in Mycobacterium tuberculosis by two-dimensional gel electrophoresis & mass spectrometry.

    Science.gov (United States)

    Sharma, Prashant; Kumar, Bhavnesh; Singhal, Neelja; Katoch, Vishwa Mohan; Venkatesan, Krishnamurthy; Chauhan, Devendra Singh; Bisht, Deepa

    2010-10-01

    The resistance of Mycobacterium tuberculosis to streptomycin, a core drug for treatment of category II tuberculosis (TB) has posed a major challenge to the health providers as well as research workers worldwide and has severely compromised the therapeutic options. A significant proportion of streptomycin resistant M. tuberculosis isolates failed to show mutations in conventional targets like rpsL and rrs. Although efflux, permeability, etc. are also known to contribute, yet a substantial proportion of isolates remains resistant suggesting involvement of other unknown mechanism. A resistant isolate may show altered gene as well as protein expression under drug induced conditions and a whole cell proteome analysis under induced conditions might help in further understanding the mechanisms of drug resistance. The present study was therefore designed with the objective to identify proteins related to streptomycin resistance in M. tuberculosis isolate grown in presence and absence of streptomycin (SM). A clinical isolate of M. tuberculosis from Mycobacterial Repository Centre at the Institute (NJIL & OMD), Agra was grown in Sauton's medium for 36 h with/without subinhibitory concentration of the drug (2 μg/ml) and the cell lysate of isolates was prepared by sonication and centrifugation. Two-dimensional (2D) gel electrophoresis was employed to study the protein profile. The selected proteins were finally identified by MALDI-TOF mass spectrometry. Our study revealed eight inducible proteins (DnaK, fabG4, DNA-binding, hypothetical, two 14 kDa antigen and two 10 kDa chaperonin) that were upregulated in the presence of drug. This preliminary study has thrown light on whether or not and how the resistant isolate responds to streptomycin at its non-toxic but sub-inhibitory concentration. An in-depth study of the upregulated proteins will give an insight into probable sites of drug action other than established primary sites.

  8. Genomic Analysis of Pathogenicity Determinants in Mycobacterium kansasii Type I

    KAUST Repository

    Guan, Qingtian

    2016-05-01

    Mycobacteria, a genus within Actinobacteria Phylum, are well known for two pathogens that cause human diseases: leprosy and tuberculosis. Other than the obligate human mycobacteria, there is a group of bacteria that are present in the environment and occasionally cause diseases in immunocompromised persons: the non-tuberculosis mycobacteria (NTM). Mycobacterium kansasii, which was first discovered in the Kansas state, is the main etiologic agent responsible for lung infections caused by NTM and raises attention because of its co-infection with human immunodeficiency virus (HIV). Five subspecies of M. kansasii (Type I-V) were described and only M. kansasii Type I is pathogenic to humans. M. kansasii is a Gram-positive bacteria that has a unique cell wall and secretion system, which is essential for its pathogenicity. We undertook a comparative genomics and transcriptomic approach to identify components of M. kansasii Type I pathogenicity. Our previous study showed that espA (ESX-1 essential protein) operon, a major component of the secretion system, is exclusively present in M. kansasii Type I. The purpose of this study was to test the functional role of the espA operon in pathogenicity and identify other components that may also be involved in pathogenicity. This study provides a new molecular diagnostic method for M. kansasii Type I infection using PCR (Polymerase Chain Reaction) technique to target the espAoperon. With detailed manual curation of the comparative genomics datasets, we found several genes exclusively present in M. kansasii Type I including ppsA/ppsC and whiB6, that we believe are involved, or have an effect on ESX-mediated secretion system. We have also highlighted, in our study, the differences in genetic components coding for the cell membrane composition between the five subspecies of M. kansasii. These results shed light on genetic components that are responsible for pathogenicity determinants in Type I M. kansasii and may help to design better

  9. Proteomic analysis of streptomycin resistant and sensitive clinical isolates of Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Venkatesan Krishnamurthy

    2010-11-01

    Full Text Available Abstract Background Streptomycin (SM is a broad spectrum antibiotic and is an important component of any anti-tuberculosis therapy regimen. Several mechanisms have been proposed to explain the emergence of resistance but still our knowledge is inadequate. Proteins form a very complex network and drugs are countered by their modification/efflux or over expression/modification of targets. As proteins manifest most of the biological processes, these are attractive targets for developing drugs, immunodiagnostics or therapeutics. The aim of present study was to analyze and compare the protein profile of whole cell extracts from Mycobacterium tuberculosis clinical isolates susceptible and resistant to SM. Results Two-dimensional gel electrophoresis (2DE and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF mass spectrometry was employed for analyzing the protein profiles. Homology and in silico characterization for identified proteins was assessed using BLAST, InterProScan and KEGG database searches. Computational studies on the possible interactions between SM and identified proteins were carried out by a battery of online servers and softwares, namely, CLUSTALW (KEGG, I-TASSER, VMD, PatchDock and FireDock. On comparing 2DE patterns, nine proteins were found consistently overexpressed in SM resistant isolates and were identified as Rv0350, Rv0440, Rv1240, Rv3075c, Rv2971, Rv3028c, Rv2145c, Rv2031c and Rv0569. In silico docking analysis showed significant interactions of SM with essential (Rv0350, Rv0440 and Rv2971 and non essential (Rv1240, Rv3075c and Rv2031c genes. Conclusions The computational results suggest high protein binding affinity of SM and suggested many possible interactions between identified proteins and the drug. Bioinformatic analysis proves attributive for analysis of diversity of proteins identified by whole proteome analysis. In-depth study of the these proteins will give an insight into probable sites of drug

  10. Whole-Genome Sequencing and Comparative Analysis of Mycobacterium brisbanense Reveals a Possible Soil Origin and Capability in Fertiliser Synthesis.

    Science.gov (United States)

    Wee, Wei Yee; Tan, Tze King; Jakubovics, Nicholas S; Choo, Siew Woh

    2016-01-01

    Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (~7.7Mbp) is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

  11. Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum.

    Science.gov (United States)

    Kenyon, Amy; Gavriouchkina, Daria; Zorman, Jernej; Napolitani, Giorgio; Cerundolo, Vincenzo; Sauka-Spengler, Tatjana

    2017-07-26

    The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β. Crispr/Cas9-mediated knockout of caspase b, which acts by proteolytic processing of il1β, results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterial infection, thus impairing granuloma development. We also show that a number of immediate early response genes (IEGs) are responsible for orchestrating the initial neutrophil response to mycobacterial infection. Further perturbation of the IEGs exposes egr3 as a key transcriptional regulator controlling il1β transcription.

  12. Phenotypic and Genotypic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Isolates from Sudanese Patients

    Directory of Open Access Journals (Sweden)

    Solima M. A. Sabeel

    2017-01-01

    Full Text Available Background. Currently, mutations in rpoB, KatG, and rrs genes and inhA promoter were considered to be involved in conferring resistance to rifampicin, isoniazid, and streptomycin in Mycobacterium tuberculosis (MTB. Objective. The aims of this study were to detect the prevalence of first-line tuberculosis (TB drug resistance among a group of previously treated and newly detected TB patients, to determine the association between prevalence of multidrug resistance (MDR and demographic information (age and sex, to explain genes correlated with MDR Mycobacterium tuberculosis, and to characterize MTB via 16S ribosomal RNA (16S rRNA analysis. Methods. A hundred MTB isolates from Sudanese pulmonary TB patients were included in the study. The proportional method of drug susceptibility test was carried out on Löwenstein-Jensen media. Multiplex PCR of rpoB and KatG genes and inhA promoter was conducted; then rrs genes were amplified by conventional PCR and were sequenced. The sequences of the PCR product were compared with known rrs gene sequences in the GenBank database by multiple sequence alignment tools. Result. The prevalence of MDR was 14.7% among old cases and 5.3% among newly diagnosed cases. Conclusion. Mutations in rrs could be considered as a diagnostic marker.

  13. Analysis of intracellular expressed proteins of Mycobacterium tuberculosis clinical isolates

    Directory of Open Access Journals (Sweden)

    Singhal Neelja

    2012-03-01

    sensitive isolate were hypothetical proteins which were functionally characterized using bioinformatic tools. Bioinformatic findings revealed that the proteins encoded by Rv0036, Rv2032c, Rv0635, Rv1827 and Rv2896c genes are involved in cellular metabolism and help in intracellular survival. Conclusions Mass spectrometry and bioinformatic analysis of both MDR and sensitive isolates of M. tuberculosis during intraphagosomal growth showed that majority of commonly upregulated/expressed proteins belonged to the cellular metabolism and respiration category. Inhibitors of the metabolic enzymes/intermediate can therefore serve as suitable drug targets against drug-resistant and sensitive subpopulations of M. tuberculosis.

  14. Interferon-γ release assays for the diagnosis of latent Mycobacterium tuberculosis infection: a systematic review and meta-analysis

    DEFF Research Database (Denmark)

    Diel, R; Goletti, D; Ferrara, G

    2011-01-01

    We conducted a systematic review and meta-analysis to compare the accuracy of the QuantiFERON-TB® Gold In-Tube (QFT-G-IT) and the T-SPOT®.TB assays with the tuberculin skin test (TST) for the diagnosis of latent Mycobacterium tuberculosis infection (LTBI). The Medline, Embase and Cochrane databases...

  15. Proposal of a new method for subtyping of Mycobacterium kansasii based upon PCR restriction enzyme analysis of the tuf gene

    NARCIS (Netherlands)

    Bakula, Z.; Modrzejewska, M.; Safianowska, A.; Ingen, J. van; Proboszcz, M.; Bielecki, J.; Jagielski, T.

    2016-01-01

    Within this study, a new, rapid method for subtyping of Mycobacterium kansasii was developed based on the sequence analysis of the tuf gene coding for the Tu (thermo-unstable) elongation factor (EF-Tu). The method involves PCR amplification of ca. 740-bp tuf gene fragment, followed by digestion with

  16. Rapid detection and immune characterization of Mycobacterium abscessus infection in cystic fibrosis patients.

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    Mathis Steindor

    Full Text Available Cystic fibrosis patients are highly susceptible to infections with non-tuberculous mycobacteria. Especially Mycobacterium abscessus infections are common but reliable diagnosis is hampered by non-specific clinical symptoms and insensitive mycobacterial culture. In the present study we established novel methods for rapid detection and immune characterization of Mycobacterium abscessus infection in cystic fibrosis patients. We performed Mycobacterium abscessus specific DNA-strip- and quantitative PCR-based analyses of non-cultured sputum samples to detect and characterize Mycobacterium abscessus infections. Concomitantly in vitro T-cell reactivation with purified protein derivatives (PPDs from different mycobacterial species was used to determine Mycobacterium abscessus specific T-cell cytokine expression of infected cystic fibrosis patients. Four of 35 cystic fibrosis patients (11.4% were Mycobacterium abscessus culture positive and showed concordant DNA-strip-test results. Quantitative PCR revealed marked differences of mycobacterial burden between cystic fibrosis patients and during disease course. Tandem-repeat analysis classified distinct Mycobacterium abscessus strains of infected cystic fibrosis patients and excluded patient-to-patient transmission. Mycobacterium abscessus specific T-cells were detected in the blood of cystic fibrosis patients with confirmed chronic infection and a subgroup of patients without evidence of Mycobacterium abscessus infection. Comparison of cytokine expression and phenotypic markers revealed increased proportions of CD40L positive T-cells that lack Interleukin-2 expression as a marker for chronic Mycobacterium abscessus infections in cystic fibrosis patients. Direct sputum examination enabled rapid diagnosis and quantification of Mycobacterium abscessus in cystic fibrosis patients. T-cell in vitro reactivation and cytokine expression analyses may contribute to diagnosis of chronic Mycobacterium abscessus

  17. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology

    Science.gov (United States)

    Mazars, Edith; Lesjean, Sarah; Banuls, Anne-Laure; Gilbert, Michèle; Vincent, Véronique; Gicquel, Brigitte; Tibayrenc, Michel; Locht, Camille; Supply, Philip

    2001-01-01

    The worldwide threat of tuberculosis to human health emphasizes the need to develop novel approaches to a global epidemiological surveillance. The current standard for Mycobacterium tuberculosis typing based on IS6110 restriction fragment length polymorphism (RFLP) suffers from the difficulty of comparing data between independent laboratories. Here, we propose a high-resolution typing method based on variable number tandem repeats (VNTRs) of genetic elements named mycobacterial interspersed repetitive units (MIRUs) in 12 human minisatellite-like regions of the M. tuberculosis genome. MIRU-VNTR profiles of 72 different M. tuberculosis isolates were established by PCR analysis of all 12 loci. From 2 to 8 MIRU-VNTR alleles were identified in the 12 regions in these strains, which corresponds to a potential of over 16 million different combinations, yielding a resolution power close to that of IS6110-RFLP. All epidemiologically related isolates tested were perfectly clustered by MIRU-VNTR typing, indicating that the stability of these MIRU-VNTRs is adequate to track outbreak episodes. The correlation between genetic relationships inferred from MIRU-VNTR and IS6110-RFLP typing was highly significant. Compared with IS6110-RFLP, high-resolution MIRU-VNTR typing has the considerable advantages of being fast, appropriate for all M. tuberculosis isolates, including strains that have a few IS6110 copies, and permitting easy and rapid comparison of results from independent laboratories. This typing method opens the way to the construction of digital global databases for molecular epidemiology studies of M. tuberculosis. PMID:11172048

  18. Use of Mycobacterium smegmatis deficient in ADP-ribosyltransferase as surrogate for Mycobacterium tuberculosis in drug testing and mutation analysis.

    Science.gov (United States)

    Agrawal, Priyanka; Miryala, Sandeep; Varshney, Umesh

    2015-01-01

    Rifampicin (Rif) is a first line drug used for tuberculosis treatment. However, the emergence of drug resistant strains has necessitated synthesis and testing of newer analogs of Rif. Mycobacterium smegmatis is often used as a surrogate for M. tuberculosis. However, the presence of an ADP ribosyltransferase (Arr) in M. smegmatis inactivates Rif, rendering it impractical for screening of Rif analogs or other compounds when used in conjunction with them (Rif/Rif analogs). Rifampicin is also used in studying the role of various DNA repair enzymes by analyzing mutations in RpoB (a subunit of RNA polymerase) causing Rif resistance. These analyses use high concentrations of Rif when M. smegmatis is used as model. Here, we have generated M. smegmatis strains by deleting arr (Δarr). The M. smegmatis Δarr strains show minimum inhibitory concentration (MIC) for Rif which is similar to that for M. tuberculosis. The MICs for isoniazid, pyrazinamide, ethambutol, ciprofloxacin and streptomycin were essentially unaltered for M. smegmatis Δarr. The growth profiles and mutation spectrum of Δarr and, Δarr combined with ΔudgB (udgB encodes a DNA repair enzyme that excises uracil) strains were similar to their counterparts wild-type for arr. However, the mutation spectrum of ΔfpgΔarr strain differed somewhat from that of the Δfpg strain (fpg encodes a DNA repair enzyme that excises 8-oxo-G). Our studies suggest M. smegmatis Δarr strain as an ideal model system in drug testing and mutation spectrum determination in DNA repair studies.

  19. Use of Mycobacterium smegmatis deficient in ADP-ribosyltransferase as surrogate for Mycobacterium tuberculosis in drug testing and mutation analysis.

    Directory of Open Access Journals (Sweden)

    Priyanka Agrawal

    Full Text Available Rifampicin (Rif is a first line drug used for tuberculosis treatment. However, the emergence of drug resistant strains has necessitated synthesis and testing of newer analogs of Rif. Mycobacterium smegmatis is often used as a surrogate for M. tuberculosis. However, the presence of an ADP ribosyltransferase (Arr in M. smegmatis inactivates Rif, rendering it impractical for screening of Rif analogs or other compounds when used in conjunction with them (Rif/Rif analogs. Rifampicin is also used in studying the role of various DNA repair enzymes by analyzing mutations in RpoB (a subunit of RNA polymerase causing Rif resistance. These analyses use high concentrations of Rif when M. smegmatis is used as model. Here, we have generated M. smegmatis strains by deleting arr (Δarr. The M. smegmatis Δarr strains show minimum inhibitory concentration (MIC for Rif which is similar to that for M. tuberculosis. The MICs for isoniazid, pyrazinamide, ethambutol, ciprofloxacin and streptomycin were essentially unaltered for M. smegmatis Δarr. The growth profiles and mutation spectrum of Δarr and, Δarr combined with ΔudgB (udgB encodes a DNA repair enzyme that excises uracil strains were similar to their counterparts wild-type for arr. However, the mutation spectrum of ΔfpgΔarr strain differed somewhat from that of the Δfpg strain (fpg encodes a DNA repair enzyme that excises 8-oxo-G. Our studies suggest M. smegmatis Δarr strain as an ideal model system in drug testing and mutation spectrum determination in DNA repair studies.

  20. Comparative Genomics and Proteomic Analysis of Four Non-tuberculous Mycobacterium Species and Mycobacterium tuberculosis Complex : Occurrence of Shared Immunogenic Proteins

    NARCIS (Netherlands)

    Gcebe, Nomakorinte; Michel, Anita; Gey van Pittius, Nicolaas C; Rutten, Victor

    2016-01-01

    The Esx and PE/PPE families of proteins are among the most immunodominant mycobacterial antigens and have thus been the focus of research to develop vaccines and immunological tests for diagnosis of bovine and human tuberculosis, mainly caused by Mycobacterium bovis and Mycobacterium tuberculosis,

  1. HLA class-II-restricted Mycobacterium leprae-reactive T-cell clones from leprosy patients established with a minimal requirement for autologous mononuclear cells

    NARCIS (Netherlands)

    Haanen, J. B.; Ottenhoff, T. H.; Voordouw, A.; Elferink, B. G.; Klatser, P. R.; Spits, H.; de Vries, R. R.

    1986-01-01

    This report describes an effective method for the cloning of Mycobacterium leprae-reactive T lymphocytes with Epstein-Barr-virus transformed autologous B cells as antigen-presenting cells. The two advantages of this method are that it drastically reduces the number of autologous peripheral blood

  2. Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b.

    Science.gov (United States)

    Benjak, Andrej; Uplekar, Swapna; Zhang, Ming; Piton, Jérémie; Cole, Stewart T; Sala, Claudia

    2016-03-05

    The ability of Mycobacterium tuberculosis to establish a latent infection (LTBI) in humans confounds the treatment of tuberculosis. Consequently, there is a need to discover new therapeutic agents that can kill M. tuberculosis both during active disease and LTBI. The streptomycin-dependent strain of M. tuberculosis, 18b, provides a useful tool for this purpose since upon removal of streptomycin (STR) it enters a non-replicating state that mimics latency both in vitro and in animal models. The 4.41 Mb genome sequence of M. tuberculosis 18b was determined and this revealed the strain to belong to clade 3 of the ancient ancestral lineage of the Beijing family. STR-dependence was attributable to insertion of a single cytosine in the 530 loop of the 16S rRNA and to a single amino acid insertion in the N-terminal domain of initiation factor 3. RNA-seq was used to understand the genetic programme activated upon STR-withdrawal and hence to gain insight into LTBI. This revealed reconfiguration of gene expression and metabolic pathways showing strong similarities between non-replicating 18b and M. tuberculosis residing within macrophages, and with the core stationary phase and microaerophilic responses. The findings of this investigation confirm the validity of 18b as a model for LTBI, and provide insight into both the evolution of tubercle bacilli and the functioning of the ribosome.

  3. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

    KAUST Repository

    Coll, Francesc

    2018-01-16

    To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.

  4. Phylogenetic analysis of vitamin B12-related metabolism in Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Douglas B. Young

    2015-03-01

    Full Text Available Comparison of genome sequences from clinical isolates of Mycobacterium tuberculosis with phylogenetically-related pathogens Mycobacterium marinum, Mycobacterium kansasii and Mycobacterium leprae reveals diversity amongst genes associated with vitamin B12-related metabolism. Diversity is generated by gene deletion events, differential acquisition of genes by horizontal transfer, and single nucleotide polymorphisms with predicted impact on protein function and transcriptional regulation. Differences in the B12 synthesis pathway, methionine biosynthesis, fatty acid catabolism, and DNA repair and replication are consistent with adaptations to different environmental niches and pathogenic lifestyles. While there is no evidence of further gene acquisition during expansion of the M. tuberculosis complex, the emergence of other forms of genetic diversity provides insights into continuing host-pathogen co-evolution and has the potential to identify novel targets for disease intervention.

  5. Analysis of CD4+ Th1 cells in immunity to intracellular Mycobacterium avium infection

    OpenAIRE

    Bakke, Marit Øien

    2013-01-01

    Mycobacterial infections are considered a major health problem internationally. Mycobacterium tuberculosis (Mtb), the infectious agent causing tuberculosis, kills 1.4 million people each year. Other non-tuberculous species such as Mycobacterium avium (M. avium) are less pathogenic but cause opportunistic infections mainly in immune-compromised people. The current treatment for different mycobacterial infections is elaborate, expensive and ineffective and new targets for treatment are needed. ...

  6. Molecular Analysis of Mycobacterium avium Isolates by Using Pulsed-Field Gel Electrophoresis and PCR

    Science.gov (United States)

    Pestel-Caron, Martine; Graff, Gabriel; Berthelot, Gilles; Pons, Jean-Louis; Lemeland, Jean-François

    1999-01-01

    Genetic relationships among 46 isolates of Mycobacterium avium recovered from 37 patients in a 2,500-bed hospital from 1993 to 1998 were assessed by pulsed-field gel electrophoresis (PFGE) and PCR amplification of genomic sequences located between the repetitive elements IS1245 and IS1311. Each technique enabled the identification of 27 to 32 different patterns among the 46 isolates, confirming that the genetic heterogeneity of M. avium strains is high in a given community. Furthermore, this retrospective analysis of sporadic isolates allowed us (i) to suggest the existence of two remanent strains in our region, (ii) to raise the question of the possibility of nosocomial acquisition of M. avium strains, and (iii) to document laboratory contamination. The methods applied in the present study were found to be useful for the typing of M. avium isolates. In general, both methods yielded similar results for both related and unrelated isolates. However, the isolates in five of the six PCR clusters were distributed among two to three PFGE patterns, suggesting that this PCR-based method may have limitations for the analysis of strains with low insertion sequence copy numbers or for resolution of extended epidemiologic relationships. PMID:10405383

  7. Phosphoproteomics analysis of a clinical Mycobacterium tuberculosis Beijing isolate: expanding the mycobacterial phosphoproteome catalog.

    Science.gov (United States)

    Fortuin, Suereta; Tomazella, Gisele G; Nagaraj, Nagarjuna; Sampson, Samantha L; Gey van Pittius, Nicolaas C; Soares, Nelson C; Wiker, Harald G; de Souza, Gustavo A; Warren, Robin M

    2015-01-01

    Reversible protein phosphorylation, regulated by protein kinases and phosphatases, mediates a switch between protein activity and cellular pathways that contribute to a large number of cellular processes. The Mycobacterium tuberculosis genome encodes 11 Serine/Threonine kinases (STPKs) which show close homology to eukaryotic kinases. This study aimed to elucidate the phosphoproteomic landscape of a clinical isolate of M. tuberculosis. We performed a high throughput mass spectrometric analysis of proteins extracted from an early-logarithmic phase culture. Whole cell lysate proteins were processed using the filter-aided sample preparation method, followed by phosphopeptide enrichment of tryptic peptides by strong cation exchange (SCX) and Titanium dioxide (TiO2) chromatography. The MaxQuant quantitative proteomics software package was used for protein identification. Our analysis identified 414 serine/threonine/tyrosine phosphorylated sites, with a distribution of S/T/Y sites; 38% on serine, 59% on threonine and 3% on tyrosine; present on 303 unique peptides mapping to 214 M. tuberculosis proteins. Only 45 of the S/T/Y phosphorylated proteins identified in our study had been previously described in the laboratory strain H37Rv, confirming previous reports. The remaining 169 phosphorylated proteins were newly identified in this clinical M. tuberculosis Beijing strain. We identified 5 novel tyrosine phosphorylated proteins. These findings not only expand upon our current understanding of the protein phosphorylation network in clinical M. tuberculosis but the data set also further extends and complements previous knowledge regarding phosphorylated peptides and phosphorylation sites in M. tuberculosis.

  8. Functional analysis of TPM domain containing Rv2345 of Mycobacterium tuberculosis identifies its phosphatase activity.

    Science.gov (United States)

    Sinha, Avni; Eniyan, Kandasamy; Sinha, Swati; Lynn, Andrew Michael; Bajpai, Urmi

    2015-07-01

    Mycobacterium tuberculosis (Mtb) is the causal agent of tuberculosis, the second largest infectious disease. With the rise of multi-drug resistant strains of M. tuberculosis, serious challenge lies ahead of us in treating the disease. The availability of complete genome sequence of Mtb has improved the scope for identifying new proteins that would not only further our understanding of biology of the organism but could also serve to discover new drug targets. In this study, Rv2345, a hypothetical membrane protein of M. tuberculosis H37Rv, which is reported to be a putative ortholog of ZipA cell division protein has been assigned function through functional annotation using bioinformatics tools followed by experimental validation. Sequence analysis showed Rv2345 to have a TPM domain at its N-terminal region and predicted it to have phosphatase activity. The TPM domain containing region of Rv2345 was cloned and expressed using pET28a vector in Escherichia coli and purified by Nickel affinity chromatography. The purified TPM domain was tested in vitro and our results confirmed it to have phosphatase activity. The enzyme activity was first checked and optimized with pNPP as substrate, followed by using ATP, which was also found to be used as substrate by the purified protein. Hence sequence analysis followed by in vitro studies characterizes TPM domain of Rv2345 to contain phosphatase activity. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Heterogeneity among Mycobacterium ulcerans from French Guiana revealed by multilocus variable number tandem repeat analysis (MLVA).

    Science.gov (United States)

    Reynaud, Yann; Millet, Julie; Couvin, David; Rastogi, Nalin; Brown, Christopher; Couppié, Pierre; Legrand, Eric

    2015-01-01

    Buruli ulcer is an emerging and neglected tropical disease caused by Mycobacterium ulcerans. Few cases have been reported so far in the Americas. With 250 cases reported since 1969, French Guiana is the only Buruli ulcer endemic area in the continent. Thus far, no genetic diversity studies of strains of M. ulcerans from French Guiana have been reported. Our goal in the present study was to examine the genetic diversity of M. ulcerans strains in this region by using the Multilocus Variable Number Tandem Repeat Analysis (MLVA) approach. A total of 23 DNA samples were purified from ulcer biopsies or derived from pure cultures. MVLA was used in the study of six previously-described Variable Number of Tandem Repeat (VNTR) markers. A total of three allelic combinations were characterized in our study: genotype I which has been described previously, genotype III which is very similar to genotype I, and genotype II which has distinctly different characteristics in comparison with the other two genotypes. This high degree of genetic diversity appears to be uncommon for M. ulcerans. Further research based on complete genome sequencing of strains belonging to genotypes I and II is in progress and should lead soon to a better understanding of genetic specificities of M. ulcerans strains from French Guiana.

  10. Mycobacterium tuberculosis complex differentiation using gyrB-restriction fragment length polymorphism analysis

    Directory of Open Access Journals (Sweden)

    Erica Chimara

    2004-11-01

    Full Text Available Mycobacterium tuberculosis complex (MTBC members are causative agents of human and animal tuberculosis. Differentiation of MTBC members is required for appropriate treatment of individual patients and for epidemiological purposes. Strains from six MTBC species - M. tuberculosis, M. bovis subsp. bovis, M. bovis BCG, M. africanum, M. pinnipedii, and "M. canetti" - were studied using gyrB-restriction fragment length polymorphism (gyrB-RFLP analysis. A table was elaborated, based on observed restriction patterns and published gyrB sequences. To evaluate applicability of gyrB-RFLP at Instituto Adolfo Lutz, São Paulo, Mycobacterial Reference Laboratory, 311 MTBC clinical isolates, previously identified using traditional methods as M. tuberculosis (306, M. bovis (3, and M. bovis BCG (2, were analyzed by gyrB-RFLP. All isolates were correctly identified by the molecular method, but no distinction between M. bovis and M. bovis BCG was obtained. Differentiation of M. tuberculosis and M. bovis is of utmost importance, because they require different treatment schedules. In conclusion, gyrB-RFLP is accurate and easy-to-perform, with potential to reduce time needed for conventional differentiation methods. However, application for epidemiological studies remains limited, because it cannot differentiate M. tuberculosis from M. africanum subtype II, and "M. canetti", M. africanum subtype I from M. pinnipedii, and. M. bovis from M. bovis BCG.

  11. Mycobacterium tuberculosis bacteremia in adults and children: a systematic review and meta-analysis.

    Science.gov (United States)

    Pavlinac, P B; Lokken, E M; Walson, J L; Richardson, B A; Crump, J A; John-Stewart, G C

    2016-07-01

    SETTINGp: Among human immunodeficiency virus (HIV) infected adults living in tuberculosis (TB) endemic settings, Mycobacterium tuberculosis is a common cause of bloodstream infections. Although young children have an increased propensity for M. tuberculosis dissemination, M. tuberculosis bacteremia is infrequently described in children. To determine the prevalence of M. tuberculosis bacteremia in adult and pediatric patients and to examine sources of heterogeneity between estimates. Systematic review and meta-analysis. Of 1077 reviewed abstracts, 27 publications met the inclusion criteria, yielding 29 independent M. tuberculosis bacteremia prevalence estimates: 22 in adults, 6 in children, and 1 not stratified by age group. The random effects pooled M. tuberculosis bacteremia prevalence in adults was 13.5% (95%CI 10.8-16.2) and 0.4% (95%CI 0-0.9) in children (P for difference = 0.004). Restricting analyses to HIV-infected participants, pooled M. tuberculosis bacteremia prevalence from 21 adult studies was 15.5% (95%CI 12.5-18.5) and 0.8% (95%CI 0-1.8) in three pediatric studies (P = 0.001). Inclusion of pre-determined study-level confounders did not account for observed differences in M. tuberculosis bacteremia prevalence between age groups. While M. tuberculosis bacteremia appears relatively common in adults, particularly those with HIV infection, bloodstream M. tuberculosis appears to be rare in children.

  12. Effect of BCG vaccination against Mycobacterium tuberculosis infection in children: systematic review and meta-analysis.

    Science.gov (United States)

    Roy, A; Eisenhut, M; Harris, R J; Rodrigues, L C; Sridhar, S; Habermann, S; Snell, L; Mangtani, P; Adetifa, I; Lalvani, A; Abubakar, I

    2014-08-05

    To determine whether BCG vaccination protects against Mycobacterium tuberculosis infection as assessed by interferon γ release assays (IGRA) in children. Systematic review and meta-analysis. Searches of electronic databases 1950 to November 2013, checking of reference lists, hand searching of journals, and contact with experts. Community congregate settings and households. Vaccinated and unvaccinated children aged under 16 with known recent exposure to patients with pulmonary tuberculosis. Children were screened for infection with M tuberculosis with interferon γ release assays. Study results relating to diagnostic accuracy were extracted and risk estimates were combined with random effects meta-analysis. The primary analysis included 14 studies and 3855 participants. The estimated overall risk ratio was 0.81 (95% confidence interval 0.71 to 0.92), indicating a protective efficacy of 19% against infection among vaccinated children after exposure compared with unvaccinated children. The observed protection was similar when estimated with the two types of interferon γ release assays (ELISpot or QuantiFERON). Restriction of the analysis to the six studies (n=1745) with information on progression to active tuberculosis at the time of screening showed protection against infection of 27% (risk ratio 0.73, 0.61 to 0.87) compared with 71% (0.29, 0.15 to 0.58) against active tuberculosis. Among those infected, protection against progression to disease was 58% (0.42, 0.23 to 0.77). BCG protects against M tuberculosis infection as well as progression from infection to disease.Trial registration PROSPERO registration No CRD42011001698 (www.crd.york.ac.uk/prospero/). © Roy et al 2014.

  13. Risk Analysis as Regulatory Science: Toward The Establishment of Standards.

    Science.gov (United States)

    Murakami, Michio

    2016-09-01

    Understanding how to establish standards is essential for risk communication and also provides perspectives for further study. In this paper, the concept of risk analysis as regulatory science for the establishment of standards is demonstrated through examples of standards for evacuation and provisional regulation values in foods and drinking water. Moreover, academic needs for further studies related to standards are extracted. The concepts of the traditional 'Standard I', which has a paternalistic orientation, and 'Standard II', established through stakeholder consensus, are then systemized by introducing the current status of the new standards-related movement that developed after the Fukushima nuclear power plant accident, and the perspectives of the standards are discussed. Preparation of standards on the basis of stakeholder consensus through intensive risk dialogue before a potential nuclear power plant accident is suggested to be a promising approach to ensure a safe society and enhance subjective well-being. © The Author 2016. Published by Oxford University Press.

  14. Risk Analysis as Regulatory Science: Toward The Establishment of Standards

    Science.gov (United States)

    Murakami, Michio

    2016-01-01

    Understanding how to establish standards is essential for risk communication and also provides perspectives for further study. In this paper, the concept of risk analysis as regulatory science for the establishment of standards is demonstrated through examples of standards for evacuation and provisional regulation values in foods and drinking water. Moreover, academic needs for further studies related to standards are extracted. The concepts of the traditional ‘Standard I’, which has a paternalistic orientation, and ‘Standard II’, established through stakeholder consensus, are then systemized by introducing the current status of the new standards-related movement that developed after the Fukushima nuclear power plant accident, and the perspectives of the standards are discussed. Preparation of standards on the basis of stakeholder consensus through intensive risk dialogue before a potential nuclear power plant accident is suggested to be a promising approach to ensure a safe society and enhance subjective well-being. PMID:27475751

  15. Structural Analysis of Mycobacterium tuberculosis Homologues of the Eukaryotic Proteasome Assembly Chaperone 2 (PAC2).

    Science.gov (United States)

    Bai, Lin; Jastrab, Jordan B; Isasa, Marta; Hu, Kuan; Yu, Hongjun; Gygi, Steven P; Darwin, K Heran; Li, Huilin

    2017-05-01

    A previous bioinformatics analysis identified the Mycobacterium tuberculosis proteins Rv2125 and Rv2714 as orthologs of the eukaryotic proteasome assembly chaperone 2 (PAC2). We set out to investigate whether Rv2125 or Rv2714 can function in proteasome assembly. We solved the crystal structure of Rv2125 at a resolution of 3.0 Å, which showed an overall fold similar to that of the PAC2 family proteins that include the archaeal PbaB and the yeast Pba1. However, Rv2125 and Rv2714 formed trimers, whereas PbaB forms tetramers and Pba1 dimerizes with Pba2. We also found that purified Rv2125 and Rv2714 could not bind to M. tuberculosis 20S core particles. Finally, proteomic analysis showed that the levels of known proteasome components and substrate proteins were not affected by disruption of Rv2125 in M. tuberculosis Our work suggests that Rv2125 does not participate in bacterial proteasome assembly or function. IMPORTANCE Although many bacteria do not encode proteasomes, M. tuberculosis not only uses proteasomes but also has evolved a posttranslational modification system called pupylation to deliver proteins to the proteasome. Proteasomes are essential for M. tuberculosis to cause lethal infections in animals; thus, determining how proteasomes are assembled may help identify new ways to combat tuberculosis. We solved the structure of a predicted proteasome assembly factor, Rv2125, and isolated a genetic Rv2125 mutant of M. tuberculosis Our structural, biochemical, and genetic studies indicate that Rv2125 and Rv2714 do not function as proteasome assembly chaperones and are unlikely to have roles in proteasome biology in mycobacteria. Copyright © 2017 American Society for Microbiology.

  16. Cell wall proteome analysis of Mycobacterium smegmatis strain MC2 155

    Directory of Open Access Journals (Sweden)

    De Buck Jeroen

    2010-04-01

    Full Text Available Abstract Background The usually non-pathogenic soil bacterium Mycobacterium smegmatis is commonly used as a model mycobacterial organism because it is fast growing and shares many features with pathogenic mycobacteria. Proteomic studies of M. smegmatis can shed light on mechanisms of mycobacterial growth, complex lipid metabolism, interactions with the bacterial environment and provide a tractable system for antimycobacterial drug development. The cell wall proteins are particularly interesting in this respect. The aim of this study was to construct a reference protein map for these proteins in M. smegmatis. Results A proteomic analysis approach, based on one dimensional polyacrylamide gel electrophoresis and LC-MS/MS, was used to identify and characterize the cell wall associated proteins of M. smegmatis. An enzymatic cell surface shaving method was used to determine the surface-exposed proteins. As a result, a total of 390 cell wall proteins and 63 surface-exposed proteins were identified. Further analysis of the 390 cell wall proteins provided the theoretical molecular mass and pI distributions and determined that 26 proteins are shared with the surface-exposed proteome. Detailed information about functional classification, signal peptides and number of transmembrane domains are given next to discussing the identified transcriptional regulators, transport proteins and the proteins involved in lipid metabolism and cell division. Conclusion In short, a comprehensive profile of the M. smegmatis cell wall subproteome is reported. The current research may help the identification of some valuable vaccine and drug target candidates and provide foundation for the future design of preventive, diagnostic, and therapeutic strategies against mycobacterial diseases.

  17. Establishment and validation of whole-cell based fluorescence assays to identify anti-mycobacterial compounds using the Acanthamoeba castellanii-Mycobacterium marinum host-pathogen system.

    Directory of Open Access Journals (Sweden)

    Sébastien Kicka

    Full Text Available Tuberculosis is considered to be one of the world's deadliest disease with 2 million deaths each year. The need for new antitubercular drugs is further exacerbated by the emergence of drug-resistance strains. Despite multiple recent efforts, the majority of the hits discovered by traditional target-based screening showed low efficiency in vivo. Therefore, there is heightened demand for whole-cell based approaches directly using host-pathogen systems. The phenotypic host-pathogen assay described here is based on the monitoring of GFP-expressing Mycobacterium marinum during infection of the amoeba Acanthamoeba castellanii. The assay showed straight-forward medium-throughput scalability, robustness and ease of manipulation, demonstrating its qualities as an efficient compound screening system. Validation with a series of known antitubercular compounds highlighted the advantages of the assay in comparison to previously published macrophage-Mycobacterium tuberculosis-based screening systems. Combination with secondary growth assays based on either GFP-expressing D. discoideum or M. marinum allowed us to further fine-tune compound characterization by distinguishing and quantifying growth inhibition, cytotoxic properties and antibiotic activities of the compounds. The simple and relatively low cost system described here is most suitable to detect anti-infective compounds, whether they present antibiotic activities or not, in which case they might exert anti-virulence or host defense boosting activities, both of which are largely overlooked by classical screening approaches.

  18. Establishment of analysis method for methane detection by gas chromatography

    Science.gov (United States)

    Liu, Xinyuan; Yang, Jie; Ye, Tianyi; Han, Zeyu

    2018-02-01

    The study focused on the establishment of analysis method for methane determination by gas chromatography. Methane was detected by hydrogen flame ionization detector, and the quantitative relationship was determined by working curve of y=2041.2x+2187 with correlation coefficient of 0.9979. The relative standard deviation of 2.60-6.33% and the recovery rate of 96.36%∼105.89% were obtained during the parallel determination of standard gas. This method was not quite suitable for biogas content analysis because methane content in biogas would be over the measurement range in this method.

  19. Comparative Genomics Analysis of Mycobacterium ulcerans for the Identification of Putative Essential Genes and Therapeutic Candidates

    Science.gov (United States)

    Tahir, Shifa; Tong, Yigang

    2012-01-01

    Mycobacterium ulcerans, the causative agent of Buruli ulcer, is the third most common mycobacterial disease after tuberculosis and leprosy. The present treatment options are limited and emergence of treatment resistant isolates represents a serious concern and a need for better therapeutics. Conventional drug discovery methods are time consuming and labor-intensive. Unfortunately, the slow growing nature of M. ulcerans in experimental conditions is also a barrier for drug discovery and development. In contrast, recent advancements in complete genome sequencing, in combination with cheminformatics and computational biology, represent an attractive alternative approach for the identification of therapeutic candidates worthy of experimental research. A computational, comparative genomics workflow was defined for the identification of novel therapeutic candidates against M. ulcerans, with the aim that a selected target should be essential to the pathogen, and have no homology in the human host. Initially, a total of 424 genes were predicted as essential from the M. ulcerans genome, via homology searching of essential genome content from 20 different bacteria. Metabolic pathway analysis showed that the most essential genes are associated with carbohydrate and amino acid metabolism. Among these, 236 proteins were identified as non-host and essential, and could serve as potential drug and vaccine candidates. Several drug target prioritization parameters including druggability were also calculated. Enzymes from several pathways are discussed as potential drug targets, including those from cell wall synthesis, thiamine biosynthesis, protein biosynthesis, and histidine biosynthesis. It is expected that our data will facilitate selection of M. ulcerans proteins for successful entry into drug design pipelines. PMID:22912793

  20. Spoligotyping and variable number tandem repeat analysis of Mycobacterium bovis isolates from cattle in Brazil

    Directory of Open Access Journals (Sweden)

    Patrícia Martins Parreiras

    2012-02-01

    Full Text Available We performed spoligotyping and 12-mycobacterial interspersed repetitive unit-variable number tandem repeats (MIRU-VNTRs typing to characterise Mycobacterium bovis isolates collected from tissue samples of bovines with lesions suggestive for tuberculosis during slaughter inspection procedures in abattoirs in Brazil. High-quality genotypes were obtained with both procedures for 61 isolates that were obtained from 185 bovine tissue samples and all of these isolates were identified as M. bovis by conventional identification procedures. On the basis of the spoligotyping, 53 isolates were grouped into nine clusters and the remaining eight isolates were unique types, resulting in 17 spoligotypes. The majority of the Brazilian M. bovis isolates displayed spoligotype patterns that have been previously observed in strains isolated from cattle in other countries. MIRU-VNTR typing produced 16 distinct genotypes, with 53 isolates forming eight of the groups, and individual isolates with unique VNTR profiles forming the remaining eight groups. The allelic diversity of each VNTR locus was calculated and only two of the 12-MIRU-VNTR loci presented scores with either a moderate (0.4, MIRU16 or high (0.6, MIRU26 discriminatory index (h. Both typing methods produced similar discriminatory indexes (spoligotyping h = 0.85; MIRU-VNTR h = 0.86 and the combination of the two methods increased the h value to 0.94, resulting in 29 distinct patterns. These results confirm that spoligotyping and VNTR analysis are valuable tools for studying the molecular epidemiology of M. bovis infections in Brazil.

  1. Spatial analysis of factors implicated in Mycobacterium ulcerans infection in Ghana

    NARCIS (Netherlands)

    Duker, A.A.

    2005-01-01

    Buruliulcer (BU), the common terminology for the disease caused by Mycobacteriumulcerans (MU) infection manifests as disfiguring skin ulceration which is difficult to treat. In its advanced

  2. DNA fingerprinting of Mycobacterium leprae strains using variable number tandem repeat (VNTR) - fragment length analysis (FLA).

    Science.gov (United States)

    Jensen, Ronald W; Rivest, Jason; Li, Wei; Vissa, Varalakshmi

    2011-07-15

    The study of the transmission of leprosy is particularly difficult since the causative agent, Mycobacterium leprae, cannot be cultured in the laboratory. The only sources of the bacteria are leprosy patients, and experimentally infected armadillos and nude mice. Thus, many of the methods used in modern epidemiology are not available for the study of leprosy. Despite an extensive global drug treatment program for leprosy implemented by the WHO, leprosy remains endemic in many countries with approximately 250,000 new cases each year. The entire M. leprae genome has been mapped and many loci have been identified that have repeated segments of 2 or more base pairs (called micro- and minisatellites). Clinical strains of M. leprae may vary in the number of tandem repeated segments (short tandem repeats, STR) at many of these loci. Variable number tandem repeat (VNTR) analysis has been used to distinguish different strains of the leprosy bacilli. Some of the loci appear to be more stable than others, showing less variation in repeat numbers, while others seem to change more rapidly, sometimes in the same patient. While the variability of certain VNTRs has brought up questions regarding their suitability for strain typing, the emerging data suggest that analyzing multiple loci, which are diverse in their stability, can be used as a valuable epidemiological tool. Multiple locus VNTR analysis (MLVA) has been used to study leprosy evolution and transmission in several countries including China, Malawi, the Philippines, and Brazil. MLVA involves multiple steps. First, bacterial DNA is extracted along with host tissue DNA from clinical biopsies or slit skin smears (SSS). The desired loci are then amplified from the extracted DNA via polymerase chain reaction (PCR). Fluorescently-labeled primers for 4-5 different loci are used per reaction, with 18 loci being amplified in a total of four reactions. The PCR products may be subjected to agarose gel electrophoresis to verify the

  3. Establishment of reference intervals and transfusion criterion for Sonoclot analysis.

    Science.gov (United States)

    Zhang, Zhen-Lu; Chen, You-Ping; Tao, Cui-Hua; Liu, Xiao-Hui; Li, Meng-Ya; Zhou, Xin

    2016-08-01

    Sonoclot analyzer has been widely used in many countries. But the reference intervals provided by the manufacturer were derived from only 45 participants, and there was no cut-off value for transfusion for Sonoclot analysis. This study aimed to establish reference intervals and transfusion criterion for Sonoclot analysis. Volunteers were recruited from healthy Chinese adults and patients undergoing cardiac surgery. Blood samples were withdrawn from forearm vein and measured for activated clotting time (ACT), clot rate (CR), platelet function (PF), activated partial thromboplastin time (APTT), fibrinogen concentration (FIB), and platelet count (PLT). The reference intervals were determined by the nonparametric method. Cut-off values were determined by the receiver operating characteristics curve. A total of 135 healthy volunteers and 281 patients were enrolled. The 95% reference intervals were 96-195 s, 22-51 signal U/min, >1.6 for ACT, CR, PF respectively. In the 281 patients, the results of APTT, FIB, PLT, ACT, CR, and PF ranged from 20.5-300.0 s, 0.28-4.11 g/L, (19.0-387.3)×109/L, 80-514 s, 2.9-74 signal U/min, and 0.1-5.1 respectively. The cut-off values for transfusion were >208, ≤14, and ≤1.3 for ACT, CR, PF respectively. The cut-off values of Sonoclot analysis were within the manufacturer's reference intervals, while they were outside the reference intervals established in this study. The results suggested that the manufacturer's reference intervals were not suitable for Chinese. The reference intervals and cut-off values established in this study will be helpful to Chinese patients.

  4. Establishment of ultra trace nuclear material analysis system

    International Nuclear Information System (INIS)

    Song, Kyuseok; Jee, Kwangyong; Lee, Changheon

    2012-05-01

    Highly accurate and precise analysis of ultra trace nuclear materials contained in swipe samples and environmental samples is required to improve the national nuclear transparency and the international nuclear security. The objectives of the first stage of this project are to develop the techniques for bulk analysis of environmental samples and the elemental techniques for particle analysis using FT-TIMS. To accomplish the objectives, state-of-the-art analytical instruments were set up followed by the development of the techniques for screening of nuclear materials, chemical treatement, particle handling, isotopic measurements using TIMS and ICP-MS, and fabrication of uranium microparticles. The verifications of the developed techniques were carried out by measurement of reference materials, and by participation to interlaboratory comparison programs. In additon, the establishement of a quality management system and the performance of the analysis of QC samples for IAEA-NWAL qualification were carried out to obtain the international accreditation for the related analytical system. In this report, the results of research and developments, and the achievements to obtain the international accreditation were summarized

  5. Simultaneous analysis of multiple Mycobacterium tuberculosis knockdown mutants in vitro and in vivo.

    Directory of Open Access Journals (Sweden)

    Antje Blumenthal

    2010-12-01

    Full Text Available Mycobacterium tuberculosis (Mtb represents one of the most persistent bacterial threats to human health and new drugs are needed to limit its impact. Conditional knockdown mutants can help validate new drug targets, but the analysis of individual mutants is laborious and time consuming. Here, we describe quantitative DNA tags (qTags and their use to simultaneously analyze conditional Mtb knockdown mutants that allowed silencing the glyoxylate and methylcitrate cycles (via depletion of isocitrate lyase, ICL, the serine protease Rv3671c, and the core subunits of the mycobacterial proteasome, PrcB and PrcA. The impact of gene silencing in multi-strain cultures was determined by measuring the relative abundance of mutant-specific qTags with real-time PCR. This achieved accurate quantification over a broad range of qTag abundances and depletion of ICL, Rv3671c, or PrcBA resulted in the expected impairment of growth of Mtb with butyrate as the primary carbon source, survival during oxidative stress, acid stress and starvation. The impact of depleting ICL, Rv3671c, or PrcBA in multi-strain mouse infections was analyzed with two approaches. We first measured the relative abundance of mutant-specific qTags in total chromosomal DNA isolated from bacteria that were recovered from infected lungs on agar plates. We then developed a two-step amplification procedure, which allowed us to measure the abundances of individual mutants directly in infected lung tissue. Both strategies confirmed that inactivation of Rv3671c and PrcBA severely reduced persistence of Mtb in mice. The multi-strain infections furthermore suggested that silencing ICL not only prevented growth of Mtb during acute infections but also prevented survival of Mtb during chronic infections. Analyses of the ICL knockdown mutant in single-strain infections confirmed this and demonstrated that silencing of ICL during chronic infections impaired persistence of Mtb to the extent that the pathogen

  6. In Silico Prediction of Antibiotic Resistance inMycobacterium ulceransAgy99 through Whole Genome Sequence Analysis.

    Science.gov (United States)

    Gupta, Sushim Kumar; Drancourt, Michel; Rolain, Jean-Marc

    2017-09-01

    Buruli ulcer is an emerging infectious disease caused by Mycobacterium ulcerans that has been reported from 33 countries. Antimicrobial agents either alone or in combination with surgery have been proved to be clinically relevant and therapeutic strategies have been deduced mainly from the empirical experience. The genome sequences of M . ulcerans strain AGY99, M. ulcerans ecovar liflandii, and three Mycobacterium marinum strains were analyzed to predict resistance in these bacteria. Fourteen putative antibiotic resistance genes from different antibiotics classes were predicted in M. ulcerans and mutation in kat G (R431G) and pnc A (T47A, V125I) genes were detected, that confer resistance to isoniazid and pyrazinamide, respectively. No mutations were detected in rpoB , gyr A, gyr B, rps L, rrs , emb , eth A, 23S ribosomal RNA genes and promoter region of inh A and ahp C genes associated with resistance. Our results reemphasize the usefulness of in silico analysis for the prediction of antibiotic resistance in fastidious bacteria.

  7. Mycobacterium tuberculosis.

    Science.gov (United States)

    Koch, Anastasia; Mizrahi, Valerie

    2018-03-23

    In this infographic, the genetics, phylogeny, physiology, and pathogenesis mechanisms of Mycobacterium tuberculosis are shown. Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), the leading cause of death due to a single infectious agent, claiming 1.7 million lives in 2016. Of the deaths attributable to TB in 2016, 22% occurred in people coinfected with HIV, and close to 5% of the 10.4 million incident cases of this disease were resistant to at least two of the first-line TB drugs. In this infographic, we describe the fundamental features of the genetics, phylogeny, and physiology of this member of the phylum Actinobacteria, which is associated increasingly with drug resistance mediated by mutations and rearrangements in its single, circular chromosome. We also highlight the key pathogenesis mechanisms employed by this slow-growing, facultative intracellular bacterium, which include avoidance of host cell clearance by arrest of the normal macrophage maturation process. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Single-nucleotide polymorphism-based population genetic analysis of Mycobacterium tuberculosis strains from 4 geographic sites.

    Science.gov (United States)

    Gutacker, Michaela M; Mathema, Barun; Soini, Hanna; Shashkina, Elena; Kreiswirth, Barry N; Graviss, Edward A; Musser, James M

    2006-01-01

    We studied genetic relationships among 5069 Mycobacterium tuberculosis strains recovered from patients enrolled in 4 population-based studies in the United States and Europe, by analysis of 36 synonymous single-nucleotide polymorphisms (SNPs). All strains were assigned to 1 of 9 major genetic clusters based on sSNP profile. The same 9 genetic clusters were revealed by analysis of 227 nonsynonymous SNPs, 121 intergenic SNPs, and concatenated profiles of 578 SNPs available for a subset of 48 representative strains. IS6110 profiles, spoligotypes, and mycobacterial interspersed repetitive unit patterns were nonrandomly associated with SNP-based phylogenetic lineages, together indicating a strongly clonal population structure. Isolates of the 9 genetic clusters were not distributed with equal frequency in all localities, reflecting geographic subdivision. The SNP-based phylogenetic framework provides new insight into the worldwide evolution of M. tuberculosis and a gateway for investigating genotype-disease phenotype relationships in large samples of strains.

  9. Genotypic analysis of Mycobacterium tuberculosis isolates from a Lisbon hospital in Portugal.

    Science.gov (United States)

    Perdigão, João; Milho, Catarina; Carrilho, Lurdes; Brum, Laura; Portugal, Isabel

    2009-01-01

    Portugal has one of the highest tuberculosis notification rates of the European Union with Lisbon Health Region having an incidence rate well above the national average. The present study analyses the transmission, drug susceptibility and characteristics of a study population from a Central Lisbon's Hospital. One hundred and thirty -two Mycobacterium tuberculosis clinical isolates were previously tested for drug susceptibility to first -line drugs. The multidrug (MDR) resistance rate was found to be 3.0%, while 13.6% of the isolates were resistant to one or more first -line drugs. HIV serology was available for 98 patients, 26 (26.5%) were positive. Genotyping was performed by MIRU -VNTR and 53 (40.2%) out of the 132 isolates were found to be distributed through 17 MIRU -VNTR clusters of two or more isolates. Lisboa strains accounted for 25.8% of all strains. We conclude that transmission of resistant and susceptible Mycobacterium tuberculosis strains is occurring, with special concern for Lisboa strains.

  10. Mutation analysis of the Mycobacterium leprae folP1 gene and dapsone resistance.

    Science.gov (United States)

    Nakata, Noboru; Kai, Masanori; Makino, Masahiko

    2011-02-01

    Diaminodiphenylsulfone (dapsone) has long been used as a first-line drug worldwide for the treatment of leprosy. Diagnosis for dapsone resistance of Mycobacterium leprae by DNA tests would be of great clinical value, but the relationship between the nucleotide substitutions and susceptibility to dapsone must be clarified before use. In this study, we constructed recombinant strains of cultivable Mycobacterium smegmatis carrying the M. leprae folP1 gene with or without a point mutation, disrupting their own folP gene on the chromosome. Dapsone susceptibilities of the recombinant bacteria were measured to examine influence of the mutations. Dapsone MICs for most of the strains with mutations at codon 53 or 55 of M. leprae folP1 were 2 to 16 times as high as the MIC for the strain with the wild-type folP1 sequence, but mutations that changed Thr to Ser at codon 53 showed somewhat lower MIC values than the wild-type sequence. Strains with mutations at codon 48 or 54 showed levels of susceptibility to dapsone comparable to the susceptibility of the strain with the wild-type sequence. This study confirmed that point mutations at codon 53 or 55 of the M. leprae folP1 gene result in dapsone resistance.

  11. Mutation Analysis of the Mycobacterium leprae folP1 Gene and Dapsone Resistance▿

    Science.gov (United States)

    Nakata, Noboru; Kai, Masanori; Makino, Masahiko

    2011-01-01

    Diaminodiphenylsulfone (dapsone) has long been used as a first-line drug worldwide for the treatment of leprosy. Diagnosis for dapsone resistance of Mycobacterium leprae by DNA tests would be of great clinical value, but the relationship between the nucleotide substitutions and susceptibility to dapsone must be clarified before use. In this study, we constructed recombinant strains of cultivable Mycobacterium smegmatis carrying the M. leprae folP1 gene with or without a point mutation, disrupting their own folP gene on the chromosome. Dapsone susceptibilities of the recombinant bacteria were measured to examine influence of the mutations. Dapsone MICs for most of the strains with mutations at codon 53 or 55 of M. leprae folP1 were 2 to 16 times as high as the MIC for the strain with the wild-type folP1 sequence, but mutations that changed Thr to Ser at codon 53 showed somewhat lower MIC values than the wild-type sequence. Strains with mutations at codon 48 or 54 showed levels of susceptibility to dapsone comparable to the susceptibility of the strain with the wild-type sequence. This study confirmed that point mutations at codon 53 or 55 of the M. leprae folP1 gene result in dapsone resistance. PMID:21115799

  12. Molecular and functional analysis of the mce4 operon in Mycobacterium smegmatis.

    Science.gov (United States)

    García-Fernández, Julia; Papavinasasundaram, Kadamba; Galán, Beatriz; Sassetti, Christopher M; García, José L

    2017-09-01

    Mycobacterium smegmatis contains 6 homologous mce (mammalian cell entry) operons which have been proposed to encode ABC-like import systems. The mce operons encode up to 10 different proteins of unknown function that are not present in conventional ABC transporters. We have analysed the consequences of individually deleting each of the genes of the mce4 operon of M. smegmatis, which mediates the transport of cholesterol. None of the mce4 mutants were able to grow in cholesterol suggesting that all these genes are required for its uptake and that none of them can be replaced by the homologous genes of the other mce operons. This result suggests that different mce operons do not provide redundant capabilities and that M. smegmatis, in contrast with Mycobacterium tuberculosis, is not able to use alternative systems to import cholesterol in the analysed culture conditions. Either deletion of the entire mce4 operon or single point mutations that eliminate the transport function cause a phenotype similar to the one observed in a mutant lacking all 6 mce operons suggesting a pleiotropic role for this system. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  13. The epidemiology of Mycobacterium bovis in wild deer and feral pigs and their roles in the establishment and spread of bovine tuberculosis in New Zealand wildlife.

    Science.gov (United States)

    Nugent, G; Gortazar, C; Knowles, G

    2015-06-01

    In New Zealand, wild deer and feral pigs are assumed to be spillover hosts for Mycobacterium bovis, and so are not targeted in efforts aimed at locally eradicating bovine tuberculosis (TB) from possums (Trichosurus vulpecula), the main wildlife host. Here we review the epidemiology of TB in deer and pigs, and assess whether New Zealand's TB management programme could be undermined if these species sometimes achieve maintenance host status. In New Zealand, TB prevalences of up to 47% have been recorded in wild deer sympatric with tuberculous possums. Patterns of lesion distribution, age-specific prevalences and behavioural observations suggest that deer become infected mainly through exposure to dead or moribund possums. TB can progress rapidly in some deer (new infection to wild deer has been halted. Tuberculosis prevalence in New Zealand feral pigs can reach 100%. Infections in lymph nodes of the head and alimentary tract predominate, indicating that TB is mostly acquired through scavenging tuberculous carrion, particularly possums. Infection is usually well contained, and transmission between pigs is rare. Large reductions in local possum density result in gradual declines (over 10 years) in TB prevalence among sympatric wild deer, and faster declines in feral pigs. Elimination of TB from possums (and livestock) therefore results in eventual disappearance of TB from feral pigs and wild deer. However, the risk of spillback infection from deer to possums substantially extends the time needed to locally eradicate TB from all wildlife (compared to that which would be required to eradicate disease from possums alone), while dispersal or translocation of pigs (e.g. by hunters) creates a risk of long-distance spread of disease. The high rate at which pigs acquire M. bovis infection from dead possums makes them useful as sentinels for detecting TB in wildlife. It is unlikely that wild deer and feral pigs act as maintenance hosts anywhere in New Zealand, because

  14. Expression, purification, crystallization and preliminary X-ray analysis of two arginine-biosynthetic enzymes from Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Moradian, Fatemeh; Garen, Craig; Cherney, Leonid; Cherney, Maia; James, Michael N. G.

    2006-01-01

    Two enzymes responsible for arginine biosynthesis in M. tuberculosis were expressed in Escherichia coli, then purified to homogeneity. Preliminary X-ray analysis of diffraction-quality crystals grown from each enzyme are reported. The gene products of two open reading frames from Mycobacterium tuberculosis (Mtb) have been crystallized using the sitting-drop vapour-diffusion method. Rv1652 encodes a putative N-acetyl-γ-glutamyl-phosphate reductase (MtbAGPR), while the Rv1656 gene product is annotated as ornithine carbamoyltransferase (MtbOTC). Both MtbAGPR and MtbOTC were expressed in Escherichia coli, purified to homogeneity and crystallized. Native data for each crystal were collected to resolutions of 2.15 and 2.80 Å, respectively. Preliminary X-ray data are presented for both enzymes

  15. Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates.

    Science.gov (United States)

    White, Alexander G; Maiello, Pauline; Coleman, M Teresa; Tomko, Jaime A; Frye, L James; Scanga, Charles A; Lin, Philana Ling; Flynn, JoAnne L

    2017-09-05

    Mycobacterium tuberculosis remains the number one infectious agent in the world today. With the emergence of antibiotic resistant strains, new clinically relevant methods are needed that evaluate the disease process and screen for potential antibiotic and vaccine treatments. Positron Emission Tomography/Computed Tomography (PET/CT) has been established as a valuable tool for studying a number of afflictions such as cancer, Alzheimer's disease, and inflammation/infection. Outlined here are a number of strategies that have been employed to evaluate PET/CT images in cynomolgus macaques that are infected intrabronchially with low doses of M. tuberculosis. Through evaluation of lesion size on CT and uptake of 18 F-fluorodeoxyglucose (FDG) in lesions and lymph nodes in PET images, these described methods show that PET/CT imaging can predict future development of active versus latent disease and the propensity for reactivation from a latent state of infection. Additionally, by analyzing the overall level of lung inflammation, these methods determine antibiotic efficacy of drugs against M. tuberculosis in the most clinically relevant existing animal model. These image analysis methods are some of the most powerful tools in the arsenal against this disease as not only can they evaluate a number of characteristics of infection and drug treatment, but they are also directly translatable to a clinical setting for use in human studies.

  16. Mycobacterium abscessus in Healthcare Settings

    Science.gov (United States)

    ... Sepsis Sharps Safety - CDC Transplant Safety Vaccine Safety Mycobacterium abscessus in Healthcare Settings Recommend on Facebook Tweet ... Mycobacterium abscessus Recommendations and Guidelines General information about Mycobacterium abscessus Mycobacterium abscessus [mī–kō–bak–tair–ee– ...

  17. Mycobacterium tuberculosis

    Science.gov (United States)

    Zhang, Susan; Burns-Huang, Kristin E; Janssen, Guido V; Li, Huilin; Ovaa, Huib; Hedstrom, Lizbeth; Darwin, K Heran

    2017-02-21

    The protein degradation machinery of Mycobacterium tuberculosis includes a proteasome and a ubiquitin-like protein (Pup). Proteasome accessory factor A (PafA) attaches Pup to proteins to target them for degradation by the proteasome. Free Pup is unstable and never observed in extracts of M. tuberculosis , an observation that led us to hypothesize that PafA may need alternative sources of Pup. Here, we show that PafA can move Pup from one proteasome substrate, inositol 1-phosphate synthetase (Ino1), to two different proteins, malonyl coenzyme A (CoA)-acyl carrier protein transacylase (FabD) and lonely guy (Log). This apparent "transpupylation" reaction required a previously unrecognized depupylase activity in PafA, and, surprisingly, this depupylase activity was much more efficient than the activity of the dedicated depupylase Dop (deamidase of Pup). Thus, PafA can potentially use both newly synthesized Pup and recycled Pup to doom proteins for degradation. IMPORTANCE Unlike eukaryotes, which contain hundreds of ubiquitin ligases, Pup-containing bacteria appear to have a single ligase to pupylate dozens if not hundreds of different proteins. The observation that PafA can depupylate and transpupylate in vitro offers new insight into how protein stability is regulated in proteasome-bearing bacteria. Importantly, PafA and the dedicated depupylase Dop are each required for the full virulence of Mycobacterium tuberculosis Thus, inhibition of both enzymes may be extremely attractive for the development of therapeutics against tuberculosis. Copyright © 2017 Zhang et al.

  18. Establishment of proteome spot profiles and comparative analysis of ...

    African Journals Online (AJOL)

    The 'Bon Rouge' pear (Pyrus communis L.) cultivar is characterized by high levels of anthocyanins, the pigments responsible for the red leaf and red fruit skin phenotype. Branches of 'Bon Rouge' pear trees planted in commercial orchards often revert to the original green phenotype. The study aimed at establishing ...

  19. Analysis of Drop Call Probability in Well Established Cellular ...

    African Journals Online (AJOL)

    Technology in Africa has increased over the past decade. The increase in modern cellular networks requires stringent quality of service (QoS). Drop call probability is one of the most important indices of QoS evaluation in a large scale well-established cellular network. In this work we started from an accurate statistical ...

  20. [A rapid screening program on the resistance to streptomycin and ethambutol in Mycobacterium tuberculosis isolates by PCR melting curve analysis].

    Science.gov (United States)

    Wang, Feng; Hu, Si-yu; Gui, Jing; Cui, Yun-yong; Liu, Xiao-li; Li, Qing-ge

    2012-05-01

    To evaluate the effects of PCR melting curve analysis assay on a rapid screening program regarding the resistance of Mycobacterium tuberculosis (MTB) clinical isolates to streptomycin and ethambutol. A total of 331 clinical isolates of MTB had been collected since 2007-2009 in Shenzhen. Mutations at codon 306, 378-380, 406 and 497 of embB gene, codon 43, 88 of rpsL gene, and 513-517, 905-908 region of rrs gene were detected by PCR melting curve analysis. Results were compared with that of conventional drug susceptibility test. Compared to drug susceptibility test, sensitivity, specificity and accuracy for streptomycin resistance were 78.6%, 90.1% and 86.7%, respectively while 83.0%, 93.3% and 91.8%, respectively for ethambutol resistance detected by PCR melting curve analysis. PCR melting curve method was in good agreement with drug susceptibility test. PCR melting curve analysis on genetic regions associated with resistance to streptomycin and ethambutol seemed to be a rapid, specific and closed-tube method so it could be used for detection of streptomycin and ethambutol resistance in MTB.

  1. XML Genetic Structure of SSR1 & SSR2 loci from Iranian Mycobacterium Avium Subspecies Paratuberculosis Isolates by a Short Sequence Repeat Analysis Approach

    OpenAIRE

    Aida Chalesh (MSc); Keyvan Tadayon ( PhD

    2016-01-01

    Background and Objective: Paratuberculosis has been repeatedly reported from Iranian ruminant herds. The extrem fastidious nature of Mycobacterium avium subspecies paratuberculsos hinders genomic diversity studies of the pathogen. Short Sequence Repeat analysis is one of the genome-based approches recently developed to overcome this difficulty. In this study we describe the application of SSR genotyping on three Iranian MAP type strains plus the III & V vaccinal strain. Methods: A...

  2. Comparative whole-genome sequence analysis of Mycobacterium tuberculosis isolated from tuberculous meningitis and pulmonary tuberculosis patients.

    Science.gov (United States)

    Faksri, Kiatichai; Xia, Eryu; Ong, Rick Twee-Hee; Tan, Jun Hao; Nonghanphithak, Ditthawat; Makhao, Nampueng; Thamnongdee, Nongnard; Thanormchat, Arirat; Phurattanakornkul, Arisa; Rattanarangsee, Somcharn; Ratanajaraya, Chate; Suriyaphol, Prapat; Prammananan, Therdsak; Teo, Yik-Ying; Chaiprasert, Angkana

    2018-03-20

    Tuberculous meningitis (TBM) is a severe form of tuberculosis with a high mortality rate. The factors associated with TBM pathogenesis are still unclear. Using comparative whole-genome sequence analysis we compared Mycobacterium tuberculosis (Mtb) isolates from cerebrospinal fluid of TBM cases (n = 73) with those from sputum of pulmonary tuberculosis (PulTB) patients (n = 220) from Thailand. The aim of this study was to seek genetic variants of Mtb associated with TBM. Regardless of Mtb lineage, we found 242 variants that were common to all TBM isolates. Among these variants, 28 were missense SNPs occurring mainly in the pks genes (involving polyketide synthesis) and the PE/PPE gene. Six lineage-independent SNPs were commonly found in TBM isolates, two of which were missense SNPs in Rv0532 (PE_PGRS6). Structural variant analysis revealed that PulTB isolates had 14 genomic regions containing 2-3-fold greater read depth, indicating higher copy number variants and half of these genes belonged to the PE/PPE gene family. Phylogenetic analysis revealed only two small clusters of TBM clonal isolates without support from epidemiological data. This study reported genetic variants of Mtb commonly found in TBM patients compared to PulTB patients. Variants associated with TBM disease warrant further investigation.

  3. Analysis of the metabolome of Anopheles gambiae mosquito after exposure to Mycobacterium ulcerans.

    Science.gov (United States)

    Hoxmeier, J Charles; Thompson, Brice D; Broeckling, Corey D; Small, Pamela; Foy, Brian D; Prenni, Jessica; Dobos, Karen M

    2015-03-18

    Infection with Mycobacterium ulcerans causes Buruli Ulcer, a neglected tropical disease. Mosquito vectors are suspected to participate in the transmission and environmental maintenance of the bacterium. However, mechanisms and consequences of mosquito contamination by M. ulcerans are not well understood. We evaluated the metabolome of the Anopheles gambiae mosquito to profile the metabolic changes associated with bacterial colonization. Contamination of mosquitoes with live M. ulcerans bacilli results in disruptions to lipid metabolic pathways of the mosquito, specifically the utilization of glycerolipid molecules, an affect that was not observed in mosquitoes exposed to dead M. ulcerans. These results are consistent with aberrations of lipid metabolism described in other mycobacterial infections, implying global host-pathogen interactions shared across diverse saprophytic and pathogenic mycobacterial species. This study implicates features of the bacterium, such as the putative M. ulcerans encoded phospholipase enzyme, which promote virulence, survival, and active adaptation in concert with mosquito development, and provides significant groundwork for enhanced studies of the vector-pathogen interactions using metabolomics profiling. Lastly, metabolic and survival data suggest an interaction which is unlikely to contribute to transmission of M. ulcerans by A. gambiae and more likely to contribute to persistence of M. ulcerans in waters cohabitated by both organisms.

  4. Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments

    Directory of Open Access Journals (Sweden)

    Morales Juan

    2008-11-01

    Full Text Available Abstract Background The recent determination of the complete nucleotide sequence of several Mycobacterium tuberculosis (MTB genomes allows the use of comparative genomics as a tool for dissecting the nature and consequence of genetic variability within this species. The multiple alignment of the genomes of clinical strains (CDC1551, F11, Haarlem and C, along with the genomes of laboratory strains (H37Rv and H37Ra, provides new insights on the mechanisms of adaptation of this bacterium to the human host. Findings The genetic variation found in six M. tuberculosis strains does not involve significant genomic rearrangements. Most of the variation results from deletion and transposition events preferentially associated with insertion sequences and genes of the PE/PPE family but not with genes implicated in virulence. Using a Perl-based software islandsanalyser, which creates a representation of the genetic variation in the genome, we identified differences in the patterns of distribution and frequency of the polymorphisms across the genome. The identification of genes displaying strain-specific polymorphisms and the extrapolation of the number of strain-specific polymorphisms to an unlimited number of genomes indicates that the different strains contain a limited number of unique polymorphisms. Conclusion The comparison of multiple genomes demonstrates that the M. tuberculosis genome is currently undergoing an active process of gene decay, analogous to the adaptation process of obligate bacterial symbionts. This observation opens new perspectives into the evolution and the understanding of the pathogenesis of this bacterium.

  5. Mutational analysis of the respiratory nitrate transporter NarK2 of Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Michelle M Giffin

    Full Text Available Mycobacterium tuberculosis induces nitrate reductase activity in response to decreasing oxygen levels. This is due to regulation of both the transcription and the activity of the nitrate transporter NarK2. A model of NarK2 structure is proposed containing 12 membrane spanning regions consistent with other members of the major facilitator superfamily. The role of the proton gradient was determined by exposing M. tuberculosis to uncouplers. Nitrite production decreased indicating that the importation of nitrate involved an H(+/nitrate symporter. The addition of nitrite before nitrate had no effect, suggesting no role for a nitrate/nitrite antiporter. In addition the NarK2 knockout mutant showed no defect in nitrite export. NarK2 is proposed to be a Type I H(+/nitrate symporter. Site directed mutagenesis was performed changing 23 amino acids of NarK2. This allowed the identification of important regions and amino acids of this transporter. Five of these mutants were inactive for nitrate transport, seven produced reduced activity and eleven mutants retained wild type activity. NarK2 is inactivated in the presence of oxygen by an unknown mechanism. However none of the mutants, including those with mutated cysteines, were altered in their response to oxygen levels. The assimilatory nitrate transporter NasA of Bacillus subtilis was expressed in the M. tuberculosis NarK2 mutant. It remained active during aerobic incubation showing that the point of oxygen control is NarK2.

  6. Secretory Proteome Analysis of Streptomycin-Resistant Mycobacterium tuberculosis Clinical Isolates.

    Science.gov (United States)

    Sharma, Divakar; Bisht, Deepa

    2017-12-01

    Tuberculosis still remains one of the most fatal infectious diseases. Streptomycin (SM) is the drug of choice, especially for patients with multidrug-resistant tuberculosis or category II patients, because it targets the protein synthesis machinery by interacting with steps of translation. Several mechanisms have been proposed to explain the resistance, but our knowledge is inadequate. Secretome often plays an important role in pathogenesis and is considered an attractive reservoir for the development of novel diagnostic markers and targets. In this study, we analyze the secretory proteins of streptomycin-resistant Mycobacterium tuberculosis isolates by 2-dimensional gel electrophoresis-matrix assisted laser desorption/ionization-time-of-flight mass spectrometry and bioinformatic tools. Fifteen overexpressed proteins were identified in a resistant isolate that belonged to various categories such as virulence/detoxification/adaptation, intermediary metabolism and respiration, and conserved hypotheticals. Among them, Rv1860, Rv1980c, Rv2140c, Rv1636, and Rv1926c were proteins of an undefined role. Molecular docking of these proteins with SM showed that it binds to their conserved domains and suggests that these might neutralize/compensate the effect of the drug. The interactome also suggests that overexpressed proteins along with their interactive partner might be involved in M. tuberculosis virulence and resistance. The cumulative effect of these overexpressed proteins could involve SM resistance, and these might be used as diagnostic markers or potential drug targets.

  7. Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis.

    Science.gov (United States)

    Bai, Lin; Hu, Kuan; Wang, Tong; Jastrab, Jordan B; Darwin, K Heran; Li, Huilin

    2016-04-05

    The human pathogen Mycobacterium tuberculosis (Mtb) requires a proteasome system to cause lethal infections in mice. We recently found that proteasome accessory factor E (PafE, Rv3780) activates proteolysis by the Mtb proteasome independently of adenosine triphosphate (ATP). Moreover, PafE contributes to the heat-shock response and virulence of Mtb Here, we show that PafE subunits formed four-helix bundles similar to those of the eukaryotic ATP-independent proteasome activator subunits of PA26 and PA28. However, unlike any other known proteasome activator, PafE formed dodecamers with 12-fold symmetry, which required a glycine-XXX-glycine-XXX-glycine motif that is not found in previously described activators. Intriguingly, the truncation of the PafE carboxyl-terminus resulted in the robust binding of PafE rings to native proteasome core particles and substantially increased proteasomal activity, suggesting that the extended carboxyl-terminus of this cofactor confers suboptimal binding to the proteasome core particle. Collectively, our data show that proteasomal activation is not limited to hexameric ATPases in bacteria.

  8. Mycobacterium saopaulense sp. nov., a rapidly growing mycobacterium closely related to members of the Mycobacterium chelonae--Mycobacterium abscessus group.

    Science.gov (United States)

    Nogueira, Christiane Lourenço; Whipps, Christopher M; Matsumoto, Cristianne Kayoko; Chimara, Erica; Droz, Sara; Tortoli, Enrico; de Freitas, Denise; Cnockaert, Margo; Palomino, Juan Carlos; Martin, Anandi; Vandamme, Peter; Leão, Sylvia Cardoso

    2015-12-01

    Five isolates of non-pigmented, rapidly growing mycobacteria were isolated from three patients and,in an earlier study, from zebrafish. Phenotypic and molecular tests confirmed that these isolates belong to the Mycobacterium chelonae-Mycobacterium abscessus group, but they could not be confidently assigned to any known species of this group. Phenotypic analysis and biochemical tests were not helpful for distinguishing these isolates from other members of the M. chelonae–M.abscessus group. The isolates presented higher drug resistance in comparison with other members of the group, showing susceptibility only to clarithromycin. The five isolates showed a unique PCR restriction analysis pattern of the hsp65 gene, 100 % similarity in 16S rRNA gene and hsp65 sequences and 1-2 nt differences in rpoB and internal transcribed spacer (ITS) sequences.Phylogenetic analysis of a concatenated dataset including 16S rRNA gene, hsp65, and rpoB sequences from type strains of more closely related species placed the five isolates together, as a distinct lineage from previously described species, suggesting a sister relationship to a group consisting of M. chelonae, Mycobacterium salmoniphilum, Mycobacterium franklinii and Mycobacterium immunogenum. DNA–DNA hybridization values .70 % confirmed that the five isolates belong to the same species, while values ,70 % between one of the isolates and the type strains of M. chelonae and M. abscessus confirmed that the isolates belong to a distinct species. The polyphasic characterization of these isolates, supported by DNA–DNA hybridization results,demonstrated that they share characteristics with M. chelonae–M. abscessus members, butconstitute a different species, for which the name Mycobacterium saopaulense sp. nov. is proposed. The type strain is EPM10906T (5CCUG 66554T5LMG 28586T5INCQS 0733T).

  9. THE IMPORTANCE OF ESTABLISHING A FINANCIAL ANALYSIS IN SERBIA

    Directory of Open Access Journals (Sweden)

    SLOBODAN POPOVIĆ

    2016-10-01

    Full Text Available As a company is a living organism, its growth and development depends on the adequacy of planning, control and analytical procedures that are in use in all aspects of their own business. Under such conditions, the accounting analysis involves primarily adequate monitoring already included in the displayed information contained in the financial statements and in particular the analysis of data that are essential to the operation of any enterprise. Knowledge and the application of modern accounting analysis will give to the company management a wide range of options in terms of uninterrupted growth and development of the company in accordance with a pre-designed and presented vision and mission.

  10. Mycobacterium Avium Complex (MAC)

    Science.gov (United States)

    ... 30, 2014 Select a Language: Fact Sheet 514 Mycobacterium Avium Complex (MAC) WHAT IS MAC? HOW DO ... INTERACTION PROBLEMS THE BOTTOM LINE WHAT IS MAC? Mycobacterium Avium Complex (MAC) is a serious illness caused ...

  11. In vitro susceptibility of Mycobacterium tuberculosis, Mycobacterium africanum, Mycobacterium bovis, Mycobacterium avium, Mycobacterium fortuitum, and Mycobacterium chelonae to ticarcillin in combination with clavulanic acid.

    OpenAIRE

    Casal, M J; Rodriguez, F C; Luna, M D; Benavente, M C

    1987-01-01

    The in vitro susceptibility of Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium avium, Mycobacterium fortuitum, and Mycobacterium chelonae (M. chelonei) to ticarcillin in combination with calvulanic acid (CA) was studied by the agar dilution method. All the M. tuberculosis, M. bovis, and M. africanum strains were inhibited at a ticarcillin concentration of 32 micrograms/ml or lower in combination with 5 micrograms of CA. M. chelonae and M. avium strains ...

  12. Rapid detection of rifampicin, isoniazid and streptomycin resistance in Mycobacterium tuberculosis clinical isolates by high-resolution melting curve analysis.

    Science.gov (United States)

    Yadav, R; Sethi, S; Mewara, A; Dhatwalia, S K; Gupta, D; Sharma, M

    2012-10-01

    This study was carried out to evaluate high-resolution melting (HRM) curve analysis assay for detection of mutations in three drug resistance-associated genes of Mycobacterium tuberculosis. Clinical isolates of Myco. tuberculosis phenotypically resistant to rifampicin (n = 29), isoniazid (n = 35) and streptomycin (n = 34) were analysed for mutations in rpoB, katG and rpsL genes, respectively, by HRM curve analysis and DNA sequencing. HRM curve assay resulted in 11 clearly distinguishable melt curves denoting eight types of mutations responsible for drug resistance. For the three drugs, respectively, the sensitivity of HRM curve assay was found to be 93·1, 80 and 61·8% compared to the phenotypic resistance patterns, and 93·1, 93·3 and 100% in comparison with the DNA sequencing. The sensitivity and specificity of HRM curve assay was found to be comparable to DNA sequencing. The assay offers the advantage of high throughput, single step, rapid work flow and cost effectiveness and can be utilized as a rapid screening method for detection of drug-resistant tuberculosis. HRM curve assay may prove to be an important tool for the development of rapid molecular diagnostic assays for detection of mutation-based drug resistance. © 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

  13. Detection of streptomycin resistance in Mycobacterium tuberculosis clinical isolates from China as determined by denaturing HPLC analysis and DNA sequencing.

    Science.gov (United States)

    Shi, Ruiru; Zhang, Jianyuan; Li, Chuanyou; Kazumi, Yuko; Sugawara, Isamu

    2007-01-01

    China is regarded by the World Health Organization as a major hot-spot region for Mycobacterium tuberculosis infection. Streptomycin has been deployed in China for over 50 years and is still widely used for tuberculosis treatment. We have developed a denaturing HPLC (DHPLC) method for detecting various gene mutations conferring drug resistance in M. tuberculosis. The present study focused on rpsL and rrs mutation analysis. Two hundred and fifteen M. tuberculosis clinical isolates (115 proved to be streptomycin-resistant and 100 susceptible by a routine proportional method) from China were tested to determine the streptomycin minimal inhibitory concentration (MIC), and subjected to DHPLC and concurrent DNA sequencing to determine rpsL and rrs mutations. The results showed that 85.2% (98/115) of streptomycin-resistant isolates harbored rpsL or rrs mutation, while rpsL mutation (76.5%, 88/115) dominated. MIC of 98 mutated isolates revealed no close correlation between mutation types and levels of streptomycin resistance. No mutation was found in any of the susceptible isolates. The DHPLC results were completely consistent with those of sequencing. The DHPLC method devised in this study can be regarded as a useful and powerful tool for detection of streptomycin resistance. This is the first report to describe DHPLC analysis of mutations in the rpsL and rrs genes of M. tuberculosis in a large number of clinical isolates.

  14. Radiochemical analysis in the nuclear research establishment (KFA) Juelich, FRG

    International Nuclear Information System (INIS)

    Anon.

    1975-01-01

    KFA Juelich is one of the two great nuclear research centres of the Federal Republic of Germany. About 3700 employees including about 700 scientists are engaged in a great number of programs and projects belonging to six main fields of research and development: high temperature reactor and energy techniques; nuclear fusion; properties of materials; materials research; life and environment; methods. In the article the radiochemical analysis work of the former Central Institute of Analytical Chemistry and its two successors is described: activation analysis, application of tracer techniques, fission product analysis. Further on the irradiation facilities are described, a short survey is given on the instrumentation, and the future work is outlined. (T.G.)

  15. A data analysis expert system for large established distributed databases

    Science.gov (United States)

    Gnacek, Anne-Marie; An, Y. Kim; Ryan, J. Patrick

    1987-01-01

    A design for a natural language database interface system, called the Deductively Augmented NASA Management Decision support System (DANMDS), is presented. The DANMDS system components have been chosen on the basis of the following considerations: maximal employment of the existing NASA IBM-PC computers and supporting software; local structuring and storing of external data via the entity-relationship model; a natural easy-to-use error-free database query language; user ability to alter query language vocabulary and data analysis heuristic; and significant artificial intelligence data analysis heuristic techniques that allow the system to become progressively and automatically more useful.

  16. Overexpression, purification and crystallographic analysis of a unique adenosine kinase from Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Wang, Yimin; Long, Mary C.; Ranganathan, Senthil; Escuyer, Vincent; Parker, William B.; Li, Rongbao

    2005-01-01

    Adenosine kinase from M. tuberculosis has been overexpressed, purified and crystallized in the presence of adenosine. Structure determination using molecular replacement with diffraction data collected at 2.2 Å reveals a dimeric structure. Adenosine kinase from Mycobacterium tuberculosis is the only prokaryotic adenosine kinase that has been isolated and characterized. The enzyme catalyzes the phosphorylation of adenosine to adenosine monophosphate and is involved in the activation of 2-methyladenosine, a compound that has demonstrated selective activity against M. tuberculosis. The mechanism of action of 2-methyladenosine is likely to be different from those of current tuberculosis treatments and this compound (or other adenosine analogs) may prove to be a novel therapeutic intervention for this disease. The M. tuberculosis adenosine kinase was overexpressed in Escherichia coli and the enzyme was purified with activity comparable to that reported previously. The protein was crystallized in the presence of adenosine using the vapour-diffusion method. The crystals diffracted X-rays to high resolution and a complete data set was collected to 2.2 Å using synchrotron radiation. The crystal belonged to space group P3 1 21, with unit-cell parameters a = 70.2, c = 111.6 Å, and contained a single protein molecule in the asymmetric unit. An initial structural model of the protein was obtained by the molecular-replacement method, which revealed a dimeric structure. The monomers of the dimer were related by twofold crystallographic symmetry. An understanding of how the M. tuberculosis adenosine kinase differs from the human homolog should aid in the design of more potent and selective antimycobacterial agents that are selectively activated by this enzyme

  17. Mycobacterium tuberculosis population structure and molecular epidemiological analysis in Sucre municipality, Miranda state, Venezuela.

    Science.gov (United States)

    Patiño, Margareth A; Abadía, Edgar; Solalba Gómez; Maes, Mailis; Muñoz, Mariana; Gómez, Daniela; Guzmán, Patricia; Méndez, María Victoria; Ramirez, Carmen; Mercedes, España; de Waard, Jacobus; Takiff, Howard

    2014-12-01

    Sucre municipality is a large, densely populated marginal area in the eastern part of Caracas, Venezuela that consistently has more cases of tuberculosis than other municipalities in the country. To identify the neighborhoods in the municipality with the highest prevalence of tuberculosis, and determine whether the Mycobacterium tuberculosis strain distribution in this municipality is different from that previously found in the western part of Caracas and the rest of Venezuela, we collected data on all tuberculosis cases in the municipality diagnosed in 2005-6. We performed two separate molecular epidemiological studies, spoligotyping 44 strains in a first study, and spoligotyping 131 strains, followed by MIRU-VNTR 15 on 21 clustered isolates in the second. With spoligotyping, the most common patterns were Shared International Type SIT17 (21%); SIT42 (15%); SIT93 (11%); SIT20 (7%); SIT53 (6%), a distribution similar to other parts of Venezuela, except that SIT42 and SIT20 were more common. MIRU-VNTR 15 showed that six of seven SIT17 strains examined belonged to a large cluster previously found circulating in Venezuela, but all of the SIT42 strains were related to a cluster centered in the neighborhoods of Unión and Maca, with a MIRU-VNTR pattern not previously seen in Venezuela. It appears that a large percentage of the tuberculosis in the Sucre municipality is caused by the active transmission of two strain families centered within distinct neighborhoods, one reflecting communication with the rest of the country, and the other suggesting the insular, isolated nature of some sectors.

  18. Microarray analysis of defined Mycobacterium tuberculosis populations using RNA amplification strategies

    Directory of Open Access Journals (Sweden)

    Butcher Philip D

    2008-02-01

    Full Text Available Abstract Background The amplification of bacterial RNA is required if complex host-pathogen interactions are to be studied where the recovery of bacterial RNA is limited. Here, using a whole genome Mycobacterium tuberculosis microarray to measure cross-genome representation of amplified mRNA populations, we have investigated two approaches to RNA amplification using different priming strategies. The first using oligo-dT primers after polyadenylation of the bacterial RNA, the second using a set of mycobacterial amplification-directed primers both linked to T7 polymerase in vitro run off transcription. Results The reproducibility, sensitivity, and the representational bias introduced by these amplification systems were examined by contrasting expression profiles of the amplified products from inputs of 500, 50 and 5 ng total M. tuberculosis RNA with unamplified RNA from the same source. In addition, as a direct measure of the effectiveness of bacterial amplification for identifying biologically relevant changes in gene expression, a model M. tuberculosis system of microaerophilic growth and non-replicating persistence was used to assess the capability of amplified RNA microarray comparisons. Mycobacterial RNA was reproducibly amplified using both methods from as little as 5 ng total RNA (~equivalent to 2 × 105 bacilli. Differential gene expression patterns observed with unamplified RNA in the switch from aerobic to microaerophilic growth were also reflected in the amplified expression profiles using both methods. Conclusion Here we describe two reproducible methods of bacterial RNA amplification that will allow previously intractable host-pathogen interactions during bacterial infection to be explored at the whole genome level by RNA profiling.

  19. HIV-1 and the Mycobacterium tuberculosis granuloma: A systematic review and meta-analysis.

    Science.gov (United States)

    Diedrich, C R; O'Hern, J; Wilkinson, R J

    2016-05-01

    Infection with HIV-1 greatly increases the risk of active tuberculosis (TB). Although hypotheses suggest HIV-1 disrupts Mycobacterium tuberculosis (Mtb) granuloma function, few studies have examined this directly. The objective of this study was to determine what evidence exists about the effect HIV-1 co-infection has upon Mtb granulomas. A systematic search of PubMed, Web of Science, and Medline up to 20 March 2015 was conducted, to identify studies comparing Mtb-infected tissue from HIV-1 infected and uninfected persons, or HIV-1 infected persons with stratified peripheral CD4 T cell (pCD4) counts. We summarized findings that focused on how HIV-1 changes granuloma formation, bacterial presence, cellular composition, and cytokine production. Nineteen studies with a combined sample size of 899 persons were included. Although studies frequently were limited by variable or inadequately described definitions of outcomes and analytical methods, HIV-1 was found to be associated with increased bacillary load within Mtb-infected tissue. Reductions in pCD4 counts within co-infected persons associated with both poorer granuloma formation and higher bacterial load. The high degree of heterogeneity among studies combined with experimental limitations made it difficult to conclusively support previously published and prevalent hypotheses about HIV-1/Mtb co-infection granulomas. To elucidate the validity of these hypotheses we have described areas that can be improved in future studies in order to clarify the influence HIV-1 co-infection has upon the Mtb granuloma. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Neutron activation analysis as an element of sculpture provenance establishing

    International Nuclear Information System (INIS)

    Panczyk, E.; Rowinska, L.; Walis, L.; Ligeza, M.; Nalepa, B.

    1998-01-01

    Investigation was carried out on the subject named ''Madonna Jackowa'' (XV cent.). The investigation object was to answer whether ''Madonna Jackowa'' was made of a native alabaster. Alabaster derived from five carious mines situated at the Cracow - Lvov line and ''Madonna Jackowa'' were analysed and the trace elements contents were compared. Instrumental neutron activation method was used for analysis of the trace. (author)

  1. Establishing Evidence for Internal Structure Using Exploratory Factor Analysis

    Science.gov (United States)

    Watson, Joshua C.

    2017-01-01

    Exploratory factor analysis (EFA) is a data reduction technique used to condense data into smaller sets of summary variables by identifying underlying factors potentially accounting for patterns of collinearity among said variables. Using an illustrative example, the 5 general steps of EFA are described with best practices for decision making…

  2. Establishing a framework for comparative analysis of genome sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bansal, A.K.

    1995-06-01

    This paper describes a framework and a high-level language toolkit for comparative analysis of genome sequence alignment The framework integrates the information derived from multiple sequence alignment and phylogenetic tree (hypothetical tree of evolution) to derive new properties about sequences. Multiple sequence alignments are treated as an abstract data type. Abstract operations have been described to manipulate a multiple sequence alignment and to derive mutation related information from a phylogenetic tree by superimposing parsimonious analysis. The framework has been applied on protein alignments to derive constrained columns (in a multiple sequence alignment) that exhibit evolutionary pressure to preserve a common property in a column despite mutation. A Prolog toolkit based on the framework has been implemented and demonstrated on alignments containing 3000 sequences and 3904 columns.

  3. The Pareto Analysis for Establishing Content Criteria in Surgical Training.

    Science.gov (United States)

    Kramp, Kelvin H; van Det, Marc J; Veeger, Nic J G M; Pierie, Jean-Pierre E N

    2016-01-01

    Current surgical training is still highly dependent on expensive operating room (OR) experience. Although there have been many attempts to transfer more training to the skills laboratory, little research is focused on which technical behaviors can lead to the highest profit when they are trained outside the OR. The Pareto principle states that in any population that contributes to a common effect, a few account for the bulk of the effect. This principle has been widely used in business management to increase company profits. This study uses the Pareto principle for establishing content criteria for more efficient surgical training. A retrospective study was conducted to assess verbal guidance provided by 9 supervising surgeons to 12 trainees performing 64 laparoscopic cholecystectomies in the OR. The verbal corrections were documented, tallied, and clustered according to the aimed change in novice behavior. The corrections were rank ordered, and a cumulative distribution curve was used to calculate which corrections accounted for 80% of the total number of verbal corrections. In total, 253 different verbal corrections were uttered 1587 times and were categorized into 40 different clusters of aimed changes in novice behaviors. The 35 highest-ranking verbal corrections (14%) and the 11 highest-ranking clusters (28%) accounted for 80% of the total number of given verbal corrections. Following the Pareto principle, we were able to identify the aspects of trainee behavior that account for most corrections given by supervisors during a laparoscopic cholecystectomy on humans. This strategy can be used for the development of new training programs to prepare the trainee in advance for the challenges encountered in the clinical setting in an OR. Copyright © 2016 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

  4. The Mycobacterium tuberculosis homologue of the Mycobacterium ...

    African Journals Online (AJOL)

    With the completion of genome sequencing of Mycobacterium tuberculosis and upsurge in the incidence of M. tuberculosis infection worldwide partly as a result of HIV pandemic, there is need for rationale approach to vaccine and chemotherapy discoveries for M. tuberculosis. The homologue of mig gene of. Mycobacterium ...

  5. Spoligotype Profile of Mycobacterium tuberculosis Complex Strains from HIV-Positive and -Negative Patients in Nigeria: a Comparative Analysis

    Science.gov (United States)

    Cadmus, Simeon; Hill, Véronique; van Soolingen, Dick; Rastogi, Nalin

    2011-01-01

    We ran a comparative analysis of all patients for whom a positive culture of Mycobacterium tuberculosis complex was available between April 2004 and October 2005 and whose HIV serology results were known, with spoligotyping results (n = 163) split into 49 HIV-positive patients and 114 HIV-negative patients. Spoligotype international type 373 (SIT373) (T1 lineage), which was highly prevalent among the HIV+ patients, was totally absent from the HIV− population, suggesting that we had a specific clone affecting nearly 1/3 of all HIV-tuberculosis (TB)-coinfected patients. Among the LAM10-CAM sublineage strains, we had only a single strain of SIT403 among HIV− patients (0.88%), as opposed to 12.25% of the HIV+ population (χ2 = 10.77; P 0.05). A total of 7/49, or 14.3%, other SITs among HIV+ patients were not found among the HIV− patients. When added to the most prevalent SIT among HIV+ patients (SIT373; n = 16), 23/49, or 47%, isolates among HIV-TB-coinfected patients were unique. We conclude that further studies should be carried out to investigate the evolution of these genotypes and others in the emergence of multidrug resistance and control of tuberculosis in Nigeria. PMID:21048016

  6. [Clustering analysis of Mycobacterium tuberculosis using the JATA(12)-VNTR system for molecular epidemiological surveillance in broad areas of Japan].

    Science.gov (United States)

    Wada, Takayuki; Tamaru, Aki; Iwamoto, Tomotada; Arikawa, Kentaro; Nakanishi, Noriko; Komukai, Jun; Matsumoto, Kenji; Hase, Atsushi

    2013-04-01

    Japan Anti-Tuberculosis Association (JATA) (12)-variable numbers of tandem repeats (VNTR) is a standard method for genotyping of clinical isolates of Mycobacterium tuberculosis in Japan. As a model study for nationwide surveillance, this study aimed to describe the tendency and frequency of genotypes of M. tuberculosis in a large number of clinical samples. Clinical isolates of M. tuberculosis (n = 1,778) were obtained from patients with tuberculosis in 3 areas, i.e., Osaka City, Osaka Prefecture, and Kobe City, during 2007 and 2008. The samples were analyzed using JATA (12)-VNTR. All genotypes were subjected to clustering analysis. In total, 1,086 (61.1%) isolates showed clustering. The most common clusters were composed of 3 members. Such clusters were considered to reflect either actual transmission or low discriminatory power of JATA (12)-VNTR. Several prevalent JATA(12)-VNTR genotypes formed large clusters and were discussed in relation with epidemiological findings of other studies. The findings of this study will aid in the construction of an effective genotyping-based surveillance system of M. tuberculosis, through improvement of interpretation of VNTR types, observation of certain particular strains in an area, and efficient detection of unidentified outbreaks.

  7. Establishment of a Policy Analysis Capability in Romania

    Directory of Open Access Journals (Sweden)

    Carole M.P. NEVES

    2000-01-01

    Full Text Available The Romanian government, like other governments of former communist countries, emerged from the collapsed Soviet Union ill prepared to confront the complex challenges of governing under a democratic, free market system. At the core of governments that formulate sound public policies, successfully implement programs, and respond effectively to rapidly changing situations is the capacity to carry out independent, high quality research and analysis that results in improved decision making. During the 21st century, the need and acceptance of the incorporation of policy analysis courses in public administration curricula in Romania is expected to grow. In time, educational programs are expected to result in the following consequences: _ Formation of a body of strong independent policy researchers employed by the national and local governments as well as by universities and non-profit institutions _ Utilization of analytical outcomes as tools of political, social and economic improvement by the executive, legislative and judicial branches and by non-profit and private sectors _ Greater public understanding of and participation in public policy processes.

  8. Establishing working standards of chromosome aberrations analysis for biological dosimetry

    International Nuclear Information System (INIS)

    Bui Thi Kim Luyen; Tran Que; Pham Ngoc Duy; Nguyen Thi Kim Anh; Ha Thi Ngoc Lien

    2015-01-01

    Biological dosimetry is an dose assessment method using specify bio markers of radiation. IAEA (International Atomic Energy Agency) and ISO (International Organization for Standardization) defined that dicentric chromosome is specify for radiation, it is a gold standard for biodosimetry. Along with the documents published by IAEA, WHO, ISO and OECD, our results of study on the chromosome aberrations induced by radiation were organized systematically in nine standards that dealing with chromosome aberration test and micronucleus test in human peripheral blood lymphocytes in vitro. This standard addresses: the reference dose-effect for dose estimation, the minimum detection levels, cell culture, slide preparation, scoring procedure for chromosome aberrations use for biodosimetry, the criteria for converting aberration frequency into absorbed dose, reporting of results. Following these standards, the automatic analysis devices were calibrated for improving biological dosimetry method. This standard will be used to acquire and maintain accreditation of the Biological Dosimetry laboratory in Nuclear Research Institute. (author)

  9. Diesel engine coolant analysis, new application for established instrumentation

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, D.P.; Lukas, M.; Lynch, B.K. [Spectro Incorporated, Littleton, MA (United States)

    1997-12-31

    Rotating disk electrode (RDE) arc emission spectrometers are user` many commercial, industrial and military laboratories throughout the world to analyze millions of oil and fuel samples each year. In fact, RDE spectrometers have been used exclusively for oil and fuel analysis for so long that it has nearly been forgotten by most practitioners that when RDE spectrometers were first introduced more than 40 years ago, they were routinely used for aqueous samples as well. This presentation reviews early methods of aqueous sample analysis using RDE technology. This presentation also describes recent work to calibrate an RDE spectrometer for both water samples and for engine coolant samples which are a mixture of approximately 50 % water and 50 % ethylene or propylene glycol. Limits of detection determined for aqueous standards are comparable to limits of detection for oil standards. Repeatability of aqueous samples is comparable to the repeatability achieved for oil samples. A comparison of results for coolant samples measured by both inductively coupled plasma (ICP) and rotating disk electrode (RDE) spectrometers is presented. Not surprisingly, RDE results are significantly higher for samples containing particles larger than a few micrometers. Although limits of detection for aqueous samples are not as low as can be achieved using the more modern ICP spectrometric method or the more cumbersome atomic absorption (AA) method, this presentation suggests that RDE spectrometers may be appropriate for certain types of aqueous samples in situations where the more sensitive ICP or AA spectrometers and the laboratory environment and skilled personnel needed for them to operate are not conveniently available. (orig.) 4 refs.

  10. Economic analysis of Mycobacterium avium subspecies paratuberculosis vaccines in dairy herds.

    Science.gov (United States)

    Cho, J; Tauer, L W; Schukken, Y H; Gómez, M I; Smith, R L; Lu, Z; Grohn, Y T

    2012-04-01

    Johne's disease, or paratuberculosis, is a chronic infectious enteric disease of ruminants, caused by infection with Mycobacterium avium ssp. paratuberculosis (MAP). Given the absence of a fail-safe method of prevention or a cure, Johne's disease can inflict significant economic loss on the US dairy industry, with an estimated annual cost of over $200 million. Currently available MAP control strategies include management measures to improve hygiene, culling MAP serologic- or fecal-positive adult cows, and vaccination. Although the 2 first control strategies have been reported to be effective in reducing the incidence of MAP infection, the changes in herd management needed to conduct these control strategies require significant effort on the part of the dairy producer. On the other hand, vaccination is relatively simple to apply and requires minor changes in herd management. Despite these advantages, only 5% of US dairy operations use vaccination to control MAP. This low level of adoption of this technology is due to limited information on its cost-effectiveness and efficacy and some important inherent drawbacks associated with current MAP vaccines. This study investigates the epidemiological effect and economic values of MAP vaccines in various stages of development. We create scenarios for the potential epidemiological effects of MAP vaccines, and then estimate economically justifiable monetary values at which vaccines become economically beneficial to dairy producers such that a net present value (NPV) of a farm's net cash flow can be higher than the NPV of a farm using no control or alternative nonvaccine controls. Any vaccination with either low or high efficacy considered in this study yielded a higher NPV compared with a no MAP control. Moreover, high-efficacy vaccines generated an even higher NPV compared with alternative controls, making vaccination economically attractive. Two high-efficacy vaccines were particularly effective in MAP control and NPV

  11. Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism.

    Directory of Open Access Journals (Sweden)

    Tsuyoshi Sekizuka

    Full Text Available Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and M. bolletii, are an environmental organism found in soil, water and other ecological niches, and have been isolated from respiratory tract infection, skin and soft tissue infection, postoperative infection of cosmetic surgery. To determine the unique genetic feature of M. massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300 (corresponding to CCUG 48898. Comparative genomic analysis was performed among Mycobacterium spp. and among M. abscessus group subspp., showing that additional ß-oxidation-related genes and, notably, the mammalian cell entry (mce operon were located on a genomic island, M. massiliense Genomic Island 1 (MmGI-1, in M. massiliense. In addition, putative anaerobic respiration system-related genes and additional mycolic acid cyclopropane synthetase-related genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also frequently possess the MmGI-1 (14/44, approximately 32% and three unique conserved regions (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%, as well as isolates of other countries (Malaysia, France, United Kingdom and United States. The well-conserved genomic island MmGI-1 may play an important role in high growth potential with additional lipid metabolism, extra factors for survival in the environment or synthesis of complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of phylogenetically distant M. avium complex (MAC, suggesting that horizontal gene transfer or genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC.

  12. Mycobacterium tuberculosis

    Science.gov (United States)

    Namugenyi, Sarah B; Aagesen, Alisha M; Elliott, Sarah R; Tischler, Anna D

    2017-07-11

    The Mycobacterium tuberculosis phosphate-specific transport (Pst) system controls gene expression in response to phosphate availability by inhibiting the activation of the SenX3-RegX3 two-component system under phosphate-rich conditions, but the mechanism of communication between these systems is unknown. In Escherichia coli , inhibition of the two-component system PhoR-PhoB under phosphate-rich conditions requires both the Pst system and PhoU, a putative adaptor protein. E. coli PhoU is also involved in the formation of persisters, a subpopulation of phenotypically antibiotic-tolerant bacteria. M. tuberculosis encodes two PhoU orthologs, PhoY1 and PhoY2. We generated phoY single- and double-deletion mutants and examined the expression of RegX3-regulated genes by quantitative reverse transcription-PCR (qRT-PCR). Gene expression was increased only in the Δ phoY1 Δ phoY2 double mutant and could be restored to the wild-type level by complementation with either phoY1 or phoY2 or by deletion of regX3 These data suggest that the PhoY proteins function redundantly to inhibit SenX3-RegX3 activation. We analyzed the frequencies of antibiotic-tolerant persister variants in the phoY mutants using several antibiotic combinations. Persister frequency was decreased at least 40-fold in the Δ phoY1 Δ phoY2 mutant compared to the frequency in the wild type, and this phenotype was RegX3 dependent. A Δ pstA1 mutant lacking a Pst system transmembrane component exhibited a similar RegX3-dependent decrease in persister frequency. In aerosol-infected mice, the Δ phoY1 Δ phoY2 and Δ pstA1 mutants were more susceptible to treatment with rifampin but not isoniazid. Our data demonstrate that disrupting phosphate sensing mediated by the PhoY proteins and the Pst system enhances the susceptibility of M. tuberculosis to antibiotics both in vitro and during infection. IMPORTANCE Persister variants, subpopulations of bacteria that are phenotypically antibiotic tolerant, contribute to

  13. Molecular analysis of Rv0679c and Rv0180c genes of Mycobacterium tuberculosis from clinical isolates of pulmonary tuberculosis

    Directory of Open Access Journals (Sweden)

    L Rupa

    2016-01-01

    Full Text Available Context: Two novel proteins/genes Rv0679c and Rv0180c of Mycobacterium tuberculosis (MTB H37Rv were classified as a hypothetical membrane and transmembrane proteins which might have a role in the invasion. Molecular analysis of these genes in human clinical isolates of pulmonary tuberculosis (PTB patients was not well characterised. Aims: To assess the molecular diversity of Rv0679c and Rv0180c genes of MTB from clinical isolates of PTB patients. Settings and Design: DNA from 97 clinical isolates was extracted and subjected to amplification using selective primers by polymerase chain reaction (PCR. The PCR product obtained was sequenced commercially. Patients and Methods: Clinical isolates obtained from tuberculosis patients were investigated for polymorphisms in the Rv0679c and Rv0180c genes by PCR and DNA sequencing. Genomic DNA isolated by cetyltrimethylammonium bromide method was used for amplification of genes. Results: Rv0679c gene was highly conserved in 61 out of 65 clinical isolates assessed for sequence homology with wild-type H37Rv gene and was identical using ClustalW. Fifty-five out of 78 (70.5% clinical isolates assessed for Rv0180c were positive for single nucleotide polymorphism (SNP at 258th position where the nucleotide G was replaced with T (G to T. In clinical isolates of untreated cases, the frequency was 54.5% for SNP at 258th position which is low compared to cases undergoing treatment where the frequency was 73.1%. Conclusions: Molecular analysis of Rv0180c in clinical isolates of PTB assessed in this study was the first report, where an SNP at 258th position G to T was identified within the gene. Rv0679c gene was highly conserved (94%, within Indian clinical isolates as compared to reports from other nations.

  14. Molecular analysis and MIRU-VNTR typing of Mycobacterium avium subsp. avium, 'hominissuis' and silvaticum strains of veterinary origin.

    Science.gov (United States)

    Rónai, Zsuzsanna; Csivincsik, Ágnes; Dán, Ádám; Gyuranecz, Miklós

    2016-06-01

    Besides Mycobacterium avium subsp. paratuberculosis (MAP), M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS), and 'M. avium subsp. hominissuis' (MAH) are equally important members of M. avium complex, with worldwide distribution and zoonotic potential. Genotypic discrimination is a prerequisite to epidemiological studies which can facilitate disease prevention through revealing infection sources and transmission routes. The primary aim of this study was to identify the genetic diversity within 135 MAA, 62 MAS, and 84 MAH strains isolated from wild and domestic mammals, reptiles and birds. Strains were tested for the presence of large sequence polymorphism LSP(A)17 and were submitted to Mycobacterial interspersed repetitive units-variable-number tandem repeat (MIRU-VNTR) analysis at 8 loci, including MIRU1, 2, 3, and 4, VNTR25, 32, and 259, and MATR9. In 12 strains hsp65 sequence code type was also determined. LSP(A)17 was present only in 19.9% of the strains. All LSP(A)17 positive strains belonged to subspecies MAH. The discriminatory power of the MIRU-VNTR loci set used reached 0.9228. Altogether 54 different genotypes were detected. Within MAH, MAA, and MAS strains 33, 16, and 5 different genotypes were observed. The described genotypes were not restricted to geographic regions or host species, but proved to be subspecies specific. Our knowledge about MAS is limited due to isolation and identification difficulties. This is the first study including a large number of MAS field strains. Our results demonstrate the high diversity of MAH and MAA strains and the relative uniformity of MAS strains. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Analysis of the bovine monocyte-derived macrophage response to Mycobacterium avium subspecies paratuberculosis infection using RNA-seq

    Directory of Open Access Journals (Sweden)

    Maura E Casey

    2015-02-01

    Full Text Available Johne’s disease, caused by infection with Mycobacterium avium subsp. paratuberculosis, (MAP, is a chronic intestinal disease of ruminants with serious economic consequences for cattle production in the United States and elsewhere. During infection, MAP bacilli are phagocytosed and subvert host macrophage processes, resulting in subclinical infections that can lead to immunopathology and dissemination of disease. Analysis of the host macrophage transcriptome during infection can therefore shed light on the molecular mechanisms and host-pathogen interplay associated with Johne’s disease. Here we describe results of an in vitro study of the bovine monocyte-derived macrophage (MDM transcriptome response during MAP infection using RNA-seq. MDM were obtained from seven age- and sex-matched Holstein-Friesian cattle and were infected with MAP across a six-hour infection time course with non-infected controls. We observed 245 and 574 differentially expressed genes in MAP-infected versus non-infected control samples (adjusted P value ≤ 0.05 at 2 and 6 hours post-infection, respectively. Functional analyses of these differentially expressed genes, including biological pathway enrichment, highlighted potential functional roles for genes that have not been previously described in the host response to infection with MAP bacilli. In addition, differential expression of pro- and anti-inflammatory cytokine genes, such as those associated with the IL-10 signaling pathway, and other immune-related genes that encode proteins involved in the bovine macrophage response to MAP infection emphasize the balance between protective host immunity and bacilli survival and proliferation. Systematic comparisons of RNA-seq gene expression results with Affymetrix® microarray data generated from the same experimental samples also demonstrated that RNA-seq represents a superior technology for studying host transcriptional responses to intracellular infection.

  16. High-resolution melting analysis for the rapid detection of fluoroquinolone and streptomycin resistance in Mycobacterium tuberculosis.

    Science.gov (United States)

    Lee, Ann S G; Ong, Danny C T; Wong, Joshua C L; Siu, Gilman K H; Yam, Wing-Cheong

    2012-01-01

    Molecular methods for the detection of drug-resistant tuberculosis are potentially more rapid than conventional culture-based drug susceptibility testing, facilitating the commencement of appropriate treatment for patients with drug resistant tuberculosis. We aimed to develop and evaluate high-resolution melting (HRM) assays for the detection of mutations within gyrA, rpsL, and rrs, for the determination of fluoroquinolone and streptomycin resistance in Mycobacterium tuberculosis (MTB). A blinded series of DNA samples extracted from a total of 92 clinical isolates of MTB were analyzed by HRM analysis, and the results were verified using DNA sequencing. The sensitivity and specificity of the HRM assays in comparison with drug susceptibility testing were 74.1% and 100.0% for the detection of fluoroquinolone resistance, and 87.5% and 100.0% for streptomycin resistance. Five isolates with low level resistance to ofloxacin had no mutations detected in gyrA, possibly due to the action of efflux pumps, or false negativity due to mixed infections. One fluoroquinolone-resistant isolate had a mutation in a region of gyrA not encompassed by our assay. Six streptomycin-resistant strains had undetectable mutations by HRM and DNA sequencing, which may be explained by the fact that not all streptomycin-resistant isolates have mutations within rpsL and rrs, and suggesting that other targets may be involved. The HRM assays described here are potentially useful adjunct tests for the efficient determination of fluoroquinolone and streptomycin resistance in MTB, and could facilitate the timely administration of appropriate treatment for patients infected with drug-resistant TB.

  17. Analysis of Mycobacterium avium subsp. paratuberculosis mutant libraries reveals loci-dependent transcription biases and strategies to novel mutant discovery

    Science.gov (United States)

    Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne’s disease in ruminants and it has been implicated as a cause of Crohn’s disease in humans. The generation of comprehensive random mutant banks by transposon mutagenesis is a fundamental wide genomic technology utilized...

  18. Analysis of Mycobacterium avium subspecies paratuberculosis mutant libraries reveals loci-dependent transposition biases and strategies to novel mutant discovery

    Science.gov (United States)

    Mycobacterium avium subsp. paratuberculosis (MAP), the etiologic agent of Johne’s disease, is one of the most important bacterial pathogens in ruminants. The lack of efficacious control measures demands a thorough understanding of MAP pathogenesis to develop new vaccines and diagnostic tests. The ge...

  19. Capillary gas chromatographic analysis of mycolic acid cleavage products, cellular fatty acids, and alcohols of Mycobacterium xenopi.

    OpenAIRE

    Luquin, M; Lopez, F; Ausina, V

    1989-01-01

    The fatty acids, alcohols, and mycolic acids of 26 strains of Mycobacterium xenopi were studied by capillary gas chromatography and thin-layer chromatography. All strains contained alpha-, keto-, and omega-carboxymycolates. The primary mycolic acid cleavage product was hexacosanoic acid. The fatty acid patterns and, especially, the presence of 2-docosanol are characteristic markers of M. xenopi.

  20. Expression, purification and preliminary crystallographic analysis of Mycobacterium tuberculosis CysQ, a phosphatase involved in sulfur metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, Anna I.; Sarsam, Reta D.; Fisher, Andrew J., E-mail: ajfisher@ucdavis.edu

    2014-05-10

    The cysQ gene from Mycobacterium tuberculosis was cloned and the expressed protein, a 3′-phosphoadenosine-5′’-phosphatase, was purified and crystallized. X-ray diffraction data were collected to 1.7 Å resolution.

  1. Bone marrow infection with Mycobacterium fortuitum in a diabetic patient.

    Science.gov (United States)

    Satti, Luqman; Abbasi, Shahid; Sattar, Abdul; Ikram, Aamer; Manzar, Muhammad Adnan; Khalid, Malik Muhammad

    2011-08-01

    Incidence and prevalence of Mycobacterium fortuitum infection vary greatly by location and death is very rare except in disseminated disease in immunocompromised individuals. We present what we believe is the first case of bone marrow infection with Mycobacterium fortuitum in an HIV negative patient. Bone marrow examination revealed presence of numerous acid fast bacilli which were confirmed as Mycobacterium fortuitum on culture and by molecular analysis. Patient was managed successfully with amikacin and ciprofloxacin.

  2. Bone marrow infection with mycobacterium fortuitum in a diabetic patient

    International Nuclear Information System (INIS)

    Satti, L.; Abbasi, S.; Sattar, A.; Ikram, A.; Manzar, M.A.; Khalid, M.M.

    2011-01-01

    Incidence and prevalence of Mycobacterium fortuitum infection vary greatly by location and death is very rare except in disseminated disease in immunocompromised individuals. We present what we believe is the first case of bone marrow infection with Mycobacterium fortuitum in an HIV negative patient. Bone marrow examination revealed presence of numerous acid fast bacilli which were confirmed as Mycobacterium fortuitum on culture and by molecular analysis. Patient was managed successfully with amikacin and ciprofloxacin. (author)

  3. Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Prem [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India); Talawar, Ramappa K.; Krishna, P. D. V.; Varshney, Umesh [Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012 (India); Vijayan, M., E-mail: mv@mbu.iisc.ernet.in [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India)

    2006-12-01

    Uracil N-glycosylase from M. tuberculosis has been crystallized in complex with a proteinaceous inhibitor (Ugi) and X-ray diffraction data have been collected. Uracil N-glycosylase is an enzyme which initiates the pathway of uracil-excision repair of DNA. The enzyme from Mycobacterium tuberculosis was co-expressed with a proteinaceous inhibitor from Bacillus subtilis phage and was crystallized in monoclinic space group C2, with unit-cell parameters a = 201.14, b = 64.27, c = 203.68 Å, β = 109.7°. X-ray data from the crystal have been collected for structure analysis.

  4. Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

    International Nuclear Information System (INIS)

    Singh, Prem; Talawar, Ramappa K.; Krishna, P. D. V.; Varshney, Umesh; Vijayan, M.

    2006-01-01

    Uracil N-glycosylase from M. tuberculosis has been crystallized in complex with a proteinaceous inhibitor (Ugi) and X-ray diffraction data have been collected. Uracil N-glycosylase is an enzyme which initiates the pathway of uracil-excision repair of DNA. The enzyme from Mycobacterium tuberculosis was co-expressed with a proteinaceous inhibitor from Bacillus subtilis phage and was crystallized in monoclinic space group C2, with unit-cell parameters a = 201.14, b = 64.27, c = 203.68 Å, β = 109.7°. X-ray data from the crystal have been collected for structure analysis

  5. Molecular Mechanisms of Intrinsic Streptomycin Resistance in Mycobacterium abscessus.

    Science.gov (United States)

    Dal Molin, Michael; Gut, Myriam; Rominski, Anna; Haldimann, Klara; Becker, Katja; Sander, Peter

    2018-01-01

    Streptomycin, the first drug used for the treatment of tuberculosis, shows limited activity against the highly resistant pathogen Mycobacterium abscessus We recently identified two aminoglycoside-acetylating genes [ aac(2') and eis2 ] which, however, do not affect susceptibility to streptomycin. This suggests the existence of a discrete mechanism of streptomycin resistance. M. abscessus BLASTP analysis identified MAB_2385 as a close homologue of the 3″- O -phosphotransferase [APH(3″)] from the opportunistic pathogen Mycobacterium fortuitum as a putative streptomycin resistance determinant. Heterologous expression of MAB_2385 in Mycobacterium smegmatis increased the streptomycin MIC, while the gene deletion mutant M. abscessus ΔMAB_2385 showed increased streptomycin susceptibility. The MICs of other aminoglycosides were not altered in M. abscessus ΔMAB_2385. This demonstrates that MAB_2385 encodes a specific and prime innate streptomycin resistance determinant in M. abscessus We further explored the feasibility of applying rpsL -based streptomycin counterselection to generate gene deletion mutants in M. abscessus Spontaneous streptomycin-resistant mutants of M. abscessus ΔMAB_2385 were selected, and we demonstrated that the wild-type rpsL is dominant over the mutated rpsL K43R in merodiploid strains. In a proof of concept study, we exploited this phenotype for construction of a targeted deletion mutant, thereby establishing an rpsL -based counterselection method in M. abscessus . Copyright © 2017 American Society for Microbiology.

  6. CANDU safety analysis system establishment; development of trip coverage and multi-dimensional hydrogen analysis methodology

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jong Ho; Ohn, M. Y.; Cho, C. H. [KOPEC, Taejon (Korea)

    2002-03-01

    The trip coverage analysis model requires the geometry network for primary and secondary circuit as well as the plant control system to simulate all the possible plant operating conditions throughout the plant life. The model was validated for the power maneuvering and the Wolsong 4 commissioning test. The trip coverage map was produced for the large break loss of coolant accident and the complete loss of class IV power event. The reliable multi-dimensional hydrogen analysis requires the high capability for thermal hydraulic modelling. To acquire such a basic capability and verify the applicability of GOTHIC code, the assessment of heat transfer model, hydrogen mixing and combustion model was performed. Also, the assessment methodology for flame acceleration and deflagration-to-detonation transition is established. 22 refs., 120 figs., 31 tabs. (Author)

  7. Drug susceptibility testing of Mycobacterium tuberculosis to fluoroquinolones

    DEFF Research Database (Denmark)

    Johansen, I S; Larsen, A R; Sandven, P

    2003-01-01

    In the first attempt to establish a quality assurance programme for susceptibility testing of Mycobacterium tuberculosis to fluoroquinolones, 20 strains with different fluoroquinolone susceptibility patterns were distributed by the Supranational Reference Laboratory in Stockholm to the other...

  8. Comparison of the capillary and agarose electrophoresis based multiple locus VNTR (variable number of tandem repeats) analysis (MLVA) on Mycobacterium bovis isolates.

    Science.gov (United States)

    Jenkins, A O; Venter, E H; Hutamo, K; Godfroid, J

    2010-09-28

    Electrophoretic techniques that can be used for genotyping of bacterial pathogens ranges from manual, low-cost, agarose gels to high-throughput capillary electrophoresis sequencing machines. These two methods are currently employed in the electrophoresis of PCR products used in multiple locus VNTR (variable number of tandem repeats) analysis (MLVA), i.e. the agarose electrophoresis (AE) and the capillary electrophoresis (CE). Some authors have suggested that clusters generated by AE are less reliable than those generated by CE and that the latter is a more sensitive technique than the former when typing Mycobacterium tuberculosis complex (MTC) isolates. Because such a claim could have significant consequences for investigators in this field, a comparison was made on 19 Belgian Mycobacterium bovis strains which had previously been genotyped using CE VNTR analysis. The VNTR profiles of the CE VNTR analysis were compared with those obtained by AE VNTR analysis at 14 VNTR loci. Our results indicated that there were no differences in copy numbers at all loci tested when the copy numbers obtained by the AE VNTR analysis were compared with those obtained by CE VNTR analysis. The use of AE VNTR analysis in mycobacterial genotyping does not alter the sensitivity of the MLVA technique compared with the CE VNTR analysis. The AE VNTR can therefore be regarded as a viable alternative in moderately equipped laboratories that cannot afford the expensive equipment required for CE VNTR analysis and data obtained by AE VNTR analysis can be shared between laboratories which use the CE VNTR method. (c) 2010 Elsevier B.V. All rights reserved.

  9. of Mycobacterium tuberculosis

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-18

    Aug 18, 2009 ... Recombinant and synthetic peptides to identify. Mycobacterium tuberculosis antigens and epitopes of diagnostic and vaccine relevance. Tuberculosis. 85: 367–376. Okkels LM, Andersen P (2004). Protein-protein interactions of proteins from the ESAT-6 family of Mycobacterium tuberculosis. J. Bacteriol.

  10. Genetic analysis of extensively drug-resistant Mycobacterium tuberculosis strains in Lisbon, Portugal.

    Science.gov (United States)

    Perdigão, João; Macedo, Rita; Malaquias, Ana; Ferreira, Ana; Brum, Laura; Portugal, Isabel

    2010-02-01

    Extensively drug-resistant (XDR) tuberculosis (TB) threatens the global control of TB worldwide. Lisbon has a high XDR-TB rate [50% of the multidrug-resistant tuberculosis (MDR-TB)], which is mainly associated with Lisboa family strains. Few studies have addressed the identification of mutations associated with resistance to second-line injectable drugs, and the relative frequency of such mutations varies geographically. The aim of this study was to characterize the genetic changes associated with the high number of XDR-TB cases in Lisbon. In the present study we analysed 26 XDR-TB clinical isolates. The gyrA, tlyA and rrs genes were screened for mutations that could be responsible for resistance to fluoroquinolones and second-line injectable drugs. Moreover, the strains under analysis were also genotyped by MIRU-VNTR ('mycobacterial interspersed repetitive unit-variable number of tandem repeats'). The mutational analysis identified the most frequent mutations in the resistance-associated genes: S91P in gyrA (42.3%); A1401G in rrs (30.8%); and Ins755GT in tlyA (42.3%). The occurrence of mutations in rrs was associated with the non-occurrence of mutations in tlyA. The genotypic analysis revealed that the strains were highly clonal, belonging to one of two MIRU-VNTR clusters, with the largest belonging to the Lisboa family. Association between mutations in gyrA and rrs or tlyA was verified. The association of specific mutations highlighted the strains' high clonality and indicates recent XDR-TB transmission. In addition, the identification of the most frequent resistance-associated mutations will be invaluable in applying XDR-TB molecular detection tests in the region in the near future.

  11. Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium.

    Science.gov (United States)

    Zhang, Dao-Feng; Chen, Xiu; Zhang, Xiao-Mei; Zhi, Xiao-Yang; Yao, Ji-Cheng; Jiang, Yi; Xiong, Zhi; Li, Wen-jun

    2013-11-01

    Two novel isolates of rapidly growing, Gram-stain-positive, non-chromogenic species of the genus Mycobacterium, strain YIM M13028(T) from a sediment sample collected from the South China Sea (19° 30.261' N 111° 0.247' E) at a depth of 42 m and strain YIM 121001(T) from a coastal zone sand sample collected in Dubai, United Arab Emirates, were obtained in our laboratory. Their taxonomic positions were determined by a polyphasic approach. Good growth of the two strains was observed at 28 °C and pH 7.0 with 0-2 % NaCl on tryptic soy agar medium. Both strains formed round orange-red colonies, strain YIM M13028(T) had a rough surface, while YIM 121001(T) was smooth. Cellular fatty acids, whole-cell protein profiles and TLC analysis of their mycolic acids show significant differences from reference stains. Phenotypic characteristics and multilocus sequence analysis (MLSA) of 16S rRNA gene, hsp65, rpoB and 16S-23S internal transcribed spacer (ITS) sequences indicated that both strains YIM M13028(T) and YIM 121001(T) belong to the genus Mycobacterium. DNA-DNA hybridization values revealed a low relatedness (<70 %) of the two isolates with the type strains Mycobacterium neoaurum DSM 44074(T) and Mycobacterium hodleri DSM 44183(T). The low DNA-DNA hybridization values (40.4±3.5 %) between strains YIM M13028(T) and YIM 121001(T) and phenotypic distinctiveness indicated that the two strains were representatives of different novel species of the genus Mycobacterium. The names proposed for these novel species are Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., and the type strains are YIM M13028(T) ( = DSM 45643(T) = KCTC 19999(T)) and YIM 121001(T) ( = DSM 45768(T) = JCM 18538(T)), respectively.

  12. Mycobacterium bovis (Bovine Tuberculosis) in Humans

    Science.gov (United States)

    Mycobacterium bovis (Bovine Tuberculosis) in Humans What is Mycobacterium bovis ? In the United States, the majority of tuberculosis (TB) cases in people are caused by Mycobacterium tuberculosis (M. tuberculosis). Mycobacterium bovis (M. bovis) is ...

  13. Molecular epidemiology of Mycobacterium tuberculosis in Lisbon

    Directory of Open Access Journals (Sweden)

    Isabel Portugal

    2008-03-01

    Full Text Available We conducted a molecular epidemiology study of Mycobacterium tuberculosis strains isolated from patients in Lisbon hospitals. We used restriction fragment length polymorphism (RFLP to detect Lisbon family strains and to determine the genetic diversity of Mycobacterium tuberculosis strains isolated in Lisbon, through identification of the most important risk factors of tuberculosis transmission analysis, with the insertion sequence IS6110 as a probe to fingerprint isolates of Mycobacterium tuberculosis. 64.8% of the 290 Mycobacterium tuberculosis isolates were grouped in clusters. This figure was 60.7% if we excluded strains with five or fewer IS6110 copies. Multidrug-resistance was observed in 4.1% of the strains and they were all in clusters. Forty-five (18.2% strains were included in the Lisbon family. Considering the relatively high percentage of strains in cluster detected in this study, we believe that active transmission is still taking place in Lisbon. Moreover, clusters of Lisbon strains represent the predominant strains circulating in Lisbon and are still related to drug resistance although presenting a lower percentage than that observed in previous studies. Resumo: Foi realizado um estudo de epidemiologia molecular a estirpes de Mycobacterium tuberculosis isoladas em hospitais de Lisboa. Analisaram-se geneticamente os isolados de Mycobacterium tuberculosis com o método restriction fragment length polymorphism (RFLP utilizando a sequência de inserção IS6110 como sonda, com o objectivo de detectar as estirpes da família Lisboa e determinar a diversidade genética das estirpes de Mycobacterium tuberculosis isoladas em Lisboa, identificando os mais importantes factores de risco de transmissão da tuberculose.Foram analisados 290 isolados de Mycobacterium tuberculosis, dos quais 64,8% se encontraram agrupados em clusters; mesmo excluindo as estirpes que apresentaram mais de 5 cópias de IS6110, a percentagem de agrupamento foi de 60

  14. Molecular analysis of the rpsL gene for rapid detection of streptomycin-resistant Mycobacterium tuberculosis: a meta-analysis.

    Science.gov (United States)

    He, Jing; Zhu, Baosheng; Yang, Zhaojie; Hu, Binbin; Lin, Lianbing; Zhang, Qi

    2014-08-01

    Drug-resistant Mycobacterium tuberculosis (MTB) is a major threat to tuberculosis (TB) control programs and public health. Most conventional methods of drug susceptibility testing (DST) are precise but time-consuming. Molecular analysis of the rpsL gene has been used widely in diagnosing streptomycin-resistant MTB since it is rapid and specific. The aim of the present study was to perform a meta-analysis to assess the accuracy of molecular assay of the rpsL gene for the rapid detection of streptomycin-resistant MTB. We searched PubMed, Web of Science, and EBSCO databases for studies that applied a molecular assay of the rpsL gene to detect streptomycin-resistant MTB with a conventional method as the reference. The sensitivity and specificity were pooled by a random effect model using Meta-DiSc software. A summary receiver operating characteristic curve (SROC) was applied to summarize the diagnostic accuracy. A total of 22 studies involving 2618 specimens with 1372 streptomycin-resistant and 1246 streptomycin-susceptible specimens met our inclusion criteria. The overall sensitivity and specificity estimates were 0.64 (95% confidence interval (CI) 0.61-0.66) and 1.00 (95% CI 0.99-1.00), respectively. The area under the SROC curve was 0.9069 and the Cochrane (Q*) index was 0.8387. This meta-analysis reveals that molecular assay of the rpsL gene is a reliable and useful method for the detection of streptomycin-resistant MTB.

  15. Two-Year Monitoring of Water Samples from Dam of Iskar and the Black Sea, Bulgaria, by Molecular Analysis: Focus on Mycobacterium spp.

    Science.gov (United States)

    Panaiotov, Stefan; Simeonovski, Ivan; Levterova, Victoria; Karamfilov, Ventzislav; Brankova, Nadia; Tankova, Kristin; Campbell, Katrina; Jacob, Pauline; Helmi, Karim; Boots, Bas; D'Ugo, Emilio; Marcheggiani, Stefania; Mancini, Laura; Breitenbach, Ulrich; Mielke, Erik; Kantardjiev, Todor

    2015-06-30

    The coast of the Bulgarian Black Sea is a popular summer holiday destination. The Dam of Iskar is the largest artificial dam in Bulgaria, with a capacity of 675 million m3. It is the main source of tap water for the capital Sofia and for irrigating the surrounding valley. There is a close relationship between the quality of aquatic ecosystems and human health as many infections are waterborne. Rapid molecular methods for the analysis of highly pathogenic bacteria have been developed for monitoring quality. Mycobacterial species can be isolated from waste, surface, recreational, ground and tap waters and human pathogenicity of nontuberculose mycobacteria (NTM) is well recognized. The objective of our study was to perform molecular analysis for key-pathogens, with a focus on mycobacteria, in water samples collected from the Black Sea and the Dam of Iskar. In a two year period, 38 water samples were collected-24 from the Dam of Iskar and 14 from the Black Sea coastal zone. Fifty liter water samples were concentrated by ultrafiltration. Molecular analysis for 15 pathogens, including all species of genus Mycobacterium was performed. Our results showed presence of Vibrio spp. in the Black Sea. Rotavirus A was also identified in four samples from the Dam of Iskar. Toxigenic Escherichia coli was present in both locations, based on markers for stx1 and stx2 genes. No detectable amounts of Cryptosporidium were detected in either location using immunomagnetic separation and fluorescence microscopy. Furthermore, mass spectrometry analyses did not detect key cyanobacterial toxins. On the basis of the results obtained we can conclude that for the period 2012-2014 no Mycobacterium species were present in the water samples. During the study period no cases of waterborne infections were reported.

  16. Two-Year Monitoring of Water Samples from Dam of Iskar and the Black Sea, Bulgaria, by Molecular Analysis: Focus on Mycobacterium spp.

    Directory of Open Access Journals (Sweden)

    Stefan Panaiotov

    2015-06-01

    Full Text Available The coast of the Bulgarian Black Sea is a popular summer holiday destination. The Dam of Iskar is the largest artificial dam in Bulgaria, with a capacity of 675 million m3. It is the main source of tap water for the capital Sofia and for irrigating the surrounding valley. There is a close relationship between the quality of aquatic ecosystems and human health as many infections are waterborne. Rapid molecular methods for the analysis of highly pathogenic bacteria have been developed for monitoring quality. Mycobacterial species can be isolated from waste, surface, recreational, ground and tap waters and human pathogenicity of nontuberculose mycobacteria (NTM is well recognized. The objective of our study was to perform molecular analysis for key-pathogens, with a focus on mycobacteria, in water samples collected from the Black Sea and the Dam of Iskar. In a two year period, 38 water samples were collected—24 from the Dam of Iskar and 14 from the Black Sea coastal zone. Fifty liter water samples were concentrated by ultrafiltration. Molecular analysis for 15 pathogens, including all species of genus Mycobacterium was performed. Our results showed presence of Vibrio spp. in the Black Sea. Rotavirus A was also identified in four samples from the Dam of Iskar. Toxigenic Escherichia coli was present in both locations, based on markers for stx1 and stx2 genes. No detectable amounts of Cryptosporidium were detected in either location using immunomagnetic separation and fluorescence microscopy. Furthermore, mass spectrometry analyses did not detect key cyanobacterial toxins. On the basis of the results obtained we can conclude that for the period 2012–2014 no Mycobacterium species were present in the water samples. During the study period no cases of waterborne infections were reported.

  17. Two-Year Monitoring of Water Samples from Dam of Iskar and the Black Sea, Bulgaria, by Molecular Analysis: Focus on Mycobacterium spp.

    Science.gov (United States)

    Panaiotov, Stefan; Simeonovski, Ivan; Levterova, Victoria; Karamfilov, Ventzislav; Brankova, Nadia; Tankova, Kristin; Campbell, Katrina; Jacob, Pauline; Helmi, Karim; Boots, Bas; D’Ugo, Emilio; Marcheggiani, Stefania; Mancini, Laura; Breitenbach, Ulrich; Mielke, Erik; Kantardjiev, Todor

    2015-01-01

    The coast of the Bulgarian Black Sea is a popular summer holiday destination. The Dam of Iskar is the largest artificial dam in Bulgaria, with a capacity of 675 million m3. It is the main source of tap water for the capital Sofia and for irrigating the surrounding valley. There is a close relationship between the quality of aquatic ecosystems and human health as many infections are waterborne. Rapid molecular methods for the analysis of highly pathogenic bacteria have been developed for monitoring quality. Mycobacterial species can be isolated from waste, surface, recreational, ground and tap waters and human pathogenicity of nontuberculose mycobacteria (NTM) is well recognized. The objective of our study was to perform molecular analysis for key-pathogens, with a focus on mycobacteria, in water samples collected from the Black Sea and the Dam of Iskar. In a two year period, 38 water samples were collected—24 from the Dam of Iskar and 14 from the Black Sea coastal zone. Fifty liter water samples were concentrated by ultrafiltration. Molecular analysis for 15 pathogens, including all species of genus Mycobacterium was performed. Our results showed presence of Vibrio spp. in the Black Sea. Rotavirus A was also identified in four samples from the Dam of Iskar. Toxigenic Escherichia coli was present in both locations, based on markers for stx1 and stx2 genes. No detectable amounts of Cryptosporidium were detected in either location using immunomagnetic separation and fluorescence microscopy. Furthermore, mass spectrometry analyses did not detect key cyanobacterial toxins. On the basis of the results obtained we can conclude that for the period 2012–2014 no Mycobacterium species were present in the water samples. During the study period no cases of waterborne infections were reported. PMID:26133133

  18. Molecular Identification of Mycobacterium Tuberculosis and Analysis of Its Resistance to Rifampin in Sputa from Tuberculosis Suspected Patients

    International Nuclear Information System (INIS)

    Syaifudin, M.

    2010-01-01

    An accurate identification of different species of Mycobacterium provides to allow appropriate treatment for Mycobacterium tuberculosis infection. Beside that, drug resistance of M. tuberculosis strains to rifampin is not clearly understood in contributing to the spread of tuberculosis in Indonesia. To assess the molecular mechanism of rifampin resistance, a number of clinical specimens of M. tuberculosis were analyzed their molecular nature of a part of the rpoB gene using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) methods. DNA's extracted from sputum samples were amplified and 32 P-labeled by PCR with the specific primers and the product was analyzed their mutation conferring resistance by MDE gel electrophoresis. Of the 70 specimens tested, 57 specimens were positive for M. tuberculosis organism only, three specimens contained a mixture of M. tuberculosis and non tuberculosis mycobacteria (NTM), and 10 specimens were negative approved by Duplex PCR. Of these sixty DNA positive samples (thus the sensitivity of PCR was 85.71%), 5 (8.3%) of them suspected to contain mutations in rpoB which were associated with rifampin resistance. Even though the frequency of mutation was low, the results from our study clearly indicate that the molecular mechanism of rifampin resistance in M. tuberculosis isolates from Indonesia involves alterations in the rpoB gene. Molecular diagnosis by PCR which is fast and easy to perform is useful for early and rapid detection of TB in sputum specimen. (author)

  19. Mycobacterium ulcerans disease

    NARCIS (Netherlands)

    van der Werf, TS; Stienstra, Y; Johnson, RC; Phillips, R; Adjei, O; Fleischer, B; Wansbrough-Jones, MH; Johnson, PDR; Portaels, F; van der Graaf, WTA; Asiedu, K

    2005-01-01

    Mycobacterium ulcerans disease (Buruli ulcer) is an important health problem in several dwest African countries. It is prevalent in scattered foci around the world, predominantly in riverine areas with a humid, hot climate. We review the epidemiology, bacteriology, transmission, immunology,

  20. The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae.

    Science.gov (United States)

    Phelan, Jody; Maitra, Arundhati; McNerney, Ruth; Nair, Mridul; Gupta, Antima; Coll, Francesc; Pain, Arnab; Bhakta, Sanjib; Clark, Taane G

    2015-09-01

    Mycobacterium aurum (M. aurum) is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related) to 96.2% for rrs (streptomycin, capreomycin). We observed two homologous genes encoding the catalase-peroxidase enzyme (katG) that is associated with resistance to isoniazid. Similarly, two embB homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum, this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae. Copyright © 2015 Asian-African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.

  1. The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

    KAUST Repository

    Phelan, Jody

    2015-06-04

    Mycobacterium aurum (M. aurum) is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02 Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related) to 96.2% for rrs (streptomycin, capreomycin). We observed two homologous genes encoding the catalase-peroxidase enzyme (katG) that is associated with resistance to isoniazid. Similarly, two embB homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum, this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae.

  2. The draft genome of Mycobacterium aurum , a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

    Directory of Open Access Journals (Sweden)

    Jody Phelan

    2015-01-01

    Full Text Available Mycobacterium aurum (M. aurum is an environmental mycobacteria that has previously been used in studies of anti-mycobacterial drugs due to its fast growth rate and low pathogenicity. The M. aurum genome has been sequenced and assembled into 46 contigs, with a total length of 6.02 Mb containing 5684 annotated protein-coding genes. A phylogenetic analysis using whole genome alignments positioned M. aurum close to Mycobacterium vaccae and Mycobacterium vanbaalenii, within a clade related to fast-growing mycobacteria. Large-scale genomic rearrangements were identified by comparing the M. aurum genome to those of Mycobacterium tuberculosis and Mycobacterium leprae. M. aurum orthologous genes implicated in resistance to anti-tuberculosis drugs in M. tuberculosis were observed. The sequence identity at the DNA level varied from 68.6% for pncA (pyrazinamide drug-related to 96.2% for rrs (streptomycin, capreomycin. We observed two homologous genes encoding the catalase-peroxidase enzyme (katG that is associated with resistance to isoniazid. Similarly, two emb B homologues were identified in the M. aurum genome. In addition to describing for the first time the genome of M. aurum , this work provides a resource to aid the use of M. aurum in studies to develop improved drugs for the pathogenic mycobacteria M. tuberculosis and M. leprae.

  3. Mycobacterium arupense, Mycobacterium heraklionense, and a Newly Proposed Species, "Mycobacterium virginiense" sp. nov., but Not Mycobacterium nonchromogenicum, as Species of the Mycobacterium terrae Complex Causing Tenosynovitis and Osteomyelitis.

    Science.gov (United States)

    Vasireddy, Ravikiran; Vasireddy, Sruthi; Brown-Elliott, Barbara A; Wengenack, Nancy L; Eke, Uzoamaka A; Benwill, Jeana L; Turenne, Christine; Wallace, Richard J

    2016-05-01

    Mycobacterium terrae complex has been recognized as a cause of tenosynovitis, with M. terrae and Mycobacterium nonchromogenicum reported as the primary etiologic pathogens. The molecular taxonomy of the M. terrae complex causing tenosynovitis has not been established despite approximately 50 previously reported cases. We evaluated 26 isolates of the M. terrae complex associated with tenosynovitis or osteomyelitis recovered between 1984 and 2014 from 13 states, including 5 isolates reported in 1991 as M. nonchromogenicum by nonmolecular methods. The isolates belonged to three validated species, one new proposed species, and two novel related strains. The majority of isolates (20/26, or 77%) belonged to two recently described species: Mycobacterium arupense (10 isolates, or 38%) and Mycobacterium heraklionense (10 isolates, or 38%). Three isolates (12%) had 100% sequence identity to each other by 16S rRNA and 99.3 to 100% identity by rpoB gene region V sequencing and represent a previously undescribed species within the M. terrae complex. There were no isolates of M. terrae or M. nonchromogenicum, including among the five isolates reported in 1991. The 26 isolates were susceptible to clarithromycin (100%), rifabutin (100%), ethambutol (92%), and sulfamethoxazole or trimethoprim-sulfamethoxazole (70%). The current study suggests that M. arupense, M. heraklionense, and a newly proposed species ("M. virginiense" sp. nov.; proposed type strain MO-233 [DSM 100883, CIP 110918]) within the M. terrae complex are the major causes of tenosynovitis and osteomyelitis in the United States, with little change over 20 years. Species identification within this complex requires sequencing methods. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  4. The comparative analysis of level of students' physical readiness of higher educational establishment.

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    Dukh T.I.

    2012-09-01

    Full Text Available Aim of research - to determine state and open up ways of perfection of students' physical preparation. In article questions of improvement of physical education of students high educational establishing are considered. It is carried out the analysis of level of physical readiness of students high educational establishing. In research has accepted 727 students of three educational establishing, the estimation of their physical readiness is given. It is defined low level of readiness in force indicators, endurance, and also speed and power qualities. Are described the coefficient of variation and level probability of results in indicators of dexterity, force - in the young man, and the dynamic force index, dexterity, high-speed endurance in the young woman. It is established insufficient level of physical readiness of students.

  5. Draft Genome Sequence of Mycobacterium chimaera Type ...

    Science.gov (United States)

    We report the draft genome sequence of the type strain Mycobacterium chimaera Fl-0169T, a member of the Mycobacterium avium complex (MAC). M. chimaera Fl-0169T was isolated from a patient in Italy and is highly similar to strains of M. chimaera isolated in Ireland, though Fl-0169T possesses unique virulence genes. Evidence suggests that M. avium, M. intracellulare, and M. chimaera are differently virulent and a comparative genomic analysis is critically needed to identify diagnostic targets that reliably differentiate species of MAC. With treatment costs for Mycobacterium infections estimated to be >$1.8 B annually in the U.S., correct species identification will result in improved treatment selection, lower costs, and improved patient outcomes.

  6. Detection of Mycobacterium avium in pet birds

    Science.gov (United States)

    Godoy, Silvia Neri; Sakamoto, Sidnei Miyoshi; de Paula, Cátia Dejuste; Catão-Dias, José Luiz; Matushima, Eliana Reiko

    2009-01-01

    The present study is a report on the presence of Mycobacterium avium in four birds of the psittaciform order kept as pets. Anatomopathological diagnosis showed lesions suggestive of the agent and presence of alcohol-acid resistant bacilli (AARB) shown by the Ziehl-Neelsen staining. The identification of Mycobacterium avium was performed by means of PRA (PCR Restriction Analysis). DNA was directly extracted from tissue of the lesions and blocked in paraffin. The role of this agent in pet bird infection is discussed, as well as its zoonotic potential. PMID:24031356

  7. Strategic analysis on establishing a natural gas trading hub in China

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    Xiaoguang Tong

    2014-12-01

    Full Text Available Since 2010, the LNG importing price premium in the Asia–Pacific markets has become increasingly high, generating great effects on the economic development in China. In addition, the natural gas dependence degree is expanding continuously, making it extremely urgent to establish a natural gas trading hub in China, with the aim to ensure national energy security, to gain the pricing power, and to build the regional benchmark prices. Through a comparative analysis of internal strength/weakness and external competitiveness, we concluded that with intensively-issued supporting policies on the natural gas sector, the initiation of spot and futures markets, the rapid growth of gas production and highly-improved infrastructures, as well as Shanghai's advantageous location, China has more advantages in establishing an Asian Natural Gas Trading Hub than other counties like Singapore, Japan and Malaysia. Moreover, based on the SWOT (strength, weakness, opportunity and threat and the marketization process analysis, the following strategies were presented: to impel the establishment of a natural gas trading hub depending on the gas supply condition, to follow the policies to complete the gas storage system, to form regional communities by taking comparative advantages, and to reinforce the marketization reform and regulation system establishment with foreign experiences for reference. This study rationalized the necessity and practicality of establishing a natural gas trading hub in China and will help China make a proper decision and find a periodical strategic path in this sector.

  8. Molecular characterization of Mycobacterium avium subspecies hominissuis isolated from humans, cattle and pigs in the Uganda cattle corridor using VNTR analysis.

    Science.gov (United States)

    Muwonge, Adrian; Oloya, James; Kankya, Clovice; Nielsen, Sigrun; Godfroid, Jacques; Skjerve, Eystein; Djønne, Berit; Johansen, Tone B

    2014-01-01

    Members of the Mycobacterium avium complex (MAC) cause disease in both human and animals. Their ubiquitous nature makes them both successful microbes and difficult to source track. The precise characterization of MAC species is a fundamental step in epidemiological studies and evaluating of possible reservoirs. This study aimed at identifying and characterizing Mycobacterium avium subsp. hominissuis isolated from human, slaughter cattle and pigs in various parts of the Uganda cattle corridor (UCC) at two temporal points using variable number of tandem repeat (VNTR) analysis. A total of 46 M. avium isolates; 31 from 997 pigs, 12 from 43 humans biopsies and three from 61 cattle lesions were identified to subspecies level using IS1245 and IS901 PCR, thereafter characterized using VNTR. Twelve loci from two previously described VNTR methods were used and molecular results were analyzed and interpreted using Bionumerics 6.1. 37 of the isolates were identified as M. avium subsp. hominissuis and four as M. avium subsp. avium, while five could not be differentiated, possibly due to mixed infection. There was distinct clustering that coincides with the temporal and spatial differences of the isolates. The isolates from humans and cattle in the North Eastern parts of the UCC shared identical VNTR genotypes. The panel of loci gave an overall discriminatory power of 0.88. Some loci were absent in several isolates, probably reflecting differences in isolates from Uganda/Africa compared to isolates previously analyzed by these methods in Europe and Asia. The findings indicate a molecular difference between M. avium subsp. hominissuis isolates from pigs in Mubende and cattle and human in the rest of the UCC. Although human and cattle shared VNTR genotypes in the North Eastern parts of the UCC, it is most likely a reflection of a shared environmental source. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Establishing Cephalometric Norms using Sagittal and Vertical Occlusal Cephalometric Analysis of Pancherz for Dakshina Kannada Children.

    Science.gov (United States)

    Sahitya, M; Shashidhar, E P; Chidanandeswara, G C; Shetty, Sharath Kumar B; Kumar, Y Mahesh

    2015-07-01

    The purpose of this study was to establish norms for the sagittal occlusal (SO) and vertical occlusal (VO) cephalometric analyses of Pancherz for Dakshina Kannada children and to analyze and compare the difference between boys and girls of same age group (10-14 years). Two hundred and sixty-three (132 boys and 131 girls) children of Dakshina Kannada were included in this study. Lateral cephalometric radiographs of children belonging to the age group of 10-14 years were taken. Dental lateral cephalometric radiographs were obtained and these cephalometric radiographs were then manually traced. All the parameters considered in the Pancherz analysis were considered while establishing the norms for Dakshina Kannada children. Statistically significant sex differences were found for 9 of 11 parameters in the sagittal occlusal analysis, and 10 of 10 in the Vertical occlusal analysis. For the sagittal and Vertical occlusal analyses of Pancherz a separate sex-specific standards are needed for Dakshina Kannada children.

  10. Effectiveness of real-time polymerase chain reaction assay for the detection of Mycobacterium tuberculosis in pathological samples: a systematic review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Emmanuel O. Babafemi

    2017-10-01

    Full Text Available Abstract Background Rapid and accurate diagnosis of tuberculosis (TB is key to manage the disease and to control and prevent its transmission. Many established diagnostic methods suffer from low sensitivity or delay of timely results and are inadequate for rapid detection of Mycobacterium tuberculosis (MTB in pulmonary and extra-pulmonary clinical samples. This study examined whether a real-time polymerase chain reaction (RT-PCR assay, with a turn-a-round time of 2 h, would prove effective for routine detection of MTB by clinical microbiology laboratories. Methods A systematic literature search was performed for publications in any language on the detection of MTB in pathological samples by RT-PCR assay. The following sources were used MEDLINE via PubMed, EMBASE, BIOSIS Citation Index, Web of Science, SCOPUS, ISI Web of Knowledge and Cochrane Infectious Diseases Group Specialised Register, grey literature, World Health Organization and Centres for Disease Control and Prevention websites. Forty-six studies met set inclusion criteria. Generated pooled summary estimates (95% CIs were calculated for overall accuracy and bivariate meta-regression model was used for meta-analysis. Results Summary estimates for pulmonary TB (31 studies were as follows: sensitivity 0.82 (95% CI 0.81–0.83, specificity 0.99 (95% CI 0.99–0.99, positive likelihood ratio 43.00 (28.23–64.81, negative likelihood ratio 0.16 (0.12–0.20, diagnostic odds ratio 324.26 (95% CI 189.08–556.09 and area under curve 0.99. Summary estimates for extra-pulmonary TB (25 studies were as follows: sensitivity 0.70 (95% CI 0.67–0.72, specificity 0.99 (95% CI 0.99–0.99, positive likelihood ratio 29.82 (17.86–49.78, negative likelihood ratio 0.33 (0.26–0.42, diagnostic odds ratio 125.20 (95% CI 65.75–238.36 and area under curve 0.96. Conclusions RT-PCR assay demonstrated a high degree of sensitivity for pulmonary TB and good sensitivity for extra-pulmonary TB. It indicated a

  11. Mycobacterium komaniense sp. nov., a rapidly growing non-tuberculous Mycobacterium species detected in South Africa.

    Science.gov (United States)

    Gcebe, Nomakorinte; Rutten, Victor P M G; van Pittius, Nicolaas Gey; Naicker, Brendon; Michel, Anita L

    2018-05-01

    Some species of non-tuberculous mycobacteria (NTM) have been reported to be opportunistic pathogens of animals and humans. Recently there has been an upsurge in the number of cases of NTM infections, such that some NTM species are now recognized as pathogens of humans and animals. From a veterinary point of view, the major significance of NTM is the cross-reactive immune response they elicit against Mycobacterium bovis antigens, leading to misdiagnosis of bovine tuberculosis. Four NTM isolates were detected from a bovine nasal swab, soil and water, during an NTM survey in South Africa. These were all found using 16S rRNA gene sequence analysis to be closely related to Mycobacterium moriokaense. The isolates were further characterised by sequence analysis of the partial fragments of hsp65, rpoB and sodA. The genome of the type strain was also elucidated. Gene (16S rRNA, hsp65, rpoB and sodA) and protein sequence data analysis of 6 kDa early secretory antigenic target (ESAT 6) and 10 kDa culture filtrate protein (CFP-10) revealed that these isolates belong to a unique Mycobacterium species. Differences in phenotypic and biochemical traits between the isolates and closely related species further supported that these isolates belong to novel Mycobacterium species. We proposed the name Mycobacterium komaniense sp. nov. for this new species. The type strain is GPK 1020 T (=CIP 110823T=ATCC BAA-2758).

  12. Establishment of appropriate protocols for analysis of tree bark for use in biomonitoring atmospheric pollution

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Eliane C.; Saiki, Mitiko, E-mail: mitiko@ipen.br, E-mail: eliane_csantos@yahoo.com.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2013-07-01

    The aim of this study was to establish appropriate protocols for collection and processing of tree barks and multielement analysis by the method of Neutron Activation Analysis (NAA). For analysis, barks of Tipuana and Sibipiruna species were cleaned and crushed. For the procedures of the Neutron activated analysis, aliquots of samples and synthetic elementary standards were irradiated in the nuclear reactor IEA-R1 then analyzed by gamma spectrometry. The quality of the results was evaluated by analysis of certified reference materials that indicated good accuracy and precision. In the analyzes of different layers of barks was verified higher concentration or the same order of magnitude for most elements in the outer layer of the barks than in the inner. For both species studied, the concentrations of Ca and K did not show significant differences with the trunk diameter differences, but for the other elements showed variability. The Tipuana species showed higher concentration for most elements in relation to Sibipiruna. From the results obtained, a procedure for sample preparation and analysis of NAA to barks for monitoring air pollution was established.

  13. A Study on the Development of Building Energy Analysis Program and the Establishment of BEPS

    Energy Technology Data Exchange (ETDEWEB)

    Kong, S.R.; Kwon, K.J.; Yoo, Y.H.; Cho, Y.K.; Kijm, Y.D.; Han, S.W. [Korea Electric Power Corp. (KEPCO), Taejon (Korea, Republic of). Research Center; Kim, M.H.; Kim, K.W.; Cho, K.H.; Lee, H.W.; Lee, Y.H.; Kim, S.J.; Song, K.S.; Heon, C.T.; Choi, J.M.; Kim, Y.I.; Suk, H.T.; Kang, J.S.; Kim, Y.D.; Kang, K.T.; Lee, J.E.; Kwark, H.S. [Seoul National Univ. (Korea, Republic of)

    1994-12-31

    The amount of energy consumption in building covers the 30% of the total energy consumption and that of electricity is much the same. Because of the improvement of the living quality, energy consumption in building part is increasing and the rate is much higher than that of other parts. So, KEPCO, one of the major domestic energy suppliers and consumers, needs to develop reliable computerized building energy analysis program and to establish building energy performance standards for the reasonable energy management and the efficient execution of energy budget and the improvement of working condition of the corp`s buildings. So the study aims to the development of computerized building energy analysis program, and the establishment energy budget level and building energy performance standards for the corp`s buildings.

  14. High frequency Analysis of Stream Chemistry to Establish Elemental Cycling Regimes of High latitude Catchments

    Science.gov (United States)

    2017-02-13

    FINAL REPORT High-frequency Analysis of Stream Chemistry to Establish Elemental Cycling Regimes of High-latitude Catchments SERDP Project RC-2507... ORGANIZATION REPORT NUMBER 9. SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S) Strategic Environmental... organic matter. Technical considerations and improvements for implementing instream sensors as part of an environmental monitoring program include

  15. Comparison of semi-automated commercial rep-PCR fingerprinting, spoligotyping, 12-locus MIRU-VNTR typing and single nucleotide polymorphism analysis of the embB gene as molecular typing tools for Mycobacterium bovis.

    Science.gov (United States)

    Armas, Federica; Camperio, Cristina; Coltella, Luana; Selvaggini, Serena; Boniotti, Maria Beatrice; Pacciarini, Maria Lodovica; Di Marco Lo Presti, Vincenzo; Marianelli, Cinzia

    2017-08-04

    Highly discriminatory genotyping strategies are essential in molecular epidemiological studies of tuberculosis. In this study we evaluated, for the first time, the efficacy of the repetitive sequence-based PCR (rep-PCR) DiversiLab Mycobacterium typing kit over spoligotyping, 12-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and embB single nucleotide polymorphism (SNP) analysis for Mycobacterium bovis typing. A total of 49 M. bovis animal isolates were used. DNA was extracted and genomic DNA was amplified using the DiversiLab Mycobacterium typing kit. The amplified fragments were separated and detected using a microfluidics chip with Agilent 2100. The resulting rep-PCR-based DNA fingerprints were uploaded to and analysed using web-based DiversiLab software through Pearson's correlation coefficient. Rep-PCR DiversiLab grouped M. bovis isolates into ten different clusters. Most isolates sharing identical spoligotype, MIRU-VNTR profile or embB gene polymorphism were grouped into different rep-PCR clusters. Rep-PCR DiversiLab displayed greater discriminatory power than spoligotyping and embB SNP analysis but a lower resolution power than the 12-locus MIRU-VNTR analysis. MIRU-VNTR confirmed that it is superior to the other PCR-based methods tested here. In combination with spoligotyping and 12-locus MIRU-VNTR analysis, rep-PCR improved the discriminatory power for M. bovis typing.

  16. Mycobacterium franklinii sp. nov., a species closely related to members of the Mycobacterium chelonae-Mycobacterium abscessus group.

    Science.gov (United States)

    Lourenço Nogueira, Christiane; Simmon, Keith E; Chimara, Erica; Cnockaert, Margo; Carlos Palomino, Juan; Martin, Anandi; Vandamme, Peter; Brown-Elliott, Barbara A; Wallace, Richard; Cardoso Leão, Sylvia

    2015-07-01

    Two isolates from water, D16Q19 and D16R27, were shown to be highly similar in their 16S rRNA, 16S-23S internal transcribed spacer (ITS), hsp65 and rpoB gene sequences to 'Mycobacterium franklinii' DSM 45524, described in 2011 but with the name not validly published. They are all nonpigmented rapid growers and are related phenotypically and genetically to the Mycobacterium chelonae-Mycobacterium abscessus group. Extensive characterization by phenotypic analysis, biochemical tests, drug susceptibility testing, PCR restriction enzyme analysis of the hsp65 gene and ITS, DNA sequencing of housekeeping genes and DNA-DNA hybridization demonstrated that 'M. franklinii' DSM 45524, D16Q19 and D16R27 belong to a single species that is separated from other members of the M. chelonae-M. abscessus group. On the basis of these results we propose the formal recognition of Mycobacterium franklinii sp. nov. Strain DSM 45524(T) ( = ATCC BAA-2149(T)) is the type strain.

  17. Mycobacterium talmoniae sp. nov., a slowly growing mycobacterium isolated from human respiratory samples.

    Science.gov (United States)

    Davidson, Rebecca M; DeGroote, Mary Ann; Marola, Jamie L; Buss, Sarah; Jones, Victoria; McNeil, Michael R; Freifeld, Alison G; Elaine Epperson, L; Hasan, Nabeeh A; Jackson, Mary; Iwen, Peter C; Salfinger, Max; Strong, Michael

    2017-08-01

    A novel slowly growing, non-chromogenic species of the class Actinobacteria was isolated from a human respiratory sample in Nebraska, USA, in 2012. Analysis of the internal transcribed spacer sequence supported placement into the genus Mycobacterium with high sequence similarity to a previously undescribed strain isolated from a patient respiratory sample from Oregon, USA, held in a collection in Colorado, USA, in 2000. The two isolates were subjected to phenotypic testing and whole genome sequencing and found to be indistinguishable. The bacteria were acid-fast stain-positive, rod-shaped and exhibited growth after 7-10 days on solid media at temperatures ranging from 25 to 42°C. Colonies were non-pigmented, rough and slightly raised. Analyses of matrix-assisted laser desorption ionization time-of-flight profiles showed no matches against a reference library of 130 mycobacterial species. Full-length 16S rRNA gene sequences were identical for the two isolates, the average nucleotide identity (ANI) between their genomes was 99.7 % and phylogenetic comparisons classified the novel mycobacteria as the basal most species in the slowly growing Mycobacterium clade. Mycobacterium avium is the most closely related species based on rpoB gene sequence similarity (92 %), but the ANI between the genomes was 81.5 %, below the suggested cut-off for differentiating two species (95 %). Mycolic acid profiles were more similar to M. avium than to Mycobacterium simiae or Mycobacterium abscessus. The phenotypic and genomic data support the conclusion that the two related isolates represent a novel Mycobacterium species for which the name Mycobacterium talmoniae sp. nov. is proposed. The type strain is NE-TNMC-100812T (=ATCC BAA-2683T=DSM 46873T).

  18. Animal-adapted members of the Mycobacterium tuberculosis complex endemic to the southern African subregion

    Directory of Open Access Journals (Sweden)

    Charlene Clarke

    2016-02-01

    Full Text Available Members of the Mycobacterium tuberculosis complex (MTC cause tuberculosis (TB in both animals and humans. In this article, three animal-adapted MTC strains that are endemic to the southern African subregion – that is, Mycobacterium suricattae, Mycobacterium mungi, and the dassie bacillus – are reviewed with a focus on clinical and pathological presentations, geographic distribution, genotyping methods, diagnostic tools and evolution. Moreover, factors influencing the transmission and establishment of TB pathogens in novel host populations, including ecological, immunological and genetic factors of both the host and pathogen, are discussed. The risks associated with these infections are currently unknown and further studies will be required for greater understanding of this disease in the context of the southern African ecosystem.Keywords: dassie bacillus; ecology; evolution; host jump; Mycobacterium mungi; Mycobacterium suricattae; Mycobacterium tuberculosis complex; phylogeny

  19. Antipyretic therapy in critically ill patients with established sepsis: a trial sequential analysis.

    Directory of Open Access Journals (Sweden)

    Zhongheng Zhang

    Full Text Available antipyretic therapy for patients with sepsis has long been debated. The present study aimed to explore the beneficial effect of antipyretic therapy for ICU patients with sepsis.systematic review and trial sequential analysis of randomized controlled trials.Pubmed, Scopus, EBSCO and EMBASE were searched from inception to August 5, 2014.Mortality was dichotomized as binary outcome variable and odds ratio (OR was chosen to be the summary statistic. Pooled OR was calculated by using DerSimonian and Laird method. Statistical heterogeneity was assessed by using the statistic I2. Trial sequential analysis was performed to account for the small number of trials and patients.A total of 6 randomized controlled trials including 819 patients were included into final analysis. Overall, there was no beneficial effect of antipyretic therapy on mortality risk in patients with established sepsis (OR: 1.02, 95% CI: 0.50-2.05. The required information size (IS was 2582 and our analysis has not yet reached half of the IS. The Z-curve did not cross the O'Brien-Fleming α-spending boundary or reach the futility, indicating that the non-significant result was probably due to lack of statistical power.our study fails to identify any beneficial effect of antipyretic therapy on ICU patients with established diagnosis of sepsis. Due to limited number of total participants, more studies are needed to make a conclusive and reliable analysis.

  20. DETECÇÃO DO COMPLEXO Mycobacterium tuberculosis NO LEITE PELA REAÇÃO EM CADEIA DA POLIMERASE SEGUIDA DE ANÁLISE DE RESTRIÇÃO DO FRAGMENTO AMPLIFICADO (PRA DETECTION OF Mycobacterium tuberculosis COMPLEX BY PCR-RESTRICTION FRAGMENT LENGTH POLYMORFISM ANALYSIS OF THE HSP65 GENE

    Directory of Open Access Journals (Sweden)

    Joab Trajano Silva

    2008-12-01

    , up to species level, is time consuming and difficult. In this work, the objective was to standardize a polymerase chain reaction followed by an enzyme restriction analysis in order to identify the M. tuberculosis complex in milk, without a microbiological isolation step. Reference strains and raw milk seeded with M. Bovis, were used as the starting material.  A 441pb fragment of the hsp65 gene was amplified and digested by two restriction enzymes BstEII and HaeIII. The obtained profile was used to identify the M. tuberculosis complex in milk. The minimum limit of detection of M. bovis in milk was 10CFU/mL. PRA methodology proved to be a specific and sensible method. It can be used to assist the microbiological and biochemical methods commonly used to identifying the bacilli in clinical samples, as milk 

    Key word: Detection limit (PRA, Mycobacterium tuberculosis complex, milk Mycobacterium bovis, Restriction Enzyme Analysis (PCR,

  1. Molecular typing of Mycobacterium tuberculosis by mycobacterial interspersed repetitive unit-variable-number tandem repeat analysis, a more accurate method for identifying epidemiological links between patients with tuberculosis

    NARCIS (Netherlands)

    van Deutekom, Henk; Supply, Philip; de Haas, Petra E. W.; Willery, Eve; Hoijng, Susan P.; Locht, Camille; Coutinho, Roel A.; van Soolingen, Dick

    2005-01-01

    IS6110 fingerprinting of Mycobacterium tuberculosis is the standard identification method in studies on transmission of tuberculosis. However, intensive epidemiological investigation may fail to confirm transmission links between patients clustered by IS6110-restriction fragment length polymorphism

  2. The new phylogenesis of the genus Mycobacterium

    Directory of Open Access Journals (Sweden)

    Enrico Tortoli

    2015-01-01

    Full Text Available Phylogenetic knowledge of the genus Mycobacterium is based on comparative analysis of their genetic sequences. The 16S rRNA has remained for many years the only target of such analyses, but in the last few years, other housekeeping genes have been investigated and the phylogeny based on their concatenated sequences become a standard. It is now clear that the robustness of the phylogenetic analysis is strictly related to the size of the genomic target used. Whole genome sequencing (WGS is nowadays becoming widely accessible and comparatively cheap. It was decided, therefore, to use this approach to reconstruct the ultimate phylogeny of the genus Mycobacterium. Over 50 types of strains of the same number of species of Mycobacterium were sequenced using the Illumina HiSeq platform. The majority of the strains of which the whole sequence was already available in GenBank were excluded from this panel with the aim of maximizing the number of the species with genome available. Following assembling and annotation with proper software, the phylogenetic analysis was conducted with PhyloPhlAn and the pan-genome analysis pipeline. The phylogenetic three which emerged was characterized by a clear-cut distinction of slowly and rapidly growing species with the latter being more ancestral. The species of the Mycobacterium terrae complex occupied an intermediate position between rapid and slow growers. Most of the species revealed clearly related and occupied specific phylogenetic branches. Thanks to the WGS technology, the genus Mycobacterium is finally approaching its definitive location.

  3. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of bacterioferritin A from Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, Vibha [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India); Gupta, Rakesh K. [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India); Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi 110021 (India); Khare, Garima [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India); Salunke, Dinakar M. [National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 (India); Tyagi, Anil K., E-mail: aniltyagi@south.du.ac.in [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India)

    2008-05-01

    The cloning, purification and crystallization of a bacterioferritin from M. tuberculosis together with preliminary X-ray characterization of its crystals are reported. Bacterioferritins (Bfrs) comprise a subfamily of the ferritin superfamily of proteins that play an important role in bacterial iron storage and homeostasis. Bacterioferritins differ from ferritins in that they have additional noncovalently bound haem groups. To assess the physiological role of this subfamily of ferritins, a greater understanding of the structural details of bacterioferritins from various sources is required. The gene encoding bacterioferritin A (BfrA) from Mycobacterium tuberculosis was cloned and expressed in Escherichia coli. The recombinant protein product was purified by affinity chromatography on a Strep-Tactin column and crystallized with sodium chloride as a precipitant at pH 8.0 using the vapour-diffusion technique. The crystals diffracted to 2.1 Å resolution and belonged to space group P4{sub 2}, with unit-cell parameters a = 123.0, b = 123.0, c = 174.6 Å.

  4. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of bacterioferritin A from Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Gupta, Vibha; Gupta, Rakesh K.; Khare, Garima; Salunke, Dinakar M.; Tyagi, Anil K.

    2008-01-01

    The cloning, purification and crystallization of a bacterioferritin from M. tuberculosis together with preliminary X-ray characterization of its crystals are reported. Bacterioferritins (Bfrs) comprise a subfamily of the ferritin superfamily of proteins that play an important role in bacterial iron storage and homeostasis. Bacterioferritins differ from ferritins in that they have additional noncovalently bound haem groups. To assess the physiological role of this subfamily of ferritins, a greater understanding of the structural details of bacterioferritins from various sources is required. The gene encoding bacterioferritin A (BfrA) from Mycobacterium tuberculosis was cloned and expressed in Escherichia coli. The recombinant protein product was purified by affinity chromatography on a Strep-Tactin column and crystallized with sodium chloride as a precipitant at pH 8.0 using the vapour-diffusion technique. The crystals diffracted to 2.1 Å resolution and belonged to space group P4 2 , with unit-cell parameters a = 123.0, b = 123.0, c = 174.6 Å

  5. Identification of Mycobacterium bovis antigens by analysis of bovine T-cell responses after infection with a virulent strain

    Directory of Open Access Journals (Sweden)

    Alito A.

    2003-01-01

    Full Text Available Purification and characterization of individual antigenic proteins are essential for the understanding of the pathogenic mechanisms of mycobacteria and the immune response against them. In the present study, we used anion-exchange chromatography to fractionate cell extracts and culture supernatant proteins from Mycobacterium bovis to identify T-cell-stimulating antigens. These fractions were incubated with peripheral blood mononuclear cells (PBMC from M. bovis-infected cattle in lymphoproliferation assays. This procedure does not denature proteins and permits the testing of mixtures of potential antigens that could be later identified. We characterized protein fractions with high stimulation indices from both culture supernatants and cell extracts. Proteins were identified by two-dimensional gel electrophoresis followed by N-terminal sequencing or MALDI-TOF. Culture supernatant fractions containing low molecular weight proteins such as ESAT6 and CFP10 and other proteins (85B, MPB70, and the novel antigens TPX and TRB-B were associated with a high stimulation index. These results reinforce the concept that some low molecular weight proteins such as ESAT6 and CFP10 play an important role in immune responses. Also, Rv3747 and L7/L12 were identified in high stimulation index cell extract fractions. These data show that protein fractions with high lymphoproliferative activity for bovine PBMC can be characterized and antigens which have been already described and new protein antigens can also be identified in these fractions.

  6. Crystallization and preliminary X-ray diffraction analysis of prephenate dehydratase from Mycobacterium tuberculosis H37Rv

    Energy Technology Data Exchange (ETDEWEB)

    Vivan, Ana Luiza [Programa de Pós Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS (Brazil); Centro de Pesquisa em Biologia Molecular e Funcional, Instituto de Pesquisas Biomédicas, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Av. Ipiranga, 6681 Prédio 92A-TECNOPUC-Partenon, CEP 90619-900, Porto Alegre, RS (Brazil); Dias, Márcio Vinícius Bertacini [Programa de Pós Graduação em Biofísica Molecular, Departamento de Física, IBILCE/UNESP, São José do Rio Preto, SP, 15054-000 (Brazil); Schneider, Cristopher Z. [Programa de Pós Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS (Brazil); Centro de Pesquisa em Biologia Molecular e Funcional, Instituto de Pesquisas Biomédicas, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Av. Ipiranga, 6681 Prédio 92A-TECNOPUC-Partenon, CEP 90619-900, Porto Alegre, RS (Brazil); Azevedo, Walter Filgueira Jr de; Basso, Luiz Augusto, E-mail: luiz.basso@pucrs.br; Santos, Diógenes Santiago, E-mail: luiz.basso@pucrs.br [Centro de Pesquisa em Biologia Molecular e Funcional, Instituto de Pesquisas Biomédicas, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Av. Ipiranga, 6681 Prédio 92A-TECNOPUC-Partenon, CEP 90619-900, Porto Alegre, RS (Brazil); Programa de Pós Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS (Brazil)

    2006-04-01

    The M. tuberculosis prephenate dehydratase was cloned, expressed, purified, crystallized by the hanging-drop vapour-diffusion method, and a complete data set collected to 3.2 Å resolution using synchrotron radiation. These results should pave the way for the three-dimensional structure determination of the enzyme and provide a framework on which to base the rational design of chemotherapeutic agents to treat tuberculosis. Tuberculosis remains the leading cause of mortality arising from a bacterial pathogen (Mycobacterium tuberculosis). There is an urgent need for the development of new antimycobacterial agents. The aromatic amino-acid pathway is essential for the survival of this pathogen and represents a target for structure-based drug design. Accordingly, the M. tuberculosis prephenate dehydratase has been cloned, expressed, purified and crystallized by the hanging-drop vapour-diffusion method using PEG 400 as a precipitant. The crystal belongs to the orthorhombic space group I222 or I2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 98.26, b = 133.22, c = 225.01 Å, and contains four molecules in the asymmetric unit. A complete data set was collected to 3.2 Å resolution using a synchrotron-radiation source.

  7. Crystallization and preliminary X-ray diffraction analysis of prephenate dehydratase from Mycobacterium tuberculosis H37Rv

    International Nuclear Information System (INIS)

    Vivan, Ana Luiza; Dias, Márcio Vinícius Bertacini; Schneider, Cristopher Z.; Azevedo, Walter Filgueira Jr de; Basso, Luiz Augusto; Santos, Diógenes Santiago

    2006-01-01

    The M. tuberculosis prephenate dehydratase was cloned, expressed, purified, crystallized by the hanging-drop vapour-diffusion method, and a complete data set collected to 3.2 Å resolution using synchrotron radiation. These results should pave the way for the three-dimensional structure determination of the enzyme and provide a framework on which to base the rational design of chemotherapeutic agents to treat tuberculosis. Tuberculosis remains the leading cause of mortality arising from a bacterial pathogen (Mycobacterium tuberculosis). There is an urgent need for the development of new antimycobacterial agents. The aromatic amino-acid pathway is essential for the survival of this pathogen and represents a target for structure-based drug design. Accordingly, the M. tuberculosis prephenate dehydratase has been cloned, expressed, purified and crystallized by the hanging-drop vapour-diffusion method using PEG 400 as a precipitant. The crystal belongs to the orthorhombic space group I222 or I2 1 2 1 2 1 , with unit-cell parameters a = 98.26, b = 133.22, c = 225.01 Å, and contains four molecules in the asymmetric unit. A complete data set was collected to 3.2 Å resolution using a synchrotron-radiation source

  8. Can 15-Locus Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Analysis Provide Insight into the Evolution of Mycobacterium tuberculosis?

    OpenAIRE

    Gibson, Andrea; Brown, Timothy; Baker, Lucy; Drobniewski, Francis

    2005-01-01

    The phylogeny and evolution of the bacterium Mycobacterium tuberculosis is still poorly understood despite the application of a variety of molecular techniques. We analyzed 469 M. tuberculosis and 49 Mycobacterium bovis isolates to evaluate if the mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR) commonly used for epidemiological studies can define the phylogeny of the M. tuberculosis complex. This population was characterized by previously identified sile...

  9. Large sample neutron activation analysis: establishment at CDTN/CNEN, Brazil

    International Nuclear Information System (INIS)

    Menezes, Maria Angela de B.C.; Jacimovic, Radojko

    2011-01-01

    In order to improve the application of the neutron activation technique at CDTN/CNEN, the large sample instrumental neutron activation analysis is being established, IAEA BRA 14798 and FAPEMIG APQ-01259-09 projects. This procedure, LS-INAA, usually requires special facilities for the activation as well as for the detection. However, the TRIGA Mark I IPR R1, CDTN/CNEN has not been adapted for the irradiation and the usual gamma spectrometry has being carried out. To start the establishment of the LS-INAA, a 5g sample - IAEA/Soil 7 reference material was analyzed by k 0 -standardized method. This paper is about the detector efficiency over the volume source using KayWin v2.23 and ANGLE V3.0 software. (author)

  10. Large sample neutron activation analysis: establishment at CDTN/CNEN, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Menezes, Maria Angela de B.C., E-mail: menezes@cdtn.b [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil); Jacimovic, Radojko, E-mail: radojko.jacimovic@ijs.s [Jozef Stefan Institute, Ljubljana (Slovenia). Dept. of Environmental Sciences. Group for Radiochemistry and Radioecology

    2011-07-01

    In order to improve the application of the neutron activation technique at CDTN/CNEN, the large sample instrumental neutron activation analysis is being established, IAEA BRA 14798 and FAPEMIG APQ-01259-09 projects. This procedure, LS-INAA, usually requires special facilities for the activation as well as for the detection. However, the TRIGA Mark I IPR R1, CDTN/CNEN has not been adapted for the irradiation and the usual gamma spectrometry has being carried out. To start the establishment of the LS-INAA, a 5g sample - IAEA/Soil 7 reference material was analyzed by k{sub 0}-standardized method. This paper is about the detector efficiency over the volume source using KayWin v2.23 and ANGLE V3.0 software. (author)

  11. hsp65 PCR-restriction analysis (PRA) with capillary electrophoresis in comparison to three other methods for identification of Mycobacterium species.

    Science.gov (United States)

    Sajduda, Anna; Martin, Anandi; Portaels, Françoise; Palomino, Juan Carlos

    2010-02-01

    We developed a scheme for rapid identification of Mycobacterium species using an automated fluorescence capillary electrophoresis instrument. A 441-bp region of the hsp65 gene was examined using PCR-restriction analysis (PRA). The assay was initially evaluated on 38 reference strains. The observed sizes of restriction fragments were consistently smaller than the real sizes for each of the species as deduced from the sequence analysis (mean variance=7bp). Nevertheless, the obtained PRA patterns were highly reproducible and resulted in correct species identifications. A blind test was then successfully performed on 64 test isolates previously characterized by conventional biochemical methods, a commercial INNO-LiPA Mycobacteria assay and/or sequence determination of the 5' end of 16S rRNA gene. A total of 14 of 64 isolates were erroneously identified by conventional methods (78% accuracy). In contrast, PRA performed very well in comparison with the LiPA (89% concordance) and especially with DNA sequencing (93.3% of concordant results). Also, PRA identified seven isolates representing five previously unreported hsp65 alleles. We conclude that hsp65 PRA based on automated capillary electrophoresis is a rapid, simple and reliable method for identification of mycobacteria. Copyright 2010 Elsevier B.V. All rights reserved.

  12. Mycobacterium ulcerans infection

    NARCIS (Netherlands)

    van der Werf, TS; van der Graaf, WTA; Tappero, JW; Asiedu, K

    1999-01-01

    After tuberculosis and leprosy, Buruli-ulcer disease (caused by infection with Mycobacterium ulcerans) is the third most common mycobacterial disease in immunocompetent people. Countries in which the disease is endemic have been identified, predominantly in areas of tropical rain forest; the

  13. Bacteriological and virulence study of a Mycobacterium chimaera isolate from a patient in China.

    Science.gov (United States)

    Liu, Guan; Chen, Su-Ting; Yu, Xia; Li, Yu-Xun; Ling, Ying; Dong, Ling-Ling; Zheng, Su-Hua; Huang, Hai-Rong

    2015-04-01

    A clinical isolate from a patient was identified as Mycobacterium chimaera, a recently identified species of nontuberculous Mycobacteria. The biochemical and molecular identity, drug sensitivity and virulence of this isolated strain were investigated. 16S rRNA, the 16S-23S ITS, hsp65 and rpoB were amplified, and their sequence similarities with other mycobacteria were analyzed. The minimum inhibitory concentrations of 22 anti-microbial agents against this isolate were established, and the virulence of the isolate was evaluated by intravenous injection into C57BL/6 mice using Mycobacterium tuberculosis H37Rv as a control strain. Growth and morphological characteristics and mycolic acid profile analysis revealed that this isolated strain was a member of the Mycobacterium avium complex. BLAST analysis of the amplified sequences showed that the isolated strain was closely related to M. chimaera. Susceptibility testing showed that the isolate was sensitive to rifabutin, rifapentine, clarithromycin, azithromycin, imipenem and cefoxitin. Bacterial load determination and tissue histopathology of the infected mice indicated that the isolate was highly virulent. The first case of M. chimaera infection in China was evaluated. The information derived from this case may offer valuable guidance for clinical diagnosis and treatment.

  14. Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis

    Science.gov (United States)

    Reynaud, Yann; Zheng, Chao; Wu, Guihui; Sun, Qun; Rastogi, Nalin

    2017-01-01

    Mycobacterium tuberculosis genetic structure, and evolutionary history have been studied for years by several genotyping approaches, but delineation of a few sublineages remains controversial and needs better characterization. This is particularly the case of T group within lineage 4 (L4) which was first described using spoligotyping to pool together a number of strains with ill-defined signatures. Although T strains were not traditionally considered as a real phylogenetic group, they did contain a few phylogenetically meaningful sublineages as shown using SNPs. We therefore decided to investigate if this observation could be corroborated using other robust genetic markers. We consequently made a first assessment of genetic structure using 24-loci MIRU-VNTRs data extracted from the SITVIT2 database (n = 607 clinical isolates collected in Russia, Albania, Turkey, Iraq, Brazil and China). Combining Minimum Spanning Trees and Bayesian population structure analyses (using STRUCTURE and TESS softwares), we distinctly identified eight tentative phylogenetic groups (T1-T8) with a remarkable correlation with geographical origin. We further compared the present structure observed with other L4 sublineages (n = 416 clinical isolates belonging to LAM, Haarlem, X, S sublineages), and showed that 5 out of 8 T groups seemed phylogeographically well-defined as opposed to the remaining 3 groups that partially mixed with other L4 isolates. These results provide with novel evidence about phylogeographically specificity of a proportion of ill-defined T group of M. tuberculosis. The genetic structure observed will now be further validated on an enlarged worldwide dataset using Whole Genome Sequencing (WGS). PMID:28166309

  15. Proteomic Analysis of the Action of the Mycobacterium ulcerans Toxin Mycolactone: Targeting Host Cells Cytoskeleton and Collagen

    Science.gov (United States)

    Gama, José B.; Ohlmeier, Steffen; Martins, Teresa G.; Fraga, Alexandra G.; Sampaio-Marques, Belém; Carvalho, Maria A.; Proença, Fernanda; Silva, Manuel T.; Pedrosa, Jorge; Ludovico, Paula

    2014-01-01

    Buruli ulcer (BU) is a neglected tropical disease caused by Mycobacterium ulcerans. The tissue damage characteristic of BU lesions is known to be driven by the secretion of the potent lipidic exotoxin mycolactone. However, the molecular action of mycolactone on host cell biology mediating cytopathogenesis is not fully understood. Here we applied two-dimensional electrophoresis (2-DE) to identify the mechanisms of mycolactone's cellular action in the L929 mouse fibroblast proteome. This revealed 20 changed spots corresponding to 18 proteins which were clustered mainly into cytoskeleton-related proteins (Dync1i2, Cfl1, Crmp2, Actg1, Stmn1) and collagen biosynthesis enzymes (Plod1, Plod3, P4ha1). In line with cytoskeleton conformational disarrangements that are observed by immunofluorescence, we found several regulators and constituents of both actin- and tubulin-cytoskeleton affected upon exposure to the toxin, providing a novel molecular basis for the effect of mycolactone. Consistent with these cytoskeleton-related alterations, accumulation of autophagosomes as well as an increased protein ubiquitination were observed in mycolactone-treated cells. In vivo analyses in a BU mouse model revealed mycolactone-dependent structural changes in collagen upon infection with M. ulcerans, associated with the reduction of dermal collagen content, which is in line with our proteomic finding of mycolactone-induced down-regulation of several collagen biosynthesis enzymes. Our results unveil the mechanisms of mycolactone-induced molecular cytopathogenesis on exposed host cells, with the toxin compromising cell structure and homeostasis by inducing cytoskeleton alterations, as well as disrupting tissue structure, by impairing the extracellular matrix biosynthesis. PMID:25101965

  16. Proteomic analysis of the action of the Mycobacterium ulcerans toxin mycolactone: targeting host cells cytoskeleton and collagen.

    Science.gov (United States)

    Gama, José B; Ohlmeier, Steffen; Martins, Teresa G; Fraga, Alexandra G; Sampaio-Marques, Belém; Carvalho, Maria A; Proença, Fernanda; Silva, Manuel T; Pedrosa, Jorge; Ludovico, Paula

    2014-08-01

    Buruli ulcer (BU) is a neglected tropical disease caused by Mycobacterium ulcerans. The tissue damage characteristic of BU lesions is known to be driven by the secretion of the potent lipidic exotoxin mycolactone. However, the molecular action of mycolactone on host cell biology mediating cytopathogenesis is not fully understood. Here we applied two-dimensional electrophoresis (2-DE) to identify the mechanisms of mycolactone's cellular action in the L929 mouse fibroblast proteome. This revealed 20 changed spots corresponding to 18 proteins which were clustered mainly into cytoskeleton-related proteins (Dync1i2, Cfl1, Crmp2, Actg1, Stmn1) and collagen biosynthesis enzymes (Plod1, Plod3, P4ha1). In line with cytoskeleton conformational disarrangements that are observed by immunofluorescence, we found several regulators and constituents of both actin- and tubulin-cytoskeleton affected upon exposure to the toxin, providing a novel molecular basis for the effect of mycolactone. Consistent with these cytoskeleton-related alterations, accumulation of autophagosomes as well as an increased protein ubiquitination were observed in mycolactone-treated cells. In vivo analyses in a BU mouse model revealed mycolactone-dependent structural changes in collagen upon infection with M. ulcerans, associated with the reduction of dermal collagen content, which is in line with our proteomic finding of mycolactone-induced down-regulation of several collagen biosynthesis enzymes. Our results unveil the mechanisms of mycolactone-induced molecular cytopathogenesis on exposed host cells, with the toxin compromising cell structure and homeostasis by inducing cytoskeleton alterations, as well as disrupting tissue structure, by impairing the extracellular matrix biosynthesis.

  17. Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Yann Reynaud

    Full Text Available Mycobacterium tuberculosis genetic structure, and evolutionary history have been studied for years by several genotyping approaches, but delineation of a few sublineages remains controversial and needs better characterization. This is particularly the case of T group within lineage 4 (L4 which was first described using spoligotyping to pool together a number of strains with ill-defined signatures. Although T strains were not traditionally considered as a real phylogenetic group, they did contain a few phylogenetically meaningful sublineages as shown using SNPs. We therefore decided to investigate if this observation could be corroborated using other robust genetic markers. We consequently made a first assessment of genetic structure using 24-loci MIRU-VNTRs data extracted from the SITVIT2 database (n = 607 clinical isolates collected in Russia, Albania, Turkey, Iraq, Brazil and China. Combining Minimum Spanning Trees and Bayesian population structure analyses (using STRUCTURE and TESS softwares, we distinctly identified eight tentative phylogenetic groups (T1-T8 with a remarkable correlation with geographical origin. We further compared the present structure observed with other L4 sublineages (n = 416 clinical isolates belonging to LAM, Haarlem, X, S sublineages, and showed that 5 out of 8 T groups seemed phylogeographically well-defined as opposed to the remaining 3 groups that partially mixed with other L4 isolates. These results provide with novel evidence about phylogeographically specificity of a proportion of ill-defined T group of M. tuberculosis. The genetic structure observed will now be further validated on an enlarged worldwide dataset using Whole Genome Sequencing (WGS.

  18. Content analysis of homeless smokers' perspectives on established and alternative smoking interventions.

    Science.gov (United States)

    Collins, Susan E; Orfaly, Victoria E; Wu, Teresa; Chang, Sunny; Hardy, Robert V; Nash, Amia; Jones, Matthew B; Mares, Leslie; Taylor, Emily M; Nelson, Lonnie A; Clifasefi, Seema L

    2018-01-01

    Cigarette smoking is 5 times more prevalent among homeless individuals than in the general population, and homeless individuals are disproportionately affected by smoking-related morbidity and mortality. Homeless smokers report interest in changing their smoking behavior; however, established smoking cessation interventions are neither desirable to nor highly effective for most members of this population. The aim of this study was to document homeless smokers' perceptions of established smoking interventions as well as self-generated, alternative smoking interventions to elucidate points for intervention enhancement. Participants (N=25) were homeless smokers who responded to semistructured interviews regarding smoking and nicotine use as well as experiences with established and alternative smoking interventions. Conventional content analysis was used to organize data and identify themes. Participants appreciated providers' initiation of conversations about smoking. They did not, however, feel simple advice to quit was a helpful approach. Instead, they suggested providers use a nonjudgmental, compassionate style, offer more support, and discuss a broader menu of options, including nonabstinence-based ways to reduce smoking-related harm and improve health-related quality of life. Most participants preferred engaging in their own self-defined, alternative smoking interventions, including obtaining nicotine more safely (e.g., vaping, using smokeless tobacco) and using behavioral (e.g., engaging in creative activities and hobbies) and cognitive strategies (e.g., reminding themselves about the positive aspects of not smoking and the negative consequences of smoking). Abrupt, unaided quit attempts were largely unsuccessful. The vast majority of participants with the lived experience of homelessness and smoking were uninterested in established smoking cessation approaches. They did, however, have creative ideas about alternative smoking interventions that providers may

  19. Analysis of DNA relaxation and cleavage activities of recombinant Mycobacterium tuberculosis DNA topoisomerase I from a new expression and purification protocol

    Directory of Open Access Journals (Sweden)

    Annamalai Thirunavukkarasu

    2009-06-01

    Full Text Available Abstract Background Mycobacterium tuberculosis DNA topoisomerase I is an attractive target for discovery of novel TB drugs that act by enhancing the accumulation of the topoisomerase-DNA cleavage product. It shares a common transesterification domain with other type IA DNA topoisomerases. There is, however, no homology between the C-terminal DNA binding domains of Escherichia coli and M. tuberculosis DNA topoisomerase I proteins. Results A new protocol for expression and purification of recombinant M. tuberculosis DNA topoisomerase I (MtTOP has been developed to produce enzyme of much higher specific activity than previously characterized recombinant enzyme. MtTOP was found to be less efficient than E. coli DNA topoisomerase I (EcTOP in removal of remaining negative supercoils from partially relaxed DNA. DNA cleavage by MtTOP was characterized for the first time. Comparison of DNA cleavage site selectivity with EcTOP showed differences in cleavage site preferences, but the preferred sites of both enzymes have a C nucleotide in the -4 position. Conclusion Recombinant M. tuberculosis DNA topoisomerase I can be expressed as a soluble protein and purified in high yield from E. coli host with a new protocol. Analysis of DNA cleavage with M. tuberculosis DNA substrate showed that the preferred DNA cleavage sites have a C nucleotide in the -4 position.

  20. Identification of Two Novel Mycobacterium avium Allelic Variants in Pig and Human Isolates from Brazil by PCR-Restriction Enzyme Analysis

    Science.gov (United States)

    Leão, Sylvia Cardoso; Briones, Marcelo R. S.; Sircili, Marcelo Palma; Balian, Simone Carvalho; Mores, Nelson; Ferreira-Neto, José Soares

    1999-01-01

    Mycobacterium avium complex (MAC) is composed of environmental mycobacteria found widely in soil, water, and aerosols that can cause disease in animals and humans, especially disseminated infections in AIDS patients. MAC consists of two closely related species, M. avium and M. intracellulare, and may also include other, less-defined groups. The precise differentiation of MAC species is a fundamental step in epidemiological studies and for the evaluation of possible reservoirs for MAC infection in humans and animals. In this study, which included 111 pig and 26 clinical MAC isolates, two novel allelic M. avium PCR-restriction enzyme analysis (PRA) variants were identified, differing from the M. avium PRA prototype in the HaeIII digestion pattern. Mutations in HaeIII sites were confirmed by DNA sequencing. Identification of these isolates as M. avium was confirmed by PCR with DT1-DT6 and IS1245 primers, nucleic acid hybridization with the AccuProbe system, 16S ribosomal DNA sequencing, and biochemical tests. The characterization of M. avium PRA variants can be useful in the elucidation of factors involved in mycobacterial virulence and routes of infection and also has diagnostic significance, since they can be misidentified as M. simiae II and M. kansasii I if the PRA method is used in the clinical laboratory for identification of mycobacteria. PMID:10405407

  1. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of succinyl-diaminopimelate desuccinylase (Rv1202, DapE) from Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Reinhard, Linda; Mueller-Dieckmann, Jochen; Weiss, Manfred S.

    2012-01-01

    M. tuberculosis succinyl-diaminopimelate desuccinylase, the enzyme which catalyzes the seventh step of the lysine-biosynthesis pathway, has been cloned, expressed, purified and crystallized. Preliminary X-ray diffraction analysis indicated the presence of pseudo-merohedral twinning in space group P2 1 , resulting in possible emulation of space group C222 1 . Succinyl-diaminopimelate desuccinylase from Mycobacterium tuberculosis (DapE, Rv1202) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Diffraction-quality crystals were obtained at acidic pH from ammonium sulfate and PEG and diffraction data were collected from two crystals to resolutions of 2.40 and 2.58 Å, respectively. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 79.7, b = 76.0, c = 82.9 Å, β = 119°. The most probable content of the asymmetric unit was two molecules of DapE, which would correspond to a solvent content of 56%. Both examined crystals turned out to be pseudo-merohedrally twinned, with twin operator −h, −k, h + l and twin fractions of approximately 0.46 and 0.16, respectively

  2. Analysis of the Phenotype of Mycobacterium tuberculosis-Specific CD4+ T Cells to Discriminate Latent from Active Tuberculosis in HIV-Uninfected and HIV-Infected Individuals

    Directory of Open Access Journals (Sweden)

    Catherine Riou

    2017-08-01

    Full Text Available Several immune-based assays have been suggested to differentiate latent from active tuberculosis (TB. However, their relative performance as well as their efficacy in HIV-infected persons, a highly at-risk population, remains unclear. In a study of 81 individuals, divided into four groups based on their HIV-1 status and TB disease activity, we compared the differentiation (CD27 and KLRG1, activation (HLA-DR, homing potential (CCR4, CCR6, CXCR3, and CD161 and functional profiles (IFNγ, IL-2, and TNFα of Mycobacterium tuberculosis (Mtb-specific CD4+ T cells using flow cytometry. Active TB disease induced major changes within the Mtb-responding CD4+ T cell population, promoting memory maturation, elevated activation and increased inflammatory potential when compared to individuals with latent TB infection. Moreover, the functional profile of Mtb-specific CD4+ T cells appeared to be inherently related to their degree of differentiation. While these specific cell features were all capable of discriminating latent from active TB, irrespective of HIV status, HLA-DR expression showed the best performance for TB diagnosis [area-under-the-curve (AUC = 0.92, 95% CI: 0.82–1.01, specificity: 82%, sensitivity: 84% for HIV− and AUC = 0.99, 95% CI: 0.98–1.01, specificity: 94%, sensitivity: 93% for HIV+]. In conclusion, these data support the idea that analysis of T cell phenotype can be diagnostically useful in TB.

  3. Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis.

    Science.gov (United States)

    Bakuła, Zofia; Brzostek, Anna; Borówka, Paulina; Żaczek, Anna; Szulc-Kiełbik, Izabela; Podpora, Agata; Parniewski, Paweł; Strapagiel, Dominik; Dziadek, Jarosław; Proboszcz, Małgorzata; Bielecki, Jacek; van Ingen, Jakko; Jagielski, Tomasz

    2018-03-13

    Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M. kansasii strains representing six subtypes (I-VI). The results of VNTR typing were compared with those of pulsed-field gel electrophoresis (PFGE) with AsnI digestion. Six VNTRs i.e. (VNTR 1, 2, 8, 14, 20 and 23) allow to differentiate analyzed strains with the same discriminatory capacities as use of a 17-loci panel. VNTR typing and PFGE in conjunction revealed 45 distinct patterns, including 11 clusters with 33 isolates and 34 unique patterns. The Hunter-Gaston's discriminatory index was 0.95 and 0.66 for PFGE and VNTR typing respectively, and 0.97 for the two methods combined. In conclusion, this study delivers a new typing scheme, based on VNTR polymorphism, and recommends it as a first-line test prior to PFGE analysis in a two-step typing strategy for M. kansasii.

  4. Determination of the antimicrobial susceptibility and molecular profile of clarithromycin resistance in the Mycobacterium abscessus complex in Japan by variable number tandem repeat analysis.

    Science.gov (United States)

    Kusuki, Mari; Osawa, Kayo; Arikawa, Kentaro; Tamura, Miho; Shigemura, Katsumi; Shirakawa, Toshiro; Nakamura, Tatsuya; Nakamachi, Yuji; Fujisawa, Masato; Saegusa, Jun; Tokimatsu, Issei

    2018-02-18

    Mycobacterium abscessus complex, including three subspecies-M. abscessus, M. massiliense, and M. bolletii-is resistant to a variety of antibiotics so limited treatment options are available. The susceptibility of these subspecies to antimicrobial agents depends in particular on the erm(41) sequevar and rrl mutations in the 23S rRNA, which are potentially related to clarithromycin (CLR) resistance. The purpose of this study was to carry out identification and molecular characterization of these subspecies based on variable number of tandem repeats (VNTR) analysis. Twenty-four M. abscessus complex strains were identified as M. abscessus and M. massiliense and these subspecies could be discriminated between based on their resistance to CLR, as determined by truncation or mutation of erm(41) or mutation of rrl, as illustrated by their VNTR patterns. In conclusion, we confirmed that the CLR susceptibility profiles could be differentiated according to the subspecies of M. abscessus complex strains by their VNTR patterns. Copyright © 2018. Published by Elsevier Inc.

  5. Pre-steady-state kinetic analysis of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Mycobacterium tuberculosis reveals partially rate-limiting product release by parallel pathways.

    Science.gov (United States)

    Liu, Juan; Murkin, Andrew S

    2012-07-03

    As part of the non-mevalonate pathway for the biosynthesis of the isoprenoid precursor isopentenyl pyrophosphate, 1-deoxy-D-xylulose-5-phosphate (DXP) reductoisomerase (DXR) catalyzes the conversion of DXP into 2-C-methyl-D-erythritol 4-phosphate (MEP) by consecutive isomerization and NADPH-dependent reduction reactions. Because this pathway is essential to many infectious organisms but is absent in humans, DXR is a target for drug discovery. In an attempt to characterize its kinetic mechanism and identify rate-limiting steps, we present the first complete transient kinetic investigation of DXR. Stopped-flow fluorescence measurements with Mycobacterium tuberculosis DXR (MtDXR) revealed that NADPH and MEP bind to the free enzyme and that the two bind together to generate a nonproductive ternary complex. Unlike the Escherichia coli orthologue, MtDXR exhibited a burst in the oxidation of NADPH during pre-steady-state reactions, indicating a partially rate-limiting step follows chemistry. By monitoring NADPH fluorescence during these experiments, the transient generation of MtDXR·NADPH·MEP was observed. Global kinetic analysis supports a model involving random substrate binding and ordered release of NADP(+) followed by MEP. The partially rate-limiting release of MEP occurs via two pathways--directly from the binary complex and indirectly via the MtDXR·NADPH·MEP complex--the partitioning being dependent on NADPH concentration. Previous mechanistic studies, including kinetic isotope effects and product inhibition, are discussed in light of this kinetic mechanism.

  6. [Etiological analysis and establishment of a discriminant model for lower respiratory tract infections in hospitalized patients].

    Science.gov (United States)

    Chen, Y S; Lin, X H; Li, H R; Hua, Z D; Lin, M Q; Huang, W S; Yu, T; Lyu, H Y; Mao, W P; Liang, Y Q; Peng, X R; Chen, S J; Zheng, H; Lian, S Q; Hu, X L; Yao, X Q

    2017-12-12

    Objective: To analyze the pathogens of lower respiratory tract infection(LRTI) including bacterial, viral and mixed infection, and to establish a discriminant model based on clinical features in order to predict the pathogens. Methods: A total of 243 hospitalized patients with lower respiratory tract infections were enrolled in Fujian Provincial Hospital from April 2012 to September 2015. The clinical data and airway (sputum and/or bronchoalveolar lavage) samples were collected. Microbes were identified by traditional culture (for bacteria), loop-mediated isothermal amplification(LAMP) and gene sequencing (for bacteria and atypical pathogen), or Real-time quantitative polymerase chain reaction (Real-time PCR)for viruses. Finally, a discriminant model was established by using the discriminant analysis methods to help to predict bacterial, viral and mixed infections. Results: Pathogens were detected in 53.9% (131/243) of the 243 cases.Bacteria accounted for 23.5%(57/243, of which 17 cases with the virus, 1 case with Mycoplasma pneumoniae and virus), mainly Pseudomonas Aeruginosa and Klebsiella Pneumonia. Atypical pathogens for 4.9% (12/243, of which 3 cases with the virus, 1 case of bacteria and viruses), all were mycoplasma pneumonia. Viruses for 34.6% (84/243, of which 17 cases of bacteria, 3 cases with Mycoplasma pneumoniae, 1 case with Mycoplasma pneumoniae and bacteria) of the cases, mainly Influenza A virus and Human Cytomegalovirus, and other virus like adenovirus, human parainfluenza virus, respiratory syncytial virus, human metapneumovirus, human boca virus were also detected fewly. Seven parameters including mental status, using antibiotics prior to admission, complications, abnormal breath sounds, neutrophil alkaline phosphatase (NAP) score, pneumonia severity index (PSI) score and CRUB-65 score were enrolled after univariate analysis, and discriminant analysis was used to establish the discriminant model by applying the identified pathogens as the

  7. Establishment of joint application system of safety analysis codes between Korea and Vietnam

    International Nuclear Information System (INIS)

    Chung, Bub Dong; Kim, Kyung Doo; Park, Cheol; Bae, Sung Won; Baek, Won Pil; Song, Cheol hwa; Jeong, Jae Jun; Lee, Seung Wook; Hwang, Moon Kyu; Lee, Chang Sup

    2011-04-01

    The following KAERI-VAEI collaboration works have been performed during the 2 year project ('09.4∼'11.4). 1) On the job training of Vietnam code users(1st training for 4 VAEI staff-3 months. 2nd training for 3 VAEI staff- 3 month), 2) Lecture of nuclear safety analysis (30 hrs basic course and 30 hrs advanced course), 3) Review of safety analysis method (IAEA safety concept and requirements), 4) Collaborative assessment of safety analysis code MARS (13 conceptual problem, 2 separate effect test problem, 1 integral effect test problem), 5) Input deck preparation of standard PWR (Preparation of APR1400 input deck and safety analysis of DBA). VAEI staffs have been familiarized to Korean PWR safety assessment technology through the collaboration assessment work using a computer code developed in Korea. The lectures for Vietnamese research will be contributed to the utilization and cultivation of Korean safety technology. The collaborated assessment works will be used for the establishment of MARS based safety analysis system which is independent from US safety assessment system

  8. Instability risk analysis and risk assessment system establishment of underground storage caverns in bedded salt rock

    Science.gov (United States)

    Jing, Wenjun; Zhao, Yan

    2018-02-01

    Stability is an important part of geotechnical engineering research. The operating experiences of underground storage caverns in salt rock all around the world show that the stability of the caverns is the key problem of safe operation. Currently, the combination of theoretical analysis and numerical simulation are the mainly adopts method of reserve stability analysis. This paper introduces the concept of risk into the stability analysis of underground geotechnical structure, and studies the instability of underground storage cavern in salt rock from the perspective of risk analysis. Firstly, the definition and classification of cavern instability risk is proposed, and the damage mechanism is analyzed from the mechanical angle. Then the main stability evaluating indicators of cavern instability risk are proposed, and an evaluation method of cavern instability risk is put forward. Finally, the established cavern instability risk assessment system is applied to the analysis and prediction of cavern instability risk after 30 years of operation in a proposed storage cavern group in the Huai’an salt mine. This research can provide a useful theoretical base for the safe operation and management of underground storage caverns in salt rock.

  9. Contextual Factors for Establishing Nursing Regulation in Iran: A Qualitative Content Analysis.

    Science.gov (United States)

    Nejatian, Ahmad; Joulaei, Hassan

    2018-04-01

    Professional regulation is one of the strategies of the governments which protect the public's right. Nursing practice is not an exception; hence, it is regulated to protect the public against nursing services' adverse effects. Although modern nursing in Iran started from 100 years ago, documents show that there was no regulation mechanism for nursing in Iran till 2016. Hence, this study was conducted to illuminate the contextual factors affecting the nursing regulation process in Iran. To explore the contextual elements of late establishment of nursing registration as an important part of nursing regulation, we applied directed qualitative content analysis. For this purpose, all the historical events and related materials including articles published in scientific journals, gray literature, statements, news articles, and interviews in the period of 2006-2016 were reviewed and analyzed by expert panel and categorized in predetermined groups. Pooled analysis data showed four contributing elements that affected the emerging nursing regulation in Iran. These elements include 1) cultural determinants, 2) structural determinants, 3) situational determinants, and 4) international or exogenous determinants. Nursing regulation is an important health policy issue in Iran which needs to be facilitated by contextual factors. These factors are complicated and country-specific. Political willingness should be accompanied by nursing association willingness to establish and improve nursing regulation. Other researches are recommended to explore actors and process and content of nursing regulation policy in Iran.

  10. Inactivation of Mycobacterium paratuberculosis and Mycobacterium tuberculosis in fresh soft cheese by gamma radiation

    Energy Technology Data Exchange (ETDEWEB)

    Badr, Hesham M., E-mail: heshambadr_aea@yahoo.co.uk [Atomic Energy Authority, Nuclear Research Center, Abou Zaabal, P.O. Box 13759 Cairo (Egypt)

    2011-11-15

    The effectiveness of gamma irradiation on the inactivation of Mycobacterium paratuberculosis, Mycobacterium bovis and Mycobacterium tuberculosis in fresh soft cheese that prepared from artificially inoculated milk samples was studied. Irradiation at dose of 2 kGy was sufficient for the complete inactivation of these mycobacteria as they were not detected in the treated samples during storage at 4{+-}1 {sup o}C for 15 days. Moreover, irradiation of cheese samples, that were prepared from un-inoculated milk, at this effective dose had no significant effects on their gross composition and contents from riboflavin, niacin and pantothenic acid, while significant decreases in vitamin A and thiamin were observed. In addition, irradiation of cheese samples had no significant effects on their pH and nitrogen fractions contents, except for the contents of ammonia, which showed a slight, but significant, increases due to irradiation. The analysis of cheese fats indicated that irradiation treatment induced significant increase in their oxidation parameters and contents from free fatty acids; however, the observed increases were relatively low. On the other hand, irradiation of cheese samples induced no significant alterations on their sensory properties. Thus, irradiation dose of 2 kGy can be effectively applied to ensure the safety of soft cheese with regards to these harmful mycobacteria. - Highlights: > We examined the effectiveness of gamma irradiation on inactivation of Mycobacterium paratuberculosis, Mycobacterium bovis and Mycobacterium tuberculosis in fresh soft cheese. > Irradiation at dose of 2 kGy was sufficient for complete inactivation of these mycobacteria. > Irradiation of cheese samples induced no significant alterations on their sensory properties.

  11. Inactivation of Mycobacterium paratuberculosis and Mycobacterium tuberculosis in fresh soft cheese by gamma radiation

    International Nuclear Information System (INIS)

    Badr, Hesham M.

    2011-01-01

    The effectiveness of gamma irradiation on the inactivation of Mycobacterium paratuberculosis, Mycobacterium bovis and Mycobacterium tuberculosis in fresh soft cheese that prepared from artificially inoculated milk samples was studied. Irradiation at dose of 2 kGy was sufficient for the complete inactivation of these mycobacteria as they were not detected in the treated samples during storage at 4±1 o C for 15 days. Moreover, irradiation of cheese samples, that were prepared from un-inoculated milk, at this effective dose had no significant effects on their gross composition and contents from riboflavin, niacin and pantothenic acid, while significant decreases in vitamin A and thiamin were observed. In addition, irradiation of cheese samples had no significant effects on their pH and nitrogen fractions contents, except for the contents of ammonia, which showed a slight, but significant, increases due to irradiation. The analysis of cheese fats indicated that irradiation treatment induced significant increase in their oxidation parameters and contents from free fatty acids; however, the observed increases were relatively low. On the other hand, irradiation of cheese samples induced no significant alterations on their sensory properties. Thus, irradiation dose of 2 kGy can be effectively applied to ensure the safety of soft cheese with regards to these harmful mycobacteria. - Highlights: → We examined the effectiveness of gamma irradiation on inactivation of Mycobacterium paratuberculosis, Mycobacterium bovis and Mycobacterium tuberculosis in fresh soft cheese. → Irradiation at dose of 2 kGy was sufficient for complete inactivation of these mycobacteria. → Irradiation of cheese samples induced no significant alterations on their sensory properties.

  12. Epidemiologia molecular de Mycobacterium tuberculosis em Lisboa

    Directory of Open Access Journals (Sweden)

    Isabel Portugal

    2008-03-01

    Full Text Available Resumo: Foi realizado um estudo de epidemiologia molecular a estirpes de Mycobacterium tuberculosis isoladas em hospitais de Lisboa. Analisaram-se geneticamente os isolados de Mycobacterium tuberculosis com o método restriction fragment length polymorphism (RFLP utilizando a sequência de inserção IS6110 como sonda, com o objectivo de detectar as estirpes da família Lisboa e determinar a diversidade genética das estirpes de Mycobacterium tuberculosis isoladas em Lisboa, identificando os mais importantes factores de risco de transmissão da tuberculose.Foram analisados 290 isolados de Mycobacterium tuberculosis, dos quais 64,8% se encontraram agrupados em clusters; mesmo excluindo as estirpes que apresentaram mais de 5 cópias de IS6110, a percentagem de agrupamento foi de 60,7%. A multirresistência foi observada em 4,1% das estirpes e encontraram-se todas em clusters. Quarenta e cinco isolados (18,2% pertenciam à família Lisboa. Considerando a percentagem relativamente alta de estirpes em cluster detectada neste estudo, cremos que a transmissão activa continua a ser uma realidade em Lisboa. Para além disso, as estirpes dos clusters Lisboa representam as estirpes predominantes que circulam em Lisboa. continuando muito relacionadas com a resistência aos antibacilares, embora correspondam a uma percentagem inferior à verificada em estudos anteriores.Rev Port Pneumol 2007; XIV (2: 239-259 Abstract: We conducted a molecular epidemiology study of Mycobacterium tuberculosis strains isolated from patients in Lisbon hospitals. We used restriction fragment length polymorphism (RFLP to detect Lisbon family strains and to determine the genetic diversity of Mycobacterium tuberculosis strains isolated in Lisbon, through identification of the most important risk factors of tuberculosis transmission analysis, with the insertion sequence IS6110 as a probe to fingerprint isolates of Mycobacterium tuberculosis. 64.8% of the 290 Mycobacterium

  13. The diagnostic value of polymerase chain reaction for Mycobacterium tuberculosis to distinguish intestinal tuberculosis from crohn's disease: A meta-analysis.

    Science.gov (United States)

    Jin, Ting; Fei, Baoying; Zhang, Yu; He, Xujun

    2017-01-01

    Intestinal tuberculosis (ITB) and Crohn's disease (CD) are important differential diagnoses that can be difficult to distinguish. Polymerase chain reaction (PCR) for Mycobacterium tuberculosis (MTB) is an efficient and promising tool. This meta-analysis was performed to systematically and objectively assess the potential diagnostic accuracy and clinical value of PCR for MTB in distinguishing ITB from CD. We searched PubMed, Embase, Web of Science, Science Direct, and the Cochrane Library for eligible studies, and nine articles with 12 groups of data were identified. The included studies were subjected to quality assessment using the revised Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. The summary estimates were as follows: sensitivity 0.47 (95% CI: 0.42-0.51); specificity 0.95 (95% CI: 0.93-0.97); the positive likelihood ratio (PLR) 10.68 (95% CI: 6.98-16.35); the negative likelihood ratio (NLR) 0.49 (95% CI: 0.33-0.71); and diagnostic odds ratio (DOR) 21.92 (95% CI: 13.17-36.48). The area under the curve (AUC) was 0.9311, with a Q* value of 0.8664. Heterogeneity was found in the NLR. The heterogeneity of the studies was evaluated by meta-regression analysis and subgroup analysis. The current evidence suggests that PCR for MTB is a promising and highly specific diagnostic method to distinguish ITB from CD. However, physicians should also keep in mind that negative results cannot exclude ITB for its low sensitivity. Additional prospective studies are needed to further evaluate the diagnostic accuracy of PCR.

  14. Prevalence and occurrence rate of Mycobacterium tuberculosis Haarlem family multi-drug resistant in the worldwide population: A systematic review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Rashid Ramazanzadeh

    2015-01-01

    Full Text Available Background: Transmission of Mycobacterium tuberculosis (M. tuberculosis can occur in different ways. Furthermore, drug resistant in M. tuberculosis family is a major problem that creates obstacles in treatment and control of tuberculosis (TB in the world. One of the most prevalent families of M. tuberculosis is Haarlem, and it is associated with drug resistant. Our objectives of this study were to determine the prevalence and occurrence rate of M. tuberculosis Haarlem family multi-drug resistant (MDR in the worldwide using meta-analysis based on a systematic review that performed on published articles. Materials and Methods: Data sources of this study were 78 original articles (2002-2012 that were published in the literatures in several databases including PubMed, Science Direct, Google Scholar, Biological abstracts, ISI web of knowledge and IranMedex. The articles were systematically reviewed for prevalence and rate of MDR. Data were analyzed using meta-analysis and random effects models with the software package Meta R, Version 2.13 (P < 0.10. Results: Final analysis included 28601 persons in 78 articles. The highest and lowest occurrence rate of Haarlem family in M. tuberculosis was in Hungary in 2006 (66.20% with negative MDR-TB and in China in 2010 (0.8%, respectively. From 2002 to 2012, the lowest rate of prevalence was in 2010, and the highest prevalence rate was in 2012. Also 1.076% were positive for MDR and 9.22% were negative (confidence interval: 95%.0020. Conclusion: Many articles and studies are performed in this field globally, and we only chose some of them. Further studies are needed to be done in this field. Our study showed that M. tuberculosis Haarlem family is prevalent in European countries. According to the presence of MDR that was seen in our results, effective control programs are needed to control the spread of drug-resistant strains, especially Haarlem family.

  15. Utilizing job/task analysis to establish content validity in the design of training programs

    Energy Technology Data Exchange (ETDEWEB)

    Nay, W.E.

    1988-01-01

    The decade of the 1980's has been a turbulent time for the Department of Energy. With concern mounting about the terrorist threat, a wave of congressional inquiries and internal inspections crossed the nation and engulfed many of the nuclear laboratories and facilities operated by DOE contractors. A typical finding was the need to improve, and increase, the training of the protective force. The immediate reaction resulted in a wide variety of responses, with most contractors feeling safer with too much, rather than not enough training. As soon as the initial pressures to upgrade subsided, a task force was established to evaluate the overall training needs. Representatives from the contractor facilities worked together to conduct a job analysis of the protective force. A generic task inventory was established, and validated at the different sites. This list has been invaluable for determining the tasks, conditions, and standards needed to develop well stated learning objectives. The enhanced training programs are being refined to ensure job content validity based on the data collected.

  16. In vitro Inhibition of Mycobacterium smegmatis and Mycobacterium ...

    African Journals Online (AJOL)

    Some Nigerian plants used in traditional medicine to treat tuberculosis and/or some of its symptoms were screened for in vitro activity against Mycobacterium smegmatis and a clinical isolate of Mycobacterium tuberculosis. Only 3 of the 6 crude methanolic extracts of the 6 plant species exhibited inhibitory activities against ...

  17. Establishment of a clean chemistry laboratory at JAERI. Clean laboratory for environmental analysis and research (CLEAR)

    Energy Technology Data Exchange (ETDEWEB)

    Hanzawa, Yukiko; Magara, Masaaki; Watanabe, Kazuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment] [and others

    2003-02-01

    The JAERI has established a facility with a cleanroom: the Clean Laboratory for Environmental Analysis and Research (CLEAR). This report is an overview of the design, construction and performance evaluation of the CLEAR in the initial stage of the laboratory operation in June 2001. The CLEAR is a facility to be used for analyses of ultra trace amounts of nuclear materials in environmental samples for the safeguards, for the CTBT verification and for researches on environmental sciences. One of the special features of the CLEAR is that it meets double requirements of a cleanroom and for handling of nuclear materials. As another feature of the CLEAR, much attention was paid to the construction materials of the cleanroom for trace analysis of metal elements using considerable amounts of corrosive acids. The air conditioning and purification system, specially designed experimental equipment to provide clean work surfaces, utilities and safety systems are also demonstrated. The potential contamination from the completed cleanroom atmosphere during the analytical procedure was evaluated. It can be concluded that the CLEAR has provided a suitable condition for reliable analysis of ultra trace amounts of nuclear materials and other heavy elements in environmental samples. (author)

  18. A framework for establishing the technical efficiency of Electricity Distribution Counties (EDCs) using Data Envelopment Analysis

    International Nuclear Information System (INIS)

    Mullarkey, Shane; Caulfield, Brian; McCormack, Sarah; Basu, Biswajit

    2015-01-01

    Highlights: • Six models are employed to establish the technical efficiency of Electricity Distribution Counties. • A diagnostic parameter is incorporated to account for differences across Electricity Distribution Counties. • The amalgamation of Electricity Distribution Counties leads to improved efficiency in the production of energy. - Abstract: European Energy market liberalization has entailed the restructuring of electricity power markets through the unbundling of electricity generation, transmission and distribution, supply activities and introducing competition into electricity generation. Under these new electricity market regimes, it is important to have an evaluation tool that is capable of examining the impacts of these market changes. The adoption of Data Envelopment Analysis as a form of benchmarking for electricity distribution regulation is one method to conduct this analysis. This paper applies a Data Envelopment Analysis framework to the electricity distribution network in Ireland to explore the merits of using this approach, to determine the technical efficiency and the potential scope for efficiency improvements through reorganizing and the amalgamation of the distribution network in Ireland. The results presented show that overall grid efficiency is improved through this restructuring. A diagnostic parameter is defined and pursued to account for aberrations across Electricity Distribution Counties as opposed to the traditionally employed environmental variables. The adoption of this diagnostic parameter leads to a more intuitive understanding of Electricity Distribution Counties

  19. Establishment and Analysis of Nuclear Structure Data DB for Nuclear Safety Regulation Technique Applications

    International Nuclear Information System (INIS)

    Lee, Young Ouk; Yoo, Jae Kwon; Gil, Choong; Cho, Young Sik; Kim, Hyung Il; Kim, Jong Woon; Kwon, Duk Hee; Lee, Jong Hwa

    2013-10-01

    The contents of the project consisting of four research fields carried out are: Ο Installation of DB with nuclear structure/decay datasets - Setup a computer system for production of nuclear structure/decay data in ENSDF format - Production of nuclear structure/decay data in ENSDF format( 211 , 215 Po, 136 Cs) and setup a data converting system from ENSDF format to ENDF-6 format. Ο Computer simulation of nuclear decay and burnup using the ENSDF DB - Calculation of decay heats of the several radioactive nuclides with Geant4 - Burnup calculation with full decay chain using Monte Carlo method Ο Comparison and analysis of nuclear structure/decay and fission product yields data. - Acquisitions and Analyses of decay and fission yields data in ENDF-6 format - Research for theoretical evaluation method of fission product yields data. Ο Analysis of SCALE(ORIGEN-s, -ARP) libraries - Analysis of ORIGEN library structure of nuclear decay/yields data. - Methodological studies to improve nuclear decay/yield ORIGEN libraries by use of nuclear structure/yield data in ENDF-6 format. The results of this project will be a basis to establish the nuclear decay and fission yield data DB in Korea. Additionally, new decay and yield data can be immediately served for the users to utilize those data for nuclear research and/or development

  20. [Analysis of Koch phenomenon of Mycobacterium tuberculosis-infected guinea pigs vaccinated with recombinant tuberculosis vaccine AEC/BC02].

    Science.gov (United States)

    Lu, J B; Cheng, B W; Deng, H Q; Su, C; Shen, X B; Du, W X; Yang, L; Wang, G Z; Xu, M

    2016-07-01

    To observe the Koch phenomenon of Mycobacterium tuberculosis(MTB)-infected guinea pigs after vaccinated with killed H37Ra bacteria or tuberculosis vaccine candidate AEC/BC02. Eighteen guinea pigs were challenged subcutaneously with 5.0×10(3) CFU MTB and after 40 days were divided into 3 groups (6 per group): NS group, AEC/BC02 group and H37Ra group, which were injected intramuscularly 3 times at 1 day interval with normal saline, AEC/BC02 vaccine and killed H37Ra bacteria respectively. Three weeks after the first vaccination, all guinea pigs were sacrificed to evaluate gross pathological scores for liver, spleen and lung, bacterial loads in lung and spleen, and lung inflammation. The gross pathological score in H37Ra group (48±26) was lower than that in NS group(62±15), but the difference was not significant (t=1.093, P=0.300). The AEC/BC02 group had a significantly lower gross pathological score (36±15) than NS group (t=2.980, P=0.014). No significant difference between H37Ra group and AEC/BC02 group was observed (t=1.009, P=0.337). The spleen bacterial load [(5.31±0.80) log10 CFU]in H37Ra group was slightly lower than that in NS group[(5.57±0.75) log10 CFU] but the difference was not significant (t=1.581, P=0.574). In AEC/BC02 group bacterial load in the spleen was (4.64±0.64) log10 CFU and significantly lower than NS group (t=2.306, P=0.044) and no significant difference between H37Ra group and AEC/BC02 group was observed (t=1.602, P=0.140). Meanwhile, the lung bacterial load in AEC/BC02 group was (3.71±1.01) log10 CFU and in H37Ra group was (3.82±1.25) log10 CFU. Compared to (4.15±0.69) log10 CFU in the NS group, no significant differences were found (t=0.881, P=0.399; t=0.566, P=0.584, respectively). For the lung inflammation, the inflamed areas in H37Ra group were significantly larger [(33.0±4.4%)] than those in both NS group [(14.8±8.4) %, t=4.719, P=0.001] and AEC/BC02 group [(14.8±8.4) %, t=3.616, P=0.005], and no significant differences were

  1. Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis

    Directory of Open Access Journals (Sweden)

    MacHugh David E

    2012-03-01

    Full Text Available Abstract Mycobacterium avium subspecies paratuberculosis is the causative agent of Johne’s disease, an intestinal disease of ruminants with major economic consequences. Infectious bacilli are phagocytosed by host macrophages upon exposure where they persist, resulting in lengthy subclinical phases of infection that can lead to immunopathology and disease dissemination. Consequently, analysis of the macrophage transcriptome in response to M. avium subsp. paratuberculosis infection can provide valuable insights into the molecular mechanisms that underlie Johne’s disease. Here, we investigate pan-genomic gene expression in bovine monocyte-derived macrophages (MDM purified from seven age-matched females, in response to in vitro infection with M. avium subsp. paratuberculosis (multiplicity of infection 2:1 at intervals of 2 hours, 6 hours and 24 hours post-infection (hpi. Differentially expressed genes were identified by comparing the transcriptomes of the infected MDM to the non-infected control MDM at each time point (adjusted P-value threshold ≤ 0.10. 1050 differentially expressed unique genes were identified 2 hpi, with 974 and 78 differentially expressed unique genes detected 6 and 24 hpi, respectively. Furthermore, in the infected MDM the number of upregulated genes exceeded the number of downregulated genes at each time point, with the fold-change in expression for the upregulated genes markedly higher than that for the downregulated genes. Inspection and systems biology analysis of the differentially expressed genes revealed an enrichment of genes involved in the inflammatory response, cell signalling pathways and apoptosis. The transcriptional changes associated with cellular signalling and the inflammatory response may reflect different immuno-modulatory mechanisms that underlie host-pathogen interactions during infection.

  2. Impact of cavity and infiltration on pulmonary function and health-related quality of life in pulmonary Mycobacterium avium complex disease: A 3-dimensional computed tomographic analysis.

    Science.gov (United States)

    Asakura, Takanori; Yamada, Yoshitake; Namkoong, Ho; Suzuki, Shoji; Niijima, Yuki; Kamata, Hirofumi; Funatsu, Yohei; Yagi, Kazuma; Okamori, Satoshi; Sugiura, Hiroaki; Ishii, Makoto; Jinzaki, Masahiro; Betsuyaku, Tomoko; Hasegawa, Naoki

    2017-05-01

    Pulmonary Mycobacterium avium complex (pMAC) disease manifests as various types of lesions, such as infiltrates, nodules, cavities, and bronchiectasis. However, the important determinants for clinical parameters in lung involvement are poorly understood. The objective of this study was to obtain quantitative parameters by 3-dimensional CT, and investigate the relationship between these parameters and the pulmonary function tests (PFTs) and health-related quality of life. Quantitative analysis using CT was performed in 67 pMAC patients. The relationship between new quantitative parameters for evaluating lung involvement using 3-dimensional CT and PFTs or St George's Respiratory Questionnaire (SGRQ) was evaluated. The ratio of infiltration to total lung volume showed significant correlation with the PFT results, especially the percent-predicted forced vital capacity (%FVC; ρ = -0.52), residual volume (ρ = -0.51), and total lung capacity (ρ = -0.59). The cavity volume was strongly correlated with the %FVC (ρ = -0.78) in the cavity group, while the ratio of infiltration to total lung volume was strongly correlated with the %FVC (ρ = -0.53) in the non-cavity group. The ratio of infiltration to total lung volume was significantly correlated with all SGRQ parameters (ρ = 0.41-0.52) in the non-cavity group. Infiltration was an important parameter for the PFTs and SGRQ in pMAC patients according to the 3-dimensional CT analysis. Moreover, cavity volume was an important parameter of the PFTs in the cavity group. Therefore, infiltration and cavity volume are key features for the management of pMAC disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Landslide Monitoring Network Establishment within Unified Datum and Stability Analysis in the Three Gorges Reservoir Area

    Directory of Open Access Journals (Sweden)

    Shengxiang Huang

    2017-01-01

    Full Text Available A landslide monitoring network construction within unified datum which combined fiducial points, working reference points, and monitoring points was intensively studied in the Three Gorges Reservoir area. With special long and narrow geographical location in the area, designing and building monitoring network was vital to the realization of landslide monitoring. To build such a network with high precision, this paper mainly focused on the following four aspects: (1 method of using multiple GPS reference stations to build a unified datum network and subnet adjustment, (2 GPS data processing algorithm with millimeter level, (3 analysis of influence on the adjustment resulting from systematic error of time evolution datum from different GPS observations, and (4 establishment and stability analysis of unified datum. Then, using global test and trial-and-error method to analyze the datum based on the GPS observations (2008~2011 of landslide monitoring network in the area, we concluded that there were moved reference points during the three years of high water impoundment, and the horizontal displacement of moved reference points was more than 4 cm, even up to 79.4 cm. The displacement direction of unstable reference points was inspected with geographical environment at sites, which revealed congruency between them.

  4. Establishment of Tools for Neurogenetic Analysis of Sexual Behavior in the Silkmoth, Bombyx mori

    Science.gov (United States)

    Kiya, Taketoshi; Morishita, Koudai; Uchino, Keiro; Iwami, Masafumi; Sezutsu, Hideki

    2014-01-01

    Background Silkmoth, Bombyx mori, is an ideal model insect for investigating the neural mechanisms underlying sex pheromone-induced innate behavior. Although transgenic techniques and the GAL4/UAS system are well established in the silkmoth, genetic tools useful for investigating brain function at the neural circuit level have been lacking. Results In the present study, we established silkmoth strains in which we could visualize neural projections (UAS-mCD8GFP) and cell nucleus positions (UAS-GFP.nls), and manipulate neural excitability by thermal stimulation (UAS-dTrpA1). In these strains, neural projections and nucleus position were reliably labeled with green fluorescent protein in a GAL4-dependent manner. Further, the behavior of silkworm larvae and adults could be controlled by GAL4-dependent misexpression of dTrpA1. Ubiquitous dTrpA1 misexpression led both silkmoth larvae and adults to exhibit seizure-like phenotypes in a heat stimulation-dependent manner. Furthermore, dTrpA1 misexpression in the sex pheromone receptor neurons of male silkmoths allowed us to control male sexual behavior by changing the temperature. Thermally stimulated male silkmoths exhibited full sexual behavior, including wing-flapping, orientation, and attempted copulation, and precisely approached a thermal source in a manner similar to male silkmoths stimulated with the sex pheromone. Conclusion These findings indicate that a thermogenetic approach using dTrpA1 is feasible in Lepidopteran insects and thermogenetic analysis of innate behavior is applicable in the silkmoth. These tools are essential for elucidating the relationships between neural circuits and function using neurogenetic methods. PMID:25396742

  5. Establishment of tools for neurogenetic analysis of sexual behavior in the silkmoth, Bombyx mori.

    Science.gov (United States)

    Kiya, Taketoshi; Morishita, Koudai; Uchino, Keiro; Iwami, Masafumi; Sezutsu, Hideki

    2014-01-01

    Silkmoth, Bombyx mori, is an ideal model insect for investigating the neural mechanisms underlying sex pheromone-induced innate behavior. Although transgenic techniques and the GAL4/UAS system are well established in the silkmoth, genetic tools useful for investigating brain function at the neural circuit level have been lacking. In the present study, we established silkmoth strains in which we could visualize neural projections (UAS-mCD8GFP) and cell nucleus positions (UAS-GFP.nls), and manipulate neural excitability by thermal stimulation (UAS-dTrpA1). In these strains, neural projections and nucleus position were reliably labeled with green fluorescent protein in a GAL4-dependent manner. Further, the behavior of silkworm larvae and adults could be controlled by GAL4-dependent misexpression of dTrpA1. Ubiquitous dTrpA1 misexpression led both silkmoth larvae and adults to exhibit seizure-like phenotypes in a heat stimulation-dependent manner. Furthermore, dTrpA1 misexpression in the sex pheromone receptor neurons of male silkmoths allowed us to control male sexual behavior by changing the temperature. Thermally stimulated male silkmoths exhibited full sexual behavior, including wing-flapping, orientation, and attempted copulation, and precisely approached a thermal source in a manner similar to male silkmoths stimulated with the sex pheromone. These findings indicate that a thermogenetic approach using dTrpA1 is feasible in Lepidopteran insects and thermogenetic analysis of innate behavior is applicable in the silkmoth. These tools are essential for elucidating the relationships between neural circuits and function using neurogenetic methods.

  6. Establishment of tools for neurogenetic analysis of sexual behavior in the silkmoth, Bombyx mori.

    Directory of Open Access Journals (Sweden)

    Taketoshi Kiya

    Full Text Available Silkmoth, Bombyx mori, is an ideal model insect for investigating the neural mechanisms underlying sex pheromone-induced innate behavior. Although transgenic techniques and the GAL4/UAS system are well established in the silkmoth, genetic tools useful for investigating brain function at the neural circuit level have been lacking.In the present study, we established silkmoth strains in which we could visualize neural projections (UAS-mCD8GFP and cell nucleus positions (UAS-GFP.nls, and manipulate neural excitability by thermal stimulation (UAS-dTrpA1. In these strains, neural projections and nucleus position were reliably labeled with green fluorescent protein in a GAL4-dependent manner. Further, the behavior of silkworm larvae and adults could be controlled by GAL4-dependent misexpression of dTrpA1. Ubiquitous dTrpA1 misexpression led both silkmoth larvae and adults to exhibit seizure-like phenotypes in a heat stimulation-dependent manner. Furthermore, dTrpA1 misexpression in the sex pheromone receptor neurons of male silkmoths allowed us to control male sexual behavior by changing the temperature. Thermally stimulated male silkmoths exhibited full sexual behavior, including wing-flapping, orientation, and attempted copulation, and precisely approached a thermal source in a manner similar to male silkmoths stimulated with the sex pheromone.These findings indicate that a thermogenetic approach using dTrpA1 is feasible in Lepidopteran insects and thermogenetic analysis of innate behavior is applicable in the silkmoth. These tools are essential for elucidating the relationships between neural circuits and function using neurogenetic methods.

  7. Mycobacterium eburneum sp. nov., a non-chromogenic, fast-growing strain isolated from sputum.

    Science.gov (United States)

    Nouioui, Imen; Carro, Lorena; Teramoto, Kanae; Igual, José M; Jando, Marlen; Del Carmen Montero-Calasanz, Maria; Sutcliffe, Iain; Sangal, Vartul; Goodfellow, Michael; Klenk, Hans-Peter

    2017-09-01

    A polyphasic study was undertaken to establish the taxonomic position of a non-chromogenic, rapidly growing Mycobacterium strain that had been isolated from sputum. The strain, CECT 8775T, has chemotaxonomic and cultural properties consistent with its classification in the genus Mycobacterium and was distinguished from the type strains of closely related mycobacterial species, notably from Mycobacterium paraense DSM 46749T, its nearest phylogenetic neighbour, based on 16S rRNA, hsp65 and rpoB gene sequence data. These organisms were also distinguished by a broad range of chemotaxonomic and phenotypic features and by a digital DNA-DNA relatedness value of 22.8 %. Consequently, the strain is considered to represent a novel species of Mycobacterium for which the name Mycobacterium eburneum sp. nov is proposed; the type strain is X82T (CECT 8775T=DSM 44358T).

  8. Lauric acid and myristic acid from Allium sativum inhibit the growth of Mycobacterium tuberculosis H37Ra: in silico analysis reveals possible binding to protein kinase B.

    Science.gov (United States)

    Muniyan, Rajiniraja; Gurunathan, Jayaraman

    2016-12-01

    The bulb of Allium sativum Linn (Alliaceae) has numerous medicinal values. Though the petroleum ether extract of the bulb has shown to exhibit antimycobacterial activity, the phytochemical(s) responsible for this inhibitory activity is not known. To characterize the bioactive compounds in the petroleum ether extract of Allium sativum (garlic) that inhibit the growth of Mycobacterium tuberculosis H37Ra. Bioactivity-guided fractionation was employed to isolate the bioactive compounds. Antimycobacterial activity was evaluated by well-diffusion method and microplate alamar blue assay (MABA). Infrared spectroscopy, mass spectrometry and nuclear magnetic resonance spectroscopy were used to characterize the bioactive compounds. Autodock was used to obtain information on molecular recognition, and molecular dynamics simulation was performed using GROMACS. The bioactive compounds that inhibited the growth of M. tuberculosis H37Ra were found to be lauric acid (LA) and myristic acid (MA). The minimal inhibitory concentration of LA and MA was found to be 22.2 and 66.7 μg/mL, respectively. In silico analysis revealed that these fatty acids could bind at the cleft between the N-terminal and C-terminal lobes of the cytosolic domain of serine/threonine protein kinase B (PknB). The inhibition activity was dependent on the alkyl chain length of the fatty acid, and the amino acid residues involved in binding to fatty acid was found to be conserved across the Pkn family of proteins. The study indicates the possibility of using fatty acid derivatives, involving Pkn family of proteins, to inhibit the signal transduction processes in M. tuberculosis.

  9. Construction and analysis of the transcription factor-microRNA co-regulatory network response to Mycobacterium tuberculosis: a view from the blood.

    Science.gov (United States)

    Lin, Yan; Duan, Zipeng; Xu, Feng; Zhang, Jiayuan; Shulgina, Marina V; Li, Fan

    2017-01-01

    Mycobacterium tuberculosis ( Mtb ) infection has been regional outbreak, recently. The traditional focus on the patterns of "reductionism" which was associated with single molecular changes has been unable to meet the demand of early diagnosis and clinical application when current tuberculosis infection happened. In this study, we employed a systems biology approach to collect large microarray data sets including mRNAs and microRNAs (miRNAs) to identify the differentially expressed mRNAs and miRNAs in the whole blood of TB patients. The aim was to identify key genes associated with the immune response in the pathogenic process of tuberculosis by analyzing the co-regulatory network that was consisted of transcription factors and miRNAs as well as their target genes. The network along with their co-regulatory genes was analyzed utilizing Transcriptional Regulatory Element Database (TRED) and Database for Annotation, Visualization and Integrated Discovery (DAVID). We got 21 (19 up-regulated and 2 down-regulated) differentially expressed genes that were co-regulated by transcription factors and miRNAs. KEGG pathway enrichment analysis showed that the 21 differentially expressed genes were predominantly involved in Tuberculosis signaling pathway, which may play a major role in tuberculosis biological process. Quantitative real-time PCR was performed to verify the over expression of co-regulatory genes ( FCGR1A and CEBPB ). The genetic expression was correlated with clinicopathological characteristics in TB patients and inferences drawn. Our results suggest the TF-miRNA gene co-regulatory network may help us further understand the molecular mechanism of immune response to tuberculosis and provide us a new angle of future biomarker and therapeutic targets.

  10. Two cases of leprosy from Žatec (Bohemia), dated to the turn of the 12th century and confirmed by DNA analysis for Mycobacterium leprae

    Czech Academy of Sciences Publication Activity Database

    Likovský, Jakub; Urbanová, M.; Hájek, Martin; Černý, Viktor; Čech, Petr

    2006-01-01

    Roč. 33, č. 9 (2006), s. 1276-1283 ISSN 0305-4403 Institutional research plan: CEZ:AV0Z80020508 Keywords : Leprosy * mediaeval * aDNA * Mycobacterium leprae * Paleopathology Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 1.322, year: 2006

  11. Establishing community-based integrated care for elderly patients through interprofessional teamwork: a qualitative analysis

    Directory of Open Access Journals (Sweden)

    Asakawa T

    2017-10-01

    Full Text Available Tomohiro Asakawa,1 Hidenobu Kawabata,1 Kengo Kisa,2 Takayoshi Terashita,3 Manabu Murakami,4 Junji Otaki1 1Department of Medical Education and General Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, 2Kutchan-Kosei General Hospital, Kutchan, Hokkaido, 3Graduate School of Radiological Technology Gunma Prefectural College of Health Sciences, Kamioki-machi, Maebashi, Gunma, 4International Relations Office, Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan Background: Working in multidisciplinary teams is indispensable for ensuring high-quality care for elderly people in Japan’s rapidly aging society. However, health professionals often experience difficulty collaborating in practice because of their different educational backgrounds, ideas, and the roles of each profession. In this qualitative descriptive study, we reveal how to build interdisciplinary collaboration in multidisciplinary teams. Methods: Semi-structured interviews were conducted with a total of 26 medical professionals, including physicians, nurses, public health nurses, medical social workers, and clerical personnel. Each participant worked as a team member of community-based integrated care. The central topic of the interviews was what the participants needed to establish collaboration during the care of elderly residents. Each interview lasted for about 60 minutes. All the interviews were recorded, transcribed verbatim, and subjected to content analysis. Results: The analysis yielded the following three categories concerning the necessary elements of building collaboration: 1 two types of meeting configuration; 2 building good communication; and 3 effective leadership. The two meetings described in the first category – “community care meetings” and “individual care meetings” – were aimed at bringing together the disciplines and discussing individual cases, respectively. Building good communication referred to the activities

  12. qPCR-High resolution melt analysis for drug susceptibility testing of Mycobacterium leprae directly from clinical specimens of leprosy patients.

    Science.gov (United States)

    Araujo, Sergio; Goulart, Luiz Ricardo; Truman, Richard W; Goulart, Isabela Maria B; Vissa, Varalakshmi; Li, Wei; Matsuoka, Masanori; Suffys, Philip; Fontes, Amanda B; Rosa, Patricia S; Scollard, David M; Williams, Diana L

    2017-06-01

    Real-Time PCR-High Resolution Melting (qPCR-HRM) analysis has been recently described for rapid drug susceptibility testing (DST) of Mycobacterium leprae. The purpose of the current study was to further evaluate the validity, reliability, and accuracy of this assay for M. leprae DST in clinical specimens. The specificity and sensitivity for determining the presence and susceptibility of M. leprae to dapsone based on the folP1 drug resistance determining region (DRDR), rifampin (rpoB DRDR) and ofloxacin (gyrA DRDR) was evaluated using 211 clinical specimens from leprosy patients, including 156 multibacillary (MB) and 55 paucibacillary (PB) cases. When comparing the results of qPCR-HRM DST and PCR/direct DNA sequencing, 100% concordance was obtained. The effects of in-house phenol/chloroform extraction versus column-based DNA purification protocols, and that of storage and fixation protocols of specimens for qPCR-HRM DST, were also evaluated. qPCR-HRM results for all DRDR gene assays (folP1, rpoB, and gyrA) were obtained from both MB (154/156; 98.7%) and PB (35/55; 63.3%) patients. All PCR negative specimens were from patients with low numbers of bacilli enumerated by an M. leprae-specific qPCR. We observed that frozen and formalin-fixed paraffin embedded (FFPE) tissues or archival Fite's stained slides were suitable for HRM analysis. Among 20 mycobacterial and other skin bacterial species tested, only M. lepromatosis, highly related to M. leprae, generated amplicons in the qPCR-HRM DST assay for folP1 and rpoB DRDR targets. Both DNA purification protocols tested were efficient in recovering DNA suitable for HRM analysis. However, 3% of clinical specimens purified using the phenol/chloroform DNA purification protocol gave false drug resistant data. DNA obtained from freshly frozen (n = 172), formalin-fixed paraffin embedded (FFPE) tissues (n = 36) or archival Fite's stained slides (n = 3) were suitable for qPCR-HRM DST analysis. The HRM-based assay was also able to

  13. qPCR-High resolution melt analysis for drug susceptibility testing of Mycobacterium leprae directly from clinical specimens of leprosy patients.

    Directory of Open Access Journals (Sweden)

    Sergio Araujo

    2017-06-01

    Full Text Available Real-Time PCR-High Resolution Melting (qPCR-HRM analysis has been recently described for rapid drug susceptibility testing (DST of Mycobacterium leprae. The purpose of the current study was to further evaluate the validity, reliability, and accuracy of this assay for M. leprae DST in clinical specimens.The specificity and sensitivity for determining the presence and susceptibility of M. leprae to dapsone based on the folP1 drug resistance determining region (DRDR, rifampin (rpoB DRDR and ofloxacin (gyrA DRDR was evaluated using 211 clinical specimens from leprosy patients, including 156 multibacillary (MB and 55 paucibacillary (PB cases. When comparing the results of qPCR-HRM DST and PCR/direct DNA sequencing, 100% concordance was obtained. The effects of in-house phenol/chloroform extraction versus column-based DNA purification protocols, and that of storage and fixation protocols of specimens for qPCR-HRM DST, were also evaluated. qPCR-HRM results for all DRDR gene assays (folP1, rpoB, and gyrA were obtained from both MB (154/156; 98.7% and PB (35/55; 63.3% patients. All PCR negative specimens were from patients with low numbers of bacilli enumerated by an M. leprae-specific qPCR. We observed that frozen and formalin-fixed paraffin embedded (FFPE tissues or archival Fite's stained slides were suitable for HRM analysis. Among 20 mycobacterial and other skin bacterial species tested, only M. lepromatosis, highly related to M. leprae, generated amplicons in the qPCR-HRM DST assay for folP1 and rpoB DRDR targets. Both DNA purification protocols tested were efficient in recovering DNA suitable for HRM analysis. However, 3% of clinical specimens purified using the phenol/chloroform DNA purification protocol gave false drug resistant data. DNA obtained from freshly frozen (n = 172, formalin-fixed paraffin embedded (FFPE tissues (n = 36 or archival Fite's stained slides (n = 3 were suitable for qPCR-HRM DST analysis. The HRM-based assay was also able

  14. Establishment of screening technique for mutant cell and analysis of base sequence in the mutation

    International Nuclear Information System (INIS)

    Sofuni, Toshio; Nomi, Takehiko; Yamada, Masami; Masumura, Kenichi

    2000-01-01

    This research project aimed to establish an easy and quick detection method for radiation-induced mutation using molecular-biological techniques and an effective analyzing method for the molecular changes in base sequence. In this year, Spi mutants derived from γ-radiation exposed mouse were analyzed by PCR method and DNA sequence method. Male transgenic mice were exposed to γ-ray at 5,10, 50 Gy and the transgene was taken out from the genome DNA from the spleen in vivo packaging method. Spi mutant plaques were obtained by infecting the recovered phage to E. coli. Sequence analysis for the mutants was made using ALFred DNA sequencer and SequiTherm TM Long-Red Cycle sequencing kit. Sequence analysis was carried out for 41 of 50 independent Spi mutants obtained. The deletions were classified into 4 groups; Group 1 included 15 mutants that were characterized with a large deletion (43 bp-10 kb) with a short homologous sequence. Group 2 included 11 mutants of a large deletion having no homologous sequence at the connecting region. Group 3 included 11 mutants having a short deletion of less than 20 bp, which occurred in the non-repetitive sequence of gam gene and possibly caused by oxidative breakage of DNA or recombination of DNA fragment produced by the breakage. Group 4 included 4 mutants having deletions as short as 20 bp or less in the repetitive sequence of gam gene, resulting in an alteration of the reading frame. Thus, the synthesis of Gam protein was terminated by the appearance of TGA between code 13 and 14 of redB gene, leading to inactivation of gam gene and redBA gene. These results indicated that most of Spi mutants had a deletion in red/gam region and the deletions in more than half mutants occurred in homologous sequences as short as 8 bp. (M.N.)

  15. Establishment of four new mesothelioma cell lines: characterization by ultrastructural and immunophenotypic analysis.

    Science.gov (United States)

    Orengo, A M; Spoletini, L; Procopio, A; Favoni, R E; De Cupis, A; Ardizzoni, A; Castagneto, B; Ribotta, M; Betta, P G; Ferrini, S; Mutti, L

    1999-03-01

    The aim of this study was to assess the biological characteristics of four new malignant mesothelioma (MM) cell lines. Since simian virus (SV)40 sequences have been recently detected in MM, SV40 large T antigen (Tag) expression was also analysed. MM cell lines were characterized by morphological, ultrastructural and cytogenetic analysis. Expression of Tag and of relevant MM markers was studied by immunocytochemistry, surface antigens by indirect immunofluorescence and immunomodulating cytokines by enzyme-linked immunosorbent assay (ELISA). The four MM cell lines, established from pleural effusions, showed a slow proliferation rate and pleomorphic changes during culture. Cell lines expressed vimentin, cytokeratins 8 and 18, and the mesothelial antigen recognized by HBME-1 monoclonal antibody, but not carcinoembryonic antigen. Surface human leukocyte antigen (HLA)-class I and intercellular adhesion molecule (ICAM)-1 molecules were present on all the cell lines. While HLA class II and CD86 were constitutively undetectable, HLA-class II was present after interferon (IFN)-gamma stimulation. All cell lines displayed abnormal karyotypes with chromosome 6 abnormalities. Transforming growth factor (TGF)-beta2 and interleukin (IL)-6 were constitutively secreted, while tumour necrosis factor (TNF)-alpha was secreted only in response to lipopolysaccharide. Intranuclear Tag was expressed in two cell lines. The persistence of large T antigen with human leukocyte antigen class I and intercellular adhesion molecule-1 positivity may point to large T antigen as a target for cytotoxic T-lymphocyte-based immunotherapy in some malignant mesothelioma patients.

  16. ANALYSIS OF THE POSSIBILITY FOR ESTABLISHING PROJECT MANAGEMENT OFFICE (PMO IN COMPANIES IN SERBIA

    Directory of Open Access Journals (Sweden)

    Dragana Milin

    2012-09-01

    Full Text Available Project Management Office (PMO is an organizational unit established to help project managers, project teams and the various levels of management in carrying out the principles of project management. The research was carried out in Serbia, in 2011, with the aim to establish which methodologies and techniques are used for project m anagement, and which of them are used the most frequently. Furthermore, the need for establishment of PMOs in Serbia is discussed. These offices should help in establishing a standardized methodology (at the organization level and thus overcome the obviou s poor use of any project management methodology at all.

  17. Anti-Mycobacterium activity of microbial peptides in a silkworm infection model with Mycobacterium smegmatis.

    Science.gov (United States)

    Yagi, Akiho; Uchida, Ryuji; Hamamoto, Hiroshi; Sekimizu, Kazuhisa; Kimura, Ken-Ichi; Tomoda, Hiroshi

    2017-05-01

    An in vivo-mimic silkworm infection model with Mycobacterium smegmatis was established. When silkworms were raised at 37 °C following an injection of M. smegmatis cells (1.25 × 10 7 CFU larva -1  g -1 ) into the silkworm hemolymph, they died within 48 h. Under these conditions, four microbial peptides with anti-M. smegmatis activity, lariatin A, calpinactam, lysocin E and propeptin, exerted therapeutic effects in a dose-dependent manner, and these are also clinically used agents that are active against Mycobacterium tuberculosis. These results indicate that the silkworm infection model with M. smegmatis is practically useful for the screening of therapeutically effective anti-M. tuberculosis antibiotics.

  18. 21 CFR 866.3370 - Mycobacterium tuberculosis immunofluorescent reagents.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Mycobacterium tuberculosis immunofluorescent... § 866.3370 Mycobacterium tuberculosis immunofluorescent reagents. (a) Identification. Mycobacterium... used to identify Mycobacterium tuberculosis directly from clinical specimens. The identification aids...

  19. Cost-benefit analysis of establishing and operating radiation oncology services in Fiji.

    Science.gov (United States)

    Kim, Eunkyoung; Cho, Yoon-Min; Kwon, Soonman; Park, Kunhee

    2017-10-01

    Rising demand for services of cancer patients has been recognised by the Government of Fiji as a national health priority. Increasing attention has been paid to the lack of service of radiation therapy or radiotherapy in Fiji. This study aims to estimate and compare the costs and benefits of introducing radiation oncology services in Fiji from the societal perspective. Time horizon for cost-benefit analysis (CBA) was 15 years from 2021 to 2035. The benefits and costs were converted to the present values of 2016. Estimates for the CBA model were taken from previous studies and expert opinions and data obtained from field visits to Fiji in January 2016. Sensitivity analyses with changing assumptions were undertaken. The estimated net benefit, applying the national minimum wage (NMW) to measure monetary value for life-year gained, was -31,624,421 FJD with 0.69 of benefit-cost (B/C) ratio. If gross national income (GNI) per capita was used for the value of life years, net benefit was 3,975,684 FJD (B/C ratio: 1.04). With a pessimistic scenario, establishing the center appeared to be not cost-beneficial, and the net benefit was -53,634,682 FJD (B/C ratio: 0.46); net benefit with an optimistic scenario was estimated 23,178,189 FJD (B/C ratio: 1.20). Based on the CBA results from using GNI per capita instead of the NMW, this project would be cost-beneficial. Introducing a radiation oncology center in Fiji would have potential impacts on financial sustainability, financial protection, and accessibility and equity of the health system. Copyright © 2017 World Health Organization. Published by Elsevier Ltd.. All rights reserved.

  20. Establishment of screening method for mutant cell and analysis of base sequence of its mutated gene

    International Nuclear Information System (INIS)

    Sofuni, Toshio; Nomi, Takehiko; Yamada, Masami; Masumura, Kenichi

    1999-01-01

    The purpose of this study was to develop a method for effective detection of the changes in DNA sequences due to radiation-induced mutation and further to establish techniques for risk evaluation and its reduction in human bodies. A transgene including E. coli gpt gene was transfected to produce a transgenic mouse model for detecting a mutation. E. coli gpt gene, a reporter gene for detection of point mutation was inserted into a shuttle vector, λEG10 and the vector was micro-injected into mouse fertilized eggs. Genome DNA was extracted from the bone marrow and the testis of its F1 mice and the presence of λEG10 DNA was confirmed by PCR method and Southern hybridization technique. A system which effectively detect a deletion mutation (Spi selection) was inserted into a shuttle vector and the mutation rate was determined using the transgenic mouse. The number of copies of the transfected gene was estimated through comparison with those for the previous transgenic mice such as Muta TM , Big Blue TM mouse. The number of copies of λEG10 DNA was about 30 in BDF1-derived mouse and 80 in C57BL16J-derived one. The rate of mutation in gpt gene was significantly increased in the bone morrow of mice intraperitoneally administered with ethylnitrosourea at 150 mg/kg of body weight. The rate of Spi mutation was dose-dependently increased in the spleen of mice exposed to γ-radiation (5, 10, 50 Gy). These results indicate that the transgenic mouse, 'gpt Δ' developed was available for in vivo detection and analysis of various types of mutation. (M.N.)

  1. Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

    Directory of Open Access Journals (Sweden)

    Weis Patrick

    2010-01-01

    Full Text Available Abstract Background The newt Notophthalmus viridescens possesses the remarkable ability to respond to cardiac damage by formation of new myocardial tissue. Surprisingly little is known about changes in gene activities that occur during the course of regeneration. To begin to decipher the molecular processes, that underlie restoration of functional cardiac tissue, we generated an EST database from regenerating newt hearts and compared the transcriptional profile of selected candidates with genes deregulated during zebrafish heart regeneration. Results A cDNA library of 100,000 cDNA clones was generated from newt hearts 14 days after ventricular injury. Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs. BLAST searches revealed 1695 sequences with potential homology to sequences from the NCBI database. BLAST searches to TrEMBL and Swiss-Prot databases assigned 1116 proteins to Gene Ontology terms. We also identified a relatively large set of 174 ORFs, which are likely to be unique for urodele amphibians. Expression analysis of newt-zebrafish homologues confirmed the deregulation of selected genes during heart regeneration. Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms. Comparison of data from regenerating zebrafish hearts identified biological processes, which were uniformly overrepresented during cardiac regeneration in newt and zebrafish. Conclusion We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles. The design of the newly established newt EST database allows identification of molecular pathways important for heart regeneration.

  2. Scaling Analysis Techniques to Establish Experimental Infrastructure for Component, Subsystem, and Integrated System Testing

    Energy Technology Data Exchange (ETDEWEB)

    Sabharwall, Piyush [Idaho National Laboratory (INL), Idaho Falls, ID (United States); O' Brien, James E. [Idaho National Laboratory (INL), Idaho Falls, ID (United States); McKellar, Michael G. [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Housley, Gregory K. [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Bragg-Sitton, Shannon M. [Idaho National Laboratory (INL), Idaho Falls, ID (United States)

    2015-03-01

    Hybrid energy system research has the potential to expand the application for nuclear reactor technology beyond electricity. The purpose of this research is to reduce both technical and economic risks associated with energy systems of the future. Nuclear hybrid energy systems (NHES) mitigate the variability of renewable energy sources, provide opportunities to produce revenue from different product streams, and avoid capital inefficiencies by matching electrical output to demand by using excess generation capacity for other purposes when it is available. An essential step in the commercialization and deployment of this advanced technology is scaled testing to demonstrate integrated dynamic performance of advanced systems and components when risks cannot be mitigated adequately by analysis or simulation. Further testing in a prototypical environment is needed for validation and higher confidence. This research supports the development of advanced nuclear reactor technology and NHES, and their adaptation to commercial industrial applications that will potentially advance U.S. energy security, economy, and reliability and further reduce carbon emissions. Experimental infrastructure development for testing and feasibility studies of coupled systems can similarly support other projects having similar developmental needs and can generate data required for validation of models in thermal energy storage and transport, energy, and conversion process development. Experiments performed in the Systems Integration Laboratory will acquire performance data, identify scalability issues, and quantify technology gaps and needs for various hybrid or other energy systems. This report discusses detailed scaling (component and integrated system) and heat transfer figures of merit that will establish the experimental infrastructure for component, subsystem, and integrated system testing to advance the technology readiness of components and systems to the level required for commercial

  3. The Permanent Establishment of Insurance: Critical Analysis of its Application from the Colombian Tax Perspective

    OpenAIRE

    Cabrera Cabrera, Omar Sebastián

    2017-01-01

    Double Taxation Conventions provide several categories of permanent establishments depending on their purpose and nature. In this sense, the United Nations tax convention set forth a special hypothesis so-called the permanent establishment of insurance, which is not a typical element in the Organisation for Economic Co-operation and Development, OECD (OCDE, in Spanish) Model. However, the scope of the current wording excludes the agents of an independent status, which has generated criticism ...

  4. Mycobacterium persicum sp. nov., a novel species closely related to Mycobacterium kansasii and Mycobacterium gastri.

    Science.gov (United States)

    Shahraki, Abdolrazagh Hashemi; Trovato, Alberto; Mirsaeidi, Mehdi; Borroni, Emanuele; Heidarieh, Parvin; Hashemzadeh, Mohamad; Shahbazi, Narges; Cirillo, Daniela M; Tortoli, Enrico

    2017-06-01

    Four strains isolated in Iran from pulmonary specimens of unrelated patients are proposed as representative of a novel Mycobacterium species. Similarity, at the phenotypic level, with Mycobacterium kansasii is remarkable with the photochromogenic yellow pigmentation of the colonies being the salient feature. They differ, however, genotypically from this species and present unique sequences in 16S rRNA, hsp65 and rpoB genes. The average nucleotide identity and the genome-to-genome distance fully support the status of an independent species. The name proposed for this species is Mycobacterium persicum sp. nov. with AFPC-000227T (=DSM 104278T=CIP 111197T) as the type strain.

  5. Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

    OpenAIRE

    Cohen, Keira A.; Abeel, Thomas; Manson McGuire, Abigail; Desjardins, Christopher A.; Munsamy, Vanisha; Shea, Terrance P.; Walker, Bruce J.; Bantubani, Nonkqubela; Almeida, Deepak V.; Alvarado, Lucia; Chapman, Sinéad B.; Mvelase, Nomonde R.; Duffy, Eamon Y.; Fitzgerald, Michael G.; Govender, Pamla

    2015-01-01

    Editors' Summary Background Tuberculosis (TB)—a contagious bacterial disease that usually infects the lungs—is a global public health problem. Every year, about 9 million people develop active TB disease, and 1.5 million people die from the disease. Mycobacterium tuberculosis, the organism that causes TB, is spread in airborne droplets when people with TB cough. The symptoms of TB include cough, weight loss, and fever. Diagnostic tests for the disease include sputum smear microscopy (microsco...

  6. Pyrosequence Analysis of the hsp65 Genes of Nontuberculous Mycobacterium Communities in Unchlorinated Drinking Water in the Netherlands

    Science.gov (United States)

    Heijnen, Leo; van der Kooij, Dick

    2013-01-01

    Studies have shown that certain opportunistic pathogenic species of nontuberculous mycobacteria (NTM) can be present in distributed drinking water. However, detailed information about NTM population composition in drinking water is lacking. Therefore, NTM communities in unchlorinated drinking water from the distribution system of five treatment plants in the Netherlands were characterized using 454 pyrosequencing of the hsp65 gene. Results showed high diversities in unchlorinated drinking water, with up to 28 different NTM operational taxonomic units (OTUs) in a single sample. Each drinking water sample had a unique NTM community, and most (81.1%) OTUs were observed only once. One OTU was observed in 14 of 16 drinking water samples, indicating that this NTM species is well adapted to unchlorinated drinking water conditions. A clear influence of season, source type (groundwater, surface water), easily assimilable organic carbon (AOC) concentration, biofilm formation rate, and active biomass in treated water on the establishment of an NTM community in drinking water was not observed. Apparently, local conditions are more important for the development of a specific NTM community in the drinking water distribution system. A low (4.2%) number of hsp65 gene sequences showed more than 97% similarity to sequences of the opportunistic pathogens M. avium, M. genavense, and M. gordonae. However, most (95.8%) NTM hsp65 gene sequences were related to not-yet-described NTM species that have not been linked to disease, indicating that most NTM species in unchlorinated drinking water from distribution systems in the Netherlands have a low public health significance. PMID:23913420

  7. Analysis of host responses to Mycobacterium tuberculosis antigens in a multi-site study of subjects with different TB and HIV infection states in sub-Saharan Africa.

    Directory of Open Access Journals (Sweden)

    Jayne S Sutherland

    Full Text Available Tuberculosis (TB remains a global health threat with 9 million new cases and 1.4 million deaths per year. In order to develop a protective vaccine, we need to define the antigens expressed by Mycobacterium tuberculosis (Mtb, which are relevant to protective immunity in high-endemic areas.We analysed responses to 23 Mtb antigens in a total of 1247 subjects with different HIV and TB status across 5 geographically diverse sites in Africa (South Africa, The Gambia, Ethiopia, Malawi and Uganda. We used a 7-day whole blood assay followed by IFN-γ ELISA on the supernatants. Antigens included PPD, ESAT-6 and Ag85B (dominant antigens together with novel resuscitation-promoting factors (rpf, reactivation proteins, latency (Mtb DosR regulon-encoded antigens, starvation-induced antigens and secreted antigens.There was variation between sites in responses to the antigens, presumably due to underlying genetic and environmental differences. When results from all sites were combined, HIV- subjects with active TB showed significantly lower responses compared to both TST(- and TST(+ contacts to latency antigens (Rv0569, Rv1733, Rv1735, Rv1737 and the rpf Rv0867; whilst responses to ESAT-6/CFP-10 fusion protein (EC, PPD, Rv2029, TB10.3, and TB10.4 were significantly higher in TST(+ contacts (LTBI compared to TB and TST(- contacts fewer differences were seen in subjects with HIV co-infection, with responses to the mitogen PHA significantly lower in subjects with active TB compared to those with LTBI and no difference with any antigen.Our multi-site study design for testing novel Mtb antigens revealed promising antigens for future vaccine development. The IFN-γ ELISA is a cheap and useful tool for screening potential antigenicity in subjects with different ethnic backgrounds and across a spectrum of TB and HIV infection states. Analysis of cytokines other than IFN-γ is currently on-going to determine correlates of protection, which may be useful for vaccine

  8. Comparative Whole-Genomic Analysis of an Ancient L2 Lineage Mycobacterium tuberculosis Reveals a Novel Phylogenetic Clade and Common Genetic Determinants of Hypervirulent Strains

    Directory of Open Access Journals (Sweden)

    Rahim Rajwani

    2018-01-01

    Full Text Available Background: Development of improved therapeutics against tuberculosis (TB is hindered by an inadequate understanding of the relationship between disease severity and genetic diversity of its causative agent, Mycobacterium tuberculosis. We previously isolated a hypervirulent M. tuberculosis strain H112 from an HIV-negative patient with an aggressive disease progression from pulmonary TB to tuberculous meningitis—the most severe manifestation of tuberculosis. Human macrophage challenge experiment demonstrated that the strain H112 exhibited significantly better intracellular survivability and induced lower level of TNF-α than the reference virulent strain H37Rv and other 123 clinical isolates.Aim: The present study aimed to identify the potential genetic determinants of mycobacterial virulence that were common to strain H112 and hypervirulent M. tuberculosis strains of the same phylogenetic clade isolated in other global regions.Methods: A low-virulent M. tuberculosis strain H54 which belonged to the same phylogenetic lineage (L2 as strain H112 was selected from a collection of 115 clinical isolates. Both H112 and H54 were whole-genome-sequenced using PacBio sequencing technology. A comparative genomics approach was adopted to identify mutations present in strain H112 but absent in strain H54. Subsequently, an extensive phylogenetic analysis was conducted by including all publically available M. tuberculosis genomes. Single-nucleotide-polymorphisms (SNPs and structural variations (SVs common to hypervirulent strains in the global collection of genomes were considered as potential genetic determinants of hypervirulence.Results:Sequencing data revealed that both H112 and H54 were identified as members of the same sub-lineage L2.2.1. After excluding the lineage-related mutations shared between H112 and H54, we analyzed the phylogenetic relatedness of H112 with global collection of M. tuberculosis genomes (n = 4,338, and identified a novel

  9. Analysis of Host Responses to Mycobacterium tuberculosis Antigens in a Multi-Site Study of Subjects with Different TB and HIV Infection States in Sub-Saharan Africa

    Science.gov (United States)

    Sutherland, Jayne S.; Lalor, Maeve K.; Black, Gillian F.; Ambrose, Lyn R.; Loxton, Andre G.; Chegou, Novel N.; Kassa, Desta; Mihret, Adane; Howe, Rawleigh; Mayanja-Kizza, Harriet; Gomez, Marie P.; Donkor, Simon; Franken, Kees; Hanekom, Willem; Klein, Michel R.; Parida, Shreemanta K.; Boom, W. Henry; Thiel, Bonnie A.; Crampin, Amelia C.; Ota, Martin; Walzl, Gerhard; Ottenhoff, Tom H. M.; Dockrell, Hazel M.; Kaufmann, Stefan H. E.

    2013-01-01

    Background Tuberculosis (TB) remains a global health threat with 9 million new cases and 1.4 million deaths per year. In order to develop a protective vaccine, we need to define the antigens expressed by Mycobacterium tuberculosis (Mtb), which are relevant to protective immunity in high-endemic areas. Methods We analysed responses to 23 Mtb antigens in a total of 1247 subjects with different HIV and TB status across 5 geographically diverse sites in Africa (South Africa, The Gambia, Ethiopia, Malawi and Uganda). We used a 7-day whole blood assay followed by IFN-γ ELISA on the supernatants. Antigens included PPD, ESAT-6 and Ag85B (dominant antigens) together with novel resuscitation-promoting factors (rpf), reactivation proteins, latency (Mtb DosR regulon-encoded) antigens, starvation-induced antigens and secreted antigens. Results There was variation between sites in responses to the antigens, presumably due to underlying genetic and environmental differences. When results from all sites were combined, HIV- subjects with active TB showed significantly lower responses compared to both TST- and TST+ contacts to latency antigens (Rv0569, Rv1733, Rv1735, Rv1737) and the rpf Rv0867; whilst responses to ESAT-6/CFP-10 fusion protein (EC), PPD, Rv2029, TB10.3, and TB10.4 were significantly higher in TST+ contacts (LTBI) compared to TB and TST- contacts fewer differences were seen in subjects with HIV co-infection, with responses to the mitogen PHA significantly lower in subjects with active TB compared to those with LTBI and no difference with any antigen. Conclusions Our multi-site study design for testing novel Mtb antigens revealed promising antigens for future vaccine development. The IFN-γ ELISA is a cheap and useful tool for screening potential antigenicity in subjects with different ethnic backgrounds and across a spectrum of TB and HIV infection states. Analysis of cytokines other than IFN-γ is currently on-going to determine correlates of protection, which may

  10. Establishing a Link Between Prescription Drug Abuse and Illicit Online Pharmacies: Analysis of Twitter Data.

    Science.gov (United States)

    Katsuki, Takeo; Mackey, Tim Ken; Cuomo, Raphael

    2015-12-16

    Youth and adolescent non-medical use of prescription medications (NUPM) has become a national epidemic. However, little is known about the association between promotion of NUPM behavior and access via the popular social media microblogging site, Twitter, which is currently used by a third of all teens. In order to better assess NUPM behavior online, this study conducts surveillance and analysis of Twitter data to characterize the frequency of NUPM-related tweets and also identifies illegal access to drugs of abuse via online pharmacies. Tweets were collected over a 2-week period from April 1-14, 2015, by applying NUPM keyword filters for both generic/chemical and street names associated with drugs of abuse using the Twitter public streaming application programming interface. Tweets were then analyzed for relevance to NUPM and whether they promoted illegal online access to prescription drugs using a protocol of content coding and supervised machine learning. A total of 2,417,662 tweets were collected and analyzed for this study. Tweets filtered for generic drugs names comprised 232,108 tweets, including 22,174 unique associated uniform resource locators (URLs), and 2,185,554 tweets (376,304 unique URLs) filtered for street names. Applying an iterative process of manual content coding and supervised machine learning, 81.72% of the generic and 12.28% of the street NUPM datasets were predicted as having content relevant to NUPM respectively. By examining hyperlinks associated with NUPM relevant content for the generic Twitter dataset, we discovered that 75.72% of the tweets with URLs included a hyperlink to an online marketing affiliate that directly linked to an illicit online pharmacy advertising the sale of Valium without a prescription. This study examined the association between Twitter content, NUPM behavior promotion, and online access to drugs using a broad set of prescription drug keywords. Initial results are concerning, as our study found over 45,000 tweets

  11. EFFECT OF SOME MEDICINAL PLANTS ON GROWTH OF MYCOBACTERIUM TUBERCULOSIS, MULTI DRUG RESISTANT MYCOBACTERIUM TUBERCULOSIS AND MYCOBACTERIUM OTHER THAN TUBERCULOSIS

    Directory of Open Access Journals (Sweden)

    Prashant Shukla

    2013-12-01

    Full Text Available Six plants of medicinal uses were tried for their inhibitory effect on Mycobacterium tuberculosis (MTB, multi drug resistant Mycobacterium tuberculosis (MDR MTB and Mycobacterium other than tuberculosis (MOTT. MTB, MDR MTB and MOTT were cultured in 12B medium vials for Bacterc 460 TB system and incubated at 37˚C. The vials were read in Bacterc 460 TB system. Garlic, Ocimum sanctum, onion and neem showed effectiveness towards Mycobacterium tuberculosis and multi drug resistant Mycobacterium tuberculosis to some extent but ginger showed no effect at all. None of the plants studied had any inhibitory effect on Mycobacterium other than tuberculosis. Aloe vera had opposite effect on the growth and it was found to be assisting the growth of Mycobacterium tuberculosis and multi drug resistant Mycobacterium tuberculosis. The tests performed were in-vitro and the authors conlude that in-vivo the results may vary.

  12. Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics.

    Science.gov (United States)

    Das, Sarbashis; Pettersson, B M Fredrik; Behra, Phani Rama Krishna; Ramesh, Malavika; Dasgupta, Santanu; Bhattacharya, Alok; Kirsebom, Leif A

    2015-06-16

    We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum, M. chubuense, and M. obuense are 6.93, 5.95, and 5.58 Mb with GC-contents of 68.4%, 69.2%, and 67.9%, respectively. Comparative genomic analysis revealed that 3,254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named Mycobacterium ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds and copper homeostasis. These are the first nonpathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. Mycobacterium tuberculosis Metabolism

    Science.gov (United States)

    Warner, Digby F.

    2015-01-01

    Metabolism underpins the physiology and pathogenesis of Mycobacterium tuberculosis. However, although experimental mycobacteriology has provided key insights into the metabolic pathways that are essential for survival and pathogenesis, determining the metabolic status of bacilli during different stages of infection and in different cellular compartments remains challenging. Recent advances—in particular, the development of systems biology tools such as metabolomics—have enabled key insights into the biochemical state of M. tuberculosis in experimental models of infection. In addition, their use to elucidate mechanisms of action of new and existing antituberculosis drugs is critical for the development of improved interventions to counter tuberculosis. This review provides a broad summary of mycobacterial metabolism, highlighting the adaptation of M. tuberculosis as specialist human pathogen, and discusses recent insights into the strategies used by the host and infecting bacillus to influence the outcomes of the host–pathogen interaction through modulation of metabolic functions. PMID:25502746

  14. Mycobacterium ulcerans disease, Peru.

    Science.gov (United States)

    Guerra, Humberto; Palomino, Juan Carlos; Falconí, Eduardo; Bravo, Francisco; Donaires, Ninoska; Van Marck, Eric; Portaels, Françoise

    2008-03-01

    Eight adult patients (ages 18-58, 5 women) with Buruli ulcer (BU) confirmed by at least 2 diagnostic methods were seen in a 10-year period. Attempts to culture Mycobacterium ulcerans failed. Five patients came from jungle areas, and 3 from the swampy northern coast of Peru. The patients had 1-5 lesions, most of which were on the lower extremities. One patient had 5 clustered gluteal lesions; another patient had 2 lesions on a finger. Three patients were lost to follow-up. All 5 remaining patients had moderate disease. Diverse treatments (antituberculous drugs, World Health Organization [WHO] recommended antimicrobial drug treatment for BU, and for 3 patients, excision surgery) were successful. Only 1 patient (patient 7) received the specific drug treatment recommended by WHO. BU is endemic in Peru, although apparently infrequent. Education of populations and training of health workers are first needed to evaluate and understand the full extent of BU in Peru.

  15. Innate Immunity Holding the Flanks until Reinforced by Adaptive Immunity against Mycobacterium tuberculosis Infection

    OpenAIRE

    Khan, Nargis; Vidyarthi, Aurobind; Javed, Shifa; Agrewala, Javed N.

    2016-01-01

    T cells play a cardinal role in imparting adaptive immunity against Mycobacterium tuberculosis (Mtb). However, ample time is required before T-cells are able to evoke efficient effector responses in the lung, where the mycobacterium inflicts disease. This delay in T cells priming, which is termed as lag phase, provides sufficient time for Mtb to replicate and establish itself within the host. In contrast, innate immunity efficiently curb the growth of Mtb during initial phase of infection thr...

  16. Does global warning increase establishment rates of invasive alien species? A centurial time series analysis

    Science.gov (United States)

    Dingcheng Huang; Robert A. Haack; Runzhi. Zhang

    2011-01-01

    The establishment rate of invasive alien insect species has been increasing worldwide during the past century. This trend has been widely attributed to increased rates of international trade and associated species introductions, but rarely linked to environmental change. To better understand and manage the bioinvasion process, it is crucial to understand the...

  17. An Analysis of the Gaps in the Newly Established South African ...

    African Journals Online (AJOL)

    The South African Department of Defence and Military Veterans can be commended for having taken a bold step in an endeavour to establish an independent entity capable of conducting oversight of its military through the introduction of the Military Ombud Act. However, said Act seems not to adequately address pertinent ...

  18. Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment

    NARCIS (Netherlands)

    Veneault-Fourrey, Claire; Commun, Carine; Kohler, Annegret; Morin, Emmanuelle; Balestrini, Raffaella; Plett, Jonathan; Danchin, Etienne; Coutinho, Pedro; Wiebenga, A.; de Vries, Ronald P; Henrissat, Bernard; Martin, Francis; van den Brink, J.

    2014-01-01

    Ectomycorrhizal fungi, living in soil forests, are required microorganisms to sustain tree growth and productivity. The establishment of mutualistic interaction with roots to form ectomycorrhiza (ECM) is not well known at the molecular level. In particular, how fungal and plant cell walls are

  19. Safety assessment in primary Mycobacterium tuberculosis smear ...

    African Journals Online (AJOL)

    . Safety assessment in primary Mycobacterium tuberculosis smear microscopy centres in Blantyre. Malawi: a facility based cross sectional survey. ABSTRACT. Introduction. Tuberculosis (TB) is caused by Mycobacterium tuberculosis and is.

  20. The genome, evolution and diversity of Mycobacterium ulcerans.

    Science.gov (United States)

    Röltgen, Katharina; Stinear, Timothy P; Pluschke, Gerd

    2012-04-01

    Mycobacterium ulcerans (M. ulcerans) causes a devastating infection of the skin and underlying tissue commonly known as Buruli ulcer (BU). Genetic analyses indicate that M. ulcerans has a common ancestor with Mycobacterium marinum (M. marinum) and has diverged from this fish and human pathogen perhaps around a million years ago. M. ulcerans is characterized by minimal genetic diversity and since it has a highly clonal population structure, genetic differences between individual isolates reflect changes that have occurred sequentially from their respective progenitors. This feature, which is shared by other bacterial pathogens with low sequence diversity, such as Yersinia pestis and Bordetella pertussis renders M. ulcerans a promising model to reveal evolutionary mechanisms. Until today transmission pathways and environmental reservoirs of M. ulcerans are not entirely explored. However, comparative genome analysis of closely related M. ulcerans isolates is anticipated to give deeper insights into the population structure of this enigmatic mycobacterium. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Mycobacterium arupense, Mycobacterium heraklionense, and a Newly Proposed Species, “Mycobacterium virginiense” sp. nov., but Not Mycobacterium nonchromogenicum, as Species of the Mycobacterium terrae Complex Causing Tenosynovitis and Osteomyelitis

    Science.gov (United States)

    Vasireddy, Sruthi; Brown-Elliott, Barbara A.; Wengenack, Nancy L.; Eke, Uzoamaka A.; Benwill, Jeana L.; Turenne, Christine; Wallace, Richard J.

    2016-01-01

    Mycobacterium terrae complex has been recognized as a cause of tenosynovitis, with M. terrae and Mycobacterium nonchromogenicum reported as the primary etiologic pathogens. The molecular taxonomy of the M. terrae complex causing tenosynovitis has not been established despite approximately 50 previously reported cases. We evaluated 26 isolates of the M. terrae complex associated with tenosynovitis or osteomyelitis recovered between 1984 and 2014 from 13 states, including 5 isolates reported in 1991 as M. nonchromogenicum by nonmolecular methods. The isolates belonged to three validated species, one new proposed species, and two novel related strains. The majority of isolates (20/26, or 77%) belonged to two recently described species: Mycobacterium arupense (10 isolates, or 38%) and Mycobacterium heraklionense (10 isolates, or 38%). Three isolates (12%) had 100% sequence identity to each other by 16S rRNA and 99.3 to 100% identity by rpoB gene region V sequencing and represent a previously undescribed species within the M. terrae complex. There were no isolates of M. terrae or M. nonchromogenicum, including among the five isolates reported in 1991. The 26 isolates were susceptible to clarithromycin (100%), rifabutin (100%), ethambutol (92%), and sulfamethoxazole or trimethoprim-sulfamethoxazole (70%). The current study suggests that M. arupense, M. heraklionense, and a newly proposed species (“M. virginiense” sp. nov.; proposed type strain MO-233 [DSM 100883, CIP 110918]) within the M. terrae complex are the major causes of tenosynovitis and osteomyelitis in the United States, with little change over 20 years. Species identification within this complex requires sequencing methods. PMID:26962085

  2. AN ANALYSIS OF THE GAPS IN THE NEWLY ESTABLISHED SOUTH AFRICAN MILITARY OMBUD

    OpenAIRE

    Boitumelo Mmusinyane; Moses Montesh

    2013-01-01

    The South African Department of Defence and Military Veterans can be commended for having taken a bold step in an endeavour to establish an independent entity capable of conducting oversight of its military through the introduction of the Military Ombud Act. However, said Act seems not to adequately address pertinent issues experienced by the defence sector. These issues include who may submit a complaint, the independence of the Military Ombud (MO) and its accountability structure. Unless th...

  3. Harmonisation of serum dihydrotestosterone analysis: establishment of an external quality assurance program.

    Science.gov (United States)

    Greaves, Ronda F; Jolly, Lisa; Hartmann, Michaela F; Ho, Chung Shun; Kam, Richard K T; Joseph, John; Boyder, Conchita; Wudy, Stefan A

    2017-03-01

    Serum dihydrotestosterone (DHT) is an important analyte for the clinical assessment of disorders of sex development. It is also reportedly a difficult analyte to measure. Currently, there are significant gaps in the standardisation of this analyte, including no external quality assurance (EQA) program available worldwide to allow for peer review performance of DHT. We therefore proposed to establish a pilot EQA program for serum DHT. DHT was assessed in the 2015 Royal College of Pathologists of Australasia Quality Assurance Programs' Endocrine program material. The material's target (i.e. "true") values were established using a measurement procedure based on isotope dilution gas chromatography (GC) tandem mass spectrometry (MS/MS). DHT calibrator values were based on weighed values of pure DHT material (>97.5% purity) from Sigma. The allowable limits of performance (ALP) were established as ±0.1 up to 0.5 nmol/L and ±15% for targets >0.5 nmol/L. Target values for the six levels of RCPAQAP material for DHT ranged from 0.02 to 0.43 nmol/L (0.01-0.12 ng/mL). The material demonstrated linearity across the six levels. There were seven participating laboratories for this pilot study. Results of the liquid chromatography (LC) MS/MS methods were within the ALP; whereas the results from the immunoassay methods were consistently higher than the target values and outside the ALP. This report provides the first peer comparison of serum DHT measured by mass spectrometry (MS) and immunoassay laboratories. Establishment of this program provides one of the pillars to achieve method harmonisation. This supports accurate clinical decisions where DHT measurement is required.

  4. Analysis of the Economic and Welfare Impacts of Establishing Irrigation Water Market in Qazvin Province

    Directory of Open Access Journals (Sweden)

    2014-03-01

    Full Text Available In this study economic and welfare impacts of establishing irrigation water market in Qazvin province as well as potentiality of irrigation water transfer under stress irrigation conditions in the cities of Qazvin province were analyzed. To achieve the above objectives, Positive Mathematical Programming model and State Wide Agricultural Production functions were used. To achieve applicable results, the production function with a constant elasticity of substitution and cost function with an exponential form were included into the Positive Mathematical Programming model was imported. The study data for the year 2011-2012 was collected by asking the relevant offices in each city of Qazvin province. The proposed model was solved in six successive stages using the GAMS software. After solving the model, amount changes in the area of irrigated crops, farmer's gross profit and labor surplus under the two conditions of “existence of water market” and “lack of water market “at the regional level were calculated. The results showed that establishing irrigation water market increases total irrigated lands for 1/2 percent, total farmer’s gross profit for 1/86 percent and total labor force employed in agriculture for 1/8 percent in the province. Ultimately, considering the supportive and constructive role of regional water markets, it is recommended to provide necessary conditions and tools to establish an optimal use of such a mechanism associated with the type of market in Qazvin province.

  5. Security Analysis and Improvements of Session Key Establishment for Clustered Sensor Networks

    Directory of Open Access Journals (Sweden)

    Jiye Kim

    2016-01-01

    Full Text Available WSN (wireless sensor network is one of the main technologies in IoT (Internet of Things applications or services. To date, several schemes have been proposed to establish a pair-wise key between two nodes in WSN, and most of them are designed to establish long-term keys used throughout the network lifetime. However, in the near future, if WSN will be used for information infrastructures in various fields such as manufacturing, distribution, or public facilities management and its life cycle can be as long as that of other common networks, it will definitely be advantageous in terms of security to encrypt messages using session keys instead of long-term keys. In this paper, we propose a session key establishment scheme for clustered sensor networks that is based on elliptic curve Diffie-Hellman (ECDH key exchange and hash chain. The proposed scheme eliminates vulnerabilities of existing schemes for WSN and has improved security. The proposed scheme is efficient in terms of energy costs compared to related schemes.

  6. Mycobacterium fortuitum causing surgical site wound infection

    International Nuclear Information System (INIS)

    Kaleem, F.; Usman, J.; Omair, M.; Din, R.U.; Hassan, A.

    2010-01-01

    Mycobacterium fortuitum, a rapidly growing mycobacterium, is ubiquitous in nature. The organism was considered to be a harmless saprophyte but now there have been several reports from different parts of the world wherein it has been incriminated in a variety of human infections. We report a culture positive case of surgical site infection caused by Mycobacterium fortuitum, who responded well to the treatment. (author)

  7. Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment.

    Science.gov (United States)

    Veneault-Fourrey, Claire; Commun, Carine; Kohler, Annegret; Morin, Emmanuelle; Balestrini, Raffaella; Plett, Jonathan; Danchin, Etienne; Coutinho, Pedro; Wiebenga, Ad; de Vries, Ronald P; Henrissat, Bernard; Martin, Francis

    2014-11-01

    Ectomycorrhizal fungi, living in soil forests, are required microorganisms to sustain tree growth and productivity. The establishment of mutualistic interaction with roots to form ectomycorrhiza (ECM) is not well known at the molecular level. In particular, how fungal and plant cell walls are rearranged to establish a fully functional ectomycorrhiza is poorly understood. Nevertheless, it is likely that Carbohydrate Active enZymes (CAZyme) produced by the fungus participate in this process. Genome-wide transcriptome profiling during ECM development was used to examine how the CAZome of Laccaria bicolor is regulated during symbiosis establishment. CAZymes active on fungal cell wall were upregulated during ECM development in particular after 4weeks of contact when the hyphae are surrounding the root cells and start to colonize the apoplast. We demonstrated that one expansin-like protein, whose expression is specific to symbiotic tissues, localizes within fungal cell wall. Whereas L. bicolor genome contained a constricted repertoire of CAZymes active on cellulose and hemicellulose, these CAZymes were expressed during the first steps of root cells colonization. L. bicolor retained the ability to use homogalacturonan, a pectin-derived substrate, as carbon source. CAZymes likely involved in pectin hydrolysis were mainly expressed at the stage of a fully mature ECM. All together, our data suggest an active remodelling of fungal cell wall with a possible involvement of expansin during ECM development. By contrast, a soft remodelling of the plant cell wall likely occurs through the loosening of the cellulose microfibrils by AA9 or GH12 CAZymes and middle lamella smooth remodelling through pectin (homogalacturonan) hydrolysis likely by GH28, GH12 CAZymes. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Mycobacterium tuberculosis Infection among Asian Elephants in Captivity.

    Science.gov (United States)

    Simpson, Gary; Zimmerman, Ralph; Shashkina, Elena; Chen, Liang; Richard, Michael; Bradford, Carol M; Dragoo, Gwen A; Saiers, Rhonda L; Peloquin, Charles A; Daley, Charles L; Planet, Paul; Narachenia, Apurva; Mathema, Barun; Kreiswirth, Barry N

    2017-03-01

    Although awareness of tuberculosis among captive elephants is increasing, antituberculosis therapy for these animals is not standardized. We describe Mycobacterium tuberculosis transmission between captive elephants based on whole genome analysis and report a successful combination treatment. Infection control protocols and careful monitoring of treatment of captive elephants with tuberculosis are warranted.

  9. Isolation of Mycobacterium tuberculosis complex (MTBC) from dairy ...

    African Journals Online (AJOL)

    ajl4

    2012-11-08

    Nov 8, 2012 ... Eleven thousand five hundred and eighty non-blood samples from dairy cows were subjected to mycobacterium culture and ... tuberculosis infection in cattle is a new risk to public health and should be paid more attention. Key words: ..... S, Zhao YL (2012). Spoligotyping and drug resistance analysis of.

  10. Model establishing and performance analysis of service stratum traffic in the integrated sensing network

    Science.gov (United States)

    Ge, Zhiqun; Wang, Ying; Zhang, Xiaolu; Zheng, Yu; Zhao, Xinqun; Sun, Xiaohan

    2017-01-01

    We propose a time-division hybrid-user data flow model scheme based on semi-Markov state-transition algorithm for multiclass business and service in Integrated Sensing Network (ISN). Two typical flow models, visual sense and auditory sense service models, are set up due to the real situation of service stratum traffic, respectively. The experimental system based on the Asynchronous Optical Packet Switching (AOPS) network simulation platform is established for the feasibility of the proposed data flow model. The results show that the proposed models achieve reasonable packet loss rate and delay time in the case of different business and service levels.

  11. Establishment of new method for analysis of starch contents and varietal differences in soybean seeds

    OpenAIRE

    Jeong, Woo-Hyeun; Harada, Kyuya; Yamada, Tetsuya; Abe, Jun; Kitamura, Keisuke

    2010-01-01

    Aside from a report claiming that soybean seeds contain less than 1% starch, little is actually known about the genetic variation of the starch content in this important crop species. We used a starch-iodine test to identify varieties with high starch content in a soybean germplasm collection and found a total of 34 cultivars that showed a strongly positive reaction (dark color). For a more accurate quantitation of starch contents, we established a new method using a heat-resistant α-amylase ...

  12. Critical analysis of the influence of the possibilities of establishing the moulding technology on obtaining the castings

    Science.gov (United States)

    Josan, A.; Pinca Bretotean, C.; Raţiu, S.

    2018-01-01

    The Romanian foundries give high priority to quality castings. Thus, the castings moulding technology decisively influences their quality. Therefore, it is necessary to study the possibilities of realization the moulds for castings. This paper presents a critical analysis of the influence of all factors of the moulding technology on the quality of steel castings. The purpose of the study is to analyze the way to establishing the separation plane, how to determine the processing allowances and technological allowances, the dimensioning of the riser, the choice of the optimal casting method of the liquid alloy. Establishing optimal moulding technology determines the optimal use of resources with direct implications for manufacturing costs.

  13. Degradation mode analysis: An approach to establish effective predictive maintenance tasks

    International Nuclear Information System (INIS)

    Sonnett, D.E.; Douglass, P.T.; Barnard, D.D.

    1991-01-01

    A significant number of nuclear generating stations have been employing Reliability Centered Maintenance methodology to arrive at applicable and effective maintenance tasks for their plant equipment. The resultant endpoint of most programs has been an increased emphasis on predictive maintenance as the task of choice for monitoring and trending plant equipment condition to address failure mechanisms of the analyses. Many of these plants have spent several years conducting reliability centered analysis before they seriously begin implementing predictive program improvements. In this paper we present another methodology, entitled Degradation Mode Analysis, which provides a more direct method to quickly and economically achieve the major benefit of reliability centered analysis, namely predictive maintenance. (author)

  14. Can You Trust Your Data? Establishing the Need for a Measurement and Analysis Infrastructure Diagnostic

    National Research Council Canada - National Science Library

    Kasunic, Mark; McCurley, James; Zubrow, David

    2008-01-01

    ... or determine how to begin improving their data This report describes common errors in measurement and analysis and the need for a criterion-based assessment method that will allow organizations to evaluate...

  15. A strategic analysis of future growth options for an established process control company

    OpenAIRE

    Levesque, Sheila Lynne

    2007-01-01

    This project speaks to the prevailing business environment presently encountered at WESTCOAST Controls Ltd (WESTCOAST), a leading process control company in British Columbia, Canada. The scope of the project covers topics such as company overview, external industry analysis, and internal company analysis including strategic tools such as Porter's 5 Forces. The project concludes with a recommendation for the restructuring of the control systems & solutions division for improved performan...

  16. Inactivation of Mycobacterium paratuberculosis and Mycobacterium tuberculosis in fresh soft cheese by gamma radiation

    Science.gov (United States)

    Badr, Hesham M.

    2011-11-01

    The effectiveness of gamma irradiation on the inactivation of Mycobacterium paratuberculosis, Mycobacterium bovis and Mycobacterium tuberculosis in fresh soft cheese that prepared from artificially inoculated milk samples was studied. Irradiation at dose of 2 kGy was sufficient for the complete inactivation of these mycobacteria as they were not detected in the treated samples during storage at 4±1 °C for 15 days. Moreover, irradiation of cheese samples, that were prepared from un-inoculated milk, at this effective dose had no significant effects on their gross composition and contents from riboflavin, niacin and pantothenic acid, while significant decreases in vitamin A and thiamin were observed. In addition, irradiation of cheese samples had no significant effects on their pH and nitrogen fractions contents, except for the contents of ammonia, which showed a slight, but significant, increases due to irradiation. The analysis of cheese fats indicated that irradiation treatment induced significant increase in their oxidation parameters and contents from free fatty acids; however, the observed increases were relatively low. On the other hand, irradiation of cheese samples induced no significant alterations on their sensory properties. Thus, irradiation dose of 2 kGy can be effectively applied to ensure the safety of soft cheese with regards to these harmful mycobacteria.

  17. Can 15-locus mycobacterial interspersed repetitive unit-variable-number tandem repeat analysis provide insight into the evolution of Mycobacterium tuberculosis?

    Science.gov (United States)

    Gibson, Andrea; Brown, Timothy; Baker, Lucy; Drobniewski, Francis

    2005-12-01

    The phylogeny and evolution of the bacterium Mycobacterium tuberculosis is still poorly understood despite the application of a variety of molecular techniques. We analyzed 469 M. tuberculosis and 49 Mycobacterium bovis isolates to evaluate if the mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR) commonly used for epidemiological studies can define the phylogeny of the M. tuberculosis complex. This population was characterized by previously identified silent single-nucleotide polymorphisms (sSNPs) or by a macroarray based on these sSNPs that was developed in this study. MIRU-VNTR phylogenetic codes capable of differentiating between phylogenetic lineages were identified. Overall, there was 90.9% concordance between the lineages of isolates as defined by the MIRU-VNTR and sSNP analyses. The MIRU-VNTR phylogenetic code was unique to M. bovis and was not observed in any M. tuberculosis isolates. The codes were able to differentiate between different M. tuberculosis strain families such as Beijing, Delhi, and East African-Indian. Discrepant isolates with similar but not identical MIRU-VNTR codes often displayed a stepwise trend suggestive of bidirectional evolution. A lineage-specific panel of MIRU-VNTR can be used to subdivide each lineage for epidemiological purposes. MIRU-VNTR is a valuable tool for phylogenetic studies and could define an evolutionarily uncharacterized population of M. tuberculosis complex organisms.

  18. Analysis of rpsL and rrs genes mutations related to streptomycin resistance in Mdr and Xdr clinical isolates of Mycobacterium tuberculosis.

    Science.gov (United States)

    Arjomandzadegan, Mohammad; Gravand, Somayeh

    2015-01-01

    Streptomycin is a bactericidal and aminoglycoside antibiotic. It is one of the most effective drugs for treatment of multi-drug Tuberculosis disease. Incidence of resistance is increasingly reported. Its action mechanism is by inhibition of binding aminoacyl tRNA to position "A" in elongation phase, which finally it causes to stop bacterial protein synthesis. In this study, resistance rapid investigation to streptomycin was conducted in clinical strains of Mycobacterium tuberculosis. In this study, among 105 strains of phlegm-positive and culture-positive Mycobacterium tuberculosis, 45 strains of resistant and sensitive to streptomycin were selected for possible mutations examination in genes rrs and rpsL. Specific primers that used for PCR were named rpsL 1, rpsL 2 and rrsR, Frrs. PCR products were sequenced. PCR Products represents 504 bp band for gene rpsL and 1027 bp for gene rrs that shows proper selection of primers and determining an amplification appropriate program. From 26 resistant strains to streptomycin 26 strain have mutation in rpsL gene and 1 strain have alteration in rrs gene. In this study 19 strains were sensitive to streptomycin that have no mutation in these gene. Streptomycin resistance is mainly related to mutation at codons 43 and 88 "rpsL" gene and to a lesser extent "rrs" that are the greatest cause of drug resistance to streptomycin.

  19. Communication component of rehabilitation establishments in Ukraine: issues of methodology of analysis

    Directory of Open Access Journals (Sweden)

    S. Y. Nedoboi

    2017-08-01

    As a result, there is a number of specific features in communication component of rehabilitation establishments. Firstly, a rehabilitation program is the first step in rehabilitation process. Effectiveness of its drafting and implementation is defined by an ability to make a contact and communication between doctor and patient. Secondly, communication and interaction between doctor and patient should continue from the beginning of treatment and even after person’s return to home life. Thirdly, a phenomenon of «therapeutic alliance» and a principle of «peer to peer» become meaningful in mentioned institutions as well as a growing role of practical nurses and other professionals in rehabilitation process.

  20. [Analysis on establishment and affecting factors of qi stagnation and blood stasis rat model].

    Science.gov (United States)

    Wang, Tingting; Jia, Cheng; Chen, Yu; Li, Xin; Cheng, Jiayi

    2012-06-01

    To study on the method for establishing the Qi stagnation and blood stasis rat model and analyze the affecting factors. The orthogonal design was adopted to study the influences of joint stimulations including noise, light, electricity, ice water bath, tail-clamping on model rats. The 'flying spot' method was used to dynamically simulate blood flow velocity in microcirculation. the pressure sensing technology of MOTO was adopted to detect hemorheology-related indicators. And the coagulation method was used to detect blood coagulation-related indicators. Compared with the negative control group, all model groups showed significant reduction in the blood flow velocity in mesenteric microcirculation and increase in the whole blood viscosity at high, medium and low shear rate, the plasma viscosity and the fibrinogen content in four blood coagulation indicators. Noise, light, electricity, tail-clamping, bondage and icewater-bath make significant impact on model rats.

  1. Establishment of animal model for the analysis of cancer cell metastasis during radiotherapy

    International Nuclear Information System (INIS)

    Park, Jong Kuk; Jang, Su Jin; Kang, Sung Wook; Park, Sunhoo; Hwang, Sang-Gu; Kim, Wun-Jae; Kang, Joo Hyun; Um, Hong-Duck

    2012-01-01

    Γ-Ionizing radiation (IR) therapy is one of major therapeutic tools in cancer treatment. Nevertheless, γ-IR therapy failed due to occurrence of metastasis, which constitutes a significant obstacle in cancer treatment. The main aim of this investigation was to construct animal model which present metastasis during radiotherapy in a mouse system in vivo and establishes the molecular mechanisms involved. The C6L transfectant cell line expressing firefly luciferase (fLuc) was treated with γ-IR, followed by immunoblotting, zymography and invasion assay in vitro. We additionally employed the C6L transfectant cell line to construct xenografts in nude mice, which were irradiated with γ-IR. Irradiated xenograft-containing mice were analyzed via survival curves, measurement of tumor size, and bioluminescence imaging in vivo and ex vivo. Metastatic lesions in organs of mice were further assessed using RT-PCR, H & E staining and immunohistochemistry. γ-IR treatment of C6L cells induced epithelial-mesenchymal transition (EMT) and increased cell invasion. In irradiated xenograft-containing mice, tumor sizes were decreased dramatically and survival rates extended. Almost all non-irradiated xenograft-containing control mice had died within 4 weeks. However, we also observed luminescence signals in about 22.5% of γ-IR-treated mice. Intestines or lungs of mice displaying luminescence signals contained several lesions, which expressed the fLuc gene and presented histological features of cancer tissues as well as expression of EMT markers. These findings collectively indicate that occurrences of metastases during γ-IR treatment accompanied induction of EMT markers, including increased MMP activity. Establishment of a murine metastasis model during γ-IR treatment should aid in drug development against cancer metastasis and increase our understanding of the mechanisms underlying the metastatic process

  2. COST ANALYSIS OF LONG ESTABLISHED AND NEWER ORAL ANTIEPILEPTIC DRUGS AVAILABLE IN THE INDIAN MARKET

    Directory of Open Access Journals (Sweden)

    Phatak Abhishek M, Hotwani Jitendra H, Deshmukhkiran R, Panchal Sagar S, Naik Madhura S

    2015-10-01

    Full Text Available Background: Large number of pharmaceutical companies manufactures antiepileptic drugs in India. The price variations among the marketed drugs are wide. Aims: The present study was aimed to find the cost of different oral antiepileptic drugs available in Indian market as monotherapy, combination therapy and number of manufacturing companies for each, to evaluate difference in cost of different brands of same dosage of same active drug by calculating percentage variation of cost. Methods and Materials: Cost of a drug being manufactured by different companies, in the same strength and dosage forms was obtained from “Indian Drug Review” Vol. XXI, Issue No.4, 2014 and “Current Index of Medical Specialties” July-October 2014. The difference in the maximum and minimum price of the same drug manufactured by different pharmaceutical companies and percentage variation in price was calculated. Results: The percentage price variation noted of long-established drugs was – Phenytoin (50mg: 140%, Carbamazepine (100mg: 1033%, Phenobarbital (30mg : 730%, Valproic acid (300mg : 420%. Newer drugs –Levetiracetam (250mg: 75%, Lamotrigine (25mg: 66%, Topiramate (50mg: 108%, Zonisamide (100mg: 19%. Combination drugs – Phenobarbital + Phenytoin (30+100 mg: 354.55%. Conclusion: The percentage price variation of different brands of the same commonly used long-established oral antiepileptic drug manufactured in India is very wide. The formulation or brand of Antiepileptic drugs (AED’s should preferably not be changed since variations in bioavailability or different pharmacokinetic profiles may increase the potential for reduced effect or excessive side effects. Hence, manufacturing companies should aim to decrease the price variation while maintaining the therapeutic efficacy.

  3. Use of benefit-cost analysis in establishing Federal radiation protection standards: a review

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, L.E.

    1979-10-01

    This paper complements other work which has evaluated the cost impacts of radiation standards on the nuclear industry. It focuses on the approaches to valuation of the health and safety benefits of radiation standards and the actual and appropriate processes of benefit-cost comparison. A brief historical review of the rationale(s) for the levels of radiation standards prior to 1970 is given. The Nuclear Regulatory Commission (NRC) established numerical design objectives for light water reactors (LWRs). The process of establishing these numerical design criteria below the radiation protection standards set in 10 CFR 20 is reviewed. EPA's 40 CFR 190 environmental standards for the uranium fuel cycle have lower values than NRC's radiation protection standards in 10 CFR 20. The task of allocating EPA's 40 CFR 190 standards to the various portions of the fuel cycle was left to the implementing agency, NRC. So whether or not EPA's standards for the uranium fuel cycle are more stringent for LWRs than NRC's numerical design objectives depends on how EPA's standards are implemented by NRC. In setting the numerical levels in Appendix I to 10 CFR 50 and 40 CFR 190 NRC and EPA, respectively, focused on the costs of compliance with various levels of radiation control. A major portion of the paper is devoted to a review and critique of the available methods for valuing health and safety benefits. All current approaches try to estimate a constant value of life and use this to vaue the expected number of lives saved. This paper argues that it is more appropriate to seek a value of a reduction in risks to health and life that varies with the extent of these risks. Additional research to do this is recommended. (DC)

  4. Establishment of Orthotopic Xuanwei Lung Cancer SCID Mouse Model 
and Analysis of Biological Properties

    Directory of Open Access Journals (Sweden)

    Yongchun ZHOU

    2012-08-01

    Full Text Available Background and objective The incidence of Xuanwei lung cancer ranks first in China, and its pathogenesis requires in-depth investigation. This study aims to establish an orthotopic Xuanwei lung cancer severe combined immunodeficiency (SCID mouse model and to provide a basic experimental platform for further study. Methods The Xuanwei lung cancer cell line XWLC-05 was inoculated into the lung tissue of SCID mice in high and low doses. The tumor formation rates, tumor characteristics, spontaneous metastases, and survival times of the mice were observed, taking a subcutaneously transplanted tumor as control. Results The tumor formation rates of the orthotopic transplantation of lung cancer cells in high and low doses were 81% and 83%, respectively, among which mice in the high-dose group appeared cachectic on day 13. Extensive invasion and adhesion were observed in the contralateral lung and thoracic cavity, but no distant metastasis was exhibited. Mice with low-dose cells in the orthotopic transplantation group appeared cachectic and distant metastasis occurred on day 25. The tumor formation rates in the subcutaneous inoculation group by the high and low doses of cells were 100% and 94.5%, respectively, and no distant metastasis was observed. The rate of metastasis within the orthotopic transplantation group and between the orthotopic and subcutaneous inoculation groups showed a significant difference (P<0.05. A significant difference was indicated by the survival rate within and between the groups (P<0.001. Conclusion We successfully established an orthotopic XWLC SCID mouse model, which lays the foundation for a more in-depth study.

  5. CRAB3: Establishing a new generation of services for distributed analysis at CMS

    Science.gov (United States)

    Cinquilli, M.; Spiga, D.; Grandi, C.; Hernàndez, J. M.; Konstantinov, P.; Mascheroni, M.; Riahi, H.; Vaandering, E.

    2012-12-01

    In CMS Computing the highest priorities for analysis tools are the improvement of the end users’ ability to produce and publish reliable samples and analysis results as well as a transition to a sustainable development and operations model. To achieve these goals CMS decided to incorporate analysis processing into the same framework as data and simulation processing. This strategy foresees that all workload tools (TierO, Tier1, production, analysis) share a common core with long term maintainability as well as the standardization of the operator interfaces. The re-engineered analysis workload manager, called CRAB3, makes use of newer technologies, such as RESTFul based web services and NoSQL Databases, aiming to increase the scalability and reliability of the system. As opposed to CRAB2, in CRAB3 all work is centrally injected and managed in a global queue. A pool of agents, which can be geographically distributed, consumes work from the central services serving the user tasks. The new architecture of CRAB substantially changes the deployment model and operations activities. In this paper we present the implementation of CRAB3, emphasizing how the new architecture improves the workflow automation and simplifies maintainability. In particular, we will highlight the impact of the new design on daily operations.

  6. CRAB3: Establishing a new generation of services for distributed analysis at CMS

    Energy Technology Data Exchange (ETDEWEB)

    Cinquilli, M. [CERN; Spiga, D. [CERN; Grandi, C. [INFN, Bologna; Hernandez, J. M. [Madrid, CIEMAT; Konstantinov, P. [CERN; Mascheroni, M. [CERN; Riahi, H. [INFN, Perugia; Vaandering, E. [Fermilab

    2012-01-01

    In CMS Computing the highest priorities for analysis tools are the improvement of the end users ability to produce and publish reliable samples and analysis results as well as a transition to a sustainable development and operations model. To achieve these goals CMS decided to incorporate analysis processing into the same framework as data and simulation processing. This strategy foresees that all workload tools (TierO, Tier1, production, analysis) share a common core with long term maintainability as well as the standardization of the operator interfaces. The re-engineered analysis workload manager, called CRAB3, makes use of newer technologies, such as RESTFul based web services and NoSQL Databases, aiming to increase the scalability and reliability of the system. As opposed to CRAB2, in CRAB3 all work is centrally injected and managed in a global queue. A pool of agents, which can be geographically distributed, consumes work from the central services serving the user tasks. The new architecture of CRAB substantially changes the deployment model and operations activities. In this paper we present the implementation of CRAB3, emphasizing how the new architecture improves the workflow automation and simplifies maintainability. In particular, we will highlight the impact of the new design on daily operations.

  7. CRAB3: Establishing a new generation of services for distributed analysis at CMS

    International Nuclear Information System (INIS)

    Cinquilli, M; Spiga, D; Konstantinov, P; Mascheroni, M; Grandi, C; Hernàndez, J M; Riahi, H; Vaandering, E

    2012-01-01

    In CMS Computing the highest priorities for analysis tools are the improvement of the end users’ ability to produce and publish reliable samples and analysis results as well as a transition to a sustainable development and operations model. To achieve these goals CMS decided to incorporate analysis processing into the same framework as data and simulation processing. This strategy foresees that all workload tools (TierO, Tier1, production, analysis) share a common core with long term maintainability as well as the standardization of the operator interfaces. The re-engineered analysis workload manager, called CRAB3, makes use of newer technologies, such as RESTFul based web services and NoSQL Databases, aiming to increase the scalability and reliability of the system. As opposed to CRAB2, in CRAB3 all work is centrally injected and managed in a global queue. A pool of agents, which can be geographically distributed, consumes work from the central services serving the user tasks. The new architecture of CRAB substantially changes the deployment model and operations activities. In this paper we present the implementation of CRAB3, emphasizing how the new architecture improves the workflow automation and simplifies maintainability. In particular, we will highlight the impact of the new design on daily operations.

  8. Establishing guidance for the review of human reliability analysis in PSA

    International Nuclear Information System (INIS)

    Reer, B.; Dang, V.N.; Hirschberg, S.; Meyer, P.

    2000-01-01

    PSI was commissioned to develop Guidelines for the Regulatory Review of the Human Reliability Analysis (HRA) within Probabilistic Safety Assessments (PSAs) for nuclear power plants. In the Guidelines, HRA quality is addressed in terms of 97 indicators. Each indicator is formulated as a question, described as a specific feature of the analysis, and then explained in detail. Two analysis stages are distinguished: the selection of the human errors to be modelled, and their quantification to determine their impact on the core damage frequency. Review findings are grouped under two headings: transparency and adequacy. An analysis is 'transparent' if an externally qualified person is able to reproduce the analysis results, and 'adequate' if such results reflect the plant-specific conditions related to safety. To allocate resources efficiently, the review is structured in two phases: (1) The Quick Review, which clarifies whether the HRA has a fundamental deficiency and, furthermore, if it points to information needs and areas of emphasis for the detailed review, and (2) The Detailed Review, which results in well-grounded findings, based on extended examinations and close-plant contacts. (authors)

  9. Establishing two-dimensional gels for the analysis of Leishmania proteomes.

    Science.gov (United States)

    Acestor, Nathalie; Masina, Slavica; Walker, John; Saravia, Nancy G; Fasel, Nicolas; Quadroni, Manfredo

    2002-07-01

    Several different sample preparation methods for two-dimensional electrophoresis (2-DE) analysis of Leishmania parasites were compared. From this work, we were able to identify a solubilization method using Nonidet P-40 as detergent, which was simple to follow, and which produced 2-DE gels of high resolution and reproducibility.

  10. Establishing a Common Vocabulary of Key Concepts for the Effective Implementation of Applied Behavior Analysis

    Science.gov (United States)

    Cihon, Traci M.; Cihon, Joseph H.; Bedient, Guy M.

    2016-01-01

    The technical language of behavior analysis is arguably necessary to share ideas and research with precision among each other. However, it can hinder effective implementation of behavior analytic techniques when it prevents clear communication between the supervising behavior analyst and behavior technicians. The present paper provides a case…

  11. APPRAISAL ANALYSIS OF AN AGRICULTURAL COMPANY AND ESTABLISHMENT OF A DEVELOPMENT STRATEGY

    Directory of Open Access Journals (Sweden)

    Ionela Mituko VLAD

    2012-01-01

    Full Text Available The paper presents the diagnostic analysis of SC Agrozootehnica Indeoendenta SA from Calarasi locality, analysis performed based on the data provided by the annual financial statements and those in the commercial, managerial, technical and technological sectors. The analysis started with the realization of the internal and external factors appraisal matrices of each branch of activity from the company, as well as the preparation of the internal and external factors global appraisal matrices (MEFI and global MEFE, based on which the development strategy was identified, by setting the values identified through matrix, in the SWOT model. The company SC Agrozootehnica Independenta SA is positioned in the IInd quadrant from the SWOT chart, quadrant that highlights the status of a company that has numerous advantages, but meets an unfavourable environment, so that it must use the strong points in order to create opportunities in other complementary activity fields or on other markets. Following our analysis, the recommendation is for SCAgrozootehnica Indeoendenta SA to adapt and implement a diversification strategy.

  12. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization.

    Science.gov (United States)

    Gcebe, Nomakorinte; Rutten, Victor; Pittius, Nicolaas Gey van; Naicker, Brendon; Michel, Anita

    2017-04-01

    Non-tuberculous mycobacteria (NTM) are ubiquitous in the environment, and an increasing number of NTM species have been isolated and characterized from both humans and animals, highlighting the zoonotic potential of these bacteria. Host exposure to NTM may impact on cross-reactive immune responsiveness, which may affect diagnosis of bovine tuberculosis and may also play a role in the variability of the efficacy of Mycobacterium bovis BCG vaccination against tuberculosis. In this study we characterized 10 NTM isolates originating from water, soil, nasal swabs of cattle and African buffalo as well as bovine tissue samples. These isolates were previously identified during an NTM survey and were all found, using 16S rRNA gene sequence analysis to be closely related to Mycobacterium moriokaense. A polyphasic approach that included phenotypic characterization, antibiotic susceptibility profiling, mycolic acid profiling and phylogenetic analysis of four gene loci, 16S rRNA, hsp65, sodA and rpoB, was employed to characterize these isolates. Sequence data analysis of the four gene loci revealed that these isolates belong to a unique species of the genus Mycobacterium. This evidence was further supported by several differences in phenotypic characteristics between the isolates and the closely related species. We propose the name Mycobacterium malmesburyense sp. nov. for this novel species. The type strain is WCM 7299T (=ATCC BAA-2759T=CIP 110822T).

  13. Analysis of Borrelia burgdorferi surface proteins as determinants in establishing host cell interactions

    Directory of Open Access Journals (Sweden)

    Virginia L Schmit

    2011-07-01

    Full Text Available Borrelia burgdorferi infection causes Lyme borreliosis in humans, a condition which can involve a systemic spread of the organism to colonize various tissues and organs. If the infection is left untreated by antimicrobials, it can lead to manifestations including, arthritis, carditis, and/or neurological problems. Identification and characterization of B. burgdorferi outer membrane proteins that facilitate cellular attachment and invasion to establish infection continue to be investigated. In this study, we sought to further define putative cell binding properties of surface-exposed B. burgdorferi proteins by observing whether cellular adherence could be blocked by antibodies. B. burgdorferi mixed separately with monoclonal antibodies against outer surface protein (Osp A, OspC, decorin-binding protein (Dbp A, BBA64, and RevA antigens were incubated with human umbilical vein endothelial cells (HUVEC and human neuroglial cells (H4. B. burgdorferi treated with anti-OspA, -DbpA, and –BBA64 monoclonal antibodies showed a significant decrease in cellular association compared to controls, whereas B. burgdorferi treated with anti-OspC and anti-RevA showed no reduction in cellular attachment. Additionally, temporal transcriptional analyses revealed upregulated expression of bba64, ospA, and dbpA during coincubation with cells. Together, the data provide evidence that OspA, DbpA, and BBA64 function in host cell adherence and infection mechanisms.

  14. Analysis of human protein replacement stable cell lines established using snoMEN-PR vector.

    Directory of Open Access Journals (Sweden)

    Motoharu Ono

    Full Text Available The study of the function of many human proteins is often hampered by technical limitations, such as cytotoxicity and phenotypes that result from overexpression of the protein of interest together with the endogenous version. Here we present the snoMEN (snoRNA Modulator of gene ExpressioN vector technology for generating stable cell lines where expression of the endogenous protein can be reduced and replaced by an exogenous protein, such as a fluorescent protein (FP-tagged version. SnoMEN are snoRNAs engineered to contain complementary sequences that can promote knock-down of targeted RNAs. We have established and characterised two such partial protein replacement human cell lines (snoMEN-PR. Quantitative mass spectrometry was used to analyse the specificity of knock-down and replacement at the protein level and also showed an increased pull-down efficiency of protein complexes containing exogenous, tagged proteins in the protein replacement cell lines, as compared with conventional co-expression strategies. The snoMEN approach facilitates the study of mammalian proteins, particularly those that have so far been difficult to investigate by exogenous expression and has wide applications in basic and applied gene-expression research.

  15. Rv2629 Overexpression Delays Mycobacterium smegmatis and Mycobacteria tuberculosis Entry into Log-Phase and Increases Pathogenicity of Mycobacterium smegmatis in Mice

    Directory of Open Access Journals (Sweden)

    Dan Liu

    2017-11-01

    Full Text Available Objective: The aim of the present study was to explore the potential biological role of Rv2629 in Mycobacterium smegmatis and Mycobacterium tuberculosis.Methods: Recombinant wild type and mutant Rv2629 strains were constructed. Rv2629 expression was evaluated by real-time PCR and western blot. Microarray and interaction network analyses were used to identify the gene interactions associated with wild type and mutant Rv2629. Bacterial growth was assessed in Balb/c mice infected with wild type and mutant Rv2629 strains using CFU assay and histological analysis of the organs.Results: Overexpression of Rv2629 could delay the entry of the Mycobacterium tuberculosis cells into the log-phase, while Rv2629 decreased the number of ribosomes and the expression of uridylate kinase in Mycobacterium smegmatis. The Gene Ontology (GO and pathway analysis indicated that 122 genes correlated with wild type Rv2629, whereas the Rv2629 mutation led to decrease in the ribosome production, oxidative phosphorylation, and virulence in Mycobacterium tuberculosis. Overexpression of Rv2629 slightly enhanced the drug resistance of Mycobacterium smegmatis to antibiotics, and increased its survival and pathogenicity in Balb/c mice.Conclusion: It is suggested that Rv2629 is involved in the survival of the clinical drug-resistant strain via bacterial growth repression and bacterial persistence induction.

  16. Establishing a Common Vocabulary of Key Concepts for the Effective Implementation of Applied Behavior Analysis

    OpenAIRE

    Traci M. CIHON; Joseph H. CIHON; Guy M. BEDIENT

    2016-01-01

    The technical language of behavior analysis is arguably necessary to share ideas and research with precision among each other. However, it can hinder effective implementation of behavior analytic techniques when it prevents clear communication between the supervising behavior analyst and behavior technicians. The present paper provides a case example of the development of a shared vocabulary, using plain English when possible, among supervisors and supervisees at a large public school distric...

  17. Establishing a protocol for element determination in human nail clippings by neutron activation analysis

    International Nuclear Information System (INIS)

    Sanches, Thalita Pinheiro; Saiki, Mitiko

    2011-01-01

    Human nail samples have been analyzed to evaluate occupational exposure, nutritional status and to diagnose certain diseases. However, sampling and washing protocols for nail analyses vary from study to study not allowing comparisons between studies. One of the difficulties in analyzing nail samples is to eliminate only surface contamination without removing elements of interest in this tissue. In the present study, a protocol was defined in order to obtain reliable results of element concentrations in human nail clippings. Nail clippings collected from all 10 fingers or toes were previously pre cleaned using an ethyl alcohol solution to eliminate microbes. Then, the clippings were cut in small pieces and submitted to different reagents for washing by shaking. Neutron activation analysis (NAA) was applied for nail samples analysis which consisted of irradiating aliquots of samples together with synthetic elemental standards in the IEA-R1 nuclear research reactor followed by gamma ray spectrometry. Comparisons made between the results obtained for nails submitted to different reagents for cleaning indicated that the procedure using acetone and Triton X100 solution is more effective than that of nitric acid solution. Analyses in triplicates of a nail sample indicated results with relative standard deviations lower than 15% for most of elements, showing the homogeneity of the prepared sample. Qualitative analyses of different nail polishes showed that the presence of elements determined in the present study is negligible in these products. Quality control of the analytical results indicated that the applied NAA procedure is adequate for human nail analysis. (author)

  18. Provenance Establishment of Stingless Bee Honey Using Multi-element Analysis in Combination with Chemometrics Techniques.

    Science.gov (United States)

    Shadan, Aidil Fahmi; Mahat, Naji A; Wan Ibrahim, Wan Aini; Ariffin, Zaiton; Ismail, Dzulkiflee

    2018-01-01

    As consumption of stingless bee honey has been gaining popularity in many countries including Malaysia, ability to identify accurately its geographical origin proves pertinent for investigating fraudulent activities for consumer protection. Because a chemical signature can be location-specific, multi-element distribution patterns may prove useful for provenancing such product. Using the inductively coupled-plasma optical emission spectrometer as well as principal component analysis (PCA) and linear discriminant analysis (LDA), the distributions of multi-elements in stingless bee honey collected at four different geographical locations (North, West, East, and South) in Johor, Malaysia, were investigated. While cross-validation using PCA demonstrated 87.0% correct classification rate, the same was improved (96.2%) with the use of LDA, indicating that discrimination was possible for the different geographical regions. Therefore, utilization of multi-element analysis coupled with chemometrics techniques for assigning the provenance of stingless bee honeys for forensic applications is supported. © 2017 American Academy of Forensic Sciences.

  19. Establishing a Common Vocabulary of Key Concepts for the Effective Implementation of Applied Behavior Analysis

    Directory of Open Access Journals (Sweden)

    Traci M. CIHON

    2016-12-01

    Full Text Available The technical language of behavior analysis is arguably necessary to share ideas and research with precision among each other. However, it can hinder effective implementation of behavior analytic techniques when it prevents clear communication between the supervising behavior analyst and behavior technicians. The present paper provides a case example of the development of a shared vocabulary, using plain English when possible, among supervisors and supervisees at a large public school district in which behavior analytic services were provided for children diagnosed with autism spectrum disorders. A list of terms and definitions are provided as well as suggestions on how to develop shared vocabularies within the readers’ own service provision context.

  20. Statistical analysis of the established salary in small and medium enterprises

    Directory of Open Access Journals (Sweden)

    Yu. S. Pin’kovetskaya

    2017-01-01

    Full Text Available The aim of the study was to analyze the present regularities, specific to the employees’ salaries of aggregates of small and medium enterprises related to the three dimensional categories and located in different regions of Russia. The following tasks were solved: the indexes, characterizing average monthly salary of employees based on the mentioned enterprises were assessed, belonging to different size categories and located in each of the regions; the relations were established between the average monthly salaries of employees of aggregates of small and medium enterprises and the cost of living in all regions of the country.Preliminary results of stopwatch reading of small and medium business activities in 2015 were used as initial data. The research was based on the comparison of indexes for the entrepreneurial sector and the full range of enterprises and organizations.Modeling differentiation of salaries’ values of small and medium enterprises aggregations, as well as its relationship to the values of the subsistence level was based on the development of the density function of normal distribution. The quality of the developed models was checked according to the Kolmogorov-Smirnov, Pearson and Shapiro-Wilk criteria.The obtained results have some theoretical significance, in particular, when conducting research related to the justification of the proposed wage of employees of enterprises different in number, the formation of measures for increasing efficiency of the entrepreneurial sector activity. Density functions of normal distribution given in the paper can be used in the justification of concepts, plans and programs of developing small and medium entrepreneurship in regions and municipalities. The practical importance of research results connected with the possibility of their use by entrepreneurs directly (especially by beginners when assessing the potential of enterprise creation and definition of employees’ proposed salaries. In

  1. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of succinyl-diaminopimelate desuccinylase (Rv1202, DapE) from Mycobacterium tuberculosis.

    Science.gov (United States)

    Reinhard, Linda; Mueller-Dieckmann, Jochen; Weiss, Manfred S

    2012-09-01

    Succinyl-diaminopimelate desuccinylase from Mycobacterium tuberculosis (DapE, Rv1202) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Diffraction-quality crystals were obtained at acidic pH from ammonium sulfate and PEG and diffraction data were collected from two crystals to resolutions of 2.40 and 2.58 Å, respectively. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 79.7, b = 76.0, c = 82.9 Å, β = 119°. The most probable content of the asymmetric unit was two molecules of DapE, which would correspond to a solvent content of 56%. Both examined crystals turned out to be pseudo-merohedrally twinned, with twin operator -h, -k, h + l and twin fractions of approximately 0.46 and 0.16, respectively.

  2. Establishing the date of Maori environmental impact in New Zealand through pollen analysis and radiocarbon dating

    Energy Technology Data Exchange (ETDEWEB)

    McGlone, M.S.; Wilmshurst, J.M. [Landcare Research, Lincoln, (New Zealand)

    1997-12-31

    Full text: Over the last decade there has been an intense debate about whether New Zealand prehistory is long ( > 1500 years) or short ( < 800 years). Pollen and charcoal analyses have played a key role in this debate by helping to pinpoint the transition from relatively undisturbed environments to those deforested by anthropogenic fires. Problems with in situ contamination, reworking of sediments, confusion of natural with anthropogenic impacts, and different theoretical expectations of growth, spread and impact of early Maori populations have led to disparate conclusions. We review pollen based studies carried out on a variety of fossil sites, including peat bogs, swamps, estuaries and lakes, and contribute new results. Different sedimentary environments show varying susceptibilities to contamination and have resulted in a wide spread of ages for initial Maori impact. Datable materials least susceptible to contamination by old or young carbon are pure peat and macrofossils, whereas lake, swamp and silty sediments are most susceptible. Analysis of the radiocarbon ages obtained for the start of Maori deforestation show that ages falling in the `long` prehistory period are exclusively derived from lake sediments and swamps. In contrast, the bulk of the ages falling in the `short` prehistory period are from pure peat and selected plant fragments. We conclude from our analysis of radiocarbon ages for pollen based deforestation that the first evidence of Maori environmental impact began about 700-550 calendar years BP (1250-1400 AD). Finer age resolution is limited by dating techniques, site limitations and the uncertainty associated with identifying the first signs of human impact. The period we have identified corresponds with the oldest dated archaeological sites and supports the short prehistory hypothesis. We discuss how to distinguish reliable fossil sites from those that have a high risk of giving misleading results.

  3. Establishing the date of Maori environmental impact in New Zealand through pollen analysis and radiocarbon dating

    International Nuclear Information System (INIS)

    McGlone, M.S.; Wilmshurst, J.M.

    1997-01-01

    Full text: Over the last decade there has been an intense debate about whether New Zealand prehistory is long ( > 1500 years) or short ( < 800 years). Pollen and charcoal analyses have played a key role in this debate by helping to pinpoint the transition from relatively undisturbed environments to those deforested by anthropogenic fires. Problems with in situ contamination, reworking of sediments, confusion of natural with anthropogenic impacts, and different theoretical expectations of growth, spread and impact of early Maori populations have led to disparate conclusions. We review pollen based studies carried out on a variety of fossil sites, including peat bogs, swamps, estuaries and lakes, and contribute new results. Different sedimentary environments show varying susceptibilities to contamination and have resulted in a wide spread of ages for initial Maori impact. Datable materials least susceptible to contamination by old or young carbon are pure peat and macrofossils, whereas lake, swamp and silty sediments are most susceptible. Analysis of the radiocarbon ages obtained for the start of Maori deforestation show that ages falling in the 'long' prehistory period are exclusively derived from lake sediments and swamps. In contrast, the bulk of the ages falling in the 'short' prehistory period are from pure peat and selected plant fragments. We conclude from our analysis of radiocarbon ages for pollen based deforestation that the first evidence of Maori environmental impact began about 700-550 calendar years BP (1250-1400 AD). Finer age resolution is limited by dating techniques, site limitations and the uncertainty associated with identifying the first signs of human impact. The period we have identified corresponds with the oldest dated archaeological sites and supports the short prehistory hypothesis. We discuss how to distinguish reliable fossil sites from those that have a high risk of giving misleading results

  4. Innate immunity to Mycobacterium tuberculosis.

    NARCIS (Netherlands)

    Crevel, R. van; Ottenhoff, T.H.; Meer, J.W.M. van der

    2002-01-01

    The different manifestations of infection with Mycobacterium tuberculosis reflect the balance between the bacillus and host defense mechanisms. Traditionally, protective immunity to tuberculosis has been ascribed to T-cell-mediated immunity, with CD4(+) T cells playing a crucial role. Recent

  5. The Analysis of the Relationship between Communication Skills and the Establishment of Clark's Management Network among Sport Managers

    Directory of Open Access Journals (Sweden)

    Rasool NAZARI

    2016-03-01

    Full Text Available The purpose of this study was to analyze the relationship between communication skills and the establishment of Clark's Management Network among sport managers. This applied research is a kind of correlational – survey study. Statistical population consist ed of 140 sport managers working for sport organizations in Isfahan Province, which have been selected by stratified random sampling. Measurement tools included two questionnaires of Communication Skill (91% and Establishment of Clark's Management Network (87%. Descriptive and inferential statistical methods applied for statistical analysis using SPSS software. Results show that there is a relationship between communication skills and the establishment of Clark's Management Network among sport managers. I n addition, the feedback component has greater contribution to prediction of Clark's management network (p 0.05. In general, it can acknowledge that the communication skills are effective in the establishment of Clark's management network and cause to i mprove the management process of sport organizations' managers and to achieve to the organizational goals with high level of productivity.

  6. Are Australians concerned about nanoparticles? A comparative analysis with established and emerging environmental health issues.

    Science.gov (United States)

    Capon, Adam; Rolfe, Margaret; Gillespie, James; Smith, Wayne

    2015-02-01

    Introducing new technologies into society raises considerable public concern. We determine the public concern about nanoparticles, and compare this concern to other environmental health issues such as wind farms and coal seam gas production. A repeat cross sectional survey examining views on environmental health issues, risk, chemicals and trust was undertaken in more than 1,300 Australian residents in 2000 and 2013. Logistic regression and principal component analysis was used to investigate predictors of nanoparticle concern and identify a component structure for environmental health issues that could explain a trend of future nanoparticle concern. Australians have a relatively low level of concern about the risks of nanoparticles to health when compared to their concerns about other environmental health issues. Items associated with concern included gender, a general wish to avoid chemicals and possibly trust in politicians. Concern over nanoparticles clustered with similar views on technological risks. Current public concern over the risks of nanoparticles is low. However, a reframing of the issue towards 'chemicals' is likely to have a negative effect on risk perceptions. This paper raises questions about appropriate channels for the effective communication of risk. © 2015 Public Health Association of Australia.

  7. Analysis of the key issues in establishing the Russian-based high technological companies

    Directory of Open Access Journals (Sweden)

    V. G. Zinov

    2016-01-01

    Full Text Available The article analyses the reasons that prevent a competitive export-oriented Russian domestic development of the robot surgical complex from being industrially prototyped and serially released for the domestic and global market. The development is completed within the framework of a «priority project» which was also highlighted as of significant importance in the Forecast analysis of the scientific-technological development of Russia for the period of up until 2030 and in the road maps of the National technological initiative and other strategic documents. The project was financed by nearly all development funds and institutes in Russia. A conclusion is drawn that the key reason behind the significant increase in a life span of a high-tech market product is the absence of a target setting and a programme of coordinated actions from committed ministries and governmental agencies, as well as the lack of a large high tech company in Russia, capable of producing in industrial volumes the export-oriented products and ensure their global sales.

  8. Amplification of Hsp 65 gene and usage of restriction endonuclease for identification of non tuberculous rapid grower mycobacterium.

    Science.gov (United States)

    Verma, Ajoy Kumar; Sarin, Rohit; Arora, Vijay Kumar; Kumar, Gavish; Arora, Jyoti; Singh, Paras; Myneedu, Vithal Prasad

    2018-01-01

    The rapid grower mycobacteria have emerged as significant group of human pathogen amongst the Runyon group IV organisms that are capable of causing infection in both the healthy and immunocompromised hosts. Study aimed to identification of species amongst rapid grower non tuberculous mycobacterial isolates by polymerase chain reaction - restriction enzyme analysis (PRA). Analysis and comparison of results with standard biochemical tests. Rapid grower non tuberculous mycobacteria had been collected from liquid culture section during the study period. All isolates were identified by conventional biochemical tests. A 441bp fragment of hsp65 genes was amplified and digested by two restriction enzymes, BstEII and HaeIII. Digested products were analyzed using polyacrilamid gel electrophoresis (PAGE). During study, 121 rapid grower mycobacterial isolates were subjected for species identification. Isolates were obtained from pulmonary samples (72) and extrapulmonary samples (49). In the PRA test 8 different types of rapid grower mycobacteria were identified after analyzing the fragments generated through restriction enzymes. Mycobacterium chelonae (57/121) was the most common isolate in pulmonary and extrapulmonary samples. Mycobacterium fortuitum (42), Mycobacterium abscessus (11), Mycobacterium immunogen (06), Mycobacterium peregrinum (02), Mycobacterium smegmatis (01), Mycobacterium wolinskyi (01), Mycobacterium goodii (01) were identified as other species of rapid grower non tuberculous mycobacteria. PRA is a rapid and accurate system for the identification of species of non tuberculous mycobacteria. Results of PRA and biochemical tests are concordant up to 98%. Copyright © 2017 Tuberculosis Association of India. Published by Elsevier B.V. All rights reserved.

  9. Characterization of a Mycobacterium leprae antigen related to the secreted Mycobacterium tuberculosis protein MPT32

    NARCIS (Netherlands)

    Wieles, B.; van Agterveld, M.; Janson, A.; Clark-Curtiss, J.; Rinke de Wit, T.; Harboe, M.; Thole, J.

    1994-01-01

    Secreted proteins may serve as major targets in the immune response to mycobacteria. To identify potentially secreted Mycobacterium leprae antigens, antisera specific for culture filtrate proteins of Mycobacterium tuberculosis were used to screen a panel of recombinant antigens selected previously

  10. Transcriptome analysis of embryonic mammary cells reveals insights into mammary lineage establishment.

    Science.gov (United States)

    Wansbury, Olivia; Mackay, Alan; Kogata, Naoko; Mitsopoulos, Costas; Kendrick, Howard; Davidson, Kathryn; Ruhrberg, Christiana; Reis-Filho, Jorge S; Smalley, Matthew J; Zvelebil, Marketa; Howard, Beatrice A

    2011-08-11

    The mammary primordium forms during embryogenesis as a result of inductive interactions between its constitutive tissues, the mesenchyme and epithelium, and represents the earliest evidence of commitment to the mammary lineage. Previous studies of embryonic mouse mammary epithelium indicated that, by mid-gestation, these cells are determined to a mammary cell fate and that a stem cell population has been delimited. Mammary mesenchyme can induce mammary development from simple epithelium even across species and classes, and can partially restore features of differentiated tissue to mouse mammary tumours in co-culture experiments. Despite these exciting properties, the molecular identity of embryonic mammary cells remains to be fully characterised. Here, we define the transcriptome of the mammary primordium and the two distinct cellular compartments that comprise it, the mammary primordial bud epithelium and mammary mesenchyme. Pathway and network analysis was performed and comparisons of embryonic mammary gene expression profiles to those of both postnatal mouse and human mammary epithelial cell sub-populations and stroma were made. Several of the genes we have detected in our embryonic mammary cell signatures were previously shown to regulate mammary cell fate and development, but we also identified a large number of novel candidates. Additionally, we determined genes that were expressed by both embryonic and postnatal mammary cells, which represent candidate regulators of mammary cell fate, differentiation and progenitor cell function that could signal from mammary lineage inception during embryogenesis through postnatal development. Comparison of embryonic mammary cell signatures with those of human breast cells identified potential regulators of mammary progenitor cell functions conserved across species. These results provide new insights into genetic regulatory mechanisms of mammary development, particularly identification of novel potential regulators of

  11. The regulation of sulfur metabolism in Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Stavroula K Hatzios

    2011-07-01

    Full Text Available Mycobacterium tuberculosis (Mtb has evolved into a highly successful human pathogen. It deftly subverts the bactericidal mechanisms of alveolar macrophages, ultimately inducing granuloma formation and establishing long-term residence in the host. These hallmarks of Mtb infection are facilitated by the metabolic adaptation of the pathogen to its surrounding environment and the biosynthesis of molecules that mediate its interactions with host immune cells. The sulfate assimilation pathway of Mtb produces a number of sulfur-containing metabolites with important contributions to pathogenesis and survival. This pathway is regulated by diverse environmental cues and regulatory proteins that mediate sulfur transactions in the cell. Here, we discuss the transcriptional and biochemical mechanisms of sulfur metabolism regulation in Mtb and potential small molecule regulators of the sulfate assimilation pathway that are collectively poised to aid this intracellular pathogen in its expert manipulation of the host. From this global analysis, we have identified a subset of sulfur-metabolizing enzymes that are sensitive to multiple regulatory cues and may be strong candidates for therapeutic intervention.

  12. Establishing the association between nonnutritive sucking behavior and malocclusions: A systematic review and meta-analysis.

    Science.gov (United States)

    Doğramacı, Esma J; Rossi-Fedele, Giampiero

    2016-12-01

    The authors studied the effects of nonnutritive sucking behavior (NNSB) on malocclusions through a systematic review of association (etiology). The authors performed a 3-step search strategy, including electronic searches. Studies of healthy participants with a history of active or previous NNSB, for whom specific malocclusion outcomes had been assessed, were eligible for inclusion. The authors considered before-and-after studies, prospective and retrospective (longitudinal) studies, case-control studies, and analytical cross-sectional studies. They excluded reviews, text- and opinion-based articles, conference abstracts, case reports, case-series, and descriptive cross-sectional studies. The authors, using standardized instruments, independently assessed methodological quality and extracted data from the included studies. In situations for which there were sufficient studies, the authors conducted meta-analyses using the random-effects model, supplemented with the fixed-effects model in situations for which statistical heterogeneity was less than 50%, which the authors assessed using the I 2 statistic. The authors included 15 identified studies. They found that NNSB was associated with varying risks of developing malocclusions. Pacifier suckers are less likely to develop an increased overjet compared with digit suckers, although the results of a meta-analysis of 7 studies whose investigators had assessed posterior crossbite in the primary dentition demonstrated a significant association with pacifier sucking over digit sucking (n = 5,560; risk ratio, 1.42; 95% confidence interval, 1.18-1.70; P = .0001). Longer duration of NNSB was associated with an increased risk of developing malocclusions. Across-study heterogeneity likely resulted from methodological and sample size differences. The authors of this study have confirmed the association between NNSB and the development of malocclusions. This study provides the highest level of evidence on this topic. Pacifiers

  13. Guidance for establishment and implementation of field sample management programs in support of EM environmental sampling and analysis activities

    International Nuclear Information System (INIS)

    1994-01-01

    The role of the National Sample Management Program (NSMP) proposed by the Department of Energy's Office of Environmental Management (EM) is to be a resource for EM programs and for local Field Sample Management Programs (FSMPs). It will be a source of information on sample analysis and data collection within the DOE complex. The purpose of this document is to establish the suggested scope of the FSMP activities to be performed under each Operations Office, list the drivers under which the program will operate, define terms and list references. This guidance will apply only to EM sampling and analysis activities associated with project planning, contracting, laboratory selection, sample collection, sample transportation, laboratory analysis and data management

  14. The application of DEA (Data Envelopment Analysis) window analysis in the assessment of influence on operational efficiencies after the establishment of branched hospitals.

    Science.gov (United States)

    Jia, Tongying; Yuan, Huiyun

    2017-04-12

    Many large-scaled public hospitals have established branched hospitals in China. This study is to provide evidence for strategy making on the management and development of multi-branched hospitals by evaluating and comparing the operational efficiencies of different hospitals before and after their establishment of branched hospitals. DEA (Data Envelopment Analysis) window analysis was performed on a 7-year data pool from five public hospitals provided by health authorities and institutional surveys. The operational efficiencies of sample hospitals measured in this study (including technical efficiency, pure technical efficiency and scale efficiency) had overall trends towards increase during this 7-year period of time, however, a temporary downturn occurred shortly after the establishment of branched hospitals; pure technical efficiency contributed more to the improvement of technical efficiency compared to scale efficiency. The establishment of branched-hospitals did not lead to a long-term negative effect on hospital operational efficiencies. Our data indicated the importance of improving scale efficiency via the optimization of organizational management, as well as the advantage of a different form of branch-establishment, merging and reorganization. This study brought an insight into the practical application of DEA window analysis on the assessment of hospital operational efficiencies.

  15. Polymorphisms of twenty regulatory proteins between Mycobacterium tuberculosis and Mycobacterium bovis

    Science.gov (United States)

    Mycobacterium tuberculosis and Mycobacterium bovis are responsible for tuberculosis in humans or animals, respectively. Both species are closely related and belong to the Mycobacterium tuberculosis complex (MTC). M. tuberculosis is the most ancient species from which M. bovis and the other members o...

  16. Mycobacterium avium Infection after Acupoint Embedding Therapy

    Directory of Open Access Journals (Sweden)

    Jiao Zhang, MD

    2017-09-01

    Full Text Available Summary:. Nontuberculous mycobacterium is a ubiquitous environmental organism that is unusual to cause a true infection, but it can cause severe cutaneous infections. In this case report, we present a successful treatment for a Chinese patient with Mycobacterium avium cutaneous infection after acupoint embedding therapy. We managed to conduct pathogenic detection, drug sensitive test, and multidisciplinary consultation. Finally, a systematic treatment strategy of nontuberculous mycobacterium was performed. Twenty-two-month follow-up revealed excellent outcome without any recurrence.

  17. Mycobacterium alsense sp. nov., a scotochromogenic slow grower isolated from clinical respiratory specimens

    DEFF Research Database (Denmark)

    Tortoli, Enrico; Richter, Elvira; Borroni, Emanuele

    2016-01-01

    "Mycobacterium alsiense", although reported in 2007, has not been validly published so far. The polyphasic characterization of the three strains available so far led us to the conclusion that they represent a distinct species within the genus Mycobacterium. The proposed new species grows slowly...... and presents pale yellow-pigmented colonies. A differentiation from other mycobacteria is not feasible on the basis of biochemical and cultural features alone while the genetic analysis, extended to eight housekeeping genes and one spacer region, reveals clear diversity from any other mycobacterium....... Mycobacterium asiaticum is the most closely related species on the basis of the 16S rRNA sequence (similarity 99.3%); the average nucleotide Identity between the genomes of the two species is 80.72%, clearly below the suggested cutoff (95-96%). The name M. alsense is proposed here for the new species...

  18. Development of a temperature-switch PCR-based SNP typing method for Mycobacterium ulcerans.

    Directory of Open Access Journals (Sweden)

    Katharina Röltgen

    Full Text Available Mycobacterium ulcerans (M. ulcerans, the causative agent of the devastating skin disease Buruli ulcer (BU, is characterized by an extremely low level of genetic diversity. Recently, we have reported the first discrimination of closely related M. ulcerans variants in the BU endemic Densu River Valley of Ghana. In the study real-time PCR-based single nucleotide polymorphism (SNP typing at 89 predefined loci revealed the presence of ten M. ulcerans haplotypes circulating in the BU endemic region. Here we describe the development of temperature-switch PCR (TSP assays that allow distinguishing these haplotypes by conventional agarose gel-based analysis of the PCR products. After validation of the accuracy of typing results, the TSP assays were successfully established in a reference laboratory in Ghana. Development of the cost-effective and rapid TSP-based genetic fingerprinting method will thus allow investigating the spread of M. ulcerans clones by regular genetic monitoring in BU endemic countries.

  19. Combating highly resistant emerging pathogen Mycobacterium abscessus and Mycobacterium tuberculosis with novel salicylanilide esters and carbamates.

    Science.gov (United States)

    Baranyai, Zsuzsa; Krátký, Martin; Vinšová, Jarmila; Szabó, Nóra; Senoner, Zsuzsanna; Horváti, Kata; Stolaříková, Jiřina; Dávid, Sándor; Bősze, Szilvia

    2015-08-28

    In the Mycobacterium genus over one hundred species are already described and new ones are periodically reported. Species that form colonies in a week are classified as rapid growers, those requiring longer periods (up to three months) are the mostly pathogenic slow growers. More recently, new emerging species have been identified to lengthen the list, all rapid growers. Of these, Mycobacterium abscessus is also an intracellular pathogen and it is the most chemotherapy-resistant rapid-growing mycobacterium. In addition, the cases of multidrug-resistant Mycobacterium tuberculosis infection are also increasing. Therefore there is an urgent need to find new active molecules against these threatening strains. Based on previous results, a series of salicylanilides, salicylanilide 5-chloropyrazinoates and carbamates was designed, synthesized and characterised. The compounds were evaluated for their in vitro activity on M. abscessus, susceptible M. tuberculosis H37Rv, multidrug-resistant (MDR) M. tuberculosis MDR A8, M. tuberculosis MDR 9449/2006 and on the extremely-resistant Praha 131 (XDR) strains. All derivatives exhibited a significant activity with minimum inhibitory concentrations (MICs) in the low micromolar range. Eight salicylanilide carbamates and two salicylanilide esters exhibited an excellent in vitro activity on M. abscessus with MICs from 0.2 to 2.1 μM, thus being more effective than ciprofloxacin and gentamicin. This finding is potentially promising, particularly, as M. abscessus is a threateningly chemotherapy-resistant species. M. tuberculosis H37Rv was inhibited with MICs from 0.2 μM, and eleven compounds have lower MICs than isoniazid. Salicylanilide esters and carbamates were found that they were effective also on MDR and XDR M. tuberculosis strains with MICs ≥1.0 μM. The in vitro cytotoxicity (IC50) was also determined on human MonoMac-6 cells, and selectivity index (SI) of the compounds was established. In general, salicylanilide

  20. [Infections due to Mycobacterium simiae].

    Science.gov (United States)

    García-Martos, Pedro; García-Agudo, Lidia; González-Moya, Enrique; Galán, Fátima; Rodríguez-Iglesias, Manuel

    2015-10-01

    Mycobacterium simiae is a slow-growing photochromogenic environmental mycobacterium, first described in 1965. Rarely associated with human infections, possibly due to its limited pathogenicity, it mainly produces lung infection in immunocompetent elderly patients with underlying lung disease, and in disseminated infections in immunosuppressed young patients with AIDS. A microbiological culture is needed to confirm the clinical suspicion, and genetic sequencing techniques are essential to correctly identify the species. Treating M. simiae infections is complicated, owing to the multiple resistance to tuberculous drugs and the lack of correlation between in vitro susceptibility data and in vivo response. Proper treatment is yet to be defined, but must include clarithromycin combined with other antimicrobials such as moxifloxacin and cotrimoxazole. It is possible that M. simiae infections are undiagnosed. Copyright © 2013 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  1. Revival and emended description of 'Mycobacterium paraffinicum' Davis, Chase and Raymond 1956 as Mycobacterium paraffinicum sp. nov., nom. rev.

    Science.gov (United States)

    Toney, Nadege; Adekambi, Toidi; Toney, Sean; Yakrus, Mitchell; Butler, W Ray

    2010-10-01

    The omission of the name 'Mycobacterium paraffinicum' from the Approved Lists of Bacterial Names was due to phenotypic confusion surrounding a close relationship with Mycobacterium scrofulaceum. Correspondingly, 'M. paraffinicum' strains grew slowly in > 7 days, stained acid-alcohol-fast and produced yellow-pigmented, smooth, waxy colonies in the dark at an optimal temperature of 35°C. However, 'M. paraffinicum' strains demonstrated no activity for urease, nicotinamidase or pyrazinamidase and lacked growth at 42°C, unlike M. scrofulaceum. The mycolic acid pattern, as determined by HPLC, clustered 'M. paraffinicum' with M. scrofulaceum, Mycobacterium avium and Mycobacterium parascrofulaceum. Strains were fully susceptible to linezolid, rifabutin, clarithromycin and amikacin. Examination of the historical reference strain of 'M. paraffinicum', ATCC 12670, and five additional isolates using comparative studies with 16S rRNA, hsp65 and rpoB gene and concatenated sequences showed that they formed a tight taxonomic group that was distinct from similar non-tuberculous mycobacteria. Multilocus enzyme electrophoresis (MEE) analysis confirmed a close association of the five additional isolates with the reference strain of 'M. paraffinicum' with a genetic distance of 0.12 and showed that all six strains were distinct from other closely related species. These genetic results provided unambiguous evidence of the uniqueness of this slowly growing, scotochromogenic species and supported the revival of the name as Mycobacterium paraffinicum (ex Davis, Chase and Raymond 1956) sp. nov., nom. rev. We propose the previously deposited reference strain ATCC 12670(T) =DSM 44181(T) =NCIMB 10420(T), located in collections worldwide, as the type strain.

  2. Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5' exonuclease activities.

    Science.gov (United States)

    Uson, Maria Loressa; Carl, Ayala; Goldgur, Yehuda; Shuman, Stewart

    2018-04-09

    Mycobacterium smegmatis FenA is a nucleic acid phosphodiesterase with flap endonuclease and 5' exonuclease activities. The 1.8 Å crystal structure of FenA reported here highlights as its closest homologs bacterial FEN-family enzymes ExoIX, the Pol1 exonuclease domain and phage T5 Fen. Mycobacterial FenA assimilates three active site manganese ions (M1, M2, M3) that are coordinated, directly and via waters, to a constellation of eight carboxylate side chains. We find via mutagenesis that the carboxylate contacts to all three manganese ions are essential for FenA's activities. Structures of nuclease-dead FenA mutants D125N, D148N and D208N reveal how they fail to bind one of the three active site Mn2+ ions, in a distinctive fashion for each Asn change. The structure of FenA D208N with a phosphate anion engaged by M1 and M2 in a state mimetic of a product complex suggests a mechanism for metal-catalyzed phosphodiester hydrolysis similar to that proposed for human Exo1. A distinctive feature of FenA is that it does not have the helical arch module found in many other FEN/FEN-like enzymes. Instead, this segment of FenA adopts a unique structure comprising a short 310 helix and surface β-loop that coordinates a fourth manganese ion (M4).

  3. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains.

    Science.gov (United States)

    Gutacker, Michaela M; Smoot, James C; Migliaccio, Cristi A Lux; Ricklefs, Stacy M; Hua, Su; Cousins, Debby V; Graviss, Edward A; Shashkina, Elena; Kreiswirth, Barry N; Musser, James M

    2002-12-01

    Several human pathogens (e.g., Bacillus anthracis, Yersinia pestis, Bordetella pertussis, Plasmodium falciparum, and Mycobacterium tuberculosis) have very restricted unselected allelic variation in structural genes, which hinders study of the genetic relationships among strains and strain-trait correlations. To address this problem in a representative pathogen, 432 M. tuberculosis complex strains from global sources were genotyped on the basis of 230 synonymous (silent) single nucleotide polymorphisms (sSNPs) identified by comparison of four genome sequences. Eight major clusters of related genotypes were identified in M. tuberculosis sensu stricto, including a single cluster representing organisms responsible for several large outbreaks in the United States and Asia. All M. tuberculosis sensu stricto isolates of previously unknown phylogenetic position could be rapidly and unambiguously assigned to one of the eight major clusters, thus providing a facile strategy for identifying organisms that are clonally related by descent. Common clones of M. tuberculosis sensu stricto and M. bovis are distinct, deeply branching genotypic complexes whose extant members did not emerge directly from one another in the recent past. sSNP genotyping rapidly delineates relationships among closely related strains of pathogenic microbes and allows construction of genetic frameworks for examining the distribution of biomedically relevant traits such as virulence, transmissibility, and host range.

  4. Methanol production by Mycobacterium smegmatis.

    OpenAIRE

    Weisman, L S; Ballou, C E

    1988-01-01

    Mycobacterium smegmatis cells produce [3H]methanol when incubated with [methyl-3H]methionine. The methanol is derived from S-adenosylmethionine rather than methyltetrahydrofolate. M. smegmatis cells carboxymethylate several proteins, and some of the methanol probably results from their demethylation, but most of the methanol may come from an unidentified component with a high gel mobility. Although methanol in the medium reached 19 microM, it was not incorporated into the methylated mannose p...

  5. High Persister Mutants in Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Heather L Torrey

    Full Text Available Mycobacterium tuberculosis forms drug-tolerant persister cells that are the probable cause of its recalcitrance to antibiotic therapy. While genetically identical to the rest of the population, persisters are dormant, which protects them from killing by bactericidal antibiotics. The mechanism of persister formation in M. tuberculosis is not well understood. In this study, we selected for high persister (hip mutants and characterized them by whole genome sequencing and transcriptome analysis. In parallel, we identified and characterized clinical isolates that naturally produce high levels of persisters. We compared the hip mutants obtained in vitro with clinical isolates to identify candidate persister genes. Genes involved in lipid biosynthesis, carbon metabolism, toxin-antitoxin systems, and transcriptional regulators were among those identified. We also found that clinical hip isolates exhibited greater ex vivo survival than the low persister isolates. Our data suggest that M. tuberculosis persister formation involves multiple pathways, and hip mutants may contribute to the recalcitrance of the infection.

  6. Measurement and Analysis of Olfactory Responses with the Aim of Establishing an Objective Diagnostic Method for Central Olfactory Disorders

    Science.gov (United States)

    Uno, Tominori; Wang, Li-Qun; Miwakeichi, Fumikazu; Tonoike, Mitsuo; Kaneda, Teruo

    In order to establish a new diagnostic method for central olfactory disorders and to identify objective indicators, we measured and analyzed brain activities in the parahippocampal gyrus and uncus, region of responsibility for central olfactory disorders. The relationship between olfactory stimulation and brain response at region of responsibility can be examined in terms of fitted responses (FR). FR in these regions may be individual indicators of changes in brain olfactory responses. In the present study, in order to non-invasively and objectively measure olfactory responses, an odor oddball task was conducted on four healthy volunteers using functional magnetic resonance imaging (fMRI) and a odorant stimulator with blast-method. The results showed favorable FR and activation in the parahippocampal gyrus or uncus in all subjects. In some subjects, both the parahippocampal gyrus and uncus were activated. Furthermore, activation was also confirmed in the cingulate gyrus, middle frontal gyrus, precentral gyrus, postcentral gyrus, superior temporal gyrus and insula. The hippocampus and uncus are known to be involved in the olfactory disorders associated with early-stage Alzheimer's disease and other olfactory disorders. In the future, it will be necessary to further develop the present measurement and analysis method to clarify the relationship between central olfactory disorders and brain activities and establish objective indicators that are useful for diagnosis.

  7. Analysis of time in establishing synchronization radio communication system with expanded spectrum conditions for communication with mobile robots

    Science.gov (United States)

    Latinovic, T. S.; Kalabic, S. B.; Barz, C. R.; Petrica, P. Paul; Pop-Vădean, A.

    2018-01-01

    This paper analyzes the influence of the Doppler Effect on the length of time to establish synchronization pseudorandom sequences in radio communications systems with an expanded spectrum. Also, this paper explores the possibility of using secure wireless communication for modular robots. Wireless communication could be used for local and global communication. We analyzed a radio communication system integrator, including the two effects of the Doppler signal on the duration of establishing synchronization of the received and locally generated pseudorandom sequence. The effects of the impact of the variability of the phase were analyzed between the said sequences and correspondence of the phases of these signals with the interval of time of acquisition of received sequences. An analysis of these impacts is essential in the transmission of signal and protection of the transfer of information in the communication systems with an expanded range (telecommunications, mobile telephony, Global Navigation Satellite System GNSS, and wireless communication). Results show that wireless communication can provide a safety approach for communication with mobile robots.

  8. Stable isotope analysis of a newly established macrofaunal food web 1.5 years after the Hebei Spirit oil spill

    International Nuclear Information System (INIS)

    Han, Eunah; Park, Hyun Je; Bergamino, Leandro; Choi, Kwang-Sik; Choy, Eun Jung; Yu, Ok Hwan; Lee, Tae Won; Park, Heung-Sik; Shim, Won Joon; Kang, Chang-Keun

    2015-01-01

    Highlights: • We examined trophic structure in a newly established community after an oil spill. • This is the most extensive in situ isotopic analysis on an oiled benthic community. • Consumer-food source δ 13 C and δ 15 N rejected influx of petroleum into the community. • A novel circular statistics rejected trophic niche change of major feeding guilds. • Prevalence of omnivory and trophic plasticity may promote the recovery process. - Abstract: We examined trophic relationships in a newly established community 1.5 years after the Hebei Spirit oil spill on the west coast of Korea. Carbon and nitrogen stable isotope ratios in consumers and their potential food sources were compared between the oil-spill site and reference site, located 13.5 km from the oil-spill spot. The isotopic mixing model and a novel circular statistics rejected the influx of petrogenic carbon into the community and identified spatial consistencies such as the high contributions of microphytobenthos, food-chain length, and the isotopic niche of each feeding guild between sites. We suggested that high level of trophic plasticity and the prevalence of omnivory of consumers may promote the robustness of food web against the oil contamination. Furthermore, we highlighted the need of holistic approaches including different functional groups to quantify changes in the food web structure and assess the influence of different perturbations including oil spill

  9. Use of descriptive analysis and preference mapping for early-stage assessment of new and established apples.

    Science.gov (United States)

    Cliff, Margaret A; Stanich, Kareen; Lu, Ran; Hampson, Cheryl R

    2016-04-01

    This research compared four new apple selections with 16 established apples using descriptive analysis (DA), instrumental analyses and preference mapping, in order to identify suitable selections for commercialization and further research. DA revealed that the new apple selections (PARC1, PARC2, PARC3, PARC4) were very similar in texture/mouthfeel (T) but differed in their flavor (F) and appearance (A) characteristics. Preference mapping revealed that consumers' T preferences were driven primarily by crispness, juiciness and lack of skin toughness, while F preferences were driven by sweetness, lack of tartness and presence of fruity flavor. Consumers' A preferences were driven by a high percentage of red color and degree of striping. The majority of consumers had similar T (82-85%) and F (88-92%) preferences for the early- and mid/late-harvest apples. In contrast, consumers' A preferences were differentiated into three subgroups (60%, 24%, 16%) for the early-harvest apples, but not for the mid/late-harvest apples. The new apple selections were among those most liked for T, F and A. This early-stage consumer research confirmed that the new apples were comparable, if not superior, to the established apples. As such, it provided the necessary feedback to industry to proceed with commercialization and optimization of cultural and storage practices. © 2015 Her Majesty the Queen in Right of Canada. Journal of the Science of Food and Agriculture © 2015 Society of Chemical Industry.

  10. A global analysis of alternative tillage and crop establishment practices for economically and environmentally efficient rice production.

    Science.gov (United States)

    Chakraborty, Debashis; Ladha, Jagdish Kumar; Rana, Dharamvir Singh; Jat, Mangi Lal; Gathala, Mahesh Kumar; Yadav, Sudhir; Rao, Adusumilli Narayana; Ramesha, Mugadoli S; Raman, Anitha

    2017-08-24

    Alternative tillage and rice establishment options should aim at less water and labor to produce similar or improved yields compared with traditional puddled-transplanted rice cultivation. The relative performance of these practices in terms of yield, water input, and economics varies across rice-growing regions. A global meta and mixed model analysis was performed, using a dataset involving 323 on-station and 9 on-farm studies (a total of 3878 paired data), to evaluate the yield, water input, greenhouse gas emissions, and cost and net return with five major tillage/crop establishment options. Shifting from transplanting to direct-seeding was advantageous but the change from conventional to zero or reduced tillage reduced yields. Direct-seeded rice under wet tillage was the best alternative with yield advantages of 1.3-4.7% (p Direct-seeding under zero tillage was another potential alternative with high savings in water input and cost of cultivation, with no yield penalty. The alternative practices reduced methane emissions but increased nitrous oxide emissions. Soil texture plays a key role in relative yield advantages, and therefore refinement of the practice to suit a specific agro-ecosystem is needed.

  11. Drug Resistance of Mycobacterium tuberculosis Complex among ...

    African Journals Online (AJOL)

    BACKGROUND: In Burkina Faso, there is no recent data about the level of drug resistance in Mycobacterium tuberculosis strains among newly diagnosed tuberculosis cases. OBJECTIVE: To provide an update of the primary drug resistance of mycobacterium tuberculosis among patients in Burkina faso. METHODS: ...

  12. Molecular Characterization of the Resistance of Mycobacterium ...

    African Journals Online (AJOL)

    Purpose: To characterize the resistance of Mycobacterium tuberculosis to second line drugs using a line probe assay. Methods: Multi-drug resistant strains of Mycobacterium tuberculosis isolated between December 2008 and December 2009 were tested for resistance to fluoroquinolones and second-line injectable drugs ...

  13. Ecotypes of the Mycobacterium tuberculosis complex.

    NARCIS (Netherlands)

    Smith, Noel H; Kremer, Kristin; Inwald, Jacqueline; Dale, James; Driscoll, Jeffrey R; Gordon, Stephen V; Soolingen, Dick van; Hewinson, R Glyn; Smith, John Maynard

    2006-01-01

    A phylogeny of the Mycobacterium tuberculosis complex has recently shown that the animal-adapted strains are found in a single lineage marked by the deletion of chromosomal region 9 (RD9) [Brosch et al., 2002. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc. Natl Acad.

  14. Molecular flexibility of Mycobacterium tuberculosis ribosome ...

    Indian Academy of Sciences (India)

    2013-11-06

    Nov 6, 2013 ... Mycobacterium tuberculosis RRF does not complement E. coli for its deficiency of RRF (in the ... [Selvaraj M, Govindan A, Seshadri A, Dubey B, Varshney U and Vijayan M 2013 Molecular flexibility of Mycobacterium tuberculosis ribosome ...... Janosi L, Mottagui-Tabar S, Isaksson LA, Sekine Y, Ohtsubo E,.

  15. Microaerobic growth and anaerobic survival of Mycobacterium avium, Mycobacterium intracellulare and Mycobacterium scrofulaceum

    Directory of Open Access Journals (Sweden)

    Amy Herndon Lewis

    2015-01-01

    Full Text Available Representative strains of Mycobacterium avium, Mycobacterium intracellulare and Mycobacterium scrofulaceum (MAIS grew at equal rates in laboratory medium at 21% (air and 12% oxygen. Growth in 6% oxygen proceeded at a 1.4–1.8-fold lower rate. Colony formation was the same at 21% (air and 6% oxygen. The MAIS strains survived rapid shifts from aerobic to anaerobic conditions as measured by two experimental approaches (Falkinham (1996 [1]. MAIS cells grown aerobically to log phase in broth were diluted, spread on agar medium, and incubated anaerobically for up to 20 days at 37 °C. Although no colonies formed anaerobically, upon transfer to aerobic conditions, greater than 25% of the colony forming units (CFU survived after 20 days of anaerobic incubation (Prince et al. (1989 [2]. MAIS cells grown in broth aerobically to log phase were sealed and vigorous agitation led to oxygen depletion (Wayne model. After 12 days anaerobic incubation, M. avium and M. scrofulaceum survival were high (>50%, while M. intracellulare survival was lower (22%. M. avium cells shifted to anaerobiosis in broth had increased levels of glycine dehydrogenase and isocitrate lyase. Growth of MAIS strains at low oxygen levels and their survival following a rapid shift to anaerobiosis is consistent with their presence in environments with fluctuating oxygen levels.

  16. Microaerobic growth and anaerobic survival of Mycobacterium avium, Mycobacterium intracellulare and Mycobacterium scrofulaceum.

    Science.gov (United States)

    Lewis, Amy Herndon; Falkinham, Joseph O

    2015-03-01

    Representative strains of Mycobacterium avium, Mycobacterium intracellulare and Mycobacterium scrofulaceum (MAIS) grew at equal rates in laboratory medium at 21% (air) and 12% oxygen. Growth in 6% oxygen proceeded at a 1.4-1.8-fold lower rate. Colony formation was the same at 21% (air) and 6% oxygen. The MAIS strains survived rapid shifts from aerobic to anaerobic conditions as measured by two experimental approaches (Falkinham (1996) [1]). MAIS cells grown aerobically to log phase in broth were diluted, spread on agar medium, and incubated anaerobically for up to 20 days at 37°C. Although no colonies formed anaerobically, upon transfer to aerobic conditions, greater than 25% of the colony forming units (CFU) survived after 20 days of anaerobic incubation (Prince et al. (1989) [2]). MAIS cells grown in broth aerobically to log phase were sealed and vigorous agitation led to oxygen depletion (Wayne model). After 12 days anaerobic incubation, M. avium and M. scrofulaceum survival were high (>50%), while M. intracellulare survival was lower (22%). M. avium cells shifted to anaerobiosis in broth had increased levels of glycine dehydrogenase and isocitrate lyase. Growth of MAIS strains at low oxygen levels and their survival following a rapid shift to anaerobiosis is consistent with their presence in environments with fluctuating oxygen levels. Copyright © 2015 Asian African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.

  17. Powerful methods to establish chromosomal markers in Lactococcus lactis: an analysis of pyrimidine salvage pathway mutants obtained by positive selections

    DEFF Research Database (Denmark)

    Martinussen, Jan; Hammer, Karin

    1995-01-01

    Using different 5-fluoropyrimidine analogues, positive selection procedures for obtaining mutants blocked in pyrimidine and purine salvage genes of Lactococcus lactis were established. Strains lacking the following enzyme activities due to mutations in the corresponding genes were isolated: uracil...... phosphoribosyltransferase (upp), uridindcytidine kinase (udk), pyrimidine nucleoside phosphorylase (pdp), cytidine/deoxycytidine deaminase (dd), thymidine kinase (tdk) and purine nucleoride phosphorylase (pup). Based on an analysis of the mutants obtained, the pathways by which L. lactis metabolizes uracil...... and the different pyrimidine nucleosides were verified. The substrate specificities of the different enzymes were determined. It was demonstrated that a single pyrimidine nucleoside phosphorylase accounts for the phosphorolytical cleavage of uridine, deoxyuridine and thymidine, and a single purine nucleoside...

  18. New-doses limits introduction analysis for the design and operation of teletherapy facilities established by IAEA

    International Nuclear Information System (INIS)

    Castaneda M, A.; Jimenez C, I.; Ramirez M, J.C.; Sanchez V, H.F.

    1996-01-01

    A design of a typical teletherapy facility was made considering a Co-60 rotating unit and using critical parameters, taking into account as a design base the dose limits established in the Safety Series No. 9 (1), and Safety Series No.115-I (2), shielding thickness when the dose limits were changed. An increment in the required thickness of 1,35 CHR for controlled areas and 2,37 CHR for non-controlled areas were found. This work considered the selection of four different types of teletherapy facilities using Co-60 sources, with different design and type of used unit. An analysis of thickness was made taking into account both the original values for the design and the real operation values in each facility. In order to determine the necessary changes for the wall thicknesses when the new recommendations are applied. (authors). 4 refs., 3 tabs

  19. Analysis of expression profile of mce operon genes (mce1, mce2, mce3 operon) in different Mycobacterium tuberculosis isolates at different growth phases.

    Science.gov (United States)

    Singh, Pratibha; Katoch, V M; Mohanty, K K; Chauhan, Devendra Singh

    2016-04-01

    Mycobacterium tuberculosis (M. tuberculosis) has four homologous mammalian cell entry (mce) operons (mce1-4) that encode exported proteins and have a possible role in the virulence mechanism of this pathogen. The expression of mce operon is considered to be complex and not completely understood. Although expression of mce operon at different in vitro growth phases has been studied earlier, its expression in different M. tuberculosis isolates under different growth phases is not yet studied. The present preliminary study was conducted on a limited number of isolates to know the trend of expression pattern of mce operon genes in different M. tuberculosis isolates under different growth stages. In this study, we monitored the transcriptional profile of selected mce operon genes (mce1A, mce1D, mce2A, mce2D, mce3A, mce3C) in different M.tuberculosis isolates (MDR1, MDR2, and sensitive isolate) at early exponential and stationary phases using real-time quantitative PCR. The expression ratio of all selected mce operon genes in all M. tuberculosis isolates was reduced at the initial phase and increased substantially at a later phase of growth. Higher expression of mce1 operon genes was found in all M. tuberculosis isolates as compared to other mce operon genes (mce2 and mce3 operons) at stationary growth phase. the higher expression of mce operon genes at stationary phase (as compared to early exponential phase) suggested growth phase dependent expression of mce operon genes. This indicated that the mce operon genes might have a role in M. tuberculosis survival and adaptation on the onset of adverse condition like stationary phase. Identification of differentially expressed genes will add to our understanding of the bacilli involved in adaptation to different growth conditions.

  20. Callogenesis and cell suspension establishment of tropical highland blackberry (Rubus adenotrichosSchltdl.) and its microscopic analysis.

    Science.gov (United States)

    Schmidt-Durán, Alexander; Alvarado-Ulloa, Carlos; Chacón-Cerdas, Randall; Alvarado-Marchena, Luis Fernando; Flores-Mora, Dora

    2016-01-01

    Blackberries are fruits produced worldwide, with 25 % of their production centered in Mexico, Central and South America. Tropical highland blackberry is a fruit that can potentially enhance human health, due to their high content in phenolic compounds, which include anthocyanins, phenolic acids, tannins (gallotannins and elagitannins) and flavonoids. Therefore, the overall aim of this study is the development of a callus induction protocol, the establishment of blackberry cell suspensions ( Rubus adenotrichos Schltdl.) and their cell analysis through optical microscopy and TEM, for the potential production of phenolic compounds. In order to produce callogenesis, segments of blackberry leaves were disinfected and placed in different concentrations of 2,4-D and the control media (0; 0.5; 1.0; 1.5; 2.0; 2.5 and 3.0 mg/l of 2,4-D); obtaining the higher size of calli in the medium with 1.5 mg/l of 2,4-D. After this determination, and for this specific treatment, a growth curve was performed through the use of fresh and dry weight parameters, in order to identify each of the growth stages. Furthermore, the calli obtained from the 1.5 mg/l of 2,4-D treatment were placed in two different culture media (MS and MS supplemented with 1.5 mg/l of 2,4-D) in order to establish the cell suspensions and the growth curve. To the best treatment, the total polyphenols were also quantified. It was determined that the MS medium is ideal for the growth and disintegration of the cell suspensions, obtaining 0.0256 mg of gallic acid/g of fresh sample. Finally, a cell callus and cell suspension analysis was performed through OM and TEM, evidencing a higher hystological differentiation in the calli, as well as the observation of antioxidant storage in the plastids.

  1. Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks.

    Directory of Open Access Journals (Sweden)

    Laurel S Burall

    Full Text Available In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra analysis plots standardized (z-score tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2. This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993-1994 and a single case from 2011 as well as

  2. Environmental contamination with Mycobacterium avium subspecies paratuberculosis within and around a dairy barn under experimental conditions

    NARCIS (Netherlands)

    Eisenberg, S.W.F.; Nielen, M.; Hoeboer, J.; Rutten, V.P.; Heederik, D.; Koets, A.P.

    2012-01-01

    To establish environmental contamination in and around a dairy barn, cows shedding Mycobacterium avium ssp. paratuberculosis (MAP) were housed in a freestall barn. Fecal samples were collected 15 times at 3-wk intervals, and samples of all animals were cultured by using the Trek Diagnostic Systems

  3. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study

    NARCIS (Netherlands)

    Ingen, J. van; Kohl, T.A.; Kranzer, K.; Hasse, B.; Keller, P.M.; Szafranska, A.K.; Hillemann, D.; Chand, M.; Schreiber, P.W.; Sommerstein, R.; Berger, C.; Genoni, M.; Ruegg, C.; Troillet, N.; Widmer, A.F.; Becker, S.L.; Herrmann, M.; Eckmanns, T.; Haller, S.; Holler, C.; Debast, S.B.; Wolfhagen, M.J.; Hopman, J.; Kluytmans, J.; Langelaar, M.; Notermans, D.W.; Oever, J. ten; Barselaar, P. van den; Vonk, A.B.; Vos, M.C.; Ahmed, N.; Brown, T.; Crook, D.; Lamagni, T.; Phin, N.; Smith, E.G.; Zambon, M.; Serr, A.; Gotting, T.; Ebner, W.; Thurmer, A.; Utpatel, C.; Sproer, C.; Bunk, B.; Nubel, U.; Bloemberg, G.V.; Bottger, E.C.; Niemann, S.; Wagner, D.; Sax, H.

    2017-01-01

    BACKGROUND: Since 2013, over 100 cases of Mycobacterium chimaera prosthetic valve endocarditis and disseminated disease were notified in Europe and the USA, linked to contaminated heater-cooler units (HCUs) used during cardiac surgery. We did a molecular epidemiological investigation to establish

  4. The effect of hyperglycaemia on in vitro cytokine production and macrophage infection with Mycobacterium tuberculosis

    NARCIS (Netherlands)

    Lachmandas, E.; Vrieling, F.; Wilson, L.G.; Joosten, S.A.; Netea, M.G.; Ottenhoff, T.H.; Crevel, R. van

    2015-01-01

    Type 2 diabetes mellitus is an established risk factor for tuberculosis but the underlying mechanisms are largely unknown. We examined the effects of hyperglycaemia, a hallmark of diabetes, on the cytokine response to and macrophage infection with Mycobacterium tuberculosis. Increasing in vitro

  5. Beta-lactamases of Mycobacterium tuberculosis and Mycobacterium kansasii.

    Science.gov (United States)

    Segura, C; Salvadó, M

    1997-09-01

    Re-emergence of infectious diseases caused by mycobacteria as well as the emergence of multiresistant strains of Mycobacterium has promoted the research on the use of beta-lactames in the treatment of such diseases. Mycobacteria produce beta-lactamases: M. tuberculosis produces a wide-spectrum beta-lactamase whose behaviour mimicks those of Gram-negative bacteria. M. kansasii produces also beta-lactamase which can be inhibited by clavulanic acid. An overview on beta-lactamases from both species is reported.

  6. Molecular Typing of Mycobacterium intracellulare Using Pulsed-Field Gel Electrophoresis, Variable-Number Tandem-Repeat Analysis, Mycobacteria Interspersed Repetitive-Unit-Variable-Number Tandem Repeat Typing, and Multilocus Sequence Typing: Molecular Characterization and Comparison of Each Typing Methods.

    Science.gov (United States)

    Jeon, Semi; Lim, Nara; Kwon, Seungjik; Shim, Taesun; Park, Misun; Kim, Bum-Joon; Kim, Seonghan

    2014-06-01

    Mycobacterium intracellulare is the major causative agent of nontuberculous mycobacteria-related pulmonary infections. The strain typing of M. intracellulare is important for the treatment and control of its infections. We compared the discrimination capacity and effective value of four different molecular typing methods. Antibiotic susceptibility testing, hsp65 and rpoB sequencing, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), mycobacteria interspersed repetitive-unit-variable-number tandem-repeat analysis (MIRU-VNTR), and VNTR assay targeting 44 M. intracellulare isolates obtained from patients with pulmonary infections were performed. All the antibiotic susceptibility patterns had no association with the molecular and sequence types tested in this study; however, the molecular and sequence types were related with each other. PFGE gave best results for discriminatory capacity, followed by VNTR, MLST, and MIRU-VNTR. The high discriminatory power of PFGE, VNTR, and MLST is enough for differentiating between reinfection and relapse, as well as for other molecular epidemiological usages. The MLST could be regarded as a representative classification method, because it showed the clearest relation with the sequence types.

  7. Mycobacterium stephanolepidis sp. nov., a rapidly growing species related to Mycobacterium chelonae, isolated from marine teleost fish, Stephanolepis cirrhifer.

    Science.gov (United States)

    Fukano, Hanako; Wada, Shinpei; Kurata, Osamu; Katayama, Kinya; Fujiwara, Nagatoshi; Hoshino, Yoshihiko

    2017-08-01

    A previously undescribed rapidly growing, non-pigmented mycobacterium was identified based on biochemical and nucleic acid analyses, as well as growth characteristics. Seven isolates were cultured from samples collected from five thread-sail filefish (Stephanolepis cirrhifer) and two farmed black scraper (Thamnaconus modestus). Bacterial growth occurred at 15-35 °C on Middlebrook 7H11 agar. The bacteria were positive for catalase activity at 68 °C and urease activity, intermediate for iron uptake, and negative for Tween 80 hydrolysis, nitrate reduction, semi-quantitative catalase activity and arylsulfatase activity at day 3. No growth was observed on Middlebrook 7H11 agar supplemented with picric acid, and very little growth was observed in the presence of 5 % NaCl. α- and α'-mycolates were identified in the cell walls, and a unique profile of the fatty acid methyl esters and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiles of the protein and cell-wall lipids were acquired. Sequence analysis revealed that the seven isolates shared identical sequences for the 16S rRNA, rpoB, hsp65, recA and sodA genes. Phylogenetic analysis of the five gene sequences confirmed that the isolates were unique, but closely related to Mycobacterium chelonae. Antibiotic susceptibility testing revealed the minimum inhibitory concentration (MIC) of clarithromycin against this novel species was Mycobacterium salmoniphilum. The hsp65 PCR restriction enzyme analysis pattern differed from those of M. chelonae and M. salmoniphilum. Based on these findings, the name Mycobacterium stephanolepidis sp. nov. is proposed for this novel species, with the type strain being NJB0901 T (=JCM 31611 T =KCTC 39843 T ).

  8. Establishment of Exposure to Organophosphorus Warfare Agents by Means of SPME-GSMS Analysis of Bodily Fluids

    International Nuclear Information System (INIS)

    Saveleva, E. I.; Koryagina, N. L.; Radilov, A. S.; Khlebnikova, N. S.; Khrustaleva, V. S.; Feld, V. E.

    2007-01-01

    Reliable chemical analytical procedures for revealing an exposure to toxic chemicals, identifying the active substance, and assessing the degree of exposure are necessary as a component of medical and forensic activities in cases of the possible use of highly toxic chemicals in war conflicts and terrorism acts, as well as emergency situations in chemical industry, specifically at chemical weapons storage and destruction facilities. According to Chemical Weapons Convention, Part XI, Appendix 4, e-17, 'samples of importance in the investigation of alleged use include biomedical samples from human or animal sources (blood, urine, excreta, tissue etc.)'. Urinary metabolites, O-alkyl esters of methylphosphic acid, offer one of the simplest means of confirming an exposure to organophosphorus warfare agents (OPWA). Urine, unlike blood or tissues, does not require invasive collection demanding in terms of sterility. Excretion with urine is the major route of elimination of OPWA from an organism. According to published data, 90% of OPWA metabolites are excreted within 48-72 h after intoxication. We developed an SPME-GCMS procedure for the determination of O-alkyl esters methylphosphonic acid in urine, with the following detection limits,: isopropyl and isobutyl esters 5 ng/ml and pinacolyl ester 1 ng/ml. The procedure involves derivatization of the target compounds directly on the microfiber. The total analysis time is 1-1.5 h. In animal experiments in vivo we could establish the exposure to OPWA at a half-LD50 level within no less than 48 h after intoxication. In principle, OPWA metabolites could be detected in urine within two weeks after intoxication but at higher doses. Retrospective analysis of urinary metabolites in cases of the exposure to low doses of OPWA requires lower detection limits (0.1-1 ng/ml). Optimal objects for the retrospective analysis of OPWA in an organism are long-lived blood protein adducts. We developed a procedure for revealing an exposure to

  9. Evaluation of the Epidemiological Relevance of Variable-Number Tandem-Repeat Genotyping of Mycobacterium bovis and Comparison of the Method with IS6110 Restriction Fragment Length Polymorphism Analysis and Spoligotyping†

    Science.gov (United States)

    Allix, Caroline; Walravens, Karl; Saegerman, Claude; Godfroid, Jacques; Supply, Philip; Fauville-Dufaux, Maryse

    2006-01-01

    Sources of Mycobacterium bovis contamination remain unclear for many cases of animal and human disease. A major limitation is the lack of sufficiently informative or epidemiologically well evaluated molecular methods for typing. Here, we report an evaluation of a high-throughput method based on 29 mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) loci to genotype 127 M. bovis isolates from cattle from 77 different Belgian farms, representative of a nationwide collection obtained from 1995 to 2003. MIRU-VNTR stability was demonstrated by analyzing a series of 74 isolates in total, obtained from different animals from a single farm or from different farms with an identified epidemiological link. The genotyping results and the genotypic diversity (h) were compared with those obtained by IS6110 restriction fragment length polymorphism (RFLP) analysis and spoligotyping. Among 68 isolates with no known epidemiological link, MIRU-VNTR typing discriminated better than either RFLP analysis or spoligotyping, with isolates taken individually (32 versus 16 and 17 genotypes; h = 0.91 versus 0.73 and 0.85, respectively) or in combination (32 versus 28 genotypes; h = 0.91 versus 0.92). Maximal resolution was already achieved with a subset of 9 loci. The observed congruence of the genetic relationships based on IS6110 RFLP analysis, spoligotyping, and MIRU-VNTR markers is consistent with a clonal population structure of M. bovis. These results support MIRU-VNTR typing as a convenient and discriminatory technique for analysis of the population structure of M. bovis in much greater detail and for addressing some still unresolved issues in the epidemiology of the pathogen. PMID:16757584

  10. Analysis of Mycobacterium ulcerans-specific T-cell cytokines for diagnosis of Buruli ulcer disease and as potential indicator for disease progression.

    Science.gov (United States)

    Nausch, Norman; Antwi-Berko, Daniel; Mubarik, Yusif; Abass, Kabiru Mohammed; Owusu, Wellington; Owusu-Dabo, Ellis; Debrah, Linda Batsa; Debrah, Alexander Yaw; Jacobsen, Marc; Phillips, Richard O

    2017-02-01

    Buruli ulcer disease (BUD), caused by Mycobacterium (M.) ulcerans, is the third most common mycobacterial disease after tuberculosis and leprosy. BUD causes necrotic skin lesions and is a significant problem for health care in the affected countries. As for other mycobacterial infections, T cell mediated immune responses are important for protection and recovery during treatment, but detailed studies investigating these immune responses in BUD patients are scarce. In this study, we aimed to characterise M. ulcerans-specific CD4+ T cell responses in BUD patients and to analyse specific cytokine-producing T cells in the context of disease severity and progression. For this case-control study, whole blood samples of BUD patients (N = 36, 1.5-17 years of age) and healthy contacts (N = 22, 3-15 years of age) were stimulated with antigen prepared from M. ulcerans and CD4+ T cells were analysed for the expression of TNFα, IFNγ and CD40L by flow cytometry. The proportions and profile of cytokine producing CD4+ T cells was compared between the two study groups and correlated with disease progression and severity. Proportions of cytokine double-positive IFNγ+TNFα+, TNFα+CD40L+, IFNγ+CD40L+ (p = 0.014, p = 0.010, p = 0.002, respectively) and triple positive IFNγ+TNFα+CD40L+ (p = 0.010) producing CD4+ T cell subsets were increased in BUD patients. In addition, TNFα+CD40L-IFNγ- CD4+ T cells differed between patients and controls (p = 0.034). TNFα+CD40L-IFNγ- CD4+ T cells were correlated with lesion size (p = 0.010) and proportion were higher in 'slow' healers compared to 'fast healers' (p = 0.030). We were able to identify M. ulcerans-specific CD4+ T cell subsets with specific cytokine profiles. In particular a CD4+ T cell subset, producing TNFα but not IFNγ and CD40L, showed association with lesion size and healing progress. Further studies are required to investigate, if the identified CD4+ T cell subset has the potential to be used as biomarker for diagnosis

  11. Proteomics of Mycobacterium Infection: Moving towards a Better Understanding of Pathogen-Driven Immunomodulation

    Directory of Open Access Journals (Sweden)

    Eik Hoffmann

    2018-01-01

    Full Text Available Intracellular bacteria are responsible for many infectious diseases in humans and have developed diverse mechanisms to interfere with host defense pathways. In particular, intracellular vacuoles are an essential niche used by pathogens to alter cellular and organelle functions, which facilitate replication and survival. Mycobacterium tuberculosis (Mtb, the pathogen causing tuberculosis in humans, is not only able to modulate its intraphagosomal fate by blocking phagosome maturation but has also evolved strategies to successfully prevent clearance by immune cells and to establish long-term survival in the host. Mass spectrometry (MS-based proteomics allows the identification and quantitative analysis of complex protein mixtures and is increasingly employed to investigate host–pathogen interactions. Major challenges are limited availability and purity of pathogen-containing compartments as well as the asymmetric ratio in protein abundance when comparing bacterial and host proteins during the infection. Recent advances in purification techniques and MS technology helped to overcome previous difficulties and enable the detailed proteomic characterization of infected host cells and their pathogen-containing vacuoles. Here, we summarize current findings of the proteomic analysis of Mycobacterium-infected host cells and highlight progress that has been made to study the protein composition of mycobacterial vacuoles. Current investigations focus on the pathogenicity during Mtb infection, which will allow to better understand pathogen-induced changes and immunomodulation of infected host cells. Consequently, future research in this field will have important implications on host response, pathogen survival, and persistence, induced adaptive immunity and metabolic changes of immune cells promoting the development of novel host-directed therapies in tuberculosis.

  12. The Use of the Position Analysis Questionnaire (PAQ) for Establishing the Job Component Validity of Tests. Report No. 5. Final Report.

    Science.gov (United States)

    McCormick, Ernest J.; And Others

    The Position Analysis Questionnaire (PAQ), a structured job analysis questionnaire that provides for the analysis of individual jobs in terms of each of 187 job elements, was used to establish the job component validity of certain commercially-available vocational aptitude tests. Prior to the general analyses reported here, a statistical analysis…

  13. Evaluation of polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis for the detection of the rpoB mutations associated with resistance to rifampicin in Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Lee, H.; Cho, S.-N.; Bang, H.-E.; Kim, S.-C.; Victor, T.C.; Jordaan, A.; Suffys, P.N.; Gomes, H.M.; Singh, U.; Suresh, V.N.; Khan, B.K.

    2003-01-01

    Resistance of Mycobacterium tuberculosis to rifampicin (RIF) has been associated with mutations of the rpoB gene, which encodes for the RNA polymerase B subunit. Based on this information, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) has been suggested as a sensitive and rapid screening test for the detection of RIF-resistant M. tuberculosis from clinical isolates. PCR-SSCP analyses with radioisotopes and without radioisotopes were employed to detect mutations of the rpoB gene associated with resistance to RIF in four laboratories, and results were compared with those of sequence analysis and the conventional proportion method of drug susceptibility test between laboratories. Radioisotopic PCR-SSCP showed an excellent correlation with sequence analysis of the 157 bp region of the rpoB gene by identifying correctly all 32 isolates analyzed in this study, with a high resolution of the banding patterns obtained. In a separate study, non-radioisotopic PCR-SSCP also gave a good correlation with sequence analysis in 22 isolates, but two (9.1%) isolates were classified as resistant by PCR-SSCP despite wild type sequences. When PCR-SSCP was compared with the results obtained using the proportion method, sensitivity of 44% to 85% were obtained in the 4 laboratories that participated in this study. Possible reasons for discordant results are discussed. It has been concluded that despite discordant results, which were sometimes observed, depending on the experimental conditions, PCR-SSCP appears to be an effective and promising method for the rapid detection of RIF-resistant M. tuberculosis, a marker of multidrug resistant tuberculosis. (author)

  14. A cost analysis of the establishment of a dedicated orthopaedic outpatient injection clinic at a single institution.

    Science.gov (United States)

    Curtin, M; O'Neill, S C; Keogh, P; Kenny, P

    2017-08-01

    Traditionally orthopaedic injections were performed in a theatre setting. A dedicated outpatient injection clinic was established at our institution to attempt to provide injections more cost effectively. Our aim was to perform a cost analysis of orthopaedic injections performed in theatre, compared to those performed in a dedicated OPD injection clinic. Patient data for all orthopaedic injections performed at a single institution from 2013 to 2014 was obtained using HIPE data. A detailed breakdown of costings for two scenarios; those performed in theatre and those in the dedicated OPD injection clinic was obtained from the hospital finance department. A unit cost per injection for theatre and OPD was derived from this financial information. A total of 487 injections were performed in 2013, with 491 performed in 2014. 134 (27.5%) injections were performed in the OPD in 2013 compared to 388 (79%) in 2014. The unit cost per injection was calculated as €52.13 for theatre and €23.85 for OPD, this represented a 115% decrease in cost per injection. The creation of a dedicated orthopaedic injection clinic resulted in considerable cost savings at our institution. We propose this may be a more cost-efficient model for delivery of injections in the orthopaedic setting.

  15. Establishment and in-house validation of stem-loop RT PCR method for MicroRNA398 expression analysis

    Directory of Open Access Journals (Sweden)

    Timotijević Gordana S.

    2015-01-01

    Full Text Available MicroRNAs (miRNAs belong to the class of small non-coding RNAs which have important roles throughout development as well as in plant response to diverse environmental stresses. Some of plant miRNAs are essential for regulation and maintenance of nutritive homeostasis when nutrients are in excess or shortage comparing to optimal concentration for certain plant species. Better understanding of miRNAs functions implies development of efficient technology for profiling their gene expression. We set out to establish validate the methodology for miRNA gene expression analysis in cucumber grown under suboptimal mineral nutrient regimes, including iron deficiency. Reverse transcription by “stem-loop” primers in combination with Real time PCR method is one of potential approaches for quantification of miRNA gene expression. In this paper we presented a method for “stem loop” primer design specific for miR398, as well as reaction optimization and determination of Real time PCR efficiency. Proving the accuracy of this method was imperative as “stem loop” RT which consider separate transcription of target and endogenous control. The method was verified by comparison of the obtained data with results of miR398 expression achieved using a commercial kit based on simultaneous conversion of all RNAs in cDNAs. [Projekat Ministarstva nauke Republike Srbije, br. 173005 i br. ON-173028

  16. Resposta imune específica de bovinos experimentalmente sensibilizados com inóculos inativados de Mycobacterium bovis e Mycobacterium avium Specific immune response of cattle to experimental sensibilization by inactivated Mycobacterium bovis and Mycobacterium avium

    Directory of Open Access Journals (Sweden)

    Robson F.C. Almeida

    2006-12-01

    Full Text Available O diagnóstico presuntivo da tuberculose bovina é baseado na análise da resposta imune celular a antígenos micobacterianos. Procedeu-se à simulação experimental de sensibilização por Mycobacterium bovis e Mycobacterium avium inativados em bovinos a fim de acompanhar a resposta imune a partir do teste cervical comparativo e da evolução da produção específica de interferon-gama, além de identificar a interferência de reações inespecíficas por M. avium nos resultados dos testes. Verificou-se que os animais desencadearam resposta de hipersensibilidade tardia contra os bacilos inativados, e que ambos os testes diagnósticos da tuberculose bovina foram eficientes na identificação dos animais sensibilizados com M. bovis e na discriminação das reações geradas pela inoculação dos bovinos com M. avium.The presumptive diagnosis of bovine tuberculosis is based on analysis of the immune response to micobacterial antigens. This experimental simulation of sensibilization by Mycobacterium bovis and Mycobacterium avium in cattle aimed to verify the immune response by both the cervical comparative test and the evolution of the specific production of gamma-interferon, and also to identify interference of unspecified reactions by M. avium on the test results. The results support that the experimental animals started a response of delayed hypersensitivity to the inactivated bacilli, and that both diagnostic tests for bovine tuberculosis were efficient for the identification of animals sensitized with M. bovis and for discrimination of reactions generated by inoculation of cattle with M. avium.

  17. Biosynthesis and Recycling of Nicotinamide Cofactors in Mycobacterium tuberculosis

    Science.gov (United States)

    Boshoff, Helena I. M.; Xu, Xia; Tahlan, Kapil; Dowd, Cynthia S.; Pethe, Kevin; Camacho, Luis R.; Park, Tae-Ho; Yun, Chang-Soo; Schnappinger, Dirk; Ehrt, Sabine; Williams, Kerstin J.; Barry, Clifton E.

    2008-01-01

    Despite the presence of genes that apparently encode NAD salvage-specific enzymes in its genome, it has been previously thought that Mycobacterium tuberculosis can only synthesize NAD de novo. Transcriptional analysis of the de novo synthesis and putative salvage pathway genes revealed an up-regulation of the salvage pathway genes in vivo and in vitro under conditions of hypoxia. [14C]Nicotinamide incorporation assays in M. tuberculosis isolated directly from the lungs of infected mice or from infected macrophages revealed that incorporation of exogenous nicotinamide was very efficient in in vivo-adapted cells, in contrast to cells grown aerobically in vitro. Two putative nicotinic acid phosphoribosyltransferases, PncB1 (Rv1330c) and PncB2 (Rv0573c), were examined by a combination of in vitro enzymatic activity assays and allelic exchange studies. These studies revealed that both play a role in cofactor salvage. Mutants in the de novo pathway died upon removal of exogenous nicotinamide during active replication in vitro. Cell death is induced by both cofactor starvation and disruption of cellular redox homeostasis as electron transport is impaired by limiting NAD. Inhibitors of NAD synthetase, an essential enzyme common to both recycling and de novo synthesis pathways, displayed the same bactericidal effect as sudden NAD starvation of the de novo pathway mutant in both actively growing and nonreplicating M. tuberculosis. These studies demonstrate the plasticity of the organism in maintaining NAD levels and establish that the two enzymes of the universal pathway are attractive chemotherapeutic targets for active as well as latent tuberculosis. PMID:18490451

  18. Expression of Mycobacterium smegmatis pyrazinamidase in Mycobacterium tuberculosis confers hypersensitivity to pyrazinamide and related amides.

    Science.gov (United States)

    Boshoff, H I; Mizrahi, V

    2000-10-01

    A pyrazinamidase (PZase)-deficient pncA mutant of Mycobacterium tuberculosis, constructed by allelic exchange, was used to investigate the effects of heterologous amidase gene expression on the susceptibility of this organism to pyrazinamide (PZA) and related amides. The mutant was highly resistant to PZA (MIC, >2,000 microg/ml), in accordance with the well-established role of pncA in the PZA susceptibility of M. tuberculosis (A. Scorpio and Y. Zhang, Nat. Med. 2:662-667, 1996). Integration of the pzaA gene encoding the major PZase/nicotinamidase from Mycobacterium smegmatis (H. I. M. Boshoff and V. Mizrahi, J. Bacteriol. 180:5809-5814, 1998) or the M. tuberculosis pncA gene into the pncA mutant complemented its PZase/nicotinamidase defect. In both pzaA- and pncA-complemented mutant strains, the PZase activity was detected exclusively in the cytoplasm, suggesting an intracellular localization for PzaA and PncA. The pzaA-complemented strain was hypersensitive to PZA (MIC, /=20 microg/ml) and was also sensitive to benzamide (MIC, 20 microg/ml), unlike the wild-type and pncA-complemented mutant strains, which were highly resistant to this amide (MIC, >500 microg/ml). This finding was consistent with the observation that benzamide is hydrolyzed by PzaA but not by PncA. Overexpression of PzaA also conferred sensitivity to PZA, nicotinamide, and benzamide on M. smegmatis (MIC, 150 microg/ml in all cases) and rendered Escherichia coli hypersensitive for growth at low pH.

  19. Effect of Fructose on Established Lipid Targets: A Systematic Review and Meta-Analysis of Controlled Feeding Trials

    Science.gov (United States)

    Chiavaroli, Laura; de Souza, Russell J; Ha, Vanessa; Cozma, Adrian I; Mirrahimi, Arash; Wang, David D; Yu, Matthew; Carleton, Amanda J; Di Buono, Marco; Jenkins, Alexandra L; Leiter, Lawrence A; Wolever, Thomas M S; Beyene, Joseph; Kendall, Cyril W C; Jenkins, David J A; Sievenpiper, John L

    2015-01-01

    Background Debate over the role of fructose in mediating cardiovascular risk remains active. To update the evidence on the effect of fructose on established therapeutic lipid targets for cardiovascular disease (low-density lipoprotein cholesterol [LDL]-C, apolipoprotein B, non-high-density lipoprotein cholesterol [HDL-C]), and metabolic syndrome (triglycerides and HDL-C), we conducted a systematic review and meta-analysis of controlled feeding trials. Methods and Results MEDLINE, EMBASE, CINHAL, and the Cochrane Library were searched through July 7, 2015 for controlled feeding trials with follow-up ≥7 days, which investigated the effect of oral fructose compared to a control carbohydrate on lipids (LDL-C, apolipoprotein B, non-HDL-C, triglycerides, and HDL-C) in participants of all health backgrounds. Two independent reviewers extracted relevant data. Data were pooled using random effects models and expressed as mean difference with 95% CI. Interstudy heterogeneity was assessed (Cochran Q statistic) and quantified (I2 statistic). Eligibility criteria were met by 51 isocaloric trials (n=943), in which fructose was provided in isocaloric exchange for other carbohydrates, and 8 hypercaloric trials (n=125), in which fructose supplemented control diets with excess calories compared to the control diets alone without the excess calories. Fructose had no effect on LDL-C, non-HDL-C, apolipoprotein B, triglycerides, or HDL-C in isocaloric trials. However, in hypercaloric trials, fructose increased apolipoprotein B (n=2 trials; mean difference = 0.18 mmol/L; 95% CI: 0.05, 0.30; P=0.005) and triglycerides (n=8 trials; mean difference = 0.26 mmol/L; 95% CI: 0.11, 0.41; Peffect on established lipid targets when added to existing diets so as to provide excess calories (+21% to 35% energy). When isocalorically exchanged for other carbohydrates, fructose had no adverse effects on blood lipids. More trials that are larger, longer, and higher quality are required. Clinical

  20. Mycobacterium shottsii sp. nov., a slowly growing species isolated from Chesapeake Bay striped bass (Morone saxatilis)

    Science.gov (United States)

    Rhodes, M.W.; Kator, H.; Kotob, S.; van Berkum, P.; Kaattari, I.; Vogelbein, W.; Quinn, F.; Floyd, M.M.; Butler, W.R.; Ottinger, C.A.

    2003-01-01

    Slowly growing, non-pigmented mycobacteria were isolated from striped bass (Morone saxatilis) during an epizootic of mycobacteriosis in the Chesapeake Bay. Growth characteristics, acid-fastness and results of 16S rRNA gene sequencing were consistent with those of the genus Mycobacterium. A unique profile of biochemical reactions was observed among the 21 isolates. A single cluster of eight peaks identified by analysis of mycolic acids (HPLC) resembled those of reference patterns but differed in peak elution times from profiles of reference species of the Mycobacterium tuberculosis complex. One isolate (M175T) was placed within the slowly growing mycobacteria by analysis of aligned 16S rRNA gene sequences and was proximate in phylogeny to Mycobacterium ulcerans and Mycobacterium marinum. However, distinct nucleotide differences were detected in the 16S rRNA gene sequence among M175T, M. ulcerans and M. marinum (99.2% similarity). Isolate M175T could be differentiated from other slowly growing, non-pigmented mycobacteria by its inability to grow at 37??C, production of niacin and urease, absence of nitrate reductase and resistance to isoniazid (1 ??g ml-1), thiacetazone and thiophene-2-carboxylic hydrazide. Based upon these genetic and phenotypic differences, isolate M175T (= ATCC 700981T = NCTC 13215T) is proposed as the type strain of a novel species, Mycobacterium shottsii sp. nov.

  1. qPCR detection of Mycobacterium leprae in biopsies and slit skin smear of different leprosy clinical forms

    OpenAIRE

    Michelle de Campos Soriani Azevedo; Natália Mortari Ramuno; Luciana Raquel Vincenzi Fachin; Mônica Tassa; Patrícia Sammarco Rosa; Andrea de Faria Fernandes Belone; Suzana Madeira Diório; Cleverson Teixeira Soares; Gustavo Pompermaier Garlet; Ana Paula Favaro Trombone

    2017-01-01

    Abstract Leprosy, whose etiological agent is Mycobacterium leprae, is a chronic infectious disease that mainly affects the skin and peripheral nervous system. The diagnosis of leprosy is based on clinical evaluation, whereas histopathological analysis and bacilloscopy are complementary diagnostic tools. Quantitative PCR (qPCR), a current useful tool for diagnosis of infectious diseases, has been used to detect several pathogens including Mycobacterium leprae. The validation of this technique ...

  2. Detection of Mycobacterium tuberculosis and Mycobacterium avium Complexes by Real-Time PCR in Bovine Milk from Brazilian Dairy Farms.

    Science.gov (United States)

    Bezerra, André Vinícius Andrade; Dos Reis, Emily Marques; Rodrigues, Rogério Oliveira; Cenci, Alexander; Cerva, Cristine; Mayer, Fabiana Quoos

    2015-05-01

    Foodborne diseases are a public health problem worldwide. The consumption of contaminated raw milk has been recognized as a major cause of transmission of bovine tuberculosis to humans. Other mycobacteria that may be present in raw milk and may cause diseases are those belonging to the Mycobacterium avium complex. In this study, molecular biology tools were applied to investigate raw milk contamination with Mycobacterium spp. in family dairy farms from Rio Grande do Sul, southern Brazil. Furthermore, different variables related to the source of the milk, herd characteristics, and management were evaluated for their effect on milk contamination. Five hundred and two samples were analyzed, of which 354 were from the Northwest region (102 farms with samples from 93 bulk tanks and 261 animals) and 148 from the South region of the state (22 farms with samples from 23 bulk tanks and 125 animals). Among them, 10 (1.99%) and 7 (1.39%) were positive for Mycobacterium tuberculosis (9 confirmed as Mycobacterium bovis) and M. avium complexes, respectively. There was no difference in the frequencies of positive samples between the regions or the sample sources. Of the positive samples, 4 were collected from a bulk tank (1 positive for M. avium and 3 for M. tuberculosis). Moreover, 1 sample was positive concomitantly for M. tuberculosis and M. avium complexes. On risk analysis, no variable was associated with raw milk contamination by M. tuberculosis complex species. However, washing the udders of all animals and drying them with paper towels were weakly classified as risk factors for M. avium contamination. Positive samples were obtained from both animals and bulk tanks, which emphasizes the importance of tuberculosis control programs and provides evidence that milk monitoring can be used as a control practice. Moreover, the findings of this study reinforce the need for awareness of the problems of raw milk consumption among the general population.

  3. mycobacterium tuberculosis genetic diversity and drug resistance ...

    African Journals Online (AJOL)

    East African Medical Journal Vol. 88 No. 12 December 2011. MYCOBACTERIUM TUBERCULOSIS GENETIC DIVERSITY AND DRUG RESISTANCE CONFERRING MUTATIONS. IN THE DEMOCRATIC REPUBLIC OF THE CONGO. L. Fenner, Institute of Social and Preventive Medicine, University of Bern, Switzerland, S.

  4. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study.

    Science.gov (United States)

    van Ingen, Jakko; Kohl, Thomas A; Kranzer, Katharina; Hasse, Barbara; Keller, Peter M; Katarzyna Szafrańska, Anna; Hillemann, Doris; Chand, Meera; Schreiber, Peter Werner; Sommerstein, Rami; Berger, Christoph; Genoni, Michele; Rüegg, Christian; Troillet, Nicolas; Widmer, Andreas F; Becker, Sören L; Herrmann, Mathias; Eckmanns, Tim; Haller, Sebastian; Höller, Christiane; Debast, Sylvia B; Wolfhagen, Maurice J; Hopman, Joost; Kluytmans, Jan; Langelaar, Merel; Notermans, Daan W; Ten Oever, Jaap; van den Barselaar, Peter; Vonk, Alexander B A; Vos, Margreet C; Ahmed, Nada; Brown, Timothy; Crook, Derrick; Lamagni, Theresa; Phin, Nick; Smith, E Grace; Zambon, Maria; Serr, Annerose; Götting, Tim; Ebner, Winfried; Thürmer, Alexander; Utpatel, Christian; Spröer, Cathrin; Bunk, Boyke; Nübel, Ulrich; Bloemberg, Guido V; Böttger, Erik C; Niemann, Stefan; Wagner, Dirk; Sax, Hugo

    2017-10-01

    Since 2013, over 100 cases of Mycobacterium chimaera prosthetic valve endocarditis and disseminated disease were notified in Europe and the USA, linked to contaminated heater-cooler units (HCUs) used during cardiac surgery. We did a molecular epidemiological investigation to establish the source of these patients' disease. We included 24 M chimaera isolates from 21 cardiac surgery-related patients in Switzerland, Germany, the Netherlands, and the UK, 218 M chimaera isolates from various types of HCUs in hospitals, from LivaNova (formerly Sorin; London, UK) and Maquet (Rastatt, Germany) brand HCU production sites, and unrelated environmental sources and patients, as well as eight Mycobacterium intracellulare isolates. Isolates were analysed by next-generation whole-genome sequencing using Illumina and Pacific Biosciences technologies, and compared with published M chimaera genomes. Phylogenetic analysis based on whole-genome sequencing of 250 isolates revealed two major M chimaera groups. Cardiac surgery-related patient isolates were all classified into group 1, in which all, except one, formed a distinct subgroup. This subgroup also comprised isolates from 11 cardiac surgery-related patients reported from the USA, most isolates from LivaNova HCUs, and one from their production site. Isolates from other HCUs and unrelated patients were more widely distributed in the phylogenetic tree. HCU contamination with M chimaera at the LivaNova factory seems a likely source for cardiothoracic surgery-related severe M chimaera infections diagnosed in Switzerland, Germany, the Netherlands, the UK, the USA, and Australia. Protective measures and heightened clinician awareness are essential to guarantee patient safety. Partly funded by the EU Horizon 2020 programme, its FP7 programme, the German Center for Infection Research (DZIF), the Swiss National Science Foundation, the Swiss Federal Office of Public Health, and National Institute of Health Research Oxford Health Protection

  5. The Leprosy Agents Mycobacterium lepromatosis and Mycobacterium leprae in Mexico

    Science.gov (United States)

    Han, Xiang Y.; Sizer, Kurt Clement; Velarde-Félix, Jesús S.; Frias-Castro, Luis O.; Vargas-Ocampo, Francisco

    2011-01-01

    Summary Background Mycobacterium leprae was the only known cause of leprosy until 2008, when a new species, named Mycobacterium lepromatosis, was found to cause diffuse lepromatous leprosy (DLL), a unique form of leprosy endemic in Mexico. Methods We sought to differentiate the leprosy agents among 120 Mexican patients with various clinical forms of leprosy and to compare their relative prevalence and disease features. Archived skin biopsy specimens from these patients were tested for both M. leprae and M. lepromatosis using polymerase chain reaction-based species-specific assays. Results Eighty-seven (72.5%) patients were confirmed for etiologic species, including 55 with M. lepromatosis, 18 with M. leprae, and 14 with both organisms. The endemic regions of each agent differed but overlapped. Patients with M. lepromatosis were younger and from more states, and their clinical diagnoses included 13 DLL, 34 lepromatous leprosy (LL), and eight other forms of leprosy. By contrast, the diagnoses of patients with M. leprae included none DLL, 15 LL and three other forms. Thus, M. lepromatosis caused DLL specifically (p=0.023). Patients with M. lepromatosis also showed more variable skin lesions and the extremities were the commonest biopsy sites. Finally, patients with dual infections manifested all clinical forms and accounted for 16.1% of all species-confirmed cases. Conclusions M. lepromatosis is another cause of leprosy and is probably more prevalent than M. leprae in Mexico. It mainly causes LL and also specifically DLL. Dual infections caused by both species may occur in endemic area. PMID:22788812

  6. Comparative analysis of Bacillus subtilis spores and monophosphoryl lipid A as adjuvants of protein-based mycobacterium tuberculosis-based vaccines: partial requirement for interleukin-17a for induction of protective immunity.

    Science.gov (United States)

    Esparza-Gonzalez, Sandra C; Troy, Amber R; Izzo, Angelo A

    2014-04-01

    The development of adjuvants for vaccines has become an important area of research as the number of protein-based vaccines against infectious pathogens increases. Currently, there are a number of adjuvant-based Mycobacterium tuberculosis vaccines in clinical trials that have shown efficacy in animal models. Despite these novel adjuvants, there is still a need to design new and more versatile adjuvants that have minimal adverse side effects but produce robust long-lasting adaptive immune responses. To this end, we hypothesized that Bacillus subtilis spores may provide the appropriate innate signals that are required to generate such vaccine-mediated responses, which would be sufficient to reduce the mycobacterial burden after infection with M. tuberculosis. In addition, we compared the response generated by B. subtilis spores to that generated by monophosphoryl lipid A (MPL), which has been used extensively to test tuberculosis vaccines. The well-characterized, 6-kDa early secretory antigenic target of M. tuberculosis (ESAT-6; Rv3875) was used as a test antigen to determine the T cell activation potential of each adjuvant. Inoculated into mice, B. subtilis spores induced a strong proinflammatory response and Th1 immunity, similar to MPL; however, unlike MPL formulated with dimethyldioctadecylammonium (DDA) bromide, it failed to induce significant levels of interleukin-17A (IL-17A) and was unable to significantly reduce the mycobacterial burden after pulmonary infection with M. tuberculosis. Further analysis of the activity of MPL-DDA suggested that IL-17A was required for protective immunity. Taken together, the data emphasize the requirement for a network of cytokines that are essential for protective immunity.

  7. Powerful methods to establish chromosomal markers in Lactococcus lactis: an analysis of pyrimidine salvage pathway mutants obtained by positive selections

    DEFF Research Database (Denmark)

    Martinussen, Jan; Hammer, Karin

    1995-01-01

    Using different 5-fluoropyrimidine analogues, positive selection procedures for obtaining mutants blocked in pyrimidine and purine salvage genes of Lactococcus lactis were established. Strains lacking the following enzyme activities due to mutations in the corresponding genes were isolated: uracil...

  8. An Analysis of Second-Tier Arms Producing Countries' Offset Policies: Technology Transfer and Defense Industrial Base Establishment

    National Research Council Canada - National Science Library

    Confer, Brian S

    2008-01-01

    The purpose of this thesis is to determine if offsets are an effective means of second-tier countries acquiring technology and if offsets enhance their ability to establish and maintain an industrial...

  9. IDENTIFICATION OF MYCOBACTERIUM GENAVENSE IN A DIANA MONKEY (CERCOPITHECUS DIANA) BY POLYMERASE CHAIN REACTION AND HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY.

    Science.gov (United States)

    Kelly, Kathleen M; Wack, Allison N; Bradway, Dan; Simons, Brian W; Bronson, Ellen; Osterhout, Gerard; Parrish, Nicole M; Montali, Richard J

    2015-06-01

    A 25-yr-old Diana monkey (Cercopithecus diana) with a 1.5-yr history of chronic colitis and diarrhea was found to have disseminated granulomatous disease with intralesional acid fast bacilli. Bacilli were identified as Mycobacterium genavense by polymerase chain reaction, sequencing of the 16S-23S ribosomal RNA intergenic spacer (ITS) gene, and mycolic acid analysis by high-performance liquid chromatography. Mycobacterium genavense is a common cause of mycobacteriosis in free-ranging and captive birds. In addition, recognition of opportunistic infection in human immunodeficiency virus-positive patients is increasing. Disease manifestations of M. genavense are similar to Mycobacterium avium complex (MAC) and include fever, wasting, and diarrhea with disseminated disease. Similar clinical signs and lesions were observed in this monkey. Mycobacterium genavense should be considered as a differential for disseminated mycobacterial disease in nonhuman primates as this agent can mimic MAC and related mycobacteria.

  10. Isolamento de Mycobacterium bovis em cão Mycobacterium bovis isolation in a dog

    Directory of Open Access Journals (Sweden)

    P.M.P.C. Mota

    2001-08-01

    Full Text Available This report describes the isolation of Mycobacterium bovis from a dog with a history of co-habitation with bufallos infected with Mycobacterium bovis. After necropsy, the microrganism was isolated from a mesenteric lymphatic node in Stonebrink media and bacterial identification was confirmed by biochemical tests.

  11. Detection of Mycobacterium bovis and Mycobacterium tuberculosis from Cattle: Possible Public Health Relevance

    DEFF Research Database (Denmark)

    Thakur, Aneesh; Sharma, Mandeep; Katoch, Vipin C.

    2012-01-01

    Mycobacterium bovis and Mycobacterium tuberculosis infect both animals and humans. The disease epidemiology by these agents differs in developed and developing countries due to the differences in the implementation of the prevention and control strategies. The present study describes the detection...

  12. Copper homeostasis in Mycobacterium tuberculosis.

    Science.gov (United States)

    Shi, Xiaoshan; Darwin, K Heran

    2015-06-01

    Copper (Cu) is a trace element essential for the growth and development of almost all organisms, including bacteria. However, Cu overload in most systems is toxic. Studies show Cu accumulates in macrophage phagosomes infected with bacteria, suggesting Cu provides an innate immune mechanism to combat invading pathogens. To counteract the host-supplied Cu, increasing evidence suggests that bacteria have evolved Cu resistance mechanisms to facilitate their pathogenesis. In particular, Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, has evolved multiple pathways to respond to Cu. Here, we summarize what is currently known about Cu homeostasis in Mtb and discuss potential sources of Cu encountered by this and other pathogens in a mammalian host.

  13. Mycobacterium chelonae infections associated with bee venom acupuncture.

    Science.gov (United States)

    Cho, Sun Young; Peck, Kyong Ran; Kim, Jungok; Ha, Young Eun; Kang, Cheol-In; Chung, Doo Ryeon; Lee, Nam Yong; Song, Jae-Hoon

    2014-03-01

    We report 3 cases of Mycobacterium chelonae infections after bee venom acupuncture. All were treated with antibiotics and surgery. Mycobacterium chelonae infections should be included in the differential diagnosis of chronic skin and soft tissue infections following bee venom acupuncture.

  14. Complete Genome Sequence of Mycobacterium phlei Type Strain RIVM601174

    KAUST Repository

    Abdallah, A. M.

    2012-05-24

    Mycobacterium phlei is a rapidly growing nontuberculous Mycobacterium species that is typically nonpathogenic, with few reported cases of human disease. Here we report the whole genome sequence of M. phlei type strain RIVM601174.

  15. Live imaging of Mycobacterium marinum infection in Dictyostelium discoideum.

    Science.gov (United States)

    Barisch, Caroline; López-Jiménez, Ana T; Soldati, Thierry

    2015-01-01

    The Dictyostelium discoideum-Mycobacterium marinum host-pathogen system is a recently established and powerful model system for mycobacterial infection. In this chapter, two simple protocols for live imaging of Dictyostelium discoideum infection are described. The first method is used to monitor the dynamics of recruitment of GFP-tagged Dictyostelium discoideum proteins at single time-points corresponding to the main stages of the infection (1.5-72 h post infection). The second method focuses at the early stages of the establishment of an infection (0-3 h post infection). In addition, several procedures to improve the imaging of the bacterium-containing compartment are described. Basic bacterial parameters such as bacterial growth and the recruitment of host proteins to the bacterium-containing compartment can be easily and precisely quantified using macros for ImageJ. These methods can be adapted to monitoring mycobacteria infection in other systems using mammalian cells.

  16. Large meta-analysis establishes the ACE insertion-deletion polymorphism as a marker of Alzheimer's disease.

    NARCIS (Netherlands)

    D.J. Lehmann (Donald); M. Cortina-Borja (Mario); D.R. Warden (Donald); A.D. Smith (David); K. Sleegers (Kristel); J.A. Prince (Jonathan); C.M. van Duijn (Cornelia); P.G. Kehoe (Patrick)

    2005-01-01

    textabstractApolipoprotein E epsilon4 (APOE*4) is the only fully established susceptibility allele for Alzheimer's disease. One of the most studied candidates is the insertion (I)/deletion (D) polymorphism (indel) of the gene for angiotensin I-converting enzyme (ACE). This study aimed to clarify its

  17. How Can School Leaders Establish Evidence-Informed Schools: An Analysis of the Effectiveness of Potential School Policy Levers

    Science.gov (United States)

    Brown, Chris; Zhang, Dell

    2017-01-01

    This article has three aims: first, it examines the notion of evidence-informed practice and its benefits, as well as recent educational policy designed to promote schools' use of evidence. Second, it examines four distinct but overlapping and interdependent factors that school leaders need to consider if they wish to establish evidence-informed…

  18. Complex multifractal nature in Mycobacterium tuberculosis genome

    Science.gov (United States)

    Mandal, Saurav; Roychowdhury, Tanmoy; Chirom, Keilash; Bhattacharya, Alok; Brojen Singh, R. K.

    2017-04-01

    The mutifractal and long range correlation (C(r)) properties of strings, such as nucleotide sequence can be a useful parameter for identification of underlying patterns and variations. In this study C(r) and multifractal singularity function f(α) have been used to study variations in the genomes of a pathogenic bacteria Mycobacterium tuberculosis. Genomic sequences of M. tuberculosis isolates displayed significant variations in C(r) and f(α) reflecting inherent differences in sequences among isolates. M. tuberculosis isolates can be categorised into different subgroups based on sensitivity to drugs, these are DS (drug sensitive isolates), MDR (multi-drug resistant isolates) and XDR (extremely drug resistant isolates). C(r) follows significantly different scaling rules in different subgroups of isolates, but all the isolates follow one parameter scaling law. The richness in complexity of each subgroup can be quantified by the measures of multifractal parameters displaying a pattern in which XDR isolates have highest value and lowest for drug sensitive isolates. Therefore C(r) and multifractal functions can be useful parameters for analysis of genomic sequences.

  19. Enfermedad por Mycobacterium simiae y "Mycobacterium sherrisii" en la Argentina

    Directory of Open Access Journals (Sweden)

    Lucía Barrera

    2010-08-01

    Full Text Available Se presenta información reunida retrospectivamente sobre casos de micobacteriosis originados por Mycobacterium simiae (n = 4 y "M. sherrisii" (n = 6. Los casos ocurrieron entre pacientes con sida (n = 6, historia de silicosis (n = 2 o tuberculosis previa (n = 1. Un caso se perdió luego de diagnosticado y nueve fueron tratados con esquemas terapéuticos basados en claritromicina, etambutol y quinolonas. La respuesta fue muy pobre: cinco pacientes fallecieron (cuatro eran HIV positivos, tres permanecieron crónicos y sólo uno curó. Estas micobacterias originaron 2.1% de los casos de micobacteriosis registrados en un período de ocho años. La distinción de estas micobacterias raras de otras más frecuentes por métodos moleculares rápidos, parece ser clínicamente útil para advertir sobre la dificultad que puede presentar el tratamiento. Sin embargo, la diferenciación genotípica entre M. simiae y "M. sherrisii" parecería no ser clínicamente relevante, dado que no quedaron expuestas características que distingan a los pacientes afectados por los dos microorganismos tan estrechamente relacionados.

  20. Differential T-cell recognition of native and recombinant Mycobacterium tuberculosis GroES

    DEFF Research Database (Denmark)

    Rosenkrands, I; Weldingh, K; Ravn, P

    1999-01-01

    Mycobacterium tuberculosis GroES was purified from culture filtrate, and its identity was confirmed by immunoblot analysis and N-terminal sequencing. Comparing the immunological recognition of native and recombinant GroES, we found that whereas native GroES elicited a strong proliferative response...

  1. Measuring bovine gamma delta T cell function at the site of Mycobacterium bovis infection

    Science.gov (United States)

    Bovine gamma delta T cells are amongst the first cells to accumulate at the site of Mycobacterium bovis infection; however, their role in the developing lesion remains unclear. We utilized transcriptomics analysis, in situ hybridization, and a macrophage/gamma delta T cell co-culture system to eluc...

  2. Epidemiology of Mycobacterium bovis Disease in Humans, the Netherlands, 1993-2007

    NARCIS (Netherlands)

    Majoor, C.J.; Magis-Escurra, C.; van Ingen, J.; Boeree, M.J.; van Soolingen, D.

    2011-01-01

    In the Netherlands, 1.4% of tuberculosis (TB) cases are caused by Mycobacterium bovis. After we admitted 3 patients with M. bovis infections to our reference hospital, we conducted a retrospective analysis of all M. bovis disease in the Netherlands during 1993-2007. We analyzed data from 231

  3. Epidemiology of Mycobacterium bovis disease in humans, The Netherlands, 1993-2007

    NARCIS (Netherlands)

    Majoor, C.J.; Magis-Escurra Ibanez, C.; Ingen, J. van; Boeree, M.J.; Soolingen, D. van

    2011-01-01

    In the Netherlands, 1.4% of tuberculosis (TB) cases are caused by Mycobacterium bovis. After we admitted 3 patients with M. bovis infections to our reference hospital, we conducted a retrospective analysis of all M. bovis disease in the Netherlands during 1993-2007. We analyzed data from 231

  4. Substantial molecular evolution and mutation rates in prolonged latent Mycobacterium tuberculosis infection in humans

    DEFF Research Database (Denmark)

    Lillebaek, Troels; Norman, Anders; Rasmussen, Erik Michael

    2016-01-01

    The genome of Mycobacterium tuberculosis (Mtb) of latently infected individuals may hold the key to understanding the processes that lead to reactivation and progression to clinical disease. We report here analysis of pairs of Mtb isolates from putative prolonged latent TB cases. We identified tw...

  5. Case of Diffuse Lepromatous Leprosy Associated with “Mycobacterium lepromatosis” ▿

    OpenAIRE

    Vera-Cabrera, Lucio; Escalante-Fuentes, Wendy G.; Gomez-Flores, Minerva; Ocampo-Candiani, Jorge; Busso, Philippe; Singh, Pushpendra; Cole, Stewart T.

    2011-01-01

    An 86-year-old female patient from northeast Mexico presented with diffuse lepromatous leprosy (DLL). Sequence analysis of four genes (rrs, rpoB, sigA, and hsp65) from the skin biopsy specimen identified “Mycobacterium lepromatosis.” This is the first independent confirmation of a case of DLL due to M. lepromatosis.

  6. Establishment of a continuous culture system for Entamoeba muris and analysis of the small subunit rRNA gene

    OpenAIRE

    Kobayashi S.; Suzuki J.; Takeuchi T.

    2009-01-01

    We established a culture system for Entamoeba muris (MG-EM-01 strain isolated from a Mongolian gerbil) using a modified Balamuth’s egg yolk infusion medium supplemented with 4% adult bovine serum and Bacteroides fragilis cocultured with Escherichia coli. Further, encystation was observed in the culture medium. The morphological characteristics of E. muris are similar to those of Entamoeba coli (E. coli); moreover, the malic isoenzyme electrophoretic band, which shows species-specific electrop...

  7. Summary and statistical analysis of environmental monitoring data in the Oarai Research Establishment, Japan Atomic Energy Research Institute

    International Nuclear Information System (INIS)

    Tamura, Katsuhiro; Kitano, Kyoshiro; Sibanuma, Yukio; Takasaki, Koichi; Ohhata, Tsutomu

    1998-03-01

    In the Oarai Research Establishment, Japan Atomic Energy Research Institute (JAERI), the environmental monitoring has been conducted for about 29 years since April 1968. The results are discussed for evaluation of long-term and short-term fluctuation in the radiological conditions in the Oarai area. This report summarises the data of the environmental monitoring in Oarai, and statistical analyses were made of the data collected from 1985 through 1994. (author)

  8. Thermal tolerance of Mycobacterium paratuberculosis.

    Science.gov (United States)

    Sung, N; Collins, M T

    1998-03-01

    D values (decimal reduction time; the time required to kill 1 log concentration of bacteria) were determined for both human and bovine strains (Dominic, Ben, BO45, and ATCC 19698) of Mycobacterium paratuberculosis in 50 mM lactate solution (pH 6.8) and in milk at four temperatures (62, 65, 68, and 71 degrees C). Viable M. paratuberculosis organisms were quantified by a radiometric culture method (BACTEC). Thermal death curves for the M. paratuberculosis strains tested were generally linear, with R2 of > or = 0.90, but a few curves (R2, 0.80 to 0.90) were better described by a quadratic equation. The human strains (Dominic and Ben) had similar D values in milk and in lactate solution. However, D values for the bovine strains (BO45 and ATCC 19698) were significantly different depending on the menstruum. D values for low-passage clinical strains (Dominic, Ben, and BO45) were lower than those of the high-passage laboratory strain (ATCC 19698). The D value based on pooled data for clinical strains of M. paratuberculosis in milk at 71 degrees C (D71 degrees C) was 11.67 s. Pooled D62 degrees C, D65 degrees C, and D68 degrees C of clinical M. paratuberculosis strains in milk were 228.8, 47.8, and 21.8 s, respectively. The Z value (the temperature required for the decimal reduction time to traverse 1 log cycle) of clinical strains in milk was 7.11 degrees C. The D values of clumped and single M. paratuberculosis cells were not significantly different. The D values of all M. paratuberculosis strains tested were considerably higher than those published for Listeria, Salmonella, and Coxiella spp. and estimated for Mycobacterium bovis, indicating that M. paratuberculosis is more thermally tolerant. This study supports the premise that M. paratuberculosis may survive high-temperature, short-time pasteurization when the initial organism concentration is greater than 10(1) cells/ml.

  9. [Establishment of a Neonatal ECMO Programme on the Basis of a Special Training Programme--A 6-year Analysis].

    Science.gov (United States)

    Förster, K M; Herber-Jonat, S; Huebener, C; Hasbargen, U; Schmitz, C; Schramm, R; Lehner, M; Stehr, M; Schulze, A; Flemmer, A W

    2015-12-01

    Internationally the need for neonatal ECMO is decreasing and the Extracorporeal Life Support Organization (ELSO) recommends that centres providing neonatal ECMO should treat at least 6 children per year. After a one-year training programme and preparation of the clinical application, neonatal ECMO was established and subsequently 41 infants [median age 1 day (1-172 days), median weight 3.25 kg (1.27-5.79 kg)] with severe respiratory failure have been treated within a 6-year period (fall 2008-fall 2014). For rescue therapy we provide inhaled nitric oxide, high-frequency oscillation and other differentiated ventilator strategies. Parallel to the clinical use of ECMO all employees have been trained in a special programme at 3-monthly intervals. By establishing an elaborate training programme and concentrating the treatment of critically ill newborns in one centre, the expertise of both running and preventing of neonatal ECMO due to pulmonary failure can be achieved. The diagnoses correlate to those of other centres which perform neonatal ECMO. 13 infants needed ECMO. The resulting overall survival rate was 11/12 (91.7%) infants treated with ECMO with a curative approach. All patients could be weaned from ECMO. In the context of a specialised university hospital with all treatment options for critically ill newborns and with the establishment of a specialised training programme, neonatal ECMO for pulmonary failure can achieve equally good results in comparison to those of national and international ECMO centres. © Georg Thieme Verlag KG Stuttgart · New York.

  10. Uracil excision repair in Mycobacterium tuberculosis cell-free extracts.

    Science.gov (United States)

    Kumar, Pradeep; Bharti, Sanjay Kumar; Varshney, Umesh

    2011-05-01

    Uracil excision repair is ubiquitous in all domains of life and initiated by uracil DNA glycosylases (UDGs) which excise the promutagenic base, uracil, from DNA to leave behind an abasic site (AP-site). Repair of the resulting AP-sites requires an AP-endonuclease, a DNA polymerase, and a DNA ligase whose combined activities result in either short-patch or long-patch repair. Mycobacterium tuberculosis, the causative agent of tuberculosis, has an increased risk of accumulating uracils because of its G + C-rich genome, and its niche inside host macrophages where it is exposed to reactive nitrogen and oxygen species, two major causes of cytosine deamination (to uracil) in DNA. In vitro assays to study DNA repair in this important human pathogen are limited. To study uracil excision repair in mycobacteria, we have established assay conditions using cell-free extracts of M. tuberculosis and M. smegmatis (a fast-growing mycobacterium) and oligomer or plasmid DNA substrates. We show that in mycobacteria, uracil excision repair is completed primarily via long-patch repair. In addition, we show that M. tuberculosis UdgB, a newly characterized family 5 UDG, substitutes for the highly conserved family 1 UDG, Ung, thereby suggesting that UdgB might function as backup enzyme for uracil excision repair in mycobacteria. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. Complete genome sequence of the frog pathogen Mycobacterium ulcerans ecovar Liflandii.

    Science.gov (United States)

    Tobias, Nicholas J; Doig, Kenneth D; Medema, Marnix H; Chen, Honglei; Haring, Volker; Moore, Robert; Seemann, Torsten; Stinear, Timothy P

    2013-02-01

    In 2004, a previously undiscovered mycobacterium resembling Mycobacterium ulcerans (the agent of Buruli ulcer) was reported in an outbreak of a lethal mycobacteriosis in a laboratory colony of the African clawed frog Xenopus tropicalis. This mycobacterium makes mycolactone and is one of several strains of M. ulcerans-like mycolactone-producing mycobacteria recovered from ectotherms around the world. Here, we describe the complete 6,399,543-bp genome of this frog pathogen (previously unofficially named "Mycobacterium liflandii"), and we show that it has undergone an intermediate degree of reductive evolution between the M. ulcerans Agy99 strain and the fish pathogen Mycobacterium marinum M strain. Like M. ulcerans Agy99, it has the pMUM mycolactone plasmid, over 200 chromosomal copies of the insertion sequence IS2404, and a high proportion of pseudogenes. However, M. liflandii has a larger genome that is closer in length, sequence, and architecture to M. marinum M than to M. ulcerans Agy99, suggesting that the M. ulcerans Agy99 strain has undergone accelerated evolution. Scrutiny of the genes specifically lost suggests that M. liflandii is a tryptophan, tyrosine, and phenylalanine auxotroph. A once-extensive M. marinum-like secondary metabolome has also been diminished through reductive evolution. Our analysis shows that M. liflandii, like M. ulcerans Agy99, has the characteristics of a niche-adapted mycobacterium but also has several distinctive features in important metabolic pathways that suggest that it is responding to different environmental pressures, supporting earlier proposals that it could be considered an M. ulcerans ecotype, hence the name M. ulcerans ecovar Liflandii.

  12. Resistance to first-line anti-TB drugs is associated with reduced nitric oxide susceptibility in Mycobacterium tuberculosis

    DEFF Research Database (Denmark)

    Idh, Jonna; Mekonnen, Mekidim; Abate, Ebba

    2012-01-01

    The relative contribution of nitric oxide (NO) to the killing of Mycobacterium tuberculosis in human tuberculosis (TB) is controversial, although this has been firmly established in rodents. Studies have demonstrated that clinical strains of M. tuberculosis differ in susceptibility to NO, but how...

  13. Molecular Typing of Mycobacterium intracellulare Using Pulsed-Field Gel Electrophoresis, Variable-Number Tandem-Repeat Analysis, Mycobacteria Interspersed Repetitive-Unit-Variable-Number Tandem Repeat Typing, and Multilocus Sequence Typing: Molecular Characterization and Comparison of Each Typing Methods

    OpenAIRE

    Jeon, Semi; Lim, Nara; Kwon, Seungjik; Shim, Taesun; Park, Misun; Kim, Bum-Joon; Kim, Seonghan

    2014-01-01

    Objectives Mycobacterium intracellulare is the major causative agent of nontuberculous mycobacteria-related pulmonary infections. The strain typing of M. intracellulare is important for the treatment and control of its infections. We compared the discrimination capacity and effective value of four different molecular typing methods. Methods Antibiotic susceptibility testing, hsp65 and rpoB sequencing, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), mycobacteria int...

  14. Chitin promotes Mycobacterium ulcerans growth.

    Science.gov (United States)

    Sanhueza, Daniel; Chevillon, Christine; Colwell, Rita; Babonneau, Jérémie; Marion, Estelle; Marsollier, Laurent; Guégan, Jean-François

    2016-06-01

    Mycobacterium ulcerans(MU) is the causative agent of Buruli ulcer, an emerging human infectious disease. However, both the ecology and life cycle of MU are poorly understood. The occurrence of MU has been linked to the aquatic environment, notably water bodies affected by human activities. It has been hypothesized that one or a combination of environmental factor(s) connected to human activities could favour growth of MU in aquatic systems. Here, we testedin vitrothe growth effect of two ubiquitous polysaccharides and five chemical components on MU at concentration ranges shown to occur in endemic regions. Real-time PCR showed that chitin increased MU growth significantly providing a nutrient source or environmental support for thebacillus, thereby, providing a focus on the association between MU and aquatic arthropods. Aquatic environments with elevated population of arthropods provide increased chitin availability and, thereby, enhanced multiplication of MU. If calcium very slightly enhanced MU growth, iron, zinc, sulphate and phosphate did not stimulate MU growth, and at the concentration ranges of this study would limit MU population in natural ecosystems. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Characterization of Mycobacterium chelonae-Like Strains by Comparative Genomics

    Directory of Open Access Journals (Sweden)

    Christiane L. Nogueira

    2017-05-01

    Full Text Available Isolates of the Mycobacterium chelonae-M. abscessus complex are subdivided into four clusters (CHI to CHIV in the INNO-LiPA® Mycobacterium spp DNA strip assay. A considerable phenotypic variability was observed among isolates of the CHII cluster. In this study, we examined the diversity of 26 CHII cluster isolates by phenotypic analysis, drug susceptibility testing, whole genome sequencing and single-gene analysis. Pairwise genome comparisons were performed using several approaches, including average nucleotide identity (ANI and genome-to-genome distance (GGD among others. Based on ANI and GGD the isolates were identified as M. chelonae (14 isolates, M. franklinii (2 isolates and M. salmoniphium (1 isolate. The remaining 9 isolates were subdivided into three novel putative genomospecies. Phenotypic analyses including drug susceptibility testing, as well as whole genome comparison by TETRA and delta differences, were not helpful in separating the groups revealed by ANI and GGD. The analysis of standard four conserved genomic regions showed that rpoB alone and the concatenated sequences clearly distinguished the taxonomic groups delimited by whole genome analyses. In conclusion, the CHII INNO-LiPa is not a homogeneous cluster; on the contrary, it is composed of closely related different species belonging to the M. chelonae-M. abscessus complex and also several unidentified isolates. The detection of these isolates, putatively novel species, indicates a wider inner variability than the presently known in this complex.

  16. Decay of Mycobacterium bovis in whole milk submitted to pasteurization parameters

    OpenAIRE

    Leandro Ribeiro; Maurício Roberto Tosti Narciso; Tatiane Hoshida Felipe; Karina Ramirez Starikoff; Gisele Oliveira de Souza; José Soares Ferreira Neto; Fernando Ferreira; Marcos Amaku; Ricardo Augusto Dias; Vítor Salvador Picão Gonçalves; Marcos Bryan Heinemann; José Henrique Hildebrand Grisi-Filho; Evelise Oliveira Telles

    2016-01-01

    Parameters for milk pasteurization were established a long time ago, considering the thermal resistance of Mycobacterium bovis, and the systematic adoption of this process has drastically reduced the incidence of human tuberculosis caused by this pathogen. However, more recently, molecular methods have allowed the identification of genetic variations in this bacterium that may lead to greater thermal resistance. The aim of this study was to investigate whether genetic variation leads to varia...

  17. Mycobacterium marinum: a potential immunotherapy for Mycobacterium tuberculosis infection

    Directory of Open Access Journals (Sweden)

    Tian WW

    2013-07-01

    Full Text Available Wei-wei Tian,1 Qian-qiu Wang,1 Wei-da Liu,2 Jian-ping Shen,1 Hong-sheng Wang11Laboratory of Mycobacterial Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, Jiangsu, People’s Republic of China; 2Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, Jiangsu, People’s Republic of ChinaPurpose: The aim of the present study was to investigate the immune response induced by Mycobacterium marinum infection in vitro and the potential of M. marinum as an immunotherapy for M. tuberculosis infection.Methods: The potential human immune response to certain bacillus infections was investigated in an immune cell–bacillus coculture system in vitro. As a potential novel immunotherapy, M. marinum was studied and compared with two other bacilli, Bacillus Calmette-Guérin (BCG and live attenuated M. tuberculosis. We examined the changes in both the bacilli and immune cells, especially the time course of the viability of mycobacteria in the coculture system and host immune responses including multinuclear giant cell formation by Wright–Giemsa modified staining, macrophage polarization by cell surface antigen expression, and cytokines/chemokine production by both mRNA expression and protein secretion.Results: The M. marinum stimulated coculture group showed more expression of CD209, CD68, CD80, and CD86 than the BCG and M. tuberculosis (an attenuated strain, H37Ra groups, although the differences were not statistically significant. Moreover, the M. marinum group expressed more interleukin (IL-1B and IL-12p40 on day 3 (IL-1B: P = 0.003 and 0.004, respectively; IL-12p40: P = 0.001 and 0.011, respectively, a higher level of CXCL10 on day 1 (P = 0.006 and 0.026, respectively, and

  18. Linking the transcriptional profiles and the physiological states of Mycobacterium tuberculosis during an extended intracellular infection.

    Directory of Open Access Journals (Sweden)

    Kyle H Rohde

    Full Text Available Intracellular pathogens such as Mycobacterium tuberculosis have evolved strategies for coping with the pressures encountered inside host cells. The ability to coordinate global gene expression in response to environmental and internal cues is one key to their success. Prolonged survival and replication within macrophages, a key virulence trait of M. tuberculosis, requires dynamic adaptation to diverse and changing conditions within its phagosomal niche. However, the physiological adaptations during the different phases of this infection process remain poorly understood. To address this knowledge gap, we have developed a multi-tiered approach to define the temporal patterns of gene expression in M. tuberculosis in a macrophage infection model that extends from infection, through intracellular adaptation, to the establishment of a productive infection. Using a clock plasmid to measure intracellular replication and death rates over a 14-day infection and electron microscopy to define bacterial integrity, we observed an initial period of rapid replication coupled with a high death rate. This was followed by period of slowed growth and enhanced intracellular survival, leading finally to an extended period of net growth. The transcriptional profiles of M. tuberculosis reflect these physiological transitions as the bacterium adapts to conditions within its host cell. Finally, analysis with a Transcriptional Regulatory Network model revealed linked genetic networks whereby M. tuberculosis coordinates global gene expression during intracellular survival. The integration of molecular and cellular biology together with transcriptional profiling and systems analysis offers unique insights into the host-driven responses of intracellular pathogens such as M. tuberculosis.

  19. Establishment of safety analysis system for emergency operating procedures of Kori 3 and 4 and YGN 1 and 2 and reference analyses

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Won Jae; Kim, Hee Cheol; Ha, Kwi Seok; Chung, Bub Dong; Jeong, Jae Jun

    1999-02-01

    This report describes the establishment of safety analysis system for emergency operating procedures(EOPs) of Kori 3 and 4 and YGN 1 and 2 and the results of reference analyses. MARS1.3.1 code has been selected as a realistic system analysis tool of the safety analysis system, and the reactor system has been modeled using a fine nodding scheme in order to capture the major thermal-hydraulic phenomena that might occur during the transients. Full power steady state operating conditions are generated based on the plant operation data. Then, the reference analyses have been carried out for the accidents that can represent the typical EOPtransients, that is, a small-break loss-of-coolant-accident,a main steam line break accident and a steam generator tube rupture accident from the full power operation. For the realistic simulation of plant transient responses, reactor control and protection systems and safety systems are modeled based on their realistic performances. Also, the operator actions are modeled based on the current EOP actions. Through the reference analyses, the soundness of the established safety analysis system and the system modeling has been verified and the effectiveness of the current EOP has been partly justified. In conclusion, the safety analysis system established through this study can be used for the generation of technical background in the development and improvement of EOP actions and in the operator training. (Author). 11 refs., 6 tabs., 48 figs.

  20. Mycobacterium chelonae y Mycobacterium abscessus: patógenos emergentes

    Directory of Open Access Journals (Sweden)

    Mónica M. Ortegón

    1996-09-01

    Full Text Available Mycobacterium chelonae es el nombre correcto para la micobacteria aislada en 1903 de los pulmones enfermos de una tortuga marina. En una especie distinta de Mycobacterium fo/tuitum, aislado de ranas en 1905, y de Mycobacterium abscessus, considerado actualmente como una subespecie de M chelonae. Estas tres especies son las únicas patógenas para el hombre dentro del grupo de micobacterias ambientales o atipicas, de crecimiento rápido, las cuales se caracterizan por formar colonias en cultivo en menos de siete días. Son agentes etiológicos de nódulos y abscesos cutáneos, localizados y diseminados, de lesiones postoperatorias, usualmente en la cicatriz quirúrgica, de lesiones pulmonares y de linfadenitis granulomatosa, de osteomielitis y de queratitis, entre otras. Las lesiones cutáneas y de los tejidos blandos son las más frecuentes y resultan generalmente de la inoculación traumática de esta micobacteria. Histopatológicamente, los nódulos y abscesos muestran un proceso inflamatorio, supurativo y granulomatoso, mixto, en el que en la cuarta parte de los casos pueden demostrarse conglomerados de bacilos ácido alcohol resistentes, que tienden a estar situados en una vacuola en el centro del absceso. En Colombia, se han descrito tres brotes de abscesos subcutáneos producidos por bacterias ambientales, secundarios a la aplicación de inyecciones contaminadas con el germen causal: en 1981, en Bucaramanga, luego de la aplicación de la vacuna contra la fiebre amarilla, en 50 personas, la mayoría niños; en 1989, en Medellin, por la inyección subcutánea de alergenos, en 13 personas; y, en 1993, en varias ciudades de la costa atlántica, luego de aplicaciones subcutáneas de xilocaína, como tratamiento bionergético, en 297 pacientes. Existen otros informes aislados de casos posttraumáticos.La enfermedad diseminada por micobacterias de rápido crecimiento, se presenta en pacientes inmunosuprimidos. En la biopsia, predominan los

  1. [Analysis of chromosome deletions of TbDl, RD6 and pks15/1 in clinical strains of Mycobacterium tuberculosis].

    Science.gov (United States)

    Likhoshvaĭ, E Iu; Kurepina, N E; Sinsimer, D; Belikov, S I; Kreiswirth, B N

    2006-01-01

    Deletions are very important sources of the variability among members of the mycobacterial tuberculosis complex (MTC). Deletion analysis of MTC clinical isolates was performed to clarify phylogenetic relationships and help to identify epidemiologically significant groups of the MTC. In this study, the variability of the TbDl, RD6 and pks15/1 chromosome loci in clinical MTC strains and comparison of those results with IS6110-RFLP (restriction fragment length polymorphism), sSNP (synonymous single nucleotide polymorphism), PGG (Principal Genetic Group) typing data were used to determine if these chromosome regions constitute good molecular markers for some of the epidemiologically important groups of the MTC. In the present study, 122, 61 and 294 clinical isolates were tested for the TbDl, RD6 and pks15/1 deletions, respectively. Specific probes were designed and used in RFLP analysis as well as sequencing techniques were applied. We found that all strains with intact TbDl region belonged to the sSNP cluster I, PGG 1 (katG463Leu and gyrA95Thr). The RD6 deletion was not determined to be a strict characteristic feature of any specific genetic group of the tested M.tb strains, but presence of this deletion is presumed for strains of high virulence, and associated with principal genetic groups 2 or 3. The genetic event that led to this deletion likely occurred in the strain that belongs to PGG 1. Identification of strains with an intact pksl5/1 gene cluster provided a potential marker for virulence. An intact pks15/1 gene cluster is required for the biosynthesis of the phenolic glycolipids (PGL-tb), production of which by clinical isolates was correlated with virulence.

  2. Therapy-resistant septic olecranon bursitis due to Mycobacterium gordonae

    Directory of Open Access Journals (Sweden)

    Konrads Christian

    2016-01-01

    Full Text Available Introduction: Septic olecranon bursitis due to atypical mycobacteria is rare. An insidious beginning can delay diagnosis and treatment. Antibacterial therapy recommendations are not well-defined for bursitis caused by atypical mycobacteria. We present a rare case of olecranon bursitis caused by Mycobacterium gordonae, reporting our experiences regarding pathogen identification and antibiotic therapy, which differs from regimes used in common septic bursitis mostly caused by staphylococcus aureus. Methods: A 35-year-old male with bursitis olecrani received open bursectomy. Microbiological culture did not reveal bacteria. Due to wound healing complications revision surgery was performed four weeks postoperatively. Finally, Mycobacterium gordonae was identified by PCR and an antibiogram could be developed. A triple antimicrobial combination therapy with Rifampicin, Clarithromycin, and Ethambutol was administered systemically for 12 months. The patient was followed-up for 24 months. Results: After the second operation with pathogen identification and antibiotic combination therapy the wound healed without any additional complications. At last follow-up 24 months after the first surgery with bursectomy and 23 months after revision surgery with debridement, the patient was still pain free with no significant clinical findings or tenderness to touch at the operation site. Elbow range of motion was full. Discussion: As septic bursitis can be caused by many different and sometimes rare and difficult to identify bacteria, intraoperative probes should be taken and histopathological and microbiological analysis should be conducted, including PCR. In a young man with olecranon bursitis due to Mycobacterium gordonae surgical treatment and an antibiotic combination therapy showed a good clinical outcome after one and two years.

  3. Correlation of bacterial viability with uptake of (14C) acetate into phenolic glycolipid-1 of Mycobacterium leprae within Schwannoma cells

    International Nuclear Information System (INIS)

    Mistry, Y.; Antia, N.H.; Mukherjee, R.

    1989-01-01

    The viability of Mycobacterium leprae, maintained within 33B Schwannoma cells, was estimated in terms of incorporation of ( 14 C) acetate into its specific phenolic glycolipid-1. This measure of viability was correlated with two other assays, viz., fluorescein diacetate/ethidium bromide staining and mouse footpad growth. Observation of a 2-fold increase in the number of intracellular Mycobacterium leprae over an experimental period of 12 days also corroborated this contention. Furthermore, on addition of anti-leprosy drugs to these intracellular Mycobacterium leprae there was significant decrease in phenolic glycolipid-1 synthesis indicative of loss of viability of the organisms. This study also established the importance of the host cell for active bacillary metabolism, as Mycobacterium leprae maintained in cell-free conditions showed no incorporation into phenolic glycolipid-1. Moreover, compromising the host's protein synthesis capacity with cycloheximide, also led to reduction in bacillary metabolism. As this system measures the metabolic synthesis of a unique Mycobacterium leprae component, it would be useful for development and screening of compounds acting against specific bacillary targets. (author). 19 refs., 5 tabs

  4. The preliminary analysis of establishing the cost control system of AP1000 for the Haiyang nuclear power project

    International Nuclear Information System (INIS)

    Li Jing; Li Xiaobing

    2012-01-01

    The AP1000 technology has been first applied to Nuclear Power Plant construction in China. Haiyang Project is the second plant which applies the new technology, and it is the key to the success of the project, that how to control the cost. The cost control of AP1000 is to manage and monitor all the cost of the project, including the cost of project management, design, procurement, construction, and startup/commissioning. For the Haiyang Project, the cost control system should be established to ensure that the evaluation of the procurement order should be covered in the original budget, and all potential commitments are evaluated and approved within the confinement of cost control, and reduce the risk of the first reactor and get the most profit. (authors)

  5. Genomic analysis of a Mycobacterium bovis bacillus [corrected] Calmette-Guérin strain isolated from an adult patient with pulmonary tuberculosis..

    Directory of Open Access Journals (Sweden)

    Xuming Li

    Full Text Available For years, bacillus Calmette-Guérin (BCG has served as the unique vaccine against tuberculosis and has generally been regarded as safe. However, a clinical strain labeled 3281 that was isolated from a TB patient was identified to be BCG. Via the combination of next-generation sequencing (NGS and comparative genomic analysis, unique 3281 genetic characteristics were revealed. A region containing the dnaA and dnaN genes that is closely related to the initial chromosome replication was found to repeat three times on the BCG Pasteur-specific tandem duplication region DU1. Due to the minimum number of epitopes in BCG strains, 3281 was inferred to have a high possibility for immune evasion. Additionally, variations in the virulence genes and predictions for potential virulence factors were analyzed. Overall, we report a pathogen that has never previously been thought to be pathogenic and initial insights that are focused on the genetic characteristics of virulent BCG.

  6. Infection by Mycobacterium bovis in a dog from Brazil

    Directory of Open Access Journals (Sweden)

    Vivianne Cambuí Figueiredo Rocha

    Full Text Available Abstract Tuberculosis (TB is a chronic disease caused by bacteria belonging to the Mycobacterium tuberculosis complex (MtbC. This disease rarely affects dogs. Canine infections are usually caused by M. tuberculosis. Mycobacterium bovis infections are rare in dogs and associated with consumption of raw milk or contaminated products. Here, we report a Boxer dog who had a M. bovis infection and was admitted to a Brazilian veterinary hospital with a presumptive diagnosis of chronic ehrlichiosis. Despite receiving treatment for chronic ehrlichiosis, it progressed to death. TB was diagnosed during post-mortem examinations using histopathological analysis. Ziehl-Neelsen staining revealed acid-fast bacilli in the kidneys, liver, mesentery, and a mass adhered to the liver. Further, PCR-restriction analysis was performed to identify mycobacteria in the samples. A restriction profile compatible with MtbC was found in the lungs. In addition, PCR-based MtbC typing deletions at different loci of chromosome 9 enabled the identification of M. bovis in the lungs. Therefore, it is very essential to perform differential diagnosis of TB in dogs with non-specific clinical signs and who do not respond to treatment, particularly those who had been in contact with TB-infected cattle or owners. Further, we highlight the use of molecular methods for the identification of bacilli, improving the diagnosis and aiding epidemiological studies.

  7. Mycobacterium aquiterrae sp. nov., a rapidly growing bacterium isolated from groundwater.

    Science.gov (United States)

    Lee, Jae-Chan; Whang, Kyung-Sook

    2017-10-01

    A strain representing a rapidly growing, Gram-stain-positive, aerobic, rod-shaped, non-motile, non-sporulating and non-pigmented species of the genus Mycobacterium, designated strain S-I-6 T , was isolated from groundwater at Daejeon in Korea. The strain grew at temperatures between 10 and 37 °C (optimal growth at 25 °C), between pH 4.0 and 9.0 (optimal growth at pH 7.0) and at salinities of 0-5 % (w/v) NaCl, growing optimally with 2 % (w/v) NaCl. Phylogenetic analyses based on multilocus sequence analysis of the 16S rRNAgene, hsp65, rpoB and the 16S-23S internal transcribed spacer indicated that strain S-I-6 T belonged to the rapidly growing mycobacteria, being most closely related to Mycobacterium sphagni. On the basis of polyphasic taxonomic analysis, the bacterial strain was distinguished from its phylogenetic neighbours by chemotaxonomic properties and other biochemical characteristics. DNA-DNA relatedness among strain S-I-6 T and the closest phylogenetic neighbour strongly support the proposal that this strain represents a novel species within the genus Mycobacterium, for which the name Mycobacterium aquiterrae sp. nov. is proposed. The type strain is S-I-6 T (=KACC 17600 T =NBRC 109805 T =NCAIM B 02535 T ).

  8. A Case of False-Positive Mycobacterium tuberculosis Caused by Mycobacterium celatum

    OpenAIRE

    Gildeh, Edward; Abdel-Rahman, Zaid; Sengupta, Ruchira; Johnson, Laura

    2016-01-01

    Mycobacterium celatum is a nontuberculous mycobacterium shown to cause symptoms similar to pulmonary M. tuberculosis. Certain strains have been shown to cross-react with the probes used to detect M. tuberculosis, making this a diagnostic challenge. We present a 56-year-old gentleman who developed signs and symptoms of lung infection with computed tomography scan of the chest showing right lung apex cavitation. Serial sputum samples were positive for acid-fast bacilli and nucleic acid amplific...

  9. Identification of Nudix Hydrolase Family Members with an Antimutator Role in Mycobacterium tuberculosis and Mycobacterium smegmatis†

    OpenAIRE

    Dos Vultos, T.; Blázquez, J.; Rauzier, J.; Matic, I.; Gicquel, B.

    2006-01-01

    Mycobacterium tuberculosis and Mycobacterium smegmatis MutT1, MutT2, MutT3, and Rv3908 (MutT4) enzymes were screened for an antimutator role. Results indicate that both MutT1, in M. tuberculosis and M. smegmatis, and MutT4, in M. smegmatis, have that role. Furthermore, an 8-oxo-guanosine triphosphatase function for MutT1 and MutT2 is suggested.

  10. Genome Analysis of the First Extensively Drug-Resistant (XDR Mycobacterium tuberculosis in Malaysia Provides Insights into the Genetic Basis of Its Biology and Drug Resistance.

    Directory of Open Access Journals (Sweden)

    Chee Sian Kuan

    Full Text Available The outbreak of extensively drug-resistant tuberculosis (XDR-TB has become an increasing problem in many TB-burdened countries. The underlying drug resistance mechanisms, including the genetic variation favored by selective pressure in the resistant population, are partially understood. Recently, the first case of XDR-TB was reported in Malaysia. However, the detailed genotype family and mechanisms of the formation of multiple drugs resistance are unknown. We sequenced the whole genome of the UM 1072388579 strain with a 2-kb insert-size library and combined with that from previously sequenced 500-bp-insert paired-end reads to produce an improved sequence with maximal sequencing coverage across the genome. In silico spoligotyping and phylogenetic analyses demonstrated that UM 1072388579 strain belongs to an ancestral-like, non-Beijing clade of East Asia lineage. This is supported by the presence of a number of lineage-specific markers, including fadD28, embA, nuoD and pks7. Polymorphism analysis showed that the drug-susceptibility profile is correlated with the pattern of resistance mutations. Mutations in drug-efflux pumps and the cell wall biogenesis pathway such as mmpL, pks and fadD genes may play an important role in survival and adaptation of this strain to its surrounding environment. In this work, fifty-seven putative promoter SNPs were identified. Among them, we identified a novel SNP located at -4 T allele of TetR/acrR promoter as an informative marker to recognize strains of East Asian lineage. Our work indicates that the UM 1072388579 harbors both classical and uncommon SNPs that allow it to escape from inhibition by many antibiotics. This study provides a strong foundation to dissect the biology and underlying resistance mechanisms of the first reported XDR M. tuberculosis in Malaysia.

  11. Analysis of Dominant HIV Quasispecies Suggests Independent Viral Evolution Within Spinal Granulomas Coinfected with Mycobacterium tuberculosis and HIV-1 Subtype C.

    Science.gov (United States)

    Danaviah, Sivapragashini; de Oliveira, Tulio; Gordon, Michelle; Govender, Shunmugam; Chelule, Paul; Pillay, Sureshnee; Naicker, Thajasvarie; Cassol, Sharon; Ndung'u, Thumbi

    2016-03-01

    Extrapulmonary tuberculosis (TB) is a significant public health challenge in South Africa and worldwide, largely fuelled by the HIV epidemic. In spinal TB, Mycobacteria infect the spinal column without dissemination to the spinal cord. The immune microenvironment, target cell characteristics, and other evolutionary forces within granulomas during HIV/TB coinfection are poorly characterized. We investigated whether spinal TB granulomas represent a sequestered anatomical site where independent HIV evolution occurs, and assessed the role of macrophages as a target cell for both HIV and mycobacteria. RNA was extracted from plasma and granulomatous tissue from six antiretroviral-naive HIV-1/spinal TB-coinfected patients, RT-PCR amplified, and the C2-V5 env segment was cloned and sequenced. Analysis of genetic diversity, phylogeny and coalescence patterns was performed on clonal sequences. To investigate their role in HIV sequestration, macrophages and the HIV-1 p24 protein were immune localized and ultrastructural features were studied. Intercompartment diversity measurements and phylogenetic reconstruction revealed anatomically distinct monophyletic HIV-1 clusters in four of six patients. Genotypic CCR5-tropic variants were predominant (98.9%) with conservation of putative N-linked glycosylation sites in both compartments. CD68(+) reactivity was associated with higher tissue viral load (r = 1.0; p 0.05). Ultrastructural imaging revealed the presence of bacterial and virus-like particles within membrane-bound intracellular compartments of macrophages. Spinal tuberculosis granulomas may form anatomically discreet sites of divergent viral evolution. Macrophages in these granulomas harbored both pathogens, suggesting that they may facilitate the process of viral sequestration within this compartment.

  12. Guidance for establishment and implementation of a national sample management program in support of EM environmental sampling and analysis activities

    International Nuclear Information System (INIS)

    1994-01-01

    The role of the National Sample Management Program (NSMP) proposed by the Department of Energy's Office of Environmental Management (EM) is to be a resource for EM programs and for local Field Sample Management Programs (FSMPs). It will be a source of information on sample analysis and data collection within the DOE complex. Therefore the NSMP's primary role is to coordinate and function as a central repository for information collected from the FSMPs. An additional role of the NSMP is to monitor trends in data collected from the FSMPs over time and across sites and laboratories. Tracking these trends will allow identification of potential problems in the sampling and analysis process

  13. Targeting phenotypically tolerant Mycobacterium tuberculosis

    Science.gov (United States)

    Gold, Ben; Nathan, Carl

    2016-01-01

    While the immune system is credited with averting tuberculosis in billions of individuals exposed to Mycobacterium tuberculosis, the immune system is also culpable for tempering the ability of antibiotics to deliver swift and durable cure of disease. In individuals afflicted with tuberculosis, host immunity produces diverse microenvironmental niches that support suboptimal growth, or complete growth arrest, of M. tuberculosis. The physiological state of nonreplication in bacteria is associated with phenotypic drug tolerance. Many of these host microenvironments, when modeled in vitro by carbon starvation, complete nutrient starvation, stationary phase, acidic pH, reactive nitrogen intermediates, hypoxia, biofilms, and withholding streptomycin from the streptomycin-addicted strain SS18b, render M. tuberculosis profoundly tolerant to many of the antibiotics that are given to tuberculosis patients in a clinical setting. Targeting nonreplicating persisters is anticipated to reduce the duration of antibiotic treatment and rate of post-treatment relapse. Some promising drugs to treat tuberculosis, such as rifampicin and bedaquiline, only kill nonreplicating M. tuberculosis in vitro at concentrations far greater than their minimal inhibitory concentrations against replicating bacilli. There is an urgent demand to identify which of the currently used antibiotics, and which of the molecules in academic and corporate screening collections, have potent bactericidal action on nonreplicating M. tuberculosis. With this goal, we review methods of high throughput screening to target nonreplicating M. tuberculosis and methods to progress candidate molecules. A classification based on structures and putative targets of molecules that have been reported to kill nonreplicating M. tuberculosis revealed a rich diversity in pharmacophores. However, few of these compounds were tested under conditions that would exclude the impact of adsorbed compound acting during the recovery phase of

  14. Increased Severity and Spread of Mycobacterium ulcerans, Southeastern Australia.

    Science.gov (United States)

    Tai, Alex Y C; Athan, Eugene; Friedman, N Deborah; Hughes, Andrew; Walton, Aaron; O'Brien, Daniel P

    2018-01-01

    Reported cases of Mycobacterium ulcerans disease (Buruli ulcer) have been increasing in southeastern Australia and spreading into new geographic areas. We analyzed 426 cases of M. ulcerans disease during January 1998-May 2017 in the established disease-endemic region of the Bellarine Peninsula and the emerging endemic region of the Mornington Peninsula. A total of 20.4% of cases-patients had severe disease. Over time, there has been an increase in the number of cases managed per year and the proportion associated with severe disease. Risk factors associated with severe disease included age, time period (range of years of diagnosis), and location of lesions over a joint. We highlight the changing epidemiology and pathogenicity of M. ulcerans disease in Australia. Further research, including genomic studies of emergent strains with increased pathogenicity, are urgently needed to improve the understanding of disease to facilitate implementation of effective public health measures to halt its spread.

  15. Evasion and subversion of antigen presentation by Mycobacterium tuberculosis.

    Science.gov (United States)

    Baena, A; Porcelli, S A

    2009-09-01

    Mycobacterium tuberculosis is one of the most successful of human pathogens and has acquired the ability to establish latent or progressive infection and persist even in the presence of a fully functioning immune system. The ability of M. tuberculosis to avoid immune-mediated clearance is likely to reflect a highly evolved and coordinated program of immune evasion strategies, including some that interfere with antigen presentation to prevent or alter the quality of T-cell responses. Here, we review an extensive array of published studies supporting the view that antigen presentation pathways are targeted at many points by pathogenic mycobacteria. These studies show the multiple potential mechanisms by which M. tuberculosis may actively inhibit, subvert or otherwise modulate antigen presentation by major histocompatibility complex class I, class II and CD1 molecules. Unraveling the mechanisms by which M. tuberculosis evades or modulates antigen presentation is of critical importance for the development of more effective new vaccines based on live attenuated mycobacterial strains.

  16. Metabolic principles of persistence and pathogenicity in Mycobacterium tuberculosis.

    Science.gov (United States)

    Ehrt, Sabine; Schnappinger, Dirk; Rhee, Kyu Y

    2018-04-24

    Metabolism was once relegated to the supply of energy and biosynthetic precursors, but it has now become clear that it is a specific mediator of nearly all physiological processes. In the context of microbial pathogenesis, metabolism has expanded outside its canonical role in bacterial replication. Among human pathogens, this expansion has emerged perhaps nowhere more visibly than for Mycobacterium tuberculosis, the causative agent of tuberculosis. Unlike most pathogens, M. tuberculosis has evolved within humans, which are both host and reservoir. This makes unrestrained replication and perpetual quiescence equally incompatible strategies for survival as a species. In this Review, we summarize recent work that illustrates the diversity of metabolic functions that not only enable M. tuberculosis to establish and maintain a state of chronic infection within the host but also facilitate its survival in the face of drug pressure and, ultimately, completion of its life cycle.

  17. Establishment of a continuous culture system for Entamoeba muris and analysis of the small subunit rRNA gene

    Directory of Open Access Journals (Sweden)

    Kobayashi S.

    2009-06-01

    Full Text Available We established a culture system for Entamoeba muris (MG-EM-01 strain isolated from a Mongolian gerbil using a modified Balamuth’s egg yolk infusion medium supplemented with 4% adult bovine serum and Bacteroides fragilis cocultured with Escherichia coli. Further, encystation was observed in the culture medium. The morphological characteristics of E. muris are similar to those of Entamoeba coli (E. coli; moreover, the malic isoenzyme electrophoretic band, which shows species-specific electrophoretic mobility, of E. muris had almost the same mobility as that observed with the malic isoenzyme electrophorectic band of E. coli (UZG-EC-01 strain isolated from a gorilla. We determined the small subunit rRNA (SSU-rRNA gene sequence of the MG-EM-01 strain, and this sequence was observed to show 82.7% homology with that of the UZG-EC-01 strain. Further, the resultant phylogenetic tree for molecular taxonomy based on the SSU-rRNA genes of the 21 strains of the intestinal parasitic amoeba species indicated that the MG-EM-01 strain was most closely related to E. coli.

  18. Tuberculosis Caused by Mycobacterium orygis in Dairy Cattle and Captured Monkeys in Bangladesh: a New Scenario of Tuberculosis in South Asia.

    Science.gov (United States)

    Rahim, Z; Thapa, J; Fukushima, Y; van der Zanden, A G M; Gordon, S V; Suzuki, Y; Nakajima, C

    2017-12-01

    Mycobacterium orygis, commonly known as the oryx bacillus and a newly proposed Mycobacterium tuberculosis complex subspecies, was isolated from 18 cattle in a dairy farm and two captured rhesus monkeys in a zoo in Bangladesh. All the infected animals had tuberculosis lesions in their lungs, suggesting transmission and infection with M. orygis by an airborne route. The 20 isolates were analysed using a range of conventional and molecular typing methods, and RD-deletion typing and sequencing of selected genes confirmed the isolates as M. orygis. Multiple-locus variable-number tandem repeat analysis (MLVA) allowed the isolates to be divided into three clusters based on the relatedness of their MLVA profiles. The two monkey isolates shared the same MLVA pattern with 15 of the cattle isolates, whereas the remaining three cattle isolates had different patterns, even though the latter animals had been kept in the same dairy farm. The diversity observed among isolates may suggest the bacteria have been established in this area for a long period. This study along with other recent findings that report the detection of M. orygis from animals as well as humans originating from South Asia potentially indicate endemic distribution of M. orygis in South Asia. © 2016 Blackwell Verlag GmbH.

  19. Anti-tubercular screening of natural products from Colombian plants: 3-methoxynordomesticine, an inhibitor of MurE ligase of Mycobacterium tuberculosis.

    Science.gov (United States)

    Guzman, Juan D; Gupta, Antima; Evangelopoulos, Dimitrios; Basavannacharya, Chandrakala; Pabon, Ludy C; Plazas, Erika A; Muñoz, Diego R; Delgado, Wilman A; Cuca, Luis E; Ribon, Wellman; Gibbons, Simon; Bhakta, Sanjib

    2010-10-01

    New anti-mycobacterial entities with novel mechanisms of action are clinically needed for treating resistant forms of tuberculosis. The purpose of this study was to evaluate anti-tubercular activity and selectivity of seven recently isolated natural products from Colombian plants. MICs were determined using a liquid medium growth inhibition assay for Mycobacterium tuberculosis H(37)Rv and both solid and liquid media growth inhibition assays for Mycobacterium bovis BCG. Escherichia coli growth inhibition and mammalian macrophage cell toxicity were evaluated to establish the degree of selectivity of the natural product against whole cell organisms. Enzymatic inhibition of ATP-dependent MurE ligase from M. tuberculosis was assayed using a colorimetric phosphate detection method. The most active compound, 3-methoxynordomesticine hydrochloride, was further investigated on M. bovis BCG for its inhibition of sigmoidal growth, acid-fast staining and viability counting analysis. Aporphine alkaloids were found to be potent inhibitors of slow-growing mycobacterial pathogens showing favourable selectivity and cytotoxicity. In terms of their endogenous action, the aporphine alkaloids were found inhibitory to M. tuberculosis ATP-dependent MurE ligase at micromolar concentrations. A significantly low MIC was detected for 3-methoxynordomesticine hydrochloride against both M. bovis BCG and M. tuberculosis H(37)Rv. Considering all the data, 3-methoxynordomesticine hydrochloride was found to be a potent anti-tubercular compound with a favourable specificity profile. The alkaloid showed MurE inhibition and is considered an initial hit for exploring related chemical space.

  20. Search for Mycobacterium leprae in wild mammals

    Directory of Open Access Journals (Sweden)

    Sílvia Cristina Barboza Pedrini

    Full Text Available Leprosy is still a worldwide public health problem. Brazil and India show the highest prevalence rates of the disease. Natural infection of armadillos Dasypus novemcinctus with Mycobacterium leprae has been reported in some regions of the United States. Identification of bacilli is difficult, particularly due to its inability to grow in vitro. The use of molecular tools represents a fast and sensitive alternative method for diagnosis of mycobacteriosis. In the present study, the diagnostic methods used were bacilloscopy, histopathology, microbiology, and PCR using specific primers for M. leprae repetitive sequences. PCR were performed using genomic DNA extracted from 138 samples of liver, spleen, lymph nodes, and skin of 44 D. novemcinctus, Euphractus sexcinctus, Cabassous unicinctus, and C. tatouay armadillos from the Middle Western region of the state of São Paulo and from the experimental station of Embrapa Pantanal, located in Pantanal da Nhecolândia of Mato Grosso do Sul state. Also, the molecular analysis of 19 samples from internal organs of other road killed species of wild animals, such as Nasua nasua (ring-tailed coati, Procyon cancrivoros (hand-skinned, Cerdocyon thous (dog-pity-bush, Cavia aperea (restless cavy, Didelphis albiventris (skunk, Sphigurrus spinosus (hedgehog, and Gallictis vittata (ferret showed PCR negative data. None of the 157 analyzed samples had shown natural mycobacterial infection. Only the armadillo inoculated with material collected from untreated multibacillary leprosy patient presented PCR positive and its genomic sequencing revealed 100% identity with M. leprae. According to these preliminary studies, based on the used methodology, it is possible to conclude that wild mammals seem not to play an important role in the epidemiology of leprosy in the Middle Western region of the São Paulo state and in the Pantanal of Mato Grosso do Sul state.

  1. Establishing a common vocabulary of key concepts for the effective ımplementation of applied behavior analysis

    OpenAIRE

    Traci M Cihon; Joseph H Cihon; Guy M. Bedient

    2016-01-01

    The technical language of behavior analysis is arguably necessary to share ideas and research with precision among each other. However, it can hinder effective implementation of behavior analytic techniques when it prevents clear communication between the supervising behavior analyst and behavior technicians. The present paper provides a case example of the development of a shared vocabulary, using plain English when possible, among supervisors and supervisees at a large public school distric...

  2. Histopathologic features of Mycobacterium ulcerans infection

    NARCIS (Netherlands)

    Guarner, J; Bartlett, J; Whitney, EAS; Raghunathan, PL; Stienstra, Y; Asamoa, K; Etuaful, S; Klutse, E; Quarshie, E; van der Werf, TS; van der Graaf, WTA; King, CH; Ashford, DA

    Because of the emergence of Buruli ulcer disease, the World Health Organization launched a Global Buruli Ulcer Initiative in 1998. This indolent skin infection is caused by Mycobacterium ulcerans. During a study of risk factors for the disease in Ghana, adequate excisional skin-biopsy specimens were

  3. Modelling the Transitional Dynamics of Mycobacterium Tuberculosis ...

    African Journals Online (AJOL)

    The World Health Organization's targets of eliminating Tuberculosis (TB) by 2050 is challenged by the emergence and spread of drug resistance TB. However, the traditional mechanism of resistance is that of acquired resistance, whereby the mycobacterium Tuberculosis (MTB) strain develops mutations under selective ...

  4. Safety assessment in primary Mycobacterium tuberculosis smear ...

    African Journals Online (AJOL)

    Introduction Tuberculosis (TB) is caused by Mycobacterium tuberculosis and is transmitted mainly through aerosolization of infected sputum which puts laboratory workers at risk in spite of the laboratory workersf risk of infection being at 3 to 9 times higher than the general public. Laboratory safety should therefore be ...

  5. ELECTROPHORETIC MOBILITY OF MYCOBACTERIUM AVIUM COMPLEX ORGANISMS

    Science.gov (United States)

    The electrophoretic mobilities (EPMs) of thirty Mycobacterium avium Complex (MAC) organisms were measured. The EPMs of fifteen clinical isolates ranged from -1.9 to -5.0 µm cm V-1s-1, and the EPMs of fifteen environmental isolates ranged from -1...

  6. Chronic leg ulcer caused by Mycobacterium immunogenum

    NARCIS (Netherlands)

    Loots, Miriam A. M.; de Jong, Menno D.; van Soolingen, Dick; Wetsteyn, José C. F. M.; Faber, William R.

    2005-01-01

    Rare tropical skin diseases are seen more frequently in Western countries because of the increased popularity of visiting tropical regions. A 55-year-old white man developed a painless leg ulcer after traveling in Guatemala and Belize. A mycobacterium was cultured from a biopsy specimen and was

  7. Identification of Immunotopes against Mycobacterium leprae as ...

    African Journals Online (AJOL)

    Purpose: To determine the surface epitopes of Mycobacterium leprae (M. leprae) and evaluate their efficacy in the production of anti-M. leprae antibodies in an animal model. Methods: Blood samples were obtained from 34 patients suffering from lepromatous leprosy. Antibodies were obtained from the samples, ...

  8. Seroprevalence of Mycobacterium avium SSP paratuberculosis ...

    African Journals Online (AJOL)

    This study aimed to determine the seroprevalence of antibodies for Mycobacterium avium subspecies paratuberculosis (MAP) in dairy cattle in the Jimma zone of Ethiopia in 2011. A random sample of 29 herds was selected, and all mature cattle within these herds had a blood sample taken. Serum was tested in duplicate, ...

  9. Molecular Characterization of the Resistance of Mycobacterium ...

    African Journals Online (AJOL)

    Abstract. Purpose: To characterize the resistance of Mycobacterium tuberculosis to second line drugs using a line probe assay. Methods: ... Marne-la-Coquette,. France). Bacterial isolates contained in 500 µl of liquid culture were heat- inactivated at 95 °C for 30 min and then sonicated for 12 min. Finally, the suspension was ...

  10. Single-nucleotide variations associated with Mycobacterium ...

    Indian Academy of Sciences (India)

    The occurrence of drug resistance in Mycobacterium tuberculosis, the aetiological agent of tuberculosis (TB), is hampering the management and .... drug response by altering cellular chemistry. The majority of. SNVs belong to the .... affects the quantum yield and kinetics of proton release and uptake by bacteriorhodopsin ...

  11. Mycobacterium tuberculosis H37Ra genome sequencing

    Indian Academy of Sciences (India)

    2007-02-09

    Feb 9, 2007 ... Home; Journals; Journal of Biosciences; Volume 32; Issue 2. Commentary: The value of comparative genomics in understanding mycobacterial virulence: Mycobacterium tuberculosis H37Ra genome sequencing – a worthwhile endeavour. Deepak Sharma Jaya Sivaswami Tyagi. Volume 32 Issue 2 March ...

  12. Mycobacterium tuberculosis complex identification by polymerase ...

    African Journals Online (AJOL)

    Mycobacterium tuberculosis complex identification by polymerase chain reaction from positive culture in patients from Jamot and Mbalmayo district hospitals. ... On the same way, MTBC were differentiated from other mycobacreia using the PNP inhibition test. DNA extracted from positive cultures was subjected to PCR ...

  13. Mitogen-activated protein kinases mediate Mycobacterium ...

    Indian Academy of Sciences (India)

    CD44, an adhesion molecule, has been reported to be a binding site for Mycobacterium tuberculosis (M. tuberculosis) in macrophages and it also mediates mycobacterial phagocytosis, macrophage recruitment and protective immunity against pulmonary tuberculosis in vivo. However, the signalling pathways that are ...

  14. Investigating Mycobacterium chelonae-abscessus Complex

    Centers for Disease Control (CDC) Podcasts

    2011-11-17

    Keith Simmon, scientist at Isentio US discusses research that was done while he was at ARUP laboratories, discusses a new classification of Mycobacterium chelonae-abscessus complex.  Created: 11/17/2011 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 11/22/2011.

  15. Mitogen-activated protein kinases mediate Mycobacterium

    Indian Academy of Sciences (India)

    CD44, an adhesion molecule, has been reported to be a binding site for Mycobacterium tuberculosis (M. tuberculosis) in macrophages and it also mediates mycobacterial phagocytosis, macrophage recruitment and protective immunity against pulmonary tuberculosis in vivo. However, the signalling pathways that are ...

  16. Spoligotyping of Mycobacterium africanum, Burkina Faso

    OpenAIRE

    Gomgnimbou, Michel K.; Refrégier, Guislaine; Diagbouga, Serge P.; Adama, Sanou; Kaboré, Antoinette; Ouiminga, Adama; Sola, Christophe

    2012-01-01

    Using Ziehl-Neelsen–positive slides collected from tuberculosis diagnostic centers in Burkina Faso, we showed that 20% of 80 spoligotyping-positive DNA samples had a characteristic Mycobacterium africanum–specific genomic signature. This result suggests that M. africanum is still present in Burkina Faso at almost the same prevalence as 15–20 years ago.

  17. Identifying past fire regimes throughout the Holocene in Ireland using new and established methods of charcoal analysis

    Science.gov (United States)

    Hawthorne, Donna; Mitchell, Fraser J. G.

    2016-04-01

    Globally, in recent years there has been an increase in the scale, intensity and level of destruction caused by wildfires. This can be seen in Ireland where significant changes in vegetation, land use, agriculture and policy, have promoted an increase in fires in the Irish landscape. This study looks at wildfire throughout the Holocene and draws on lacustrine charcoal records from seven study sites spread across Ireland, to reconstruct the past fire regimes recorded at each site. This work utilises new and accepted methods of fire history reconstruction to provide a recommended analytical procedure for statistical charcoal analysis. Digital charcoal counting was used and fire regime reconstructions carried out via the CharAnalysis programme. To verify this record new techniques are employed; an Ensemble-Member strategy to remove the objectivity associated with parameter selection, a Signal to Noise Index to determine if the charcoal record is appropriate for peak detection, and a charcoal peak screening procedure to validate the identified fire events based on bootstrapped samples. This analysis represents the first study of its kind in Ireland, examining the past record of fire on a multi-site and paleoecological timescale, and will provide a baseline level of data which can be built on in the future when the frequency and intensity of fire is predicted to increase.

  18. [Establishment and assessment of QA/QC method for sampling and analysis of atmosphere background CO2].

    Science.gov (United States)

    Liu, Li-xin; Zhou, Ling-xi; Xia, Ling-jun; Wang, Hong-yang; Fang, Shuang-xi

    2014-12-01

    To strengthen scientific management and sharing of greenhouse gas data obtained from atmospheric background stations in China, it is important to ensure the standardization of quality assurance and quality control method for background CO2 sampling and analysis. Based on the greenhouse gas sampling and observation experience of CMA, using portable sampling observation and WS-CRDS analysis technique as an example, the quality assurance measures for atmospheric CO,sampling and observation in the Waliguan station (Qinghai), the glass bottle quality assurance measures and the systematic quality control method during sample analysis, the correction method during data processing, as well as the data grading quality markers and data fitting interpolation method were systematically introduced. Finally, using this research method, the CO2 sampling and observation data at the atmospheric background stations in 3 typical regions were processed and the concentration variation characteristics were analyzed, indicating that this research method could well catch the influences of the regional and local environmental factors on the observation results, and reflect the characteristics of natural and human activities in an objective and accurate way.

  19. [Analysis of serum lipids levels and the establishment of reference intervals for serum lipids in middle and late pregnancy].

    Science.gov (United States)

    Ying, Chunmei; Yue, Chaoyan; Zhang, Chunyi; Li, Xiaotian

    2015-12-01

    To explore the serum lipids levels in healthy pregnant women, and to establish the reference intervals of serum lipids in middle and late pregnancy. Triglyceride (TG), total cholesterol (TCH), high density lipoprotein (HDL), low density lipoprotein (LDL), apo-lipoprotein-A(APO-A) and apo-lipoprotein-B (APO-B) were measured in 3 200 pregnant women and 3 200 healthy women of childbearing age(the control group) from January 2014 to Febuary 2015 in Obstetrics and Gynecology Hospital of Fudan University. In the healthy pregnant women, serum lipids were measured at 14-20, 24-28 and 37-40 gestational weeks, respectively. All the parameters were detected by Hitachi 7180 automatic biochemical analyzer. The test results were calculated and determined by the C28-A3 standard of the National Clinical and Laboratory Standards Institute. And the normal reference intervals of serum lipids in middle and late pregnancy were defined as 2.5%-97.5%. (1) The levels of TG, TCH, HDL, LDL, APO-A and APO-B in the control group were 0.8, 4.2, 1.0, 2.7 mmol/L and 1.1, 0.8 g/L, respectively. The levels of TG, TCH, HDL, LDL, APO-A and APO-B in middle and late pregnancy were significantly higher than those in the control group (Plipids levels at 14-20, 24-28 and 37-40 gestational weeks in healthy pregnant women were compared with the control group as following. The TG levels were 1.9, 3.8 and 4.4 folds of the control group; the TCH levels were 1.1, 1.5 and 1.5 folds of the control group; the HDL levels were 1.2, 1.6 and 1.5 folds of the control group; the LDL levels were 1.1, 1.4 and 1.4 folds of the control group; the APO-A levels were 1.3, 1.4 and 1.5 folds of the control group; and the APO-B levels were 1.1, 1.5 and 1.5 fold of the control group respectively. The TG level was the most increased, and it increased gradually with gestational age (Plipids at 14-20, 24-28 and 37-40 gestational weeks in healthy pregnant women were as following. The TG levels were 0.7-3.9, 1.7-6.3 and 1.6-8.1 mmol

  20. Establishment and validation of a microfluidic capillary gel electrophoresis platform method for purity analysis of therapeutic monoclonal antibodies.

    Science.gov (United States)

    Smith, Michael T; Zhang, Shu; Adams, Troy; DiPaolo, Byron; Dally, Jennifer

    2017-05-01

    Capillary and microfluidic chip electrophoresis technologies are heavily utilized for development, characterization, release, and stability testing of biopharmaceuticals. Within the biopharmaceutical industry, CE-SDS and M-CGE are commonly used for purity determination by separation and quantitation of size-based variants. M-CGE is used primarily as an R&D tool for product and process development, while cGMP release and stability testing applications are commonly reserved for CE-SDS. This paper describes the establishment of an M-CGE platform method to be used for R&D and cGMP applications, including release and stability testing, for monoclonal antibodies. The M-CGE platform method enables testing for product development support and cGMP release and stability using the same method, and utilization of one CE technology for the entire lifecycle of a biopharmaceutical product. Critical method parameters were identified, and the analytical design space of those critical parameters was defined using design of experiments (DOE) studies. Once defined through DOE studies, the method design space was validated according to ICH Q2 (R1) guidelines. Additional molecules of the same validated class were verified for use in the method by experimental confirmation of accuracy, specificity, and stability indicating capabilities. The platform method model facilitates rapid utilization of the method in development and GMP testing environments, and eliminates the need for individual validations for assets of the same class entering early stage development. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Lymphadenitis in children is caused by Mycobacterium avium hominissuis and not related to 'bird tuberculosis'

    NARCIS (Netherlands)

    Bruijnesteijn van Coppenraet, L.E.S.; de Haas, P.E.W.; Lindeboom, J.A.; Kuijper, E.J.; van Soolingen, D.

    2008-01-01

    Mycobacterium avium is the most commonly encountered mycobacterium species among non-Mycobacterium tuberculosis complex (nontuberculous mycobacteria) isolates worldwide and frequently causes lymphadenitis in children. During a multi-centre study in The Netherlands that was performed to determine the

  2. Field-based detection of biological samples for forensic analysis: Established techniques, novel tools, and future innovations.

    Science.gov (United States)

    Morrison, Jack; Watts, Giles; Hobbs, Glyn; Dawnay, Nick

    2018-02-21

    Field based forensic tests commonly provide information on the presence and identity of biological stains and can also support the identification of species. Such information can support downstream processing of forensic samples and generate rapid intelligence. These approaches have traditionally used chemical and immunological techniques to elicit the result but some are known to suffer from a lack of specificity and sensitivity. The last 10 years has seen the development of field-based genetic profiling systems, with specific focus on moving the mainstay of forensic genetic analysis, namely STR profiling, out of the laboratory and into the hands of the non-laboratory user. In doing so it is now possible for enforcement officers to generate a crime scene DNA profile which can then be matched to a reference or database profile. The introduction of these novel genetic platforms also allows for further development of new molecular assays aimed at answering the more traditional questions relating to body fluid identity and species detection. The current drive for field-based molecular tools is in response to the needs of the criminal justice system and enforcement agencies, and promises a step-change in how forensic evidence is processed. However, the adoption of such systems by the law enforcement community does not represent a new strategy in the way forensic science has integrated previous novel approaches. Nor do they automatically represent a threat to the quality control and assurance practices that are central to the field. This review examines the historical need and subsequent research and developmental breakthroughs in field-based forensic analysis over the past two decades with particular focus on genetic methods Emerging technologies from a range of scientific fields that have potential applications in forensic analysis at the crime scene are identified and associated issues that arise from the shift from laboratory into operational field use are discussed

  3. Establishing a common vocabulary of key concepts for the effective ımplementation of applied behavior analysis

    Directory of Open Access Journals (Sweden)

    Traci M Cihon

    2016-12-01

    Full Text Available The technical language of behavior analysis is arguably necessary to share ideas and research with precision among each other. However, it can hinder effective implementation of behavior analytic techniques when it prevents clear communication between the supervising behavior analyst and behavior technicians. The present paper provides a case example of the development of a shared vocabulary, using plain English when possible, among supervisors and supervisees at a large public school district in which behavior analytic services were provided for children diagnosed with autism spectrum disorders. A list of terms and definitions are provided as well as suggestions on how to develop shared vocabularies within the readers’ own service provision context.

  4. Profiled Roller Stress/Fatigue Life Analysis Methodology and Establishment of an Appropriate Stress/Life Exponent

    Science.gov (United States)

    1997-01-01

    The objective of this work was to determine the three dimensional volumetric stress field, surface pressure distribution and actual contact area between a 0.50" square roller with different crown profiles and a flat raceway surface using Finite Element Analysis. The 3-dimensional stress field data was used in conjunction with several bearing fatigue life theories to extract appropriate values for stress-life exponents. Also, results of the FEA runs were used to evaluate the laminated roller model presently used for stress and life prediction.

  5. An analysis of chick limb bud intercellular adhesion underlying the establishment of cartilage aggregates in suspension culture.

    Science.gov (United States)

    Bee, J A; von der Mark, K

    1990-07-01

    To examine the mechanism of intercellular adhesion in the establishment of limb skeletal elements we have investigated the process of limb bud cell aggregation in vitro. Limb bud cells are aggregation-competent immediately after their trypsin:collagenase dissociation in the absence of calcium. This aggregation is largely Ca2(+)-independent (CI) and is completely and reversibly inhibited by cycloheximide. In contrast, when limb bud cells are first allowed to recover from Ca2(+)-free trypsin:collagenase dissociation, aggregation of the surviving population is exclusively Ca2(+)-dependent (CD) and completely and reversibly inhibited by cycloheximide. The presence of exogenous calcium during initial cell dissociation retains a functional CD aggregation mechanism. However, incubation of such cells with EGTA releases the CD component and converts the cells to a predominantly CI aggregation. Rabbits were immunized with limb bud cells exhibiting the recovered CD aggregation mechanism and the resulting immune sera were screened for their effect on cell aggregation. Relative to pre-immune sera, intact immune IgG agglutinated dissociated limb bud cells whilst immune Fab fragments inhibited their aggregation. The aggregation-inhibiting antiserum recognizes five major limb bud cell surface components with apparent molecular weights of 72K, 50K, 23K, 14.5K and 8.5K (K = 10(3) Mr), respectively. Limb bud cell surface plasma membranes were isolated by sucrose gradient density centrifugation and detergent-solubilized proteins coupled to Sepharose 4B with cyanogen bromide. Equivalent cell surface plasma membrane proteins were 125I-iodinated and applied to the affinity column. Limb bud cell surface protein affinity chromatography in the presence of exogenous calcium yields a single protein with an apparent molecular weight of approximately 8.5 K. This protein molecule elutes at 0.6 M NaCl, indicating a high affinity, is recognized by the aggregation-inhibiting antiserum, and is

  6. Establishing the natural history and growth rate of ameloblastoma with implications for management: systematic review and meta-analysis.

    Science.gov (United States)

    Chae, Michael P; Smoll, Nicolas R; Hunter-Smith, David J; Rozen, Warren Matthew

    2015-01-01

    Ameloblastoma is the second most common odontogenic tumor, known to be slow-growing, persistent, and locally aggressive. Recent data suggests that ameloblastoma is best treated with wide resection and adequate margins. Following primary excision, bony reconstruction is often necessary for a functional and aesthetically satisfactory outcome, making early diagnosis paramount. Despite earlier diagnosis potentially limiting the extent of resection and reconstruction, an understanding of the growth rate and natural history of ameloblastoma has been notably lacking from the literature. A systematic review of the literature was conducted by reviewing relevant articles from PubMed and Web of Science databases. Each article's level of evidence was formally appraised according to the Centre of Evidence Based Medicine (CEBM), with data from each utilized in a meta-analysis of growth rates for ameloblastoma. Literature regarding the natural history of ameloblastoma is limited since the tumor is immediately acted upon at its initial detection, unless the patient voluntarily refuses a surgical intervention. From the limited data, it is derived that the highest estimated growth rate is associated with solid, multicystic type and the lowest rate with peripheral ameloblastomas. After meta-analysis, the calculated mean specific grow rate is 87.84% per year. The growth rate of ameloblastoma has been demonstrated, offering prognostic and management information, particularly in cases where a delay in management is envisaged.

  7. An analysis of the proposed MITR-III core to establish thermal-hydraulic limits at 10 MW. Final report

    International Nuclear Information System (INIS)

    Harling, O.K.; Lanning, D.D.; Bernard, J.A.; Meyer, J.E.; Henry, A.F.

    1997-01-01

    The 5 MW Massachusetts Institute of Technology Research Reactor (MITR-II) is expected to operate under a new license beginning in 1999. Among the options being considered is an upgrade in the heat removal system to allow operation at 10 MW. The purpose of this study is to predict the Limiting Safety System Settings and Safety Limits for the upgraded reactor (MITR-III). The MITR Multi-Channel Analysis Code was written to analyze the response of the MITR system to a series of anticipated transients in order to determine the Limiting Safety System Settings and Safety Limits under various operating conditions. The MIT Multi-Channel Analysis Code models the primary and secondary systems, with special emphasis placed on analyzing the thermal-hydraulic conditions in the core. The code models each MITR fuel element explicitly in order to predict the behavior of the system during flow instabilities. The results of the code are compared to experimental data from MITR-II and other sources. New definitions are suggested for the Limiting Safety System Settings and Safety Limits. MITR Limit Diagrams are included for three different heat removal system configurations. It is concluded that safe, year-round operating at 10 MW is possible, given that the primary and secondary flow rates are both increased by approximately 40%

  8. Mycobacterium alsense sp. nov., a scotochromogenic slow grower isolated from clinical respiratory specimens.

    Science.gov (United States)

    Tortoli, Enrico; Richter, Elvira; Borroni, Emanuele; Cabibbe, Andrea M; Capitolo, Eleonora; Cittaro, Davide; Engel, Regina; Hendricks, Oliver; Hillemann, Doris; Kristiansen, Jette E; Mariottini, Alessandro; Schubert, Sabine; Cirillo, Daniela M

    2016-01-01

    The name 'Mycobacterium alsiense', although reported in 2007, has not been validly published. Polyphasic characterization of three available strains of this species led us to the conclusion that they represent a distinct species within the genus Mycobacterium. The proposed novel species grows slowly and presents pale yellow-pigmented colonies. Differentiation from other mycobacteria is not feasible on the basis of biochemical and cultural features alone while genetic analysis, extended to eight housekeeping genes and one spacer region, reveals its clear distinction from all other mycobacteria. Mycobacterium asiaticum is the most closely related species on the basis of 16S rRNA gene sequences (similarity 99.3 %); the average nucleotide identity between the genomes of the two species is 80.72 %, clearly below the suggested cut-off (95-96 %). The name Mycobacterium alsense sp. nov. is proposed here for the novel species and replaces the name 'M. alsiense', ex Richter et al. 2007, given at the time of isolation of the first strain. The type strain is TB 1906T ( = DSM 45230T = CCUG 56586T).

  9. Systems-based approaches to probing metabolic variation within the Mycobacterium tuberculosis complex.

    Directory of Open Access Journals (Sweden)

    Emma K Lofthouse

    Full Text Available The Mycobacterium tuberculosis complex includes bovine and human strains of the tuberculosis bacillus, including Mycobacterium tuberculosis, Mycobacterium bovis and the Mycobacterium bovis BCG vaccine strain. M. bovis has evolved from a M. tuberculosis-like ancestor and is the ancestor of the BCG vaccine. The pathogens demonstrate distinct differences in virulence, host range and metabolism, but the role of metabolic differences in pathogenicity is poorly understood. Systems biology approaches have been used to investigate the metabolism of M. tuberculosis, but not to probe differences between tuberculosis strains. In this study genome scale metabolic networks of M. bovis and M. bovis BCG were constructed and interrogated, along with a M. tuberculosis network, to predict substrate utilisation, gene essentiality and growth rates. The models correctly predicted 87-88% of high-throughput phenotype data, 75-76% of gene essentiality data and in silico-predicted growth rates matched measured rates. However, analysis of the metabolic networks identified discrepancies between in silico predictions and in vitro data, highlighting areas of incomplete metabolic knowledge. Additional experimental studies carried out to probe these inconsistencies revealed novel insights into the metabolism of these strains. For instance, that the reduction in metabolic capability observed in bovine tuberculosis strains, as compared to M. tuberculosis, is not reflected by current genetic or enzymatic knowledge. Hence, the in silico networks not only successfully simulate many aspects of the growth and physiology of these mycobacteria, but also provide an invaluable tool for future metabolic studies.

  10. Isolation and characterization of a Mycobacterium strain that metabolizes the insecticide endosulfan.

    Science.gov (United States)

    Sutherland, T D; Horne, I; Harcourt, R L; Russell, R J; Oakeshott, J G

    2002-01-01

    The aim of this study was to isolate and characterize a bacterium capable of metabolizing endosulfan. A endosulfan-degrading bacterium (strain ESD) was isolated from soil inoculum after repeated culture with the insecticide as the sole source of sulfur. Analysis of its 16S rRNA gene sequence, and morphological and physiological characteristics revealed it to be a new fast-growing Mycobacterium, closely related to other Mycobacterium species with xenobiotic-degrading capabilities. Degradation of endosulfan by strain ESD involved both oxidative and sulfur-separation reactions. Strain ESD did not degrade endosulfan when sulfite, sulphate or methionine were present in the medium along with the insecticide. Partial degradation occurred when the culture was grown, with endosulfan, in the presence of MOPS (3-(N-morpholino)propane sulphonic acid), DMSO (dimethyl sulfoxide), cysteine or sulphonane and complete degradation occurred in the presence of gutathione. When both beta-endosulfan and low levels of sulphate were provided as the only sources of sulfur, biphasic exponential growth was observed with endosulfan metabolism being restricted to the latter phase of exponential growth. This study isolated a Mycobacterium strain (strain ESD) capable of metabolizing endosulfan by both oxidative and sulfur-separation reactions. The endosulfan-degrading reactions are a result of the sulfur-starvation response of this bacterium. This describes the isolation of a Mycobacterium strain capable of degrading the insecticide endosulfan. This bacterium is a valuable source of enzymes for use in enzymatic bioremediation of endosulfan residues.

  11. Isolation and Identification of Pyrene Mineralizing Mycobacterium spp. from Contaminated and Uncontaminated Sources

    Directory of Open Access Journals (Sweden)

    Christopher W. M. Lease

    2011-01-01

    Full Text Available Mycobacterium isolates obtained from PAH-contaminated and uncontaminated matrices were evaluated for their ability to degrade three-, four- and five-ring PAHs. PAH enrichment studies were prepared using pyrene and inocula obtained from manufacturing gas plant (MGP soil, uncontaminated agricultural soil, and faeces from Macropus fuliginosus (Western Grey Kangaroo. Three pyrene-degrading microorganisms isolated from the corresponding enrichment cultures had broad substrate ranges, however, isolates could be differentiated based on surfactant, phenol, hydrocarbon and PAH utilisation. 16S rRNA analysis identified all three isolates as Mycobacterium sp. The Mycobacterium spp. could rapidly degrade phenanthrene and pyrene, however, no strain had the capacity to utilise fluorene or benzo[a]pyrene. When pyrene mineralisation experiments were performed, 70–79% of added 14C was evolved as 14CO2 after 10 days. The present study demonstrates that PAH degrading microorganisms may be isolated from a diverse range of environmental matrices. The present study demonstrates that prior exposure to PAHs was not a prerequisite for PAH catabolic activity for two of these Mycobacterium isolates.

  12. Isolation and Identification of Pyrene Mineralizing Mycobacterium spp. from Contaminated and Uncontaminated Sources

    International Nuclear Information System (INIS)

    Lease, C.W.M; Bentham, R.H; Gaskin, S.E; Juhasz, A.L

    2011-01-01

    Mycobacterium isolates obtained from PAH-contaminated and uncontaminated matrices were evaluated for their ability to degrade three-, four- and five-ring PAHs. PAH enrichment studies were prepared using pyrene and inocula obtained from manufacturing gas plant (MGP) soil, uncontaminated agricultural soil, and faeces from Macropus fuliginosus (Western Grey Kangaroo). Three pyrene-degrading microorganisms isolated from the corresponding enrichment cultures had broad substrate ranges, however, isolates could be differentiated based on surfactant, phenol, hydrocarbon and PAH utilisation. 16S rRNA analysis identified all three isolates as Mycobacterium sp. The Mycobacterium spp. could rapidly degrade phenanthrene and pyrene, however, no strain had the capacity to utilise fluorene or benzo[a]pyrene. When pyrene mineralisation experiments were performed, 70-79% of added 14 C was evolved as 14 CO 2 after 10 days. The present study demonstrates that PAH degrading microorganisms may be isolated from a diverse range of environmental matrices. The present study demonstrates that prior exposure to PAHs was not a prerequisite for PAH catabolic activity for two of these Mycobacterium isolates.

  13. Conditional silencing of topoisomerase I gene of Mycobacterium tuberculosis validates its essentiality for cell survival.

    Science.gov (United States)

    Ahmed, Wareed; Menon, Shruti; Godbole, Adwait Anand; Karthik, Pullela V D N B; Nagaraja, Valakunja

    2014-04-01

    Topoisomerases are an important class of enzymes for regulating the DNA transaction processes. Mycobacterium tuberculosis (Mtb) is one of the most formidable pathogens also posing serious challenges for therapeutic interventions. The organism contains only one type IA topoisomerase (Rv3646c), offering an opportunity to test its potential as a candidate drug target. To validate the essentiality of M. tuberculosis topoisomerase I (TopoI(Mt) ) for bacterial growth and survival, we have generated a conditionally regulated strain of topoI in Mtb. The conditional knockdown mutant exhibited delayed growth on agar plate. In liquid culture, the growth was drastically impaired when TopoI expression was suppressed. Additionally, novobiocin and isoniazid showed enhanced inhibitory potential against the conditional mutant. Analysis of the nucleoid revealed its altered architecture upon TopoI depletion. These studies establish the essentiality of TopoI for the M. tuberculosis growth and open up new avenues for targeting the enzyme. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  14. Cutting edge: Vitamin D regulates lipid metabolism in Mycobacterium tuberculosis infection.

    Science.gov (United States)

    Salamon, Hugh; Bruiners, Natalie; Lakehal, Karim; Shi, Lanbo; Ravi, Janani; Yamaguchi, Ken D; Pine, Richard; Gennaro, Maria Laura

    2014-07-01

    Vitamin D has long been linked to resistance to tuberculosis, an infectious respiratory disease that is increasingly hard to treat because of multidrug resistance. Previous work established that vitamin D induces macrophage antimicrobial functions against Mycobacterium tuberculosis. In this article, we report a novel, metabolic role for vitamin D in tuberculosis identified through integrated transcriptome and mechanistic studies. Transcriptome analysis revealed an association between vitamin D receptor (VDR) and lipid metabolism in human tuberculosis and infected macrophages. Vitamin D treatment of infected macrophages abrogated infection-induced accumulation of lipid droplets, which are required for intracellular M. tuberculosis growth. Additional transcriptomics results showed that vitamin D downregulates the proadipogenic peroxisome proliferator-activated receptor γ (PPARγ) in infected macrophages. PPARγ agonists reversed the antiadipogenic and the antimicrobial effects of VDR, indicating a link between VDR and PPARγ signaling in regulating both vitamin D functions. These findings suggest the potential for host-based, adjunct antituberculosis therapy targeting lipid metabolism. Copyright © 2014 by The American Association of Immunologists, Inc.

  15. Proteins with complex architecture as potential targets for drug design: a case study of Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Bálint Mészáros

    2011-07-01

    Full Text Available Lengthy co-evolution of Homo sapiens and Mycobacterium tuberculosis, the main causative agent of tuberculosis, resulted in a dramatically successful pathogen species that presents considerable challenge for modern medicine. The continuous and ever increasing appearance of multi-drug resistant mycobacteria necessitates the identification of novel drug targets and drugs with new mechanisms of action. However, further insights are needed to establish automated protocols for target selection based on the available complete genome sequences. In the present study, we perform complete proteome level comparisons between M. tuberculosis, mycobacteria, other prokaryotes and available eukaryotes based on protein domains, local sequence similarities and protein disorder. We show that the enrichment of certain domains in the genome can indicate an important function specific to M. tuberculosis. We identified two families, termed pkn and PE/PPE that stand out in this respect. The common property of these two protein families is a complex domain organization that combines species-specific regions, commonly occurring domains and disordered segments. Besides highlighting promising novel drug target candidates in M. tuberculosis, the presented analysis can also be viewed as a general protocol to identify proteins involved in species-specific functions in a given organism. We conclude that target selection protocols should be extended to include proteins with complex domain architectures instead of focusing on sequentially unique and essential proteins only.

  16. Identification, activity and disulfide connectivity of C-di-GMP regulating proteins in Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Kajal Gupta

    2010-11-01

    Full Text Available C-di-GMP, a bacterial second messenger plays a key role in survival and adaptation of bacteria under different environmental conditions. The level of c-di-GMP is regulated by two opposing activities, namely diguanylate cyclase (DGC and phosphodiesterase (PDE-A exhibited by GGDEF and EAL domain, respectively in the same protein. Previously, we reported a bifunctional GGDEF-EAL domain protein, MSDGC-1 from Mycobacterium smegmatis showing both these activities (Kumar and Chatterji, 2008. In this current report, we have identified and characterized the homologous protein from Mycobacterium tuberculosis (Rv 1354c named as MtbDGC. MtbDGC is also a bifunctional protein, which can synthesize and degrade c-di-GMP in vitro. Further we expressed Mtbdgc in M. smegmatis and it was able to complement the MSDGC-1 knock out strain by restoring the long term survival of M. smegmatis. Another protein Rv 1357c, named as MtbPDE, is an EAL domain protein and degrades c-di-GMP to pGpG in vitro. Rv1354c and 1357c have seven cysteine amino acids in their sequence, distributed along the full length of the protein. Disulfide bonds play an important role in stabilizing protein structure and regulating protein function. By proteolytic digestion and mass spectrometric analysis of MtbDGC, connectivity between cysteine pairs Cys94-Cys584, Cys2-Cys479 and Cys429-Cys614 was determined, whereas the third cysteine (Cys406 from N terminal was found to be free in MtbDGC protein, which was further confirmed by alkylation with iodoacetamide labeling. Bioinformatics modeling investigations also supported the pattern of disulfide connectivity obtained by Mass spectrometric analysis. Cys406 was mutated to serine by site directed mutagenesis and the mutant MtbC406S was not found to be active and was not able to synthesize or degrade c-di-GMP. The disulfide connectivity established here would help further in understanding the structure - function relationship in MtbDGC.

  17. A Study on establishing Top-Down model - development of Global CGE model for Kyoto mechanism analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Gyeong Lyeong [Korea Energy Economics Institute, Euiwang (Korea)

    1999-07-01

    In Korea, it is true that studies on the Convention on Climate Change is behind compared with the developed countries. As a result, a clear goal on negotiation and a reasonable alternative to persuade other countries were not prepared and a negative and passive attitude of negotiation was showed when entering into negotiations with other countries. However, fortunately, the Convention on Climate Change is not completely reached an agreement. It means that there still remains time to contrive for terms favorable to Korea. To do this, a precise negotiating strategy should be prepared based on a reasonable and systematic study and with diplomatic negotiating power to assist it. Also, it should prepare for a next stage after the negotiation through the analyses of several scenarios. Developing a model for a simulation analysis is absolutely needed to set a more systematic and reasonable negotiation strategy for the Convention on Climate Change. (author). 32 refs., 14 fig., 36 tabs.

  18. Enfermedad por Mycobacterium simiae y "Mycobacterium sherrisii" en la Argentina Disease due to Mycobacterium simiae and "Mycobacterium sherrisii" in Argentina

    Directory of Open Access Journals (Sweden)

    Lucía Barrera

    2010-08-01

    Full Text Available Se presenta información reunida retrospectivamente sobre casos de micobacteriosis originados por Mycobacterium simiae (n = 4 y "M. sherrisii" (n = 6. Los casos ocurrieron entre pacientes con sida (n = 6, historia de silicosis (n = 2 o tuberculosis previa (n = 1. Un caso se perdió luego de diagnosticado y nueve fueron tratados con esquemas terapéuticos basados en claritromicina, etambutol y quinolonas. La respuesta fue muy pobre: cinco pacientes fallecieron (cuatro eran HIV positivos, tres permanecieron crónicos y sólo uno curó. Estas micobacterias originaron 2.1% de los casos de micobacteriosis registrados en un período de ocho años. La distinción de estas micobacterias raras de otras más frecuentes por métodos moleculares rápidos, parece ser clínicamente útil para advertir sobre la dificultad que puede presentar el tratamiento. Sin embargo, la diferenciación genotípica entre M. simiae y "M. sherrisii" parecería no ser clínicamente relevante, dado que no quedaron expuestas características que distingan a los pacientes afectados por los dos microorganismos tan estrechamente relacionados.A revision of mycobacterial disease due to M simiae (n = 4 and "M. sherrisii" (n = 6 identified during an eight-year period is presented. Cases occurred among patients with AIDS (n = 6, previous history of silicosis (n = 2 or tuberculosis (n = 2. One case was lost to follow-up and the remaining nine responded poorly to chemotherapy based on clarithromycin, ethambutol and fluoroquinolones. Five patients died of whom four were HIV-positive, three remained chronic and one was cured. These microorganisms originated 2.1% of mycobacterioses cases detected in an eight-year period. Timely identification of this group of uncommon mycobacteria by molecular methods seems to be clinically relevant in order to warn of difficulties inherent to the treatment. However, the distinction between both closely related microorganisms might not be crucial for case

  19. The location of midfacial landmarks according to the method of establishing the midsagittal reference plane in three-dimensional computed tomography analysis of facial asymmetry

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Min Sun; Lee, Eun Joo; Lee, Jae Seo; Kang, Byung Cheock; Yoon, Suk Ja [Dental Science Research Institute, Chonnam National University, Gwangju (Korea, Republic of); Song, In Ja [Dept. of Nursing, Kwangju Women' s University, Gwangju (Korea, Republic of)

    2015-12-15

    The purpose of this study was to evaluate the influence of methods of establishing the midsagittal reference plane (MRP) on the locations of midfacial landmarks in the three-dimensional computed tomography (CT) analysis of facial asymmetry. A total of 24 patients (12 male and 12 female; mean age, 22.5 years; age range, 18.2-29.7 years) with facial asymmetry were included in this study. The MRP was established using two different methods on each patient's CT image. The x-coordinates of four midfacial landmarks (the menton, nasion, upper incisor, and lower incisor) were obtained by measuring the distance and direction of the landmarks from the MRP, and the two methods were compared statistically. The direction of deviation and the severity of asymmetry found using each method were also compared. The x-coordinates of the four anatomic landmarks all showed a statistically significant difference between the two methods of establishing the MRP. For the nasion and lower incisor, six patients (25.0%) showed a change in the direction of deviation. The severity of asymmetry also changed in 16 patients (66.7%). The results of this study suggest that the locations of midfacial landmarks change significantly according to the method used to establish the MRP.

  20. A single or multistage mycobacterium avium subsp. paratuberculosis subunit vaccine

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention provides one or more immunogenic polypeptides for use in a preventive or therapeutic vaccine against latent or active infection in a human or animal caused by a Mycobacterium species, e.g. Mycobacterium avium subsp. paratuberculosis. Furthermore a single or multi-phase vaccine...... comprising the one or more immunogenic polypeptides is provided for administration for the prevention or treatment of infection with a Mycobacterium species, e.g. Mycobacterium avium subsp. paratuberculosis. Additionally, nucleic acid vaccines, capable of in vivo expression of the multi-phase vaccine...... comprising the one or more immunogenic polypeptides, is provided for prevention or treatment of infection with a Mycobacterium species, e.g. Mycobacterium avium subsp. paratuberculosis....

  1. Using a Six Sigma Fishbone Analysis Approach To Evaluate the Effect of Extreme Weather Events on Salmonella Positives in Young Chicken Slaughter Establishments.

    Science.gov (United States)

    Linville, John W; Schumann, Douglas; Aston, Christopher; Defibaugh-Chavez, Stephanie; Seebohm, Scott; Touhey, Lucy

    2016-12-01

    A six sigma fishbone analysis approach was used to develop a machine learning model in SAS, Version 9.4, by using stepwise linear regression. The model evaluated the effect of a wide variety of variables, including slaughter establishment operational measures, normal (30-year average) weather, and extreme weather events on the rate of Salmonella -positive carcasses in young chicken slaughter establishments. Food Safety and Inspection Service (FSIS) verification carcass sampling data, as well as corresponding data from the National Oceanographic and Atmospheric Administration and the Federal Emergency Management Agency, from September 2011 through April 2015, were included in the model. The results of the modeling show that in addition to basic establishment operations, normal weather patterns, differences from normal and disaster events, including time lag weather and disaster variables, played a role in explaining the Salmonella percent positive that varied by slaughter volume quartile. Findings show that weather and disaster events should be considered as explanatory variables when assessing pathogen-related prevalence analysis or research and slaughter operational controls. The apparent significance of time lag weather variables suggested that at least some of the impact on Salmonella rates occurred after the weather events, which may offer opportunities for FSIS or the poultry industry to implement interventions to mitigate those effects.

  2. Trend analysis of GIMMS and MODIS NDVI time series for establishing a land degradation neutrality national baseline

    Science.gov (United States)

    Gichenje, Helene; Godinho, Sergio

    2017-04-01

    Land degradation is a key global environment and development problem that is recognized as a priority by the international development community. The Sustainable Development Goals (SDGs) were adopted by the global community in 2015, and include a goal related to land degradation and the accompanying target to achieve a land degradation-neutral (LDN) world by 2030. The LDN concept encompasses two joint actions of reducing the rate of degradation and increasing the rate of restoration. Using Kenya as the study area, this study aims to develop and test a spatially explicit methodology for assessing and monitoring the operationalization of a land degradation neutrality scheme at the national level. Time series analysis is applied to Normalized Difference Vegetation Index (NDVI) satellite data records, based on the hypothesis that the resulting NDVI residual trend would enable successful detection of changes in vegetation photosynthetic capacity and thus serve as a proxy for land degradation and regeneration processes. Two NDVI data sets are used to identify the spatial and temporal distribution of degraded and regenerated areas: the long term coarse resolution (8km, 1982-2015) third generation Global Inventory Modeling and Mapping Studies (GIMMS) NDVI3g data record; and the shorter-term finer resolution (250m, 2001-2015) Moderate Resolution Imaging Spectroradiometer (MODIS) derived NDVI data record. Climate data (rainfall, temperature and soil moisture) are used to separate areas of human-induced vegetation productivity decline from those driven by climate dynamics. Further, weekly vegetation health (VH) indexes (4km, 1982-2015) developed by National Oceanic and Atmospheric Administration (NOAA), are assessed as indicators for early detection and monitoring of land degradation by estimating vegetation stress (moisture, thermal and combined conditions).

  3. Mangrove and Freshwater Wetland Conservation Through Carbon Offsets: A Cost-Benefit Analysis for Establishing Environmental Policies.

    Science.gov (United States)

    Vázquez-González, César; Moreno-Casasola, Patricia; Hernández, María Elizabeth; Campos, Adolfo; Espejel, Ileana; Fermán-Almada, José Luis

    2017-02-01

    Mexico has extensive coastal wetlands (4,243,137 ha), and one of its most important sites is the Alvarado Lagoon System, located in the Papaloapan River Basin on the Gulf of Mexico. The land cover dedicated to livestock and sugarcane has increased: by 25 % in 2005 and 50 % in 2010, with a loss of wetland vegetation and the carbon that it stores. We found that the Net Present Value of mangrove carbon offsets profit is equal to $5822.71, that of broad-leaved marshes is $7958.86, cattail marshes $5250.33, and forested wetlands $8369.41 per hectare, during a 30-year-carbonoffset contract. However, the opportunity cost from conserving wetland instead of growing sugarcane is positive according to REDD+ methodology, e.g., broad-leaved marsh conservation ranged from $6.73 to $20 USD/t CO2e, that of cattail marshes from $12.20 to $32.65 USD/t CO2e, and forested wetlands from $7.15 to $20.60 USD/t CO2e, whereas the opportunity cost between conservation and livestock was negative, it means that conservation is more profitable. The cost-benefit analysis for assessing investment projects from a governmental perspective is useful to determine the viability of conserving coastal wetlands through carbon offset credits. It also shows why in some areas it is not possible to conserve ecosystems due to the opportunity cost of changing from one economic activity (livestock and sugarcane) to carbon offsets for protecting wetlands. Furthermore, it allows for a comparison of carbon markets and assessment in terms of REDD+ and its methods for determining the social cost per ton of carbon avoided.

  4. Gamma/delta T lymphocytes in Mycobacterium tuberculosis infection

    OpenAIRE

    Baliko, Z.; Szereday, L.; Szekeres-Bartho, J.

    1997-01-01

    BACKGROUND: Data on the percentage of gamma/delta T lymphocytes in the peripheral blood of patients infected with Mycobacterium tuberculosis are few and contradictory. The percentage of gamma/delta T lymphocytes in the peripheral blood of tuberculin positive and tuberculin negative patients with Mycobacterium tuberculosis infection and healthy controls was compared. METHODS: Thirty six patients infected with Mycobacterium tuberculosis and 11 healthy controls were studied. Lymphocytes we...

  5. Origins and properties of Mycobacterium tuberculosis isolates in London.

    Science.gov (United States)

    Dale, Jeremy W; Bothamley, Graham H; Drobniewski, Francis; Gillespie, Stephen H; McHugh, Timothy D; Pitman, Richard

    2005-06-01

    Using similarities of IS6110 banding patterns, isolates of Mycobacterium tuberculosis from a population-based study in London were assigned to 12 large groups termed 'superfamilies' (sfams). Analysis of patient data showed a marked geographical association in the distribution of these sfams. In particular, isolates from patients born in Europe were from different sfams than those born elsewhere, indicating that there had been relatively little transmission of tuberculosis in London from immigrant communities into the endogenous population. Multivariate analysis showed that certain sfams were significantly associated with pulmonary rather than extrapulmonary disease, or with sputum smear negativity, independently of country of birth or ethnicity, suggesting that the properties of the infecting organism play a role in the nature of the disease process.

  6. Different transcriptional profiles of human monocyte-derived dendritic cells infected with distinct strains of Mycobacterium tuberculosis and Mycobacterium bovis bacillus Calmette-Guérin.

    Science.gov (United States)

    Sanarico, Nunzia; Colone, Alessia; Grassi, Manuela; Speranza, Viviana; Giovannini, Daniela; Ciaramella, Antonio; Colizzi, Vittorio; Mariani, Francesca

    2011-01-01

    In order to analyze dendritic cells (DCs) activation following infection with different mycobacterial strains, we studied the expression profiles of 165 genes of human monocyte-derived DCs infected with H37Rv, a virulent Mycobacterium tuberculosis (MTB) laboratory strain, CMT97, a clinical MTB isolate, Mycobacterium bovis bacillus Calmette-Guérin (BCG), Aventis Pasteur, and BCG Japan, both employed as vaccine against tuberculosis. The analysis of the gene expression reveals that, despite a set of genes similarly modulated, DCs response resulted strain dependent. In particular, H37Rv significantly upregulated EBI3 expression compared with BCG Japan, while it was the only strain that failed to release a significant IL-10 amount. Of note, BCG Japan showed a marked increase in CCR7 and TNF-α expression regarding both MTB strains and it resulted the only strain failing in exponential intracellular growth. Our results suggest that DCs display the ability to elicit a tailored strain-specific immune response.

  7. Mycobacterium pseudoshottsii sp. nov., a slowly growing chromogenic species isolated from Chesapeake Bay striped bass (Morone saxatilis)

    Science.gov (United States)

    Rhodes, M.W.; Kator, H.; McNabb, A.; Deshayes, C.; Reyrat, J.-M.; Brown-Elliott, B. A.; Wallace, R.; Trott, K.A.; Parker, J.M.; Lifland, B.; Osterhout, G.; Kaattari, I.; Reece, K.; Vogelbein, W.; Ottinger, C.A.

    2005-01-01

    A group of slowly growing photochromogenic mycobacteria was isolated from Chesapeake Bay striped bass (Morone saxatilis) during an epizootic of mycobacteriosis. Growth characteristics, acid-fastness and 16S rRNA gene sequencing results were consistent with those of the genus Mycobacterium. Biochemical reactions, growth characteristics and mycolic acid profiles (HPLC) resembled those of Mycobacterium shottsii, a non-pigmented mycobacterium also isolated during the same epizootic. Sequencing of the 16S rRNA genes, the gene encoding the exported repeated protein (erp) and the gene encoding the 65 kDa heat-shock protein (hsp65) and restriction enzyme analysis of the hsp65 gene demonstrated that this group of isolates is unique. Insertion sequences associated with Mycobacterium ulcerans, IS2404 and IS2606, were detected by PCR. These isolates could be differentiated from other slowly growing pigmented mycobacteria by their inability to grow at 37 ??C, production of niacin and urease, absence of nitrate reductase, negative Tween 80 hydrolysis and resistance to isoniazid (1 ??g ml-1), p-nitrobenzoic acid, thiacetazone and thiophene-2-carboxylic hydrazide. On the basis of this polyphasic study, it is proposed that these isolates represent a novel species, Mycobacterium pseudoshottsii sp. nov. The type strain, L15T, has been deposited in the American Type Culture Collection as ATCC BAA-883T and the National Collection of Type Cultures (UK) as NCTC 13318T. ?? 2005 IUMS.

  8. Successful outcomes with oral fluoroquinolones combined with rifampicin in the treatment of Mycobacterium ulcerans: an observational cohort study.

    Science.gov (United States)

    O'Brien, Daniel P; McDonald, Anthony; Callan, Peter; Robson, Mike; Friedman, N Deborah; Hughes, Andrew; Holten, Ian; Walton, Aaron; Athan, Eugene

    2012-01-01

    The World Health Organization currently recommends combined streptomycin and rifampicin antibiotic treatment as first-line therapy for Mycobacterium ulcerans infections. Alternatives are needed when these are not tolerated or accepted by patients, contraindicated, or neither accessible nor affordable. Despite in vitro effectiveness, clinical evidence for fluoroquinolone antibiotic use against Mycobacterium ulcerans is lacking. We describe outcomes and tolerability of fluoroquinolone-containing antibiotic regimens for Mycobacterium ulcerans in south-eastern Australia. Analysis was performed of prospectively collected data including all primary Mycobacterium ulcerans infections treated at Barwon Health between 1998 and 2010. Medical treatment involved antibiotic use for more than 7 days; surgical treatment involved surgical excision of a lesion. Treatment success was defined as complete lesion healing without recurrence at 12 months follow-up. A complication was defined as an adverse event attributed to an antibiotic that required its cessation. A total of 133 patients with 137 lesions were studied. Median age was 62 years (range 3-94 years). 47 (34%) had surgical treatment alone, and 90 (66%) had combined surgical and medical treatment. Rifampicin and ciprofloxacin comprised 61% and rifampicin and clarithromycin 23% of first-line antibiotic regimens. 13/47 (30%) treated with surgery alone failed treatment compared to 0/90 (0%) of those treated with combination medical and surgical treatment (pMycobacterium ulcerans infections, and fluoroquinolone combined with rifampicin-containing antibiotic regimens can provide an effective and safe oral treatment option.

  9. Evidence of presence of Mycobacterium tuberculosis in bovine tissue samples by multiplex PCR: possible relevance to reverse zoonosis.

    Science.gov (United States)

    Mittal, M; Chakravarti, S; Sharma, V; Sanjeeth, B S; Churamani, C P; Kanwar, N S

    2014-04-01

    Bovine tuberculosis, caused by Mycobacterium bovis, remains one of the most important zoonotic health concerns worldwide. The transmission of Mycobacterium tuberculosis from humans to animals also occurs especially in countries where there is close interaction of humans with the animals. In the present study, thirty bovine lung tissue autopsy samples from an organized dairy farm located in North India were screened for the presence of Mycobacterium tuberculosis complex by smear microscopy, histopathological findings and PCR. Differential diagnosis of M. tuberculosis and M. bovis was made based on the deletion of mce-3 operon in M. bovis. The present study found eight of these samples positive for M. tuberculosis by multiplex PCR. Sequencing was performed on two PCR-positive representative samples and on annotation, and BLAST analysis confirmed the presence of gene fragment specific to Mycobacterium tuberculosis. The presence of M. tuberculosis in all the positive samples raises the possibility of human-to-cattle transmission and possible adaptation of this organism in bovine tissues. This study accentuates the importance of screening and differential diagnosis of Mycobacterium tuberculosis complex in humans and livestock for adopting effective TB control and eradication programmes. © 2014 Blackwell Verlag GmbH.

  10. Strengthening cost-effectiveness analysis in Thailand through the establishment of the health intervention and technology assessment program.

    Science.gov (United States)

    Tantivess, Sripen; Teerawattananon, Yot; Mills, Anne

    2009-01-01

    Capacity is limited in the developing world to conduct cost-effectiveness analysis (CEA) of health interventions. In Thailand, there have been concerted efforts to promote evidence-based policy making, including the introduction of economic appraisals within health technology assessment (HTA). This paper reviews the experience of this lower middle-income country, with an emphasis on the creation of the Health Intervention and Technology Assessment Program (HITAP), including its mission, management structures and activities. Over the past 3 decades, several HTA programmes were implemented in Thailand but not sustained or developed further into a national institute. As a response to increasing demands for HTA evidence including CEA information, the HITAP was created in 2007 as an affiliate unit of a semi-autonomous research arm of the Ministry of Public Health. An advantage of this HTA programme over previous initiatives was that it was hosted by a research institute with long-term experience in conducting health systems and policy research and capacity building of its research staff, and excellent research and policy networks. To deal with existing impediments to conducting health economics research, the main strategies of the HITAP were carefully devised to include not only capacity strengthening of its researchers and administrative staff, but also the development of essential elements for the country's health economic evaluation methodology. These included, for example, methodological guidelines, standard protocols and benchmarks for resource allocation, many of which have been adopted by national policy-making bodies including the three major public health insurance plans. Networks and collaborations with domestic and foreign institutes have been sought as a means of resource mobilization and exchange. Although the HITAP is well financed by a number of government agencies and international organizations, the programme is vulnerable to shortages of qualified

  11. Mycobacterium bovis and Other Uncommon Members of the Mycobacterium tuberculosis Complex.

    Science.gov (United States)

    Esteban, Jaime; Muñoz-Egea, Maria-Carmen

    2016-12-01

    Since its discovery by Theobald Smith, Mycobacterium bovis has been a human pathogen closely related to animal disease. At present, M. bovis tuberculosis is still a problem of importance in many countries and is considered the main cause of zoonotic tuberculosis throughout the world. Recent development of molecular epidemiological tools has helped us to improve our knowledge about transmission patterns of this organism, which causes a disease indistinguishable from that caused by Mycobacterium tuberculosis. Diagnosis and treatment of this mycobacterium are similar to those for conventional tuberculosis, with the important exceptions of constitutive resistance to pyrazinamide and the fact that multidrug-resistant and extremely drug-resistant M. bovis strains have been described. Among other members of this complex, Mycobacterium africanum is the cause of many cases of tuberculosis in West Africa and can be found in other areas mainly in association with immigration. M. bovis BCG is the currently available vaccine for tuberculosis, but it can cause disease in some patients. Other members of the M. tuberculosis complex are mainly animal pathogens with only exceptional cases of human disease, and there are even some strains, like "Mycobacterium canettii," which is a rare human pathogen that could have an important role in the knowledge of the evolution of tuberculosis in the history.

  12. A single or multistage mycobacterium avium subsp. paratuberculosis subunit vaccine

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention provides one or more immunogenic polypeptides for use in a preventive or therapeutic vaccine against latent or active infection in a human or animal caused by a Mycobacterium species, e.g. Mycobacterium avium subsp. paratuberculosis. Furthermore a single or multi-phase vaccine...... comprising the one or more immunogenic polypeptides is provided for administration for the prevention or treatment of infection with a Mycobacterium species, e.g. Mycobacterium avium subsp. paratuberculosis. Additionally, nucleic acid vaccines, capable of in vivo expression of the multi-phase vaccine...

  13. Establishment of Relational Model of Congenital Heart Disease Markers and GO Functional Analysis of the Association between Its Serum Markers and Susceptibility Genes.

    Science.gov (United States)

    Liu, Min; Zhao, Luosha; Yuan, Jiaying

    2016-01-01

    The purpose of present study was to construct the best screening model of congenital heart disease serum markers and to provide reference for further prevention and treatment of the disease. Documents from 2006 to 2014 were collected and meta-analysis was used for screening susceptibility genes and serum markers closely related to the diagnosis of congenital heart disease. Data of serum markers were extracted from 80 congenital heart disease patients and 80 healthy controls, respectively, and then logistic regression analysis and support vector machine were utilized to establish prediction models of serum markers and Gene Ontology (GO) functional annotation. Results showed that NKX2.5, GATA4, and FOG2 were susceptibility genes of congenital heart disease. CRP, BNP, and cTnI were risk factors of congenital heart disease (p heart disease (p markers' relational model established by support vector machine was only 85%. GO analysis suggested that NKX2.5, GATA4, and FOG2 were functionally related to Lp(a) and BNP. The combined markers model of BNP and cTnI had the highest accuracy rate, providing a theoretical basis for the diagnosis of congenital heart disease.

  14. Co-infecção por Mycobacterium tuberculosis e vírus da imunodeficiência humana: uma análise epidemiológica em Taubaté (SP Co-infection with Mycobacterium tuberculosis and human immunodeficiency virus: an epidemiological analysis in the city of Taubaté, Brazil

    Directory of Open Access Journals (Sweden)

    Luiz Gustavo Miranda de Carvalho

    2006-10-01

    Full Text Available OBJETIVO: Discutir os principais aspectos da co-infecção por Mycobacterium tuberculosis e vírus da imunodeficiência humana no município de Taubaté (SP nos anos de 2001 e 2002. MÉTODOS: Este trabalho apresenta o levantamento epidemiológico dos casos de tuberculose ocorridos em Taubaté em 2001 e 2002. RESULTADOS: Foram analisados 250 casos de tuberculose, dos quais 70 corresponderam a casos de sorologia positiva para o vírus da imunodeficiência humana (28%, 95 de sorologia negativa (38%, e para 85 pacientes a sorologia não foi realizada (34%. Com relação ao primeiro grupo houve predomínio do sexo masculino e da faixa etária de 30 a 40 anos, a forma clínica de tuberculose mais comum foi a pulmonar (65,71% e a taxa de cura foi de 59,38% . No grupo de pacientes para os quais não se comprovou a co-infecção também predominou o sexo masculino e ocorrência na mesma faixa etária, sendo a forma clínica mais comum também a pulmonar (70,55% e a taxa de cura foi de 81,63%. CONCLUSÃO: Concluiu-se que o vírus da imunodeficiência humana é importante na epidemiologia da tuberculose e, portanto, o teste sorológico para o vírus da imunodeficiência humana deve ser realizado quando se diagnostica a presença de tuberculose.OBJECTIVE: To discuss the main aspects of co-infection with Mycobacterium tuberculosis and human immunodeficiency virus in the city of Taubaté (located in the state of São Paulo, Brazil in 2001 and 2002. METHODS: This study presents epidemiological data on tuberculosis cases occurring in Taubaté in 2001 and 2002. RESULTS: Of the 250 cases of tuberculosis analyzed, 70 (28% presented human immunodeficiency virus seropositivity, 95 (38% presented human immunodeficiency virus seronegativity, and 85 (34% were patients who had not been submitted to serological testing. In the first group (tuberculosis and human immunodeficiency virus seropositivity, males from 30 to 40 years of age predominated, the most common clinical

  15. Mycobacterium ulcerans infection in two alpacas.

    Science.gov (United States)

    O'Brien, C; Kuseff, G; McMillan, E; McCowan, C; Lavender, C; Globan, M; Jerrett, I; Oppedisano, F; Johnson, P; Fyfe, J

    2013-07-01

    An ulcerative dermopathy caused by Mycobacterium ulcerans is described in two alpacas (Vicugna pacos) domiciled in endemic areas of Victoria, Australia. The diagnosis was confirmed in both cases by PCR targeting the M. ulcerans-specific insertion sequence, IS2404. Extensive wound debridement and bandaging was effective in controlling local disease in one alpaca, although the animal was eventually euthanased because of suspected disease recurrence at other anatomical sites. Treatment was not undertaken in the second animal, but the results of a complete necropsy are described. Investigation of the environs of the second animal yielded low levels of M. ulcerans DNA associated with a variety of samples. The potential use of adjunctive antibiotic therapies directed against M. ulcerans infection in this species is discussed. Mycobacterium ulcerans infection should be suspected in alpacas domiciled in endemic areas and presented with ulcerative skin disease. © 2013 The Authors. Australian Veterinary Journal © 2013 Australian Veterinary Association.

  16. Mycobacterium chelonae infection of the parotid gland

    Directory of Open Access Journals (Sweden)

    Hamid S Shaaban

    2012-01-01

    Full Text Available Mycobacterium chelonae can cause numerous infections, including lung disease, local cutaneous disease, osteomyelitis, joint infections and ocular disease. With the exception of lung disease, these syndromes commonly develop after direct inoculation. The most common clinical presentation in immunocompetent individuals is skin and soft tissue infection. We present a case of M. chelonae infection of the parotid gland that was successfully treated with clarithromycin monotherapy. To our knowledge, this is the first case report of M. chelonae parotitis in an adult.

  17. A Dermal Piercing Complicated by Mycobacterium fortuitum

    Science.gov (United States)

    Scroggins-Markle, Leslie; Kelly, Brent

    2013-01-01

    Background. Dermal piercings have recently become a fashion symbol. Common complications include hypertrophic scarring, rejection, local infection, contact allergy, and traumatic tearing. We report a rare case of Mycobacterium fortuitum following a dermal piercing and discuss its medical implications and treatments. Case. A previously healthy 19-year-old woman presented complaining of erythema and edema at the site of a dermal piercing on the right fourth dorsal finger. She was treated with a 10-day course of trimethoprim-sulfamethoxazole and one course of cephalexin by her primary care physician with incomplete resolution. The patient stated that she had been swimming at a local water park daily. A punch biopsy around the dermal stud was performed, and cultures with sensitivities revealed Mycobacterium fortuitum. The patient was treated with clarithromycin and ciprofloxacin for two months receiving full resolution. Discussion. Mycobacterium fortuitum is an infrequent human pathogen. This organism is a Runyon group IV, rapidly growing nontuberculous mycobacteria, often found in water,soil, and dust. Treatment options vary due to the size of the lesion. Small lesions are typically excised, while larger lesions require treatment for 2–6 months with antibiotics. We recommend a high level of suspicion for atypical mycobacterial infections in a piercing resistant to other therapies. PMID:24073343

  18. A Dermal Piercing Complicated by Mycobacterium fortuitum

    Directory of Open Access Journals (Sweden)

    Trisha Patel

    2013-01-01

    Full Text Available Background. Dermal piercings have recently become a fashion symbol. Common complications include hypertrophic scarring, rejection, local infection, contact allergy, and traumatic tearing. We report a rare case of Mycobacterium fortuitum following a dermal piercing and discuss its medical implications and treatments. Case. A previously healthy 19-year-old woman presented complaining of erythema and edema at the site of a dermal piercing on the right fourth dorsal finger. She was treated with a 10-day course of trimethoprim-sulfamethoxazole and one course of cephalexin by her primary care physician with incomplete resolution. The patient stated that she had been swimming at a local water park daily. A punch biopsy around the dermal stud was performed, and cultures with sensitivities revealed Mycobacterium fortuitum. The patient was treated with clarithromycin and ciprofloxacin for two months receiving full resolution. Discussion. Mycobacterium fortuitum is an infrequent human pathogen. This organism is a Runyon group IV, rapidly growing nontuberculous mycobacteria, often found in water,soil, and dust. Treatment options vary due to the size of the lesion. Small lesions are typically excised, while larger lesions require treatment for 2–6 months with antibiotics. We recommend a high level of suspicion for atypical mycobacterial infections in a piercing resistant to other therapies.

  19. Mechanisms of fluoroquinolone resistance in Mycobacterium tuberculosis.

    Science.gov (United States)

    Zhang, Yu-jiao; Li, Xiao-jing; Mi, Kai-xia

    2016-10-20

    Tuberculosis, caused by the pathogen Mycobacterium tuberculosis, is one of the world's deadliest bacterial infectious disease. It is still a global-health threat, particularly because of the drug-resistant forms. Fluoroquinolones, with target of gyrase, are among the drugs used to treat tuberculosis. However, their widespread use has led to bacterial resistance. The molecular mechanisms of fluoroquinolone resistance in mycobacterium tuberculosis have been reported, such as DNA gyrase mutations, drug efflux pumps system, bacterial cell wall thickness and pentapeptide proteins (MfpA) mediated regulation of gyrase. Mutations in gyrase conferring quinolone resistance play important roles and have been extensively studied. Recent studies have shown that the regulation of DNA gyrase affects mycobacterial drug resistance, but the mechanisms, especially by post-translational modification and regulatory proteins, are poorly understood. In this review, we summarize the fluoroquinolone drug development, and the molecular genetics of fluoroquinolone resistance in mycobacteria. Comprehensive understanding of the mechanisms of fluoroquinolone resistance in Mycobacterium tuberculosis will open a new view on understanding drug resistance in mycobacteria and lead to novel strategies to develop new accurate diagnosis methods.

  20. Re-establishing dignity

    DEFF Research Database (Denmark)

    Høy, Bente; Hall, E.O.C

    2012-01-01

    study with 29 nurses and nurse assistants was performed following Van Manen’s hermeneutic phenomenology. Findings show that caring mainly concerns ‘re-establishing dignity’ especially through ‘seeing the patient as a unique person’, ‘assisting in getting rid of the bed’ and ‘supporting patient...... appearance’. The study documents that caring for older people is about creating small everyday circumstances in which patient dignity can flourish. Shortcomings of a secondary analysis are discussed and suggestions for future research, such as how older hospital patients experience caring and dignity...

  1. Establishment of a System for Monitoring and Control of Cross Contamination in the Laboratory of Microbiological Analysis of Food during 2009

    Directory of Open Access Journals (Sweden)

    Corpa- Iguarán Eduardo Javid

    2012-03-01

    Full Text Available Within the activities for quality control in the laboratory, the final results of a particular analyteare now recognized as intermediates, due to the relevance given to quality assurance, as the ultimategoal of programs for quality management. This concept makes it necessary to establishmentof integral tools, to detect events such as cross-contamination, and measures to avoid affectingthe analysis method. Objective: to established a system for monitoring and control of crosscontaminationin the laboratory of microbiological analysis of food. Materials and methods:Flowcharts were developed to control the proceedings on the populations of aerobe mesophilicsand molds originated from pollution in the environment, surfaces, sterile material and culturemedia, which included a decision tree designed to perform control actions based on tolerance intervals,which were established as objective tool to decision-making leading to normalize countsof microbial populations in question. Results: Warning limits stricter were obtained for aerobicmesophilic and mold populations in the different controls, except for environment of media preparationand the corresponding for sterile material. Conclusion: The process developed allowedto complement the system of internal quality control in the laboratory, to provide of an objectivetool for closing nonconformities because of cross-contamination.

  2. A novel peptide interferes with Mycobacterium tuberculosis virulence and survival

    Directory of Open Access Journals (Sweden)

    Sachin Kumar Samuchiwal

    2014-01-01

    Full Text Available Tuberculosis (TB is a huge global burden, with new and resistant strains emerging at an alarming rate, necessitating an urgent need for a new class of drug candidates. Here, we report that SL3, a novel 33-amino acid peptide, causes debilitating effects on mycobacterial morphology. Treatment with SL3 drastically inhibits the growth of Mycobacterium tuberculosis in vitro as well as in a pre-clinical mouse model for M.tb infection. Microarray analysis of SL3-expressing strain demonstrates wide-scale transcriptional disruption in M.tb. We therefore believe that SL3 and similar peptides may herald a new approach towards discovering new molecules for TB therapy.

  3. Replication rates of Mycobacterium tuberculosis in human macrophages do not correlate with mycobacterial antibiotic susceptibility.

    Directory of Open Access Journals (Sweden)

    Johanna Raffetseder

    Full Text Available The standard treatment of tuberculosis (TB takes six to nine months to complete and this lengthy therapy contributes to the emergence of drug-resistant TB. TB is caused by Mycobacterium tuberculosis (Mtb and the ability of this bacterium to switch to a dormant phenotype has been suggested to be responsible for the slow clearance during treatment. A recent study showed that the replication rate of a non-virulent mycobacterium, Mycobacterium smegmatis, did not correlate with antibiotic susceptibility. However, the question whether this observation also holds true for Mtb remains unanswered. Here, in order to mimic physiological conditions of TB infection, we established a protocol based on long-term infection of primary human macrophages, featuring Mtb replicating at different rates inside the cells. During conditions that restricted Mtb replication, the bacterial phenotype was associated with reduced acid-fastness. However, these phenotypically altered bacteria were as sensitive to isoniazid, pyrazinamide and ethambutol as intracellularly replicating Mtb. In support of the recent findings with M. smegmatis, we conclude that replication rates of Mtb do not correlate with antibiotic tolerance.

  4. Replication rates of Mycobacterium tuberculosis in human macrophages do not correlate with mycobacterial antibiotic susceptibility.

    Science.gov (United States)

    Raffetseder, Johanna; Pienaar, Elsje; Blomgran, Robert; Eklund, Daniel; Patcha Brodin, Veronika; Andersson, Henrik; Welin, Amanda; Lerm, Maria

    2014-01-01

    The standard treatment of tuberculosis (TB) takes six to nine months to complete and this lengthy therapy contributes to the emergence of drug-resistant TB. TB is caused by Mycobacterium tuberculosis (Mtb) and the ability of this bacterium to switch to a dormant phenotype has been suggested to be responsible for the slow clearance during treatment. A recent study showed that the replication rate of a non-virulent mycobacterium, Mycobacterium smegmatis, did not correlate with antibiotic susceptibility. However, the question whether this observation also holds true for Mtb remains unanswered. Here, in order to mimic physiological conditions of TB infection, we established a protocol based on long-term infection of primary human macrophages, featuring Mtb replicating at different rates inside the cells. During conditions that restricted Mtb replication, the bacterial phenotype was associated with reduced acid-fastness. However, these phenotypically altered bacteria were as sensitive to isoniazid, pyrazinamide and ethambutol as intracellularly replicating Mtb. In support of the recent findings with M. smegmatis, we conclude that replication rates of Mtb do not correlate with antibiotic tolerance.

  5. Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis

    OpenAIRE

    Dos Vultos, Tiago; Mestre, Olga; Rauzier, Jean; Golec, Marcin; Rastogi, Nalin; Rasolofo, Voahangy; Tonjum, Tone; Sola, Christophe; Matic, Ivan; Gicquel, Brigitte

    2008-01-01

    International audience; BACKGROUND: Mycobacterium tuberculosis complex species display relatively static genomes and 99.9% nucleotide sequence identity. Studying the evolutionary history of such monomorphic bacteria is a difficult and challenging task. PRINCIPAL FINDINGS: We found that single-nucleotide polymorphism (SNP) analysis of DNA repair, recombination and replication (3R) genes in a comprehensive selection of M. tuberculosis complex strains from across the world, yielded surprisingly ...

  6. The Response of Mycobacterium Tuberculosis to Reactive Oxygen and Nitrogen Species

    OpenAIRE

    Voskuil, Martin I.; Bartek, Iona L.; Visconti, Kevin; Schoolnik, Gary K.

    2011-01-01

    The bacteriostatic and bactericidal effects and the transcriptional response of Mycobacterium tuberculosis to representative oxidative and nitrosative stresses were investigated by growth and survival studies and whole genome expression analysis. The M. tuberculosis reaction to a range of hydrogen peroxide (H2O2) concentrations fell into three distinct categories: (1) low level exposure resulted in induction of a few highly sensitive H2O2-responsive genes, (2) intermediate exposure resulted i...

  7. Surviving within the amoebal exocyst: the Mycobacterium avium complex paradigm

    Directory of Open Access Journals (Sweden)

    Drancourt Michel

    2010-04-01

    Full Text Available Abstract Background Most of environmental mycobacteria have been previously demonstrated to resist free-living amoeba with subsequent increased virulence and resistance to antibiotics and biocides. The Mycobacterium avium complex (MAC comprises of environmental organisms that inhabit a wide variety of ecological niches and exhibit a significant degree of genetic variability. We herein studied the intra-ameobal location of all members of the MAC as model organisms for environmental mycobacteria. Results Type strains for M. avium, Mycobacterium intracellulare, Mycobacterium chimaera, Mycobacterium colombiense, Mycobacterium arosiense, Mycobacterium marseillense, Mycobacterium timonense and Mycobacterium bouchedurhonense were co-cultivated with the free-living amoeba Acanthamoeba polyphaga strain Linc-AP1. Microscopic analyses demonstrated the engulfment and replication of mycobacteria into vacuoles of A. polyphaga trophozoites. Mycobacteria were further entrapped within amoebal cysts, and survived encystment as demonstrated by subculturing. Electron microscopy observations show that, three days after entrapment into A. polyphaga cysts, all MAC members typically resided within the exocyst. Conclusions Combined with published data, these observations indicate that mycobacteria are unique among amoeba-resistant bacteria, in residing within the exocyst.

  8. Risk factors for Mycobacterium tuberculosis infection among children in Greenland

    DEFF Research Database (Denmark)

    Søborg, Bolette; Andersen, Aase Bengaard; Melbye, Mads

    2011-01-01

    To examine the risk factors for Mycobacterium tuberculosis infection (MTI) among Greenlandic children for the purpose of identifying those at highest risk of infection.......To examine the risk factors for Mycobacterium tuberculosis infection (MTI) among Greenlandic children for the purpose of identifying those at highest risk of infection....

  9. Complete Genome Sequence of Mycobacterium vaccae Type Strain ATCC 25954

    KAUST Repository

    Ho, Y. S.

    2012-10-26

    Mycobacterium vaccae is a rapidly growing, nontuberculous Mycobacterium species that is generally not considered a human pathogen and is of major pharmaceutical interest as an immunotherapeutic agent. We report here the annotated genome sequence of the M. vaccae type strain, ATCC 25954.

  10. Mycobacterium marinum kan være vanskelig at diagnosticere

    DEFF Research Database (Denmark)

    Lønnberg, Ann Sophie; Seersholm, Niels; Nielsen, Signe Ledou

    2012-01-01

    The diagnosis of cutaneous Mycobacterium marinum infection is often delayed for months after presentation. In this case the diagnosis and correct treatment was delayed for ten months resulting in possible irreversible damage to the patient's infected finger. The main reason for the delay is lack...... of knowledge of the mycobacterium....

  11. Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169

    Science.gov (United States)

    We report the draft genome sequence of the type strain Mycobacterium chimaera Fl-0169T, a member of the Mycobacterium avium complex (MAC). M. chimaera Fl-0169T was isolated from a patient in Italy and is highly similar to strains of M. chimaera isolated in Ireland, though Fl-016...

  12. An orphan gyrB in the Mycobacterium smegmatis genome

    Indian Academy of Sciences (India)

    DNA gyrase is an essential topoisomerase found in all bacteria. It is encoded by gyrB and gyrA genes. These genes are organized differently in different bacteria. Direct comparison of Mycobacterium tuberculosis and Mycobacterium smegmatis genomes reveals presence of an additional gyrB in M. smegmatis flanked by ...

  13. Update on Medicinal Plants with Potency on Mycobacterium ulcerans.

    Science.gov (United States)

    Tsouh Fokou, Patrick Valere; Nyarko, Alexander Kwadwo; Appiah-Opong, Regina; Tchokouaha Yamthe, Lauve Rachel; Ofosuhene, Mark; Boyom, Fabrice Fekam

    2015-01-01

    Mycobacterium ulcerans disease has been a serious threat for people living in rural remote areas. Due to poverty or availability of traditional medicine these populations rely on herbal remedies. Currently, data on the anti-Mycobacterium ulcerans activity of plants, so far considered community-based knowledge, have been scientifically confirmed, concomitantly with some medicinal plants used to treat infectious diseases in general. Products derived from plants usually responsible for the biological properties may potentially control Mycobacterium ulcerans disease; numerous studies have aimed to describe the chemical composition of these plant antimicrobials. Thus, the present work provides the first compilation of medicinal plants that demonstrated inhibitory potential on Mycobacterium ulcerans. This work shows that the natural products represent potential alternatives to standard therapies for use as curative medicine for Mycobacterium ulcerans disease.

  14. Update on Medicinal Plants with Potency on Mycobacterium ulcerans

    Science.gov (United States)

    Tsouh Fokou, Patrick Valere; Nyarko, Alexander Kwadwo; Appiah-Opong, Regina; Tchokouaha Yamthe, Lauve Rachel; Ofosuhene, Mark; Boyom, Fabrice Fekam

    2015-01-01

    Mycobacterium ulcerans disease has been a serious threat for people living in rural remote areas. Due to poverty or availability of traditional medicine these populations rely on herbal remedies. Currently, data on the anti-Mycobacterium ulcerans activity of plants, so far considered community-based knowledge, have been scientifically confirmed, concomitantly with some medicinal plants used to treat infectious diseases in general. Products derived from plants usually responsible for the biological properties may potentially control Mycobacterium ulcerans disease; numerous studies have aimed to describe the chemical composition of these plant antimicrobials. Thus, the present work provides the first compilation of medicinal plants that demonstrated inhibitory potential on Mycobacterium ulcerans. This work shows that the natural products represent potential alternatives to standard therapies for use as curative medicine for Mycobacterium ulcerans disease. PMID:26779539

  15. A PULMONARY INFECTION CAUSED BY MYCOBACTERIUM PEREGRINUM– A CASE REPORT.

    Directory of Open Access Journals (Sweden)

    Tatina T. Todorova

    2015-12-01

    Full Text Available Mycobacterium peregrinum is a member of the group of rapidly growing Nontuberculous Mycobacteria (NTM. It can be found in high frequency in natural and laboratory environments and is considered to be uncommonrare pathogen for both immunocompetent and immunosuppressed individuals. Currently, pulmonary infections caused by Mycobacterium peregrinum are unusual and diagnosed only in limited number of cases. Here, we present a clinical case of elderly man (72 years with 1 month history of non-specific respiratory symptomatic. The patient was without underlying immunosuppressive condition or lung disease. Chest X-ray demonstrated persistent pleural effusion, opacities and cavitations in the right lobe. One of the sputum culturesgrewa rapidly growing mycobacterium and the isolated strain was found to be Mycobacterium peregrinumas identified by molecular genetic detection (PCR and DNA strip technology. To our knowledge, this is the third case in the world to report Mycobacterium peregrinumas a possible causative agent of pulmonary infection.

  16. Mycobacterium grossiae sp. nov., a rapidly growing, scotochromogenic species isolated from human clinical respiratory and blood culture specimens.

    Science.gov (United States)

    Paniz-Mondolfi, Alberto Enrique; Greninger, Alexander L; Ladutko, Lynn; Brown-Elliott, Barbara A; Vasireddy, Ravikiran; Jakubiec, Wesley; Vasireddy, Sruthi; Wallace, Richard J; Simmon, Keith E; Dunn, Bruce E; Jackoway, Gary; Vora, Surabhi B; Quinn, Kevin K; Qin, Xuan; Campbell, Sheldon

    2017-11-01

    A previously undescribed, rapidly growing, scotochromogenic species of the genus Mycobacterium (represented by strains PB739 T and GK) was isolated from two clinical sources - the sputum of a 76-year-old patient with severe chronic obstructive pulmonary disease, history of tuberculosis exposure and Mycobacterium avium complex isolated years prior; and the blood of a 15-year-old male with B-cell acute lymphoblastic leukaemia status post bone marrow transplant. The isolates grew as dark orange colonies at 25-37 °C after 5 days, sharing features in common with other closely related species. Analysis of the complete 16S rRNA gene sequence (1492 bp) of strain PB739 T demonstrated that the isolate shared 98.8 % relatedness with Mycobacterium wolinskyi. Partial 429 bp hsp65 and 744 bp rpoB region V sequence analyses revealed that the sequences of the novel isolate shared 94.8 and 92.1 % similarity with those of Mycobacterium neoaurum and Mycobacterium aurum, respectively. Biochemical profiling, antimicrobial susceptibility testing, HPLC/gas-liquid chromatography analyses and multilocus sequence typing support the taxonomic status of these isolates (PB739 T and GK) as representatives of a novel species. Both isolates were susceptible to the Clinical and Laboratory Standards Institute recommended antimicrobials for susceptibility testing of rapidly growing mycobacteria including amikacin, ciprofloxacin, moxifloxacin, doxycycline/minocycline, imipenem, linezolid, clarithromycin and trimethropin/sulfamethoxazole. Both isolates PB739 T and GK showed intermediate susceptibility to cefoxitin. We propose the name Mycobacterium grossiae sp. nov. for this novel species and have deposited the type strain in the DSMZ and CIP culture collections. The type strain is PB739 T (=DSM 104744 T =CIP 111318 T ).

  17. HANFORD DOUBLE SHELL TANK (DST) THERMAL & SEISMIC PROJECT ESTABLISHMENT OF METHODOLOGY FOR TIME DOMAIN SOIL STRUCTURE INTERACTION ANALYSIS OF HANFORD DST

    Energy Technology Data Exchange (ETDEWEB)

    MACKEY, T.C.

    2006-03-14

    the frequency domain, but frequency domain analysis is limited to systems with linear responses. The nonlinear character of the coupled SSI model and tank structural model requires that the seismic analysis be solved in the time domain. However, time domain SSI analysis is somewhat nontraditional and requires that the appropriate methodology be developed and demonstrated. Moreover, the analysis of seismically induced fluid-structure interaction between the explicitly modeled waste and the primary tank must be benchmarked against known solutions to simpler problems before being applied to the more complex analysis of the DSTs. The objective of this investigation is to establish the methodology necessary to perform the required SSI analysis of the DSTs in the time domain. Specifically, the analysis establishes the capabilities and limitations of the time domain codes ANSYS and Dytran for performing seismic SSI analysis of the DSTs. The benchmarking of the codes Dytran and ANSYS for performing seismically induced fluid-structure interaction (FSI) between the contained waste and the DST primary tank are documented in Abatt (2006) and Carpenter and Abatt (2006), respectively. The results of those two studies show that both codes have the capability to analyze the fluid-structure interaction behavior of the primary tank and contained waste. As expected, Dytran appears to have more robust capabilities for FSI analysis. The ANSYS model used in that study captures much of the FSI behavior, but does have some limitations for predicting the convective response of the waste and possibly the response of the waste in the knuckle region of the primary tank. While Dytran appears to have somewhat stronger capabilities for the analysis of the FSI behavior in the primary tank, it is more practical for the overall analysis to use ANSYS. Thus, Dytran served the purpose of helping to identify limitations in the ANSYS FSI analysis so that those limitations can be addressed in the structural

  18. Immunological crossreactivity of the Mycobacterium leprae CFP-10 with its homologue in Mycobacterium tuberculosis

    NARCIS (Netherlands)

    Geluk, A.; van Meijgaarden, K. E.; Franken, K. L. M. C.; Wieles, B.; Arend, S. M.; Faber, W. R.; Naafs, B.; Ottenhoff, T. H. M.

    2004-01-01

    Mycobacterium tuberculosis culture filtrate protein-10 (CFP-10) (Rv3874) is considered a promising antigen for the immunodiagnosis of tuberculosis (TB) together with early secreted antigens of M. tuberculosis (ESAT-6). Both ESAT-6 and CFP-10 are encoded by the RD1 region that is deleted from all

  19. Bacteriological diagnosis and molecular strain typing of Mycobacterium bovis and Mycobacterium caprae.

    Science.gov (United States)

    Gormley, E; Corner, L A L; Costello, E; Rodriguez-Campos, S

    2014-10-01

    The primary isolation of a Mycobacterium sp. of the Mycobacterium tuberculosis complex from an infected animal provides a definitive diagnosis of tuberculosis. However, as Mycobacterium bovis and Mycobacterium caprae are difficult to isolate, particularly for animals in the early stages of disease, success is dependent on the optimal performance of all aspects of the bacteriological process, from the initial choice of tissue samples at post-mortem examination or clinical samples, to the type of media and conditions used to cultivate the microorganism. Each step has its own performance characteristics, which can contribute to sensitivity and specificity of the procedure, and may need to be optimized in order to achieve the gold standard diagnosis. Having isolated the slow-growing mycobacteria, species identification and fine resolution strain typing are keys to understanding the epidemiology of the disease and to devise strategies to limit transmission of infection. New technologies have emerged that can now even discriminate different isolates from the same animal. In this review we highlight the key factors that contribute to the accuracy of bacteriological diagnosis of M. bovis and M. caprae, and describe the development of advanced genotyping techniques that are increasingly used in diagnostic laboratories for the purpose of supporting detailed epidemiological investigations. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. High resolution discrimination of clinical Mycobacterium tuberculosis complex strains based on single nucleotide polymorphisms.

    Directory of Open Access Journals (Sweden)

    Susanne Homolka

    Full Text Available Recently, the diversity of the Mycobacterium tuberculosis complex (MTBC population structure has been described in detail. Based on geographical separation and specific host pathogen co-evolution shaping MTBC virulence traits, at least 20 major lineages/genotypes have evolved finally leading to a clear influence of strain genetic background on transmissibility, clinical presentation/outcome, and resistance development. Therefore, high resolution genotyping for characterization of strains in larger studies is mandatory for understanding mechanisms of host-pathogen-interaction and to improve tuberculosis (TB control. Single nucleotide polymorphisms (SNPs represent the most reliable markers for lineage classification of clinical isolates due to the low levels of homoplasy, however their use is hampered either by low discriminatory power or by the need to analyze a large number of genes to achieve higher resolution. Therefore, we carried out de novo sequencing of 26 genes (approx. 20000 bp per strain in a reference collection of MTBC strains including all major genotypes to define a highly discriminatory gene set. Overall, 161 polymorphisms were detected of which 59 are genotype-specific, while 13 define deeper branches such as the Euro-American lineage. Unbiased investigation of the most variable set of 11 genes in a population based strain collection (one year, city of Hamburg, Germany confirmed the validity of SNP analysis as all strains were classified with high accuracy. Taken together, we defined a diagnostic algorithm which allows the identification of 17 MTBC phylogenetic lineages with high confidence for the first time by sequencing analysis of just five genes. In conclusion, the diagnostic algorithm developed in our study is likely to open the door for a low cost high resolution sequence/SNP based differentiation of the MTBC with a very high specificity. High throughput assays can be established which will be needed for large association

  1. [Cloning and sequence analysis of the DHBV genome of the brown ducks in Guilin region and establishment of the quantitative method for detecting DHBV].

    Science.gov (United States)

    Su, He-Ling; Huang, Ri-Dong; He, Song-Qing; Xu, Qing; Zhu, Hua; Mo, Zhi-Jing; Liu, Qing-Bo; Liu, Yong-Ming

    2013-03-01

    Brown ducks carrying DHBV were widely used as hepatitis B animal model in the research of the activity and toxicity of anti-HBV dugs. Studies showed that the ratio of DHBV carriers in the brown ducks in Guilin region was relatively high. Nevertheless, the characters of the DHBV genome of Guilin brown duck remain unknown. Here we report the cloning of the genome of Guilin brown duck DHBV and the sequence analysis of the genome. The full length of the DHBV genome of Guilin brown duck was 3 027bp. Analysis using ORF finder found that there was an ORF for an unknown peptide other than S-ORF, PORF and C-ORF in the genome of the DHBV. Vector NTI 8. 0 analysis revealed that the unknown peptide contained a motif which binded to HLA * 0201. Aligning with the DHBV sequences from different countries and regions indicated that there were no obvious differences of regional distribution among the sequences. A fluorescence quantitative PCR for detecting DHBV was establishment based on the recombinant plasmid pGEM-DHBV-S constructed. This study laid the groundwork for using Guilin brown duck as a hepatitis B animal model.

  2. Mycobacterium sarraceniae sp. nov. and Mycobacterium helvum sp. nov., isolated from the pitcher plant Sarracenia purpurea.

    Science.gov (United States)

    Tran, Phuong M; Dahl, John L

    2016-11-01

    Several fast- to intermediate-growing, acid-fast, scotochromogenic bacteria were isolated from Sarracenia purpurea pitcher waters in Minnesota sphagnum peat bogs. Two strains (DL734T and DL739T) were among these isolates. On the basis of 16S rRNA gene sequences, the phylogenetic positions of both strains is in the genus Mycobacterium with no obvious relation to any characterized type strains of mycobacteria. Phenotypic characterization revealed that neither strain was similar to the type strains of known species of the genus Mycobacterium in the collective properties of growth, pigmentation or fatty acid composition. Strain DL734T grew at temperatures between 28 and 32 °C, was positive for 3-day arylsulfatase production, and was negative for Tween 80 hydrolysis, urease and nitrate reduction. Strain DL739T grew at temperatures between 28 and 37 °C, and was positive for Tween 80 hydrolysis, urea, nitrate reduction and 3-day arylsulfatase production. Both strains were catalase-negative while only DL739T grew with 5 % NaCl. Fatty acid methyl ester profiles were unique for each strain. DL739T showed an ability to survive at 8 °C with little to no cellular replication and is thus considered to be psychrotolerant. Therefore, strains DL734T and DL739T represent two novel species of the genus Mycobacterium with the proposed names Mycobacterium sarraceniae sp. nov. and Mycobacterium helvum sp. nov., respectively. The type strains are DL734T (=JCM 30395T=NCCB 100519T) and DL739T (=JCM 30396T=NCCB 100520T), respectively.

  3. System-wide coordinates of higher order functions in host-pathogen environment upon Mycobacterium tuberculosis infection.

    Science.gov (United States)

    Parvati Sai Arun, P V; Miryala, Sravan Kumar; Rana, Aarti; Kurukuti, Sreenivasulu; Akhter, Yusuf; Yellaboina, Sailu

    2018-03-22

    Molecular signatures and their interactions behind the successful establishment of infection of Mycobacterium tuberculosis (Mtb) inside macrophage are largely unknown. In this work, we present an inter-system scale atlas of the gene expression signatures, their interactions and higher order gene functions of macrophage-Mtb environment at the time of infection. We have carried out large-scale meta-analysis of previously published gene expression microarray studies andhave identified a ranked list of differentially expressed genes and their higher order functions in intracellular Mtb as well as the infected macrophage. Comparative analysis of gene expression signatures of intracellular Mtb with the in vitro dormant Mtb at different hypoxic and oxidative stress conditions led to the identification of the large number of Mtb functional groups, namely operons, regulons and pathways that were common and unique to the intracellular environment and dormancy state. Some of the functions that are specific to intracellular Mtb are cholesterol degradation and biosynthesis of immunomodulatory phenolic compounds. The molecular signatures we have identified to be involved in adaptation to different stress conditions in macrophage environment may be critical for designing therapeutic interventions against tuberculosis. And, our approach may be broadly applicable for investigating other host-pathogen interactions.

  4. Mycobacterium minnesotense sp. nov., a photochromogenic bacterium isolated from sphagnum peat bogs.

    Science.gov (United States)

    Hannigan, Geoffrey D; Krivogorsky, Bogdana; Fordice, Daniel; Welch, Jacqueline B; Dahl, John L

    2013-01-01

    Several intermediate-growing, photochromogenic bacteria were isolated from sphagnum peat bogs in northern Minnesota, USA. Acid-fast staining and 16S rRNA gene sequence analysis placed these environmental isolates in the genus Mycobacterium, and colony morphologies and PCR restriction analysis patterns of the isolates were similar. Partial sequences of hsp65 and dnaJ1 from these isolates showed that Mycobacterium arupense ATCC BAA-1242(T) was the closest mycobacterial relative, and common biochemical characteristics and antibiotic susceptibilities existed between the isolates and M. arupense ATCC BAA-1242(T). However, compared to nonchromogenic M. arupense ATCC BAA-1242(T), the environmental isolates were photochromogenic, had a different mycolic acid profile and had reduced cell-surface hydrophobicity in liquid culture. The data reported here support the conclusion that the isolates are representatives of a novel mycobacterial species, for which the name Mycobacterium minnesotense sp. nov. is proposed. The type strain is DL49(T) (=DSM 45633(T) = JCM 17932(T) = NCCB 100399(T)).

  5. Mycobacterium abscessus Displays Fitness for Fomite Transmission.

    Science.gov (United States)

    Malcolm, Kenneth C; Caceres, Silvia M; Honda, Jennifer R; Davidson, Rebecca M; Epperson, L Elaine; Strong, Michael; Chan, Edward D; Nick, Jerry A

    2017-10-01

    Mycobacterium abscessus is a rapidly growing nontuberculous mycobacterium (NTM) increasingly reported in soft tissue infections and chronic lung diseases, including cystic fibrosis. The environmental source of M. abscessus has not been definitively identified, but NTM have been detected in soil and water. To determine the potential of soil-derived M. abscessus as an infectious source, we explored the association, growth, and survival of M. abscessus with defined mineral particulates, including kaolin, halloysite, and silicone dioxide, and house dust as possible M. abscessus fomites. M. abscessus physically associated with particulates, and the growth of M. abscessus was enhanced in the presence of both kaolin and house dust. M. abscessus survived desiccation for 2 weeks but was not viable after 3 weeks. The rate of decline of M. abscessus viability during desiccation was reduced in the presence of house dust. The evidence for enhanced growth and survival of M. abscessus during alternating growth and drying periods suggests that dissemination could occur when in wet or dry environments. These studies are important to understand environmental survival and acquisition of NTM. IMPORTANCE The environmental source of pulmonary Mycobacterium abscessus infections is not known. Fomites are nonliving carriers of infectious agents and may contribute to acquisition of M. abscessus This study provides evidence that M. abscessus growth is enhanced in the presence of particulates, using kaolin, an abundant natural clay mineral, and house dust as experimental fomites. Moreover, M. abscessus survived desiccation for up to 2 weeks in the presence of house dust, kaolin, and several chemically defined mineral particulates; mycobacterial viability during extended periods of dessication was enhanced by the presence of house dust. The growth characteristics of M. abscessus with particulates suggest that a fomite mechanism of transmission may contribute to M. abscessus acquisition, which

  6. Disseminated infection due to Mycobacterium chelonae with scleritis, spondylodiscitis and spinal epidural abscess

    Directory of Open Access Journals (Sweden)

    Humberto Metta

    Full Text Available Mycobacteria other than tuberculosis (MOTT have a low incidence as pathogens in human pathology. The most frequent clinical expression is the disseminated disease in subjects with compromised cellular immunity. Bacteriological characteristics in culture can generate confusion with other pathogens, which delays the appropriate diagnosis and treatment. We present a case of a disseminated infection due to Mycobacterium chelonae with scleritis, spondylodiscitis and spinal epidural abscess in a man with a medical background of cellular immunity deficit induced by therapeutic drugs. The antibiotic scheme of twenty-one weeks, during the follow-up period, controlled the infection, however, the optimum duration of treatment has not been established.

  7. Mycobacterium chimaera Infections Associated With Contaminated Heater-Cooler Devices for Cardiac Surgery: Outbreak Management.

    Science.gov (United States)

    Marra, Alexandre R; Diekema, Daniel J; Edmond, Michael B

    2017-08-15

    The global outbreak of Mycobacterium chimaera infections associated with heater-cooler devices (HCDs) presents several important, unique challenges for the infection prevention community. The primary focus of this article is to assist hospitals in establishing a rapid response for identification, notification, and evaluation of exposed patients, and management of HCDs with regard to placement and containment, environmental culturing, and disinfection. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

  8. Mycobacterium chimaera left ventricular assist device infections.

    Science.gov (United States)

    Balsam, Leora B; Louie, Eddie; Hill, Fred; Levine, Jamie; Phillips, Michael S

    2017-06-01

    A global outbreak of invasive Mycobacterium chimaera infections after cardiac surgery has recently been linked to bioaerosols from contaminated heater-cooler units. The majority of cases have occurred after valvular surgery or aortic graft surgery and nearly half have resulted in death. To date, infections in patients with left ventricular assist devices (LVADs) have not been characterized in the literature. We report two cases of device-associated M. chimaera infection in patients with continuous-flow LVADs and describe challenges related to diagnosis and management in this population. © 2017 Wiley Periodicals, Inc.

  9. Transcriptional Profiling Mycobacterium tuberculosis from Patient Sputa.

    Science.gov (United States)

    Wildner, Leticia Muraro; Gould, Katherine A; Waddell, Simon J

    2018-01-01

    The emergence of drug resistance threatens to destroy tuberculosis control programs worldwide, with resistance to all first-line drugs and most second-line drugs detected. Drug tolerance (or phenotypic drug resistance) is also likely to be clinically relevant over the 6-month long standard treatment for drug-sensitive tuberculosis. Transcriptional profiling the response of Mycobacterium tuberculosis to antimicrobial drugs offers a novel interpretation of drug efficacy and mycobacterial drug-susceptibility that likely varies in dynamic microenvironments, such as the lung. This chapter describes the noninvasive sampling of tuberculous sputa and techniques for mRNA profiling M. tb bacilli during patient therapy to characterize real-world drug actions.

  10. Skin granulomas due to Mycobacterium gordonae.

    Science.gov (United States)

    Gengoux, P; Portaels, F; Lachapelle, J M; Minnikin, D E; Tennstedt, D; Tamigneau, P

    1987-04-01

    A 38-year-old woman presented with small, ulcerated, red or bluish nodules on the right hand, clinically resembling mycobacterial granulomas; these appeared a few months after a bite by a rat, while the patient was collecting frogs in a pond in the Belgian Ardennes. The histopathologic picture was compatible with a diagnosis of mycobacterial infection and rare acid-fast bacilli could be found. Repeated bacteriologic investigations were performed and these led to the identification of a strain displaying characteristics of Mycobacterium gordonae. The skin condition responded well to rifampicin (300 mg/day) within 6 months.

  11. Mycobacterium tuberculosis effectors interfering host apoptosis signaling.

    Science.gov (United States)

    Liu, Minqiang; Li, Wu; Xiang, Xiaohong; Xie, Jianping

    2015-07-01

    Tuberculosis remains a serious human public health concern. The coevolution between its pathogen Mycobacterium tuberculosis and human host complicated the way to prevent and cure TB. Apoptosis plays subtle role in this interaction. The pathogen endeavors to manipulate the apoptosis via diverse effectors targeting key signaling nodes. In this paper, we summarized the effectors pathogen used to subvert the apoptosis, such as LpqH, ESAT-6/CFP-10, LAMs. The interplay between different forms of cell deaths, such as apoptosis, autophagy, necrosis, is also discussed with a focus on the modes of action of effectors, and implications for better TB control.

  12. Bacteremia with an Unusual Pathogen: Mycobacterium neoaurum

    Directory of Open Access Journals (Sweden)

    Hesham Awadh

    2016-01-01

    Full Text Available Mycobacterium neoaurum (M. neoaurum is an infrequently encountered cause of infection in humans. It is a member of the rapidly growing mycobacteria family. It predominately afflicts those with a compromised immune status and a chronically indwelling vascular access. Isolation of this organism is challenging yet the advent of 16s ribosomal sequencing paved the way for more sensitive detection. No treatment guidelines are available and treatment largely depends on the experience of the treating physician and nature of the isolate. We report a case of M. neoaurum bacteremia in an immune competent host, with a chronically placed peripherally inserted central catheter (PICC line.

  13. Mycobacterium fortuitum abdominal wall abscesses following liposuction

    Directory of Open Access Journals (Sweden)

    Al Soub Hussam

    2008-01-01

    Full Text Available We describe here a case of abdominal abscesses due to Mycobacterium fortuitum following liposuction. The abscesses developed three months after the procedure and diagnosis was delayed for five months. The clues for diagnosis were persistent pus discharge in spite of broad spectrum antibiotics and failure to grow any organisms on routine culture. This condition has been rarely reported; however, the increasing number of liposuction procedures done and awareness among physicians will probably result in the identification of more cases. Combination antibiotic therapy with surgical drainage in more extensive diseases is essential for cure.

  14. Automated ultrasound edge-tracking software comparable to established semi-automated reference software for carotid intima-media thickness analysis.

    Science.gov (United States)

    Shenouda, Ninette; Proudfoot, Nicole A; Currie, Katharine D; Timmons, Brian W; MacDonald, Maureen J

    2017-04-26

    Many commercial ultrasound systems are now including automated analysis packages for the determination of carotid intima-media thickness (cIMT); however, details regarding their algorithms and methodology are not published. Few studies have compared their accuracy and reliability with previously established automated software, and those that have were in asymptomatic adults. Therefore, this study compared cIMT measures from a fully automated ultrasound edge-tracking software (EchoPAC PC, Version 110.0.2; GE Medical Systems, Horten, Norway) to an established semi-automated reference software (Artery Measurement System (AMS) II, Version 1.141; Gothenburg, Sweden) in 30 healthy preschool children (ages 3-5 years) and 27 adults with coronary artery disease (CAD; ages 48-81 years). For both groups, Bland-Altman plots revealed good agreement with a negligible mean cIMT difference of -0·03 mm. Software differences were statistically, but not clinically, significant for preschool images (P = 0·001) and were not significant for CAD images (P = 0·09). Intra- and interoperator repeatability was high and comparable between software for preschool images (ICC, 0·90-0·96; CV, 1·3-2·5%), but slightly higher with the automated ultrasound than the semi-automated reference software for CAD images (ICC, 0·98-0·99; CV, 1·4-2·0% versus ICC, 0·84-0·89; CV, 5·6-6·8%). These findings suggest that the automated ultrasound software produces valid cIMT values in healthy preschool children and adults with CAD. Automated ultrasound software may be useful for ensuring consistency among multisite research initiatives or large cohort studies involving repeated cIMT measures, particularly in adults with documented CAD. © 2017 Scandinavian Society of Clinical Physiology and Nuclear Medicine. Published by John Wiley & Sons Ltd.

  15. Developing and Validating an Age-Independent Equation Using Multi-Frequency Bioelectrical Impedance Analysis for Estimation of Appendicular Skeletal Muscle Mass and Establishing a Cutoff for Sarcopenia

    Directory of Open Access Journals (Sweden)

    Yosuke Yamada

    2017-07-01

    Full Text Available Background: Appendicular skeletal muscle (or lean mass (ALM estimated using dual-energy X-ray absorptiometry (DXA is considered to be a preferred method for sarcopenia studies. However, DXA is expensive, has limited portability, and requires radiation exposure. Bioelectrical impedance analysis (BIA is inexpensive, easy to use, and portable; thus BIA might be useful in sarcopenia investigations. However, a large variety of models have been commercially supplied by different companies, and for most consumer products, the equations estimating ALM are not disclosed. It is therefore difficult to use these equations for research purposes. In particular, the BIA equation is often age-dependent, which leads to fundamental difficulty in examining age-related ALM loss. The aims of the current study were as follows: (1 to develop and validate an equation to estimate ALM using multi-frequency BIA (MF-BIA based on theoretical models, and (2 to establish sarcopenia cutoff values using the equation for the Japanese population. Methods: We measured height (Ht, weight, and ALM obtained using DXA and a standing-posture 8-electrode MF-BIA (5, 50, 250 kHz in 756 Japanese individuals aged 18 to 86-years-old (222 men and 301 women as developing equation group and 97 men and 136 women as a cross validation group. The traditional impedance index (Ht2/Z50 and impedance ratio of high and low frequency (Z250/Z5 of hand to foot values were calculated. Multiple regression analyses were conducted with ALM as dependent variable in men and women separately. Results: We created the following equations: ALM = (0.6947 × (Ht2/Z50 + (−55.24 × (Z250/Z5 + (−10,940 × (1/Z50 + 51.33 for men, and ALM = (0.6144 × (Ht2/Z50 + (−36.61 × (Z250/Z5 + (−9332 × (1/Z50 + 37.91 for women. Additionally, we conducted measurements in 1624 men and 1368 women aged 18 to 40 years to establish sarcopenia cutoff values in the Japanese population. The mean values minus 2 standard deviations

  16. Developing and Validating an Age-Independent Equation Using Multi-Frequency Bioelectrical Impedance Analysis for Estimation of Appendicular Skeletal Muscle Mass and Establishing a Cutoff for Sarcopenia.

    Science.gov (United States)

    Yamada, Yosuke; Nishizawa, Miyuki; Uchiyama, Tomoka; Kasahara, Yasuhiro; Shindo, Mikio; Miyachi, Motohiko; Tanaka, Shigeho

    2017-07-19

    Background: Appendicular skeletal muscle (or lean) mass (ALM) estimated using dual-energy X-ray absorptiometry (DXA) is considered to be a preferred method for sarcopenia studies. However, DXA is expensive,