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Journal articles on the topic "MLSA"
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Abe, R., J. J. Ryan, and R. J. Hodes. "Mls is not a single gene, allelic system. Different stimulatory Mls determinants are the products of at least two nonallelic, unlinked genes." Journal of Experimental Medicine 166, no. 4 (October 1, 1987): 1150–55. http://dx.doi.org/10.1084/jem.166.4.1150.
Full textAbstract:
Mls determinants share with MHC products the unique property of stimulating T cells at extraordinarily high precursor frequencies. The Mls system was originally described as a single locus on chromosome 1, with four alleles, Mlsa, Mlsb, Mlsc, and Mlsd, that encode polymorphic cell surface structures. However, the fundamental issues of polymorphism and allelism in the Mls system remain controversial. To clarify these questions, a formal segregation analysis of the genes encoding Mlsa and Mlsc determinants was carried out by testing the capacity of spleen cells from progeny of (Mlsa X Mlsc)F1 X Mlsb breedings to stimulate responses by unprimed T cells and by Mlsa- and Mlsc-specific cloned T cells. The results of this analysis indicated that the gene encoding Mlsa determinants is neither allelic to nor linked to the gene encoding Mlsc determinants. Together with previous findings, these results also suggest that another strongly stimulatory type, Mlsd, in fact results from the independent expression of unlinked Mlsa and Mlsc gene products. Based on these observations, it is concluded that, contrary to conventional concepts, the stimulatory phenotypes designated as Mlsa, Mlsc, and Mlsd can be accounted for by the independent expression of the products of at least two unlinked gene loci.
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Ryan, J. J., J. J. Mond, and F. D. Finkelman. "The Mlsd-defined primary mixed lymphocyte reaction: a composite response to Mlsa and Mlsc determinants." Journal of Immunology 138, no. 12 (June 15, 1987): 4085–92. http://dx.doi.org/10.4049/jimmunol.138.12.4085.
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Abstract Considerable disagreement exists among immunologists regarding the polymorphic nature of the murine Mls system. An estimate of the capacity of a given putative Mls allelic gene product expressed on a stimulator population to elicit proliferation of H-2-compatible Mls-disparate unprimed T cells may vary widely among different groups of investigators. This laboratory has shown previously that preactivation of B lymphocytes in a splenocyte stimulator population by exposure to goat anti-mouse IgD (GaMD) before irradiation dramatically enhanced the in vitro presentation not only of the strongly stimulatory (and highly cross-reactive) Mlsa and Mlsd, but also the more poorly stimulatory Mlsc specificity. Therefore, by the use of GaMD-treated splenocytes that optimally present the various Mls non-H-2 stimulatory epitopes, we attempted in this study to obtain a clearer understanding of Mls polymorphism by re-examining the conflicting claims associated with the mixed lymphocyte reaction (MLR) stimulatory capacity of different Mls specificities. Among H-2k responder cells of the Mls null, Mlsa, Mlsb, or Mlsd genotypes, only T cells from Mlsd-bearing CBA/J mice did not respond to Mlsc determinants present on GaMD-treated C3H/HeJ stimulator cells. Crossing CBA/J with an Mlsc-responsive mouse strain yielded an F1 animal in which nonresponsiveness to Mlsc was dominant. Although Mlsa (AKR/J) and Mlsc (C3H/HeJ) parental T cells both proliferated vigorously to Mlsd (CBA/J) stimulator cells, the Mlsa/c (AKR X C3H)F1 T cells responded poorly to GaMD-treated Mlsd stimulator cells. In addition, Mlsd (CBA/J) T cells were nonresponsive to Mlsa (AKR/J), Mlsc (C3H/HeJ), and Mlsa/c (AKR X C3H)F1 GaMD-treated stimulator cells. Because Mlsa (AKR/J) and Mlsc (C3H/HeJ) specificities are mutually stimulatory, at least limited polymorphism must exist in the Mls system. However, because Mlsa/c (AKR X C3H) and Mlsd (CBA/J) specificities are mutually nonstimulatory, T cell proliferation in an Mlsd-defined primary MLR is most likely due to a composite response to Mlsa and Mlsc epitopes present on CBA/J stimulator cells.
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Abe, R., J. J. Ryan, and R. J. Hodes. "Clonal analysis of the Mls system. A reappraisal of polymorphism and allelism among Mlsa, Mlsc, and Mlsd." Journal of Experimental Medicine 165, no. 4 (April 1, 1987): 1113–29. http://dx.doi.org/10.1084/jem.165.4.1113.
Full textAbstract:
Only two sets of antigenic determinants are recognized by T lymphocytes at uniquely high precursor frequencies: those encoded by the MHC and those encoded by Mls. The structural as well as functional characteristics of MHC products have been extensively analyzed. In contrast, little information concerning the nature of Mls genes or their products is available. Although it was originally described (5, 6) that the Mls locus on chromosome 1 is composed of four alleles that encode polymorphic cell surface structures, the issues of polymorphism and allelism in the Mls system have been controversial for some time. In the present study, T cell clones were generated by continuous stimulation of B10.BR (H-2k, Mlsb) T cells by CBA/J (H-2k, Mlsd) stimulators and they were used to analyze the relationship of putative Mlsa, Mlsc, and Mlsd determinants. All clones proliferated in response to determinants expressed by CBA/J stimulators. In addition, each of these clones exhibited a second reactivity to either AKR/J (H-2k, Mlsa) or C3H/HeJ (H-2k, Mlsc) stimulators. No clone responded to both AKR/J and C3H/HeJ. These second specificities were defined to be for Mlsa or Mlsc determinants, respectively, by the response patterns of clones and unprimed T cells to stimulators derived from congenic strains, recombinant inbred (RI) strains, and backcross mice. Moreover, a segregation analysis of the (CBA/J X B10.BR)F1 X B10.BR backcross indicated that the Mlsa-like and Mlsc-like determinants expressed on CBA/J (Mlsd) cells are in fact encoded by nonallelic, unlinked genes. These findings suggest a new concept of the polymorphism and genetics of the Mls system. It is proposed that two distinct and nonallelic gene products express, respectively, the noncrossreacting Mlsa and Mlsc determinants, and that the Mlsd phenotype does not represent an independent genotype but rather reflects the concurrent expression of Mlsa and Mlsc. The Mls system, therefore, consists of at least two systems that are distinct both genetically and antigenically, and that may be of different biologic or physiologic significance as well.
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Abe, R., J. J. Ryan, F. D. Finkelman, and R. J. Hodes. "T cell recognition of Mls. T cell clones demonstrate polymorphism between Mlsa, Mlsc, and Mlsd." Journal of Immunology 138, no. 2 (January 15, 1987): 373–79. http://dx.doi.org/10.4049/jimmunol.138.2.373.
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Abstract The determinants encoded by the minor lymphocyte stimulating locus (Mls) are defined as determinants that induce strong T cell proliferative responses in primary mixed lymphocyte reactions. Although the Mls locus was originally described as having four alleles, a, b, c, and d, a number of recent observations have led several investigators to challenge the idea that Mls is truly a polymorphic system. To better define this system of determinants recognized at high frequency by T cells, the present studies were undertaken to evaluate the polymorphism of Mls products. In the present study, the in vitro proliferative responses of Mlsa- and Mlsc-specific T cell clones were employed to analyze Mls products. The identification of determinants recognized by Mlsa- and Mlsc-reactive clones was established by the pattern of responses to stimulators derived from congenic strains, recombinant inbred strains, and backcross mice. T cell clones and unprimed T cells gave concordant responses that confirmed the Mlsa or Mlsc specificity of the cloned populations. With the use of these two sets of Mls-specific T cell clones, the existence or absence of polymorphism of Mls-encoded gene products was examined. It was found that Mlsa-specific cloned T cells responded to Mlsa but not Mlsc stimulators, whereas Mlsc-specific clones responded to Mlsc but not Mlsa. This reciprocal pattern of specificity indicates that the Mls system as currently defined is therefore truly polymorphic. In addition, it was observed that both Mlsa- and Mlsc-specific clones were stimulated by Mlsd stimulators. In particular, the possibility that Mlsa and Mlsc are not alleles but products of different loci and that Mlsd strains are those that express both Mlsa and Mlsc is considered.
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Click, R. E., A. M. Adelmann, and M. M. Azar. "Immune responses in vitro. XIII. MLR detectability of Mlsa-, Mlsb-, Mlsc-, and Mlsd-encoded products." Journal of Immunology 134, no. 5 (May 1, 1985): 2948–52. http://dx.doi.org/10.4049/jimmunol.134.5.2948.
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Abstract The Mls locus was originally defined to have four alleles; all controlled products that were detectable in MLR except b, which was described as being null. More recent evidence led other investigators to postulate that the Mls locus is nonpolymorphic, being composed of only the b null allele and a singly expressed allele previously ascribed to be the a and d alleles. Our results indicate that Mlsa and Mlsd control products that are antigenically distinct and, therefore, the products cannot be controlled by the same allele. In addition, the product of Mlsb was easily detectable by Mlsa and Mlsd responding cells and cannot be considered null. Alternative explanations are considered for these conflicting results.
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DeKruyff, R. H., S. T. Ju, J. Laning, H. Cantor, and M. E. Dorf. "Activation requirements of cloned inducer T cells. III. Need for two stimulator cells in the response of a cloned line to Mls determinants." Journal of Immunology 137, no. 4 (August 15, 1986): 1109–14. http://dx.doi.org/10.4049/jimmunol.137.4.1109.
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Abstract To gain insight into the nature of Mls determinants, we examined the stimulator cells responsible for the activation of inducer T cell clones by Mls determinants. Two types of clones responding to Mls determinants were identified. One type responded to purified B cells, but not to splenic adherent cells (SAC), from mice bearing Mls stimulatory determinants. The other type of Mls-reactive T cell clone, including the representative clone Ly1-N5, demonstrated a vigorous response to unfractionated spleen cells, but showed little or no response to B cells alone or to SAC alone from mice bearing the Mlsa or Mlsd stimulatory determinant. The response of these clones to Mls determinants required stimulation by two cell types. The failure of clone Ly1-N5 to respond to Mlsa-bearing B cells was reversed by the addition of SAC taken from mice bearing the Mlsa allele. In addition, SAC from mice bearing the nonstimulatory Mlsb allele could synergize with B cells from Mlsa-bearing animals. B cells were required to provide the Mlsa determinant, because the combination of Mlsa-bearing SAC and Mlsb-bearing B cells did not activate the clone. The response of clone Ly1-N5 to Mls is restricted by Ia determinants (shared by H-2b, H-2d, and H-2k haplotypes but not by the H-2q haplotype). The permissive H-2 alleles can be present either on the stimulator B cell or on the SAC. The optimal response of the clone was obtained by using B cells bearing Mlsa and the permissive Ia epitopes. However, a significant response of the clone to B cells bearing Mlsa but an inappropriate Ia (Iaq) was also seen in the presence of SAC bearing the nonstimulatory Mlsb allele but the permissive Ia epitopes.
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Speiser, D. E., R. Schneider, H. Hengartner, H. R. MacDonald, and R. M. Zinkernagel. "Clonal deletion of self-reactive T cells in irradiation bone marrow chimeras and neonatally tolerant mice. Evidence for intercellular transfer of Mlsa." Journal of Experimental Medicine 170, no. 2 (August 1, 1989): 595–600. http://dx.doi.org/10.1084/jem.170.2.595.
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Tolerance to Mlsa has been shown to be associated with clonal deletion of cells carrying TCR beta chain variable regions V beta 6 or V beta 8.1 in mice possessing I-E antigens. To evaluate the rules of tolerance induction to Mlsa we prepared irradiation bone marrow chimeras expressing Mlsa or Mlsb and I-E by different cell types. Deletion of V beta 6+, Mlsa-reactive T cells required the presence of Mlsa and I-E products either on bone marrow-derived cells or on irradiated recipient cells. Tolerance was induced when Mlsa and I-E were expressed by distinct cells of the chimera. Also neonatally tolerized mice exhibited depletion of V beta 6+ cells after injection of I-E- Mlsa spleen cells (DBA/1) into newborn I-E+ Mlsb mice (BALB/c x B10.G)F1. These results suggest that the product of the Mlsa locus is soluble and/or may be transferred from cell to cell and bound to I-E antigens. The chimera experiments also showed that tolerance to Mlsa is H-2 allele independent, i.e., is apparently unrestricted. Differentiation of chimeric (H-2d/Mlsa x H-2q/Mlsb)F1 stem cells in either an H-2d or an H-2q thymus revealed that tolerance assessed by absence of V beta 6+ T cells is not dependent on the thymically determined restriction specificity of T cells.
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Click, R. E., G. Cahill, D. Schneider, A. Adelmann, M. M. Azar, J. J. Tarquinio, and A. B. Peck. "Nonresponsiveness to Mlsd in F1 hybrid mice carrying Mlsa and Mlsc genes." Journal of Immunology 139, no. 2 (July 15, 1987): 321–25. http://dx.doi.org/10.4049/jimmunol.139.2.321.
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Abstract Neither the biological function nor a basic understanding of the enigmatic chromosome 1-encoded Mls locus of the mouse has yet been uncovered despite extensive investigations. The present report is a continuation of our genetic analyses of the Mls locus in an attempt to better define the system. Data presented here indicate that in contrast to cells of mice expressing either the Mlsa or Mlsc allele which respond in mixed leukocyte reactions to cells expressing the Mlsd allelic products, cells from (Mlsa X Mlsc)F1-hybrid mice do not. In addition, the nonresponder phenotype appears to segregate as a single autosomal genetic system in backcross animals. These findings fail to support two recently advanced hypotheses: first, that the Mls locus is nonpolymorphic, or second, that the Mls locus controls differential expression of Ia antigenic determinants. Although the mechanism by which a (responder X responder) converts to a nonresponder remains unknown, three models involving gene complementation are discussed.
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Hämmerling, U., M. Toulon, M. Chun, S. Palfree, and M. K. Hoffmann. "Bidirectionality of mixed lymphocyte stimulation (Mls) response. Effects of Mlsb stimulator cells on Mlsa helper cells." Journal of Immunology 140, no. 8 (April 15, 1988): 2543–48. http://dx.doi.org/10.4049/jimmunol.140.8.2543.
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Abstract The activation of BALB/c lymphocytes in the mixed lymphocyte reaction to Mls-disparate APC has been shown to encompass up to 20% of the mature resting helper T lymphocyte population. In addition to these overtly Mls-responsive cells, our studies have revealed a second population that respond to the Mls difference of DBA/2 spleen cells in conjunction with the mitogen Con A. This part of the Mls response is therefore latent. As mitogen and Mls-stimulating effect act in synergy, it is likely that both stimuli act on the same cell, and hence the Mls effect can be regarded as a regulatory interaction between APC and Th cell. By use of congenic BALB.Mlsa mice, the regulatory effect has been mapped to the Mls locus. The regulatory influence has also been demonstrated in DBA/2 Th cells (Mlsa) stimulated simultaneously with mitogen and Mls-disparate (Mlsb) APC, consistently causing inhibition of mitogen-induced proliferation in this reverse Mls direction. This antagonistic effect has also been linked to the Mls locus. We conclude that the Mls reaction governed by the a and b alleles is bidirectional, producing synergy with class II-dependent activation signals in the direction of Mlsa----Mlsb, and antagonism in the direction Mlsb----Mlsa. Both the classical Mls and the reverse Mls effects have been demonstrated at the clonal level. These results are in accord with the previously proposed hypothesis that the Mls molecule serves as a down-regulatory stimulus in the activation of Th cells. Mls responses of Mlsb T cells are explained as the consequence of a diminished down-regulation by Mlsa APC. Conversely, the reverse Mls response described here can be considered a consequence of inordinately high down-regulation of the Mlsa T cell responses by Mlsb APC.
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Ryan, J. J., H. B. LeJeune, J. J. Mond, and F. D. Finkelman. "Genetic analysis of the presentation of minor lymphocyte-stimulating determinants. II. Differing non-MHC control of super-stimulatory and more poorly stimulatory Mls phenotypes." Journal of Immunology 144, no. 7 (April 1, 1990): 2506–17. http://dx.doi.org/10.4049/jimmunol.144.7.2506.
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Abstract Analysis of the capacity of splenocytes from non-prototypic Mlsa or Mlsc mouse strains to stimulate allogeneic H-2k-compatible T cells in a primary Mls-defined MLR provided interesting examples of exceptions to the usually stated characterization of Mlsa and Mlsc determinants as highly stimulatory of weakly stimulatory, respectively. Across the Mlsa barrier, MA/My stimulator cells had a significantly reduced capacity to elicit responder proliferation in comparison with prototypic AKR/J or less well studied C58/J, CE/J, or RF/J splenocytes. Across the Mlsc barrier, a gradient of stimulatory ability was observed with RF/J splenocytes being virtually nonstimulatory, prototypic C3H/HeJ splenocytes having an intermediate capacity, and CE/J and C58/J being highly stimulatory presenters of this non-MHC specificity. The differing capacity of each of these H-2k stimulator cells to elicit unprimed responder cell proliferation across an Mlsa or Mlsc difference correlated with the T cell growth factor activity that was secreted into the MLR supernatants. The super stimulatory form of Mlsc was expressed in an autosomal dominant fashion by (Mlsc poorly stimulatory x Mlsc super-stimulatory)F1 animals, (BALB.K x C58/J)F1 or (RF/J x CE/J)F1. The segregation of Mlsc stimulatory ability among first backcross and F2 animals derived from the former F1 was compatible with a single non-MHC gene controlling the expression and presentation of the super-stimulatory form of Mlsc. The regulatory nature of this gene was indicated by the observation that F1 animals generated from the Mlsc nonprototypic and poorly stimulatory BALB/c parental strain were self-tolerant to the super-stimulatory form of Mlsc. The existence of an Mls specificity other than a and c was suggested by positive non-MHC MLR responses in certain responder/stimulator cell combinations of Mls prototypic and nonprototypic mouse strains.
Dissertations / Theses on the topic "MLSA"
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Cunty, Amandine. "Caractérisation de Pseudomonas syringae pv. actinidiae l’agent responsable de l’émergence d’une épidémie de chancre bactérien du kiwi en France et description de Pseudomonas syringae pv. actinidifoliorum, agent causal de taches foliaires sur kiwi." Thesis, Angers, 2015. http://www.theses.fr/2015ANGE0018/document.
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La bactérie responsable de chancre sur bois, Pseudomonas syringae pv. actinidiae (Psa), a causé trois épidémies depuis les années 1980 et se décline en trois biovars. La plus récente et dévastatrice (causée par Psa biovar 3), a été détectée pour la première fois en 2008 en Italie et s’est rapidement répandue dans la majorité des pays producteurs de kiwi, dont en France en 2010. Nous avons analysé la diversité de 280 souches de P. syringae isolées de kiwi en France. La caractérisation biologique et l’analyse phylogénétique des souches par MLSA ont révélé que les biovars 1, 2 et 3 appartenaient à une même lignée génétique, groupant également P. s. pv. theae. Les souches de biovar 4 constituent un ensemble de 4 lignées génétiques distinctes qui ont été rassemblées au sein d’un nouveau pathovar (Pseudomonas syringae pv. actinidifoliorum (Psaf)). Ces souches sont caractérisées par une pathogénie réduite (taches foliaires mais pas de chancre). Cette nouvelle classification permet une meilleure gestion des épidémies de chancre bactérien du kiwi. Le développement d’un schéma MLVA composé de 11 VNTRs a permis d’étudier la structuration génétique de populations de Psa biovar 3, de révéler de la diversité au sein de ce pathovar et d’identifier l’origine italienne de l’épidémie en France. Le séquençage du génome de cinq souches de Psaf et la comparaison de ces séquences avec celles d’autres génomes de Psa et Psaf, disponibles sur NCBI, a permis le développement d’un nouvel outil de détection par PCR temps réel, plus spécifique de chaque biovar de Psa et de Psaf. La MLVA et la PCR temps réel développées ici contribueront à l’amélioration de la surveillance de Psa dans le mondeThe causal agent of bacterial canker, Pseudomonas syringae pv. actinidiae (Psa),has been responsible ofthree epidemics since 1980’s.Psa is divided in three biovars. The most recent and severe outbreak (causedby Psa biovar 3) was detected for the first time in Italy in 2008. It has spread very quickly in the main kiwifruit producing countries, as in France in 2010. We analyzed the diversity of 280 strains of P. syringae isolated fromkiwifruit in France. The biological characterization and the phylogenetic analysis of the strains by MLSArevealed that the biovars 1, 2 and 3 belong to the same genetic lineage, which include P. s. pv. theae, as well.The biovar 4 strains, which are structured in 4 distinct genetic lineages, have been grouped in a new pathovar(Pseudomonas syringae pv. actinidifoliorum (Psaf)). These strains are characterized by a low virulence (onlyspots on leaves and no canker on wood). This new classification help with the management of the bacterialkiwifruit canker outbreaks. The development of an MLVA scheme composed of 11 VNTRs allowed to studythe genetic structuration of Psa biovar 3 populations, to reveal the diversity within this pathovar and to identifythe Italian origin of the epidemic in France. The genome sequencing of five Psaf strains and the comparisonbetween these sequences and those of Psa and Psaf genomes already available on NCBI, allowed thedevelopment of a new detection tool by real-time PCR, specific of each Psa biovar and of Psaf. The MLVA andthe real-time PCR based detection technique developed here will contribute to the improvement of the monitoringof kiwifruit bacterial canker around the world
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Afonso, Mendes-Yahiaoui Noura. "Épidémiologie moléculaire du complexe d’espèces Ralstonia solanacearum, agent du flétrissement bactérien, dans les îles du Sud-Ouest de l’océan Indien." Thesis, La Réunion, 2018. http://www.theses.fr/2018LARE0014.
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Dans les îles du sud-ouest de l'océan Indien (SOOI) (Comores, Maurice, Mayotte, Réunion, Rodrigues et Seychelles), le flétrissement bactérien causé par le complexe d'espèces Ralstonia solanacearum (ceRs) est une phytobactériose considérée comme l'une des plus nuisibles pour les productions vivrières ou d'exportation. Les travaux de thèse présentés dans ce manuscrit avaient pour principal objectif l'exploration du niveau et de la distribution de la diversité génétique du ce Rs et de la structure génétique de ses populations dans le SOOI. Nous avons mené de vastes campagnes d'échantillonnage qui ont permis de constituer une large collection de 1704 isolats, principalement à partir de Solanacées (tomate, pomme de terre, piment, aubergine, poivron) et de géranium rosat. L'assignation phylogénétique des isolats a montré une très forte prévalence du phylotype I (88 %), qui est distribué dans chaque île du SOOI, tandis que les phylotypes II (9 %) et III (3 %) ne sont trouvés qu'à La Réunion. Deux souches de phylotype IV ont par ailleurs été signalées à l'île Maurice, représentant le premier rapport de ce groupe phylogénétique dans le SOOI. Une approche phylogénétique et de génotypage (MLSA/MLST) basée sur l'analyse de séquences de 6 gènes de ménage et 1 gène associé à la virulence (egl) a permis de révéler les relations génétiques entre 145 souches représentatives (diversité géographique + hôte d'isolement) du SOOI et 90 souches mondiales de référence. Le développement et l'application d'un schéma MLVA basé sur 17 séquences répétées en tandem (VNTR) sur près de 1300 souches a permis de révéler que les populations de phylotype I sont organisées en complexes clonaux dans le SOOI et que le niveau de diversité génétique est très contrasté selon les îles, Maurice présentant la plus forte diversité génétique. Un résultat majeur de cette thèse est la mise en évidence du déploiement d’une lignée génétique (sequevar I-31 ; STI-13 ; MT-035), surreprésentée dans les îles du SOOI, qui pourrait avoir été introduite via du matériel végétal contaminé depuis l'Afrique de Sud ou l’Afrique de l'Ouest. Nos études préliminaires montrent que l'haplotype majoritaire MT-035 (i) est le probable haplotype fondateur du complexe clonal le plus prévalent dans le SOOI, (ii) présente un pouvoir pathogène élevé (large gamme d'hôtes comprenant des plantes cultivées et des adventices, et forte agressivité sur Solanacées) et (iii) possède une forte aptitude à la compétition dans l'environnement via la production de bactériocines. Ces travaux permettront in fine de renforcer l'épidémiosurveillance et orienter les stratégies de lutte vis-à-vis de cet agent phytopathogène, notamment via le déploiement de cultivars résistantsIn the southwest Indian Ocean (SWIO) islands (Comoros, Mauritius, Mayotte, Réunion, Rodrigues and Seychelles), bacterial wilt caused by the Ralstonia solanacearum species complex (Rssc) is considered one of the most harmful plant disease for food crops or export. The main objective of this work presented in this manuscript was to explore the level and the distribution of the genetic diversity of Rssc and the genetic structure of its populations in SWIO. We conducted extensive sampling campaigns that resulted in a large collection of 1704 isolates, mainly from Solanaceae (tomato, potato, chilli, eggplant, pepper) and geranium rosat. The phylogenetic assignment of the isolates showed a very high prevalence of phylotype I (88 %), which is distributed in each island of the SWIO, while phylotypes II (9 %) and III (3 %) are found only in Réunion. Two phylotype IV strains have also been reported in Mauritius, representing the first report of this phylogenetic group in SWIO. A phylogenetic and genotyping approach (MLSA/MLST) based on sequence analysis of 6 housekeeping genes and 1 gene associated with virulence (egl) revealed the genetic relationships between 145 representative SWIO strains (geographic diversity + host) and 90 global reference strains. The development and application of MLVA scheme based on 17 variable number of tandem repeat sequences (VNTR) on nearly 1300 strains revealed that phylotype I populations are organized into clonal complexes in SWIO and that the level of genetic diversity is highly contrasted according to the islands, with Mauritius having the highest genetic diversity. This work highlights the deployment of a genetic lineage (Sequevar I-31, STI-13, MT-035), overrepresented in SWIO islands, which could have been introduced via contaminated plant material from South Africa or West Africa. Our preliminary studies show that the main haplotype MT-035 (i) is the probable founding haplotype of the most prevalent clonal complex in SWIO, (ii) has high pathogenicity (wide range of hosts including cultivated plants and weeds, and high aggressiveness on Solanaceae) and (iii) has a strong ability to compete in the environment via the production of bacteriocins. This work will ultimately strengthen epidemiosurveillance and guide control strategies of this plant pathogen, including the deployment of resistant cultivars
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Ramos, Patrícia Locosque. "Taxonomia do gênero Stenotrophomonas através de Multi Locus Sequence Analysis (MLSA)." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-26012012-170618/.
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As Stenotrophomonas são comumente encontradas no trato respiratório de pacientes com doenças pulmonares crônicas e também na rizosfera de plantas. Esse gênero apresenta resistência a diversos antibióticos, promove o crescimento de plantas e algumas espécies apresentam a capacidade de fixar o nitrogênio atmosférico. O Multi Locus Sequence Analysis (MLSA) é uma metodologia baseada em genes constitutivos para definição e alocação taxonômica de novas espécies. O objetivo geral do presente trabalho foi caracterizar taxonomicamente uma coleção ampla de Stenotrophomonas composta por isolados endófitos, linhagens-tipo e de referência. Para tanto, foi estabelecido um sistema de classificação e identificação de Stenotrophomonas por meio de MLSA. Foi possível através da metodologia de MLSA definir 9 novas espécies, detectar a presença de um novo gênero e estabelecer um sistema online de taxonomia para Stenotrophomonas.The genus Stenotrophomonas is found in the respiratory treatment of patients with chronic pulmonary and also in the rizhosfera of plants. It presents resistance to several antibiotics, promotes the growth of plants and some species present the ability to fix atmospheric nitrogen. The Multi Locus Sequence Analysis (MLSA) is a methodology based on constitutive genes for definition and taxonomic allocation of new species. The general objective of the present work was to characterize a wide collection constituted by Stenotrophomonas from isolated endophytic, type and reference strains. In such a way, a system of classification and identification of Stenotrophomonas by means of MLSA was established. It was possible through the MLSA methodology to define 9 new species, to detect the presence of a new genus and to establish an online system for Stenotrophomonas taxonomy.
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Rahman, Mohammad Shamsur. "Molecular Characterization of Vibrio spp. in Shellfish using Multilocus Sequence Analysis." Doctoral thesis, Università degli studi di Padova, 2013. http://hdl.handle.net/11577/3423397.
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Fish and shellfish are the second largest source of protein for man after meat products and in some countries, such as Japan, constitute the main source of protein. In recent years, indigenous marine bacteria were responsible for 20% of all diseases and 99% of fatalities associated with the consumption of fishery products (Cozzi and Ciccaglioni, 2005). Among these, the main causes of diseases are some species of Vibrionaceae, which can cause gastroenteritis, especially after the consumption of fish products, raw or undercooked, from temperate and warm Seas. Vibrio is a very diverse genus responsible of different human and animal diseases. The accurate identification of Vibrio spp. is very important to assess the risks in regard to public health and diseases of aquatic organisms. Thus, analyses of population structure for a reliable bacteria characterization in different ecological environments are necessary. In particular, sequence based identification methods are preferable over classical biochemical approaches. In this study, a Multilocus Sequence Analysis scheme was developed on the basis of four housekeeping genes (gyrB, pyrH, recA and atpA) applied to 3 set of Vibrio strains (154 isolates from mollusks in 2007; 92 isolates from crustacean and 22 isolates form mollusks in 2011 ) and 29 reference strains. Concatenated sequences were used for phylogenetic and population analyses and the results were compared with biochemical identification tests (Alsina’s scheme). The phylogeny provided a good clustering, showing 15 clusters and 6 single strains in the first set of strains; 10 clusters and 4 singletons in second set; and 4 clusters and 4 singletons in the third set of strains. The population analysis highlighted 17 subpopulations in first set and 12 subpopulations in second set of Vibrio strains that were well supported by phylogeny with few exceptions. Overestimations of risk due to biochemical identification have been found for V. parahaemolyticus and V. vulnificus and no V. cholerae strains were identified. The false negative results of Alsina’s scheme need to be considered as it might represent a potential public health risk. These findings highlight the need of a rapid and robust identification of shellfish associated foodborne Vibrio spp. and, in addition, the connection of environmental information to genetic data could enhance the Vibrio spp. characterization.
Second part of the study gave special emphasis on the species Vibrio parahaemolyticus, a potential emerging pathogen in the North Adriatic Sea. Pathogenic strains of V. parahaemolyticus represent one of the main causes of foodborne gastroenteritis, especially in Asia and USA (Su and Liu, 2007). The study examined 160 strains isolated from 43 edible mollusks sampled between January and October 2011, identified biochemically as Vibrio parahaemolyticus in the Food Microbiology laboratory of Istituto Zooprofilattico (IZSVe). The strains were characterized for the presence of genes typical for the species Vibrio parahaemolyticus (toxR and tlh) in order to confirm the biochemical identification and virulence genes (tdh and trh). Dubious or misidentified strains were subjected to MLSA (Multilocus Sequence Analysis) by evaluating the sequence of 4 housekeeping genes. Finally, 102 Vibrio parahaemolyticus strains were analyzed by the MLST protocol: portions of 7 genes (dnaE, gyrB, recA, dtdS, pntA, pyrC and tnaA) were sequenced and concatenated. With the obtained MLST information phylogenetic analyses were performed to determine the relationships between the different strains isolated in this study and secondly, any links with worldwide isolates. All strains of V. parahaemolyticus were found positive for toxR and tlh, no strain was tdh positive, while 6 strains had the positive reaction for trh gene. 72 non-redundant (63 new) STs were identified. A total of 54 clonal groups were highlighted, in which 17 are clonal complex. Two distinct populations of V. parahaemolyticus were marked by phylogenetic, structure and recombination analyses. The main result is that despite the high percentage of positive samples for V. parahaemolyticus, only a few strains were potentially pathogenic for humans. However, some possible genetic relationships with strains can emerge from a comparative study with the STs in the world database. The characterization could help to identify suspect genotypes and thus clarify the dynamics of the spread of potentially pathogenic strains.I prodotti ittici sono la seconda fonte di proteine per l’alimentazione dell'uomo e in alcuni Paesi, quali il Giappone, ne costituiscono la principale fonte. Negli ultimi anni, i batteri marini della flora indigena sono risultati responsabili del 20% delle malattie nell’uomo e del 99% dei decessi derivati dal consumo dei prodotti della pesca. Tra questi, le principali cause di malattie sono da ascrivere ad alcune specie di Vibrionaceae in particolare al genere Vibrio, che possono causare gastroenteriti, soprattutto a seguito di consumo di prodotti crudi o poco cotti, provenienti da mari temperati e caldi. L'identificazione accurata dei batteri appartenenti al genere Vibrio risulta quindi molto importante per valutare i rischi in materia di salute pubblica e per l’identificazione puntuale delle malattie degli organismi acquatici. Risulta quindi necessario sviluppare ed applicare metodi affidabili che possano caratterizzare le specie di vibrioni residenti nei prodotti commercializzati (es. molluschi bivalivi e crostacei). In particolare, i metodi di identificazione basati sull’analisi delle sequenze geniche sono preferibili rispetto ai classici approcci biochimici. In questo studio è stato sviluppato uno schema MLSA Multilocus Sequence Analysis impiegando quattro geni housekeeping (gyrB, pyrH, recA e atpA), tale schema è stato valutato in 3 differenti data set di ceppi (154 isolati da molluschi nel 2007; 92 isolati di crostacei e 22 da molluschi isolati nel 2011) e 29 ceppi di riferimento e Type strain. I concatenameri sono stati utilizzati per le analisi filogenetiche e per gli studi di popolazione dei Vibrio isolati, confrontando al contempo i risultati dell’identificazione di specie con i test biochimici (schema di Alsina) applicati di routine all’identificazione dei Vibrioni. L’analisi della struttura di popolazione mediante il software STRUCTURE e l’analisi filogenetica risultano concordi nell’assegnazione dei principali taxa evidenziando una simile clusterizzazione dei gruppi in sottopopolazioni. Al contrario, il confronto tra la classificazione mediante MLSA e i test biochimici ha evidenziato varie discrepanze tra le quali una sovrastima di ceppi classificati come V. parahaemolyticus e V. vulnificus. Al contempo alcuni ceppi di V. parahaemolyticus sono risultati falsi negativi. Questi riscontri potrebbero indicare una limitazione dell’utilizzo delle prove biochimiche adottate di routine alla classificazione dei Vibrio potenzialmente patogeni per l’uomo e tale riscontro si riflette in un possibile rischio per la salute pubblica. La seconda parte dello studio ha considerato nel dettaglio la caratterizzazione molecolare di V. parahaemolyticus. Questo batterio è oggi un patogeno emergente derivato dal consumo di prodotti ittici, infatti ceppi patogeni di V. parahaemolyticus rappresentano una delle principali cause di gastroenterite di origine alimentare, in particolare in alcuni paesi dell’Asia e negli Stati Uniti. Questo batterio, a causa di mutamenti ambientali e delle abitudini dei consumatori (consumo di prodotti crudi provenienti da aree contaminate) potrebbe rappresentare una problematica igienico sanitaria anche nel Mare Adriatico settentrionale. In questa parte dello studio sono stati esaminati 160 ceppi isolati da 43 campioni di molluschi commestibili campionati tra gennaio e ottobre 2011 e identificati a livello biochimico dal laboratorio di microbiologia dell’Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe). I ceppi sono stati caratterizzati per la presenza dei marker genici specie specifici (toxR e tlh - Vibrio parahaemolyticus) per confermare l'identificazione biochimica e quindi dei geni per i fattori di virulenza (tdh e trh). I ceppi risultati di dubbia o errata identificazione sono stati sottoposti a MLSA (Multilocus Sequence Analysis) valutando la sequenza dei 4 geni housekeeping. Infine tutti i ceppi risultati Vibrio parahaemolyticus (n° 102) sono stati analizzati mediante il protocollo MLST (http://pubmlst.org/vparahaemolyticus/.). Lo schema prevede l’analisi di sequenza di 7 porzioni geniche (dnaE, gyrB, recA, dtdS, pntA, pyrC and tnaA). I concatenameri ottenuti sono stati utilizzati nelle analisi bioinformatiche di popolazione per determinare le relazioni tra i diversi ceppi isolati in questo studio e, in seconda battuta, per evidenziare eventuali collegamenti con ceppi isolati a livello mondiale. Per quanto concerne i fattori di virulenza tutti i ceppi di V. parahaemolyticus sono risultati tdh negativi, mentre 6 ceppi hanno presentato la positività per il gene trh. Nel complesso sono stati identificati 72 profili ST non ridondanti, 63 dei quali di nuova attribuzione rispetto al database on-line. L’analisi clonale dell’intero database ha evidenziato la presenza di 54 gruppi clonali dei quali 17 risultano essere ascritti entro un complesso clonale. Le analisi di popolazione nel loro complesso delineano la presenza di due gruppi principali di V. parahaemolyticus. Dallo studio emerge che, nonostante sia stata riscontrata un’alta percentuale di campioni positivi per V. parahaemolyticus, solo pochi ceppi risultano potenzialmente patogeni per l'uomo. Tuttavia, alcune possibili relazioni genetiche con ceppi isolati da casi di gastroenteriti in varie parti del mondo emergono dallo studio comparativo con il database on-line. La caratterizzazione molecolare potrebbe aiutare a individuare genotipi sospetti e quindi chiarire la dinamica della diffusione di ceppi potenzialmente patogeni.
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Gomes, Catarina dos Santos Teles. "Identification and phylogenetic characterization of Ralstonia solanacearum species complex isolates collected in Portugal." Master's thesis, ISA, 2017. http://hdl.handle.net/10400.5/15089.
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Helene, Luisa Caroline Ferraz. "Diversidade entre estirpes do gênero Bradyrhizobium avaliada por Multilocus Sequence Analysis (MLSA) e análise polifásica." Universidade Estadual de Londrina. Centro de Ciências Biológicas. Programa de Pós-Graduação em Microbiologia, 2015. http://www.bibliotecadigital.uel.br/document/?code=vtls000201471.
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Bactérias simbióticas fixadoras de nitrogênio, também denominadas popularmente de rizóbios, têm grande relevância agronômica, pois fornecem quantidades significativas de nitrogênio para as plantas e colaboram para a recuperação de solos e ambientes degradados. Nos últimos anos, com o avanço das técnicas moleculares, diversos trabalhos têm demonstrado que essas bactérias apresentam uma elevada diversidade genética, resultando em reclassificações taxonômicas e na descrição de novas espécies. Apesar de o gene ribossomal 16S (16S RNAr) ainda ser utilizado em análises filogenéticas de procariotos, sua alta conservação não é capaz de revelar diferenças entre espécies de diversos gêneros, incluindo Bradyrhizobium. Outras metodologias, como o MLSA (Multilocus Sequence Analysis), estão sendo utilizadas para elucidar esses casos, com bons resultados. Neste trabalho, 15 estirpes de Bradyrhizobium sem posicionamento taxonômico claro foram utilizadas em estudos de filogenia e taxonomia com base na técnica de MLSA e análise polifásica. Para isso, três genes housekeeping?glnII, gyrB e recA?foram sequenciados e suas sequências foram concatenadas e utilizadas para a construção de uma árvore filogenética. Das 15 estirpes, sete agruparam com a espécie Bradyrhizobium pachyrhizi, enquanto as SEMIAS 6159, 6405 e 6408 ocuparam posições isoladas, e dois grupos (SEMIAS 6399 e 6404, e SEMIAS 690, 6387 e 6428) não apresentaram similaridade filogenética com nenhuma espécie descrita. Esses grupos merecem estudos mais detalhados, pois apresentam grande potencial de representarem espécies novas. As estirpes SEMIA 690 (isolada de Centrosema pubescens), SEMIA 6387 e SEMIA 6428, (isoladas de Acacia spp.) foram selecionadas para análises complementares, visando à descrição de uma nova espécie, tendo início um estudo polifásico (análises genéticas, fenotípicas e filogenéticas). O perfil de BOX-PCR agrupou as estirpes com mais de 73% de similaridade entre si, e inferiores a 66% com as espécies de Bradyrhizobium já descritas. Os ácidos graxos identificados como principais na SEMIA 690 foram a fração molecular total 8 e a fração individual C19:0 ciclo ?8c. A SEMIA 690 apresentou identidade nucleotídica média do genoma inferior a 91% com todas as estirpes tipo das espécies relacionadas. O conteúdo G + C da SEMIA 690 foi determinado em 63,46%. Os testes fenotípicos (fontes de carbono utilizadas, características morfológicas, condições de crescimento) foram congruentes entre as estirpes representantes da provável nova espécie. Os resultados obtidos confirmam que a técnica de MLSA é eficiente para estudos filogenéticos de procariotos, mostrando ser uma ferramenta segura e rápida de análise da diversidade dos gêneros e identificação de possíveis novas espécies. Os resultados suportam a descrição de uma nova espécie de Bradyrhizobium.Symbiotic nitrogen-fixing bacteria, also commonly called rhizobia, have great agronomic relevance because they can provide significant amounts of nitrogen to plants and help in the recovery of soils and degraded environments. In recent years, with the advances in molecular techniques, several studies have shown that these bacteria have a high level of genetic diversity, resulting in taxonomic reclassifications and description of new species. Although the 16S ribosomal genes (16S rRNA) are still used in phylogenetic analyses of prokaryotes, their high conservation do not allow to reveal differences between species of several genera, including Bradyrhizobium. Other methodologies such as the MLSA (Multilocus Sequence Analysis) are being used to elucidate these cases, with good results. In this study, 15 strains of Bradyrhizobium without clear taxonomic position were used in studies of phylogeny and taxonomy based on the MLSA technique. Tree housekeeping genes?glnII, gyrB and recA?were sequenced and their sequences were concatenated and used for the construction of a phylogenetic tree. Of the 15 strains, seven grouped with the species Bradyrhizobium pachyrhizi, while the SEMIAS 6159, 6405 and 6408 strains occupied isolated locations, and two groups (SEMIAS 6399 and 6404, and SEMIAS 690, 6387 and 6428) showed no genetic similarity with any described species. These groups deserve more detailed studies, since they have great potential to represent new species. Strains SEMIA 690 (isolated from Centrosema pubescens), SEMIA 6387 and SEMIA 6428, (isolated from Acacia spp.) were selected for a polyphasic study (genetic, phenotypic and phylogenetic analyzes) aimed at the description of a new species. The BOX-PCR profile clustered the strains with more than 73% of similarity, and less than 66% with closer Bradyrhizobium described species. Fatty acids identified as key in SEMIA 690 were summed features 8 and individual fraction C19:0 cycle ?8c. The genomic analysis of ANI (average nucleotide identity) between SEMIA 690 and closer type strains of Bradyrhizobium species was less than 91%. The G + C content from SEMIA 690 was of 63.46%. The phenotypic tests (carbon sources used, morphological characteristics, growth conditions) were congruent among the strains representative of the new putative species. The results confirm that the MLSA technique is efficient for phylogenetic studies of prokaryotes, representing a reliable and fast tool to analyze the diversity of genes and to identify possible new rhizobial species. The results obtained in this study also support the description of a new species of Bradyrhizobium.
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Menezes, Cláudia Beatriz Afonso de. "Análise da diversidade genética por MLSA e avaliação da atividade antitumoral de linhagens de Chromobacterium sp." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-17042009-115257/.
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A diversidade genética dos isolados de Chromobacterium sp. foi avaliada por Multilocus sequence analysis com base nas análises dos genes conservados rpoA, lepA, gyrB, fusA e rRNA 16S. A análise do gene rRNA 16S e MLSA agrupou os isolados no gênero Chromobacterium, entretanto, cinco dos isolados estão distantes filogeneticamente das linhagens tipo, C. violaceum e C. subtsugae, sugerindo duas novas espécies. Os extratos brutos, obtidos por soxhlet, dos isolados de Chromobacterium sp., testados em ensaios in vitro em células tumorais humanas, apresentaram atividades antitumorais potenciais e seletivas para determinadas linhagens celulares. Os extratos brutos e frações foram analisados por HPLC-DAD para avaliação da presença ou ausência da violaceína. Além disso, outros metábólitos secundários que não a violaceína podem estar relacionados à atividade antitumoral.The genetic diversity of strains of Chromobacterium sp was evaluated by Multilocus sequence analysis (MLSA) based on the analysis of conserved genes rpoA, recA, lepA, gyrB, fusA and rRNA 16S. The analysis of 16S ribosomal RNA gene grouped all isolates in the genus Chromobacterium, however, the five isolates are phylogenetically distant of type strain C. violaceum and C. subtsugae, suggesting new species. The crude extracts of the isolates from Chromobacterium sp., obtained by soxlhlet, evaluated in vitro tests on human tumor cells, showed potential and selective antitumor activities for certain cell lines. In addition, other secondary metabolites than violacein may be related with antitumor activity.
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Delamuta, Jakeline Renata Marçon. "Taxonomia e filogenia de estirpes de Bradyrhizobium utilizados em inoculantes comerciais brasileiros pela metodologia de MLSA (Multilocus Sequence Analysis)." Universidade Estadual de Londrina.Centro de Ciências Biológicas. Programa de Pós-Graduação em Microbiologia, 2011. http://www.bibliotecadigital.uel.br/document/?code=vtls000164000.
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O gênero Bradyrhizobium compreende um diverso grupo de bactérias com capacidade de fazer simbiose com plantas da família Leguminosae. Estudos com Bradyrhizobium têm demonstrado uma elevada diversidade genética, principalmente com estirpes isoladas em regiões tropicais. A análise do gene ribossomal 16S (16S RNAr) tem sido a principal ferramenta utilizada em estudos de diversidade, taxonomia e também de filogenia bacteriana, mas devido ao alto nível de conservação da sequência nucleotídica deste gene, as informações obtidas podem limitar a determinação de novas espécies, como é o caso do gênero Bradyrhizobium. Desse modo, a metodologia de MLSA (Multilocus Sequence Analysis) tem sido recentemente proposta como uma ferramenta complementar em estudos de filogenia e taxonomia, bem como de diversidade em procariotos. Prévios estudos com as estirpes de Bradyrhizobium utilizadas neste trabalho demonstraram elevada diversidade genética do gene 16S RNAr com a hipótese de possíveis novas espécies. Utilizando a metodologia de MLSA, o objetivo do presente trabalho foi elucidar as relações filogenéticas de 12 estirpes de Bradyrhizobium e, assim, determinar sua posição taxonômica. Além do gene 16S RNAr, outros cinco genes housekeeping foram utilizados (atpD, glnII, gyrB, recA e rpoB). A árvore filogenética resultante da análise do MLSA dividiu as estirpes em dois grandes grupos com subgrupos bem definidos, sugerindo a descrição de novas espécies. O primeiro grande grupo incluiu as estirpes tipo de B. japonicum, B. liaoningense, B. yuanmingense, B. betae e B. canariense e o segundo grande grupo incluiu a estirpe tipo de B. elkanii USDA 76T. Uma grande diversidade foi observada na árvore filogenética do gene atpD, com a formação de um terceiro grande grupo formado por 4 estirpes e as estirpes tipo de B. betae LMG 21987T e B. liaoningense LMG 18230T. Os resultados obtidos demonstram uma elevada diversidade genética de Bradyrhizobium utilizados como inoculantes comerciais brasileiros, confirmando a existência de possíveis novas espécies. Portanto, a técnica de MLSA demonstrou ser um método rápido e eficaz em estudos filogenético e taxonômico de Bradyrhizobium.The genus Bradyrhizobium encompasses a variety of bacteria that can live in symbiosis with plants of the family Leguminosae. Studies with Bradyrhizobium strains have indicated a high genetic diversity, mainly with strains belonging tropical regions. The analysis of the 16S ribosomal gene (16S rRNA) has been the main tool in studies of phylogeny, taxonomy and also diversity of bacteria, but due to the high conservation of the nucleotide sequence, the information obtained may limit the determination of new species, such as occurs in the genus Bradyrhizobium. Thus, MLSA (Multilocus Sequence Analysis) method has been recently proposed as a strategy to determine the diversity in studies of taxonomy and phylogeny of prokaryotes. Previous studies using the 16S rRNA showed high diversity in the Bradyrhizobium strains of this work and the suggestion of the new species has been proposed. Using the MLSA method, the aim of this work was to elucidate the phylogenetic relationships and taxonomic positions of 12 Bradyrhizobium strains. In addition of the 16S rRNA gene, five housekeeping genes (atpD, glnII, gyrB, recA and rpoB) were used in the analysis. The phylogenetic tree resulting from analysis of MLSA divided the strains in two great groups with subgroups well defined, suggesting the description of new species. The first great group included the type strains of B. japonicum, B. liaoningense, B. yuanmingense, B. betae and B. canariense, and the second great group included the type strain of B. elkanii USDA 76T. The greatest variability was observed in the phylogenetic tree of atpD gene, and a third group formed by four strains and B. betae LMG 21987T and B. liaoningense LMG 18230T was observed. The results obtained showed a high genetic diversity of Bradyrhizobium strains used in commercial inoculants in Brazil and confirms the presence of new species. Thus, the MLSA method is a rapid and reliable tool to provide information about phylogenetic relationships and identify Bradyrhizobium strains potentially representative of novel species.
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Bautista, Guerrero Hector Hugo. "Phylogenomic study and specific diversity depiction of frankia genus : special focus on non-cultivable strains and ecological implications." Phd thesis, Université Claude Bernard - Lyon I, 2010. http://tel.archives-ouvertes.fr/tel-00838567.
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The depiction of the phylogenetic structure of the genus Frankia is still troublesome and the evolutionary forces guiding the speciation, dispersion and diversity are not well documented. The current phylogeny has been defined on the basis of the comparative analysis of the 16S rRNA gene sequence while de genomospecies definition is still subjected to DNA-DNA hybridization trials. Aiming to bring to light the genomic variability of the genus and its translation into the ecological and specific diversity, our studies consisted in, firstly, evaluating the specific diversity within the genus and the ability of the Amplified Fragment Length Polymorphism technique (AFLP) to describe Frankia genomospecies and their phylogenetic liaisons. Moreover this technique was also tested for the study of the non isolated Frankia directly in the actinorhizal nodules. Secondly, we defined a MLSA (Multilocus Sequence analysis) scheme which allowed us to establish a phylogeny of the genus by using a hundred of strains and for the first time to describe the phylogenetic divergence of a group of non culturable strains exhibiting the particular ability (phenotype) of sporulating in planta (Sp+). The Sp+ strains are distributed into two divergent clades whose structure is highly correlated to the host genotype. The importance of genetic markers having impact over ecology of the strains has been revised. In this regard we have studied the phylogenetic analysis and the occurrence of the genetic components for the siderophore production and of the sodF gene in Frankia.
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Menezes, Cláudia Beatriz Afonso de 1977. "Taxonomia polifásica com ênfase em Multilocus Sequence Analysis (MLSA) e bioprospecção de compostos bioativos de actinomicetos isolados de ambiente marinho." [s.n.], 2015. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316710.
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Orientador: Fabiana Fantinatti GarbogginiTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: O ambiente marinho representa uma importante fonte de diversidade biológica com grande potencial para descoberta de novos metabólitos secundários biologicamente ativos. Dentro desse ambiente, pode-se destacar os actinomicetos marinhos, cujos estudos podem contribuir para a melhor compreensão de suas funções ecológicas e para seu uso como uma fonte importante de novos metabólitos. A taxonomia dos actinomicetos é bastante complexa e a metodologia de MLSA, ferramenta alternativa em estudos de sistemática microbiana, pode ser uma técnica importante na caracterização de actinomicetos. Novos metabólitos secundários tem sido isolados de actinomicetos marinhos, sendo as atividades antibacteriana e anticâncer as principais descritas,porém pouco se conhece sobre a atividade antiviral deste grupo de micro-organimos. Neste contexto, o presente trabalho teve por objetivo avaliar a diversidade de actinomicetos associados ao ambiente marinho, utilizando uma abordagem polifásica, associada à avaliação das atividades antimicrobiana e antiviral destas bactérias. No total, foram obtidos 579 isolados de bactérias oriundos de macro-organismos marinhos coletados no litoral norte do Estado de São Paulo, Brasil. Desses, 72 foram identificados por análise de sequência do gene RNA ribossomal 16S, como actinomicetos, e nove isolados foram descritos como novas espécies de actinobactérias pertencentes aos gêneros Gordonia (B204), Marmoricola (B374), Williamsia (B138, B375 e B452), Serinicoccus (B736), Kineococcus (B366), Knoellia (B175) e Janibacter (B742). A caracterização polifásica dessas novas espécies de actinobactérias foi realizada pela técnica de hibridação DNA-DNA, Multilocus Sequence Analysis (MLSA) utilizando genes conservados (rpoB, rpoA, gyrB, recA e trpB), análise de perfil de ácidos graxos e microscopia eletrônica. A caracterização dos isolados foi complementada por testes fisiológicos e quimiotaxonômicos, tais como a determinação do conteúdo de GC, lipídios polares, menaquinonas, testes de utilização de fontes de carbono, atividade enzimática, degradação de compostos e tolerância a antibióticos, pH e temperatura. Quanto ao potencial biotecnológico dos 72 isolados de actinobactérias avaliados, 16 isolados apresentaram potencial antimicrobiano e 13 potencial antiviral. Os extratos dos isolados B175 (CIM = 1 mg/mL), B375 (CIM = 2 mg/mL), B138 (CIM = 1 mg/mL) e B366 (CIM = 2 mg/mL) apresentaram atividade antimicrobiana frente a Staphylococcus aureus ATCC 6538. O extrato do isolado B374 apresentou atividade antiviral frente ao vírus Metapneumovírus aviário (aMPV), os isolados B366 e B742, frente ao herpes vírus simplex do tipo 1 (HSV-1), os isolados B138 e B452 frente ao vírus Calicivírus Felino (FCV) e o isolado B204 frente ao vírus da diarréia viral bovina (BVDV). A partir deste trabalho, pode-se concluir que existe grande diversidade de micro-organismos marinhos a ser descoberta e explorada, como fonte de novas espécies e compostos com potencial biotecnológico
Abstract: O ambiente marinho representa uma importante fonte de diversidade biológica com grande potencial para descoberta de novos metabólitos secundários biologicamente ativos. Dentro desse ambiente, pode-se destacar os actinomicetos marinhos, cujos estudos podem contribuir para a melhor compreensão de suas funções ecológicas e para seu uso como uma fonte importante de novos metabólitos. A taxonomia dos actinomicetos é bastante complexa e a metodologia de MLSA, ferramenta alternativa em estudos de sistemática microbiana, pode ser uma técnica importante na caracterização de actinomicetos. Novos metabólitos secundários tem sido isolados de actinomicetos marinhos, sendo as atividades antibacteriana e anticâncer as principais descritas,porém pouco se conhece sobre a atividade antiviral deste grupo de micro-organimos. Neste contexto, o presente trabalho teve por objetivo avaliar a diversidade de actinomicetos associados ao ambiente marinho, utilizando uma abordagem polifásica, associada à avaliação das atividades antimicrobiana e antiviral destas bactérias. No total, foram obtidos 579 isolados de bactérias oriundos de macro-organismos marinhos coletados no litoral norte do Estado de São Paulo, Brasil. Desses, 72 foram identificados por análise de sequência do gene RNA ribossomal 16S, como actinomicetos, e nove isolados foram descritos como novas espécies de actinobactérias pertencentes aos gêneros Gordonia (B204), Marmoricola (B374), Williamsia (B138, B375 e B452), Serinicoccus (B736), Kineococcus (B366), Knoellia (B175) e Janibacter (B742). A caracterização polifásica dessas novas espécies de actinobactérias foi realizada pela técnica de hibridação DNA-DNA, Multilocus Sequence Analysis (MLSA) utilizando genes conservados (rpoB, rpoA, gyrB, recA e trpB), análise de perfil de ácidos graxos e microscopia eletrônica. A caracterização dos isolados foi complementada por testes fisiológicos e quimiotaxonômicos, tais como a determinação do conteúdo de GC, lipídios polares, menaquinonas, testes de utilização de fontes de carbono, atividade enzimática, degradação de compostos e tolerância a antibióticos, pH e temperatura. Quanto ao potencial biotecnológico dos 72 isolados de actinobactérias avaliados, 16 isolados apresentaram potencial antimicrobiano e 13 potencial antiviral. Os extratos dos isolados B175 (CIM = 1 mg/mL), B375 (CIM = 2 mg/mL), B138 (CIM = 1 mg/mL) e B366 (CIM = 2 mg/mL) apresentaram atividade antimicrobiana frente a Staphylococcus aureus ATCC 6538. O extrato do isolado B374 apresentou atividade antiviral frente ao vírus Metapneumovírus aviário (aMPV), os isolados B366 e B742, frente ao herpes vírus simplex do tipo 1 (HSV-1), os isolados B138 e B452 frente ao vírus Calicivírus Felino (FCV) e o isolado B204 frente ao vírus da diarréia viral bovina (BVDV). A partir deste trabalho, pode-se concluir que existe grande diversidade de micro-organismos marinhos a ser descoberta e explorada, como fonte de novas espécies e compostos com potencial biotecnológico
Doutorado
Microbiologia
Doutora em Genética e Biologia Molecular
Books on the topic "MLSA"
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The Wadsworth guide to MLA documentation: 2009 MLA update. 2nd ed. Boston, MA: Wadsworth, Cengage Learning, 2011.
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Modern Language Association of America. and EBSCO Publishing (Firm), eds. MLA international bibliography. Ipswich, Mass: EBSCO Publishing, 2000.
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1942-, Gibaldi Joseph, and Modern Language Association of America., eds. The MLA style manual. New York: Modern Language Association of America, 1985.
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Association, Medical Library, ed. MLA 1992 salary survey. Chicago, Ill: Medical Library Association, 1992.
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Association, Medical Library, ed. MLA 1989 salary survey. Chicago, Ill: Medical Library Association, 1989.
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Houghton, Peggy M. MLA: The easy way! Edited by Houghton Timothy J. 1961- and Pratt Michele M. Flint, Mich: Houghton & Houghton, 2008.
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Modern Language Association of America. and EBSCO Publishing (Firm), eds. MLA directory of periodicals. Ipswich, Mass: EBSCO Publishing, 2000.
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1961-, Houghton Timothy J., Pratt Michele M, and Valensky Sandra W, eds. MLA: The easy way! ; [a quick and simplified guide to MLA writing style]. 7th ed. Flint, Mich: Baker College, 2009.
Find full textBook chapters on the topic "MLSA"
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Moeller, J., L. Hültner, E. Schmitt, and P. Dörmer. "Purification of a Mast Cell Growth-Enhancing Activity (MEA) Derived from a Murine Interleukin-2-Dependent, Mlsa-Specific T Cell Line." In Cytokines in Hemopoiesis, Oncology, and AIDS, 299–304. Berlin, Heidelberg: Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-75510-1_41.
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Arnemann, J. "MLPA." In Springer Reference Medizin, 1669–70. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-48986-4_3533.
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Arnemann, J. "MLPA." In Lexikon der Medizinischen Laboratoriumsdiagnostik, 1–2. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-662-49054-9_3533-1.
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Bensard, Denis D., Philip F. Stahel, Jorge Cerdá, Babak Sarani, Sajid Shahul, Daniel Talmor, Peter M. Hammer, et al. "MLSB Resistance." In Encyclopedia of Intensive Care Medicine, 1412. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-00418-6_3207.
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Janusik, Laura A. "Metacognitive Listening Strategies Instrument (MLSI)." In The Sourcebook of Listening Research, 438–44. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2017. http://dx.doi.org/10.1002/9781119102991.ch46.
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Ohnesorg, Thomas, Erin Turbitt, and Stefan J. White. "The Many Faces of MLPA." In Methods in Molecular Biology, 193–205. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-944-4_13.
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Maupas, Hélène, Dominique Kervadec, and Jean-Louis Chermant. "Damage Creep in SiCf-MLAS Composites." In Fracture Mechanics of Ceramics, 527–38. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4615-5853-8_40.
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Berbegall, Ana Pilar, Eva Villamón, Samuel Navarro, and Rosa Noguera. "Multiplex Ligation-dependent Probe Amplification (MLPA)." In Guidelines for Molecular Analysis in Archive Tissues, 215–24. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17890-0_33.
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Jelocnik, Martina, Adam Polkinghorne, and Yvonne Pannekoek. "Multilocus Sequence Typing (MLST) of Chlamydiales." In Chlamydia trachomatis, 69–86. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9694-0_7.
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Ohnesorg, Thomas, Stefanie Eggers, and Stefan J. White. "Detecting DNaseI-Hypersensitivity Sites with MLPA." In Methods in Molecular Biology, 201–10. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-292-2_12.
Full textConference papers on the topic "MLSA"
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Haijun Geng, Xia Yin, Xingang Shi, and Zhiliang Wang. "MLSA: A link-state multipath routing algorithm." In 2013 IEEE Symposium on Computers and Communications (ISCC). IEEE, 2013. http://dx.doi.org/10.1109/iscc.2013.6754968.
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Liang, Hongliang, Lei Wang, Dongyang Wu, and Jiuyun Xu. "MLSA: A static bugs analysis tool based on LLVM IR." In 2016 17th IEEE/ACIS International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (SNPD). IEEE, 2016. http://dx.doi.org/10.1109/snpd.2016.7515932.
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Octaviana, Senlie, Tjandrawati Mozef, and Joachim Wink. "Assessment of multilocus sequences analysis (MLSA) for the identification of myxobacteria strains." In THE FIRST INTERNATIONAL CONFERENCE ON NEUROSCIENCE AND LEARNING TECHNOLOGY (ICONSATIN 2021). AIP Publishing, 2023. http://dx.doi.org/10.1063/5.0118330.
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Ghozzi, Y., C. Labergere, and P. Villon. "Numerical Simulation Based on Meshless Formulation: Application to 2D Solid Mechanics." In ASME 2012 11th Biennial Conference on Engineering Systems Design and Analysis. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/esda2012-82330.
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This paper presents the development of Meshless Methods based on Moving Least Square Approximation (MLSA) [3][10][14]. In the case of solid mechanics, the shape displacement functions are computed for each node with a centered scheme approximation [3][12] associated with a specific weight function [10]. Both interpolated and approximated weight functions are studied [10][9][15]. We propose to build a new C1 weight function based on a 2d boundary line. The Galerkin Method is used to solve the mechanical equilibrium balance problems [14]. A 2-dimensional example is presented to validate the Meshless Method.
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Lin, Dongyun, Yi Cheng, Yiqun Li, Shitala Prasad, and Aiyuan Guo. "MLSA-UNet: End-to-End Multi-Level Spatial Attention Guided UNet for Industrial Defect Segmentation." In 2022 IEEE International Conference on Image Processing (ICIP). IEEE, 2022. http://dx.doi.org/10.1109/icip46576.2022.9897416.
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Helene, Luisa Caroline Ferraz, Jakeline Renata Marçon Delamuta, Renan Augusto Ribeiro, and Mariangela Hungria. "Estudo das Relações Filogenéticas de Estirpes de Rizóbios através da Metodologia Multilocus Sequence Analysis (MLSA) com Identificação de Espécies Novas." In V Simpósio de Bioquímica e Biotecnologia. São Paulo: Editora Edgard Blücher, 2015. http://dx.doi.org/10.5151/biochem-vsimbbtec-22452.
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Chim, T. W., Lucas C. K. Hui, S. M. Yiu, and Victor O. K. Li. "MLAS." In the 6th ACM Symposium. New York, New York, USA: ACM Press, 2011. http://dx.doi.org/10.1145/1966913.1966982.
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Al-Obeidallah, Mohammed, Miltos Petridis, and Stelios Kapetanakis. "MLDA." In the International Conference. New York, New York, USA: ACM Press, 2017. http://dx.doi.org/10.1145/3093241.3093244.
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"MLSD 2018 Copyright." In 2018 Eleventh International Conference "Management of large-scale system development" (MLSD). IEEE, 2018. http://dx.doi.org/10.1109/mlsd.2018.8551830.
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"MLSD 2019 Topics." In 2019 Twelfth International Conference "Management of large-scale system development" (MLSD). IEEE, 2019. http://dx.doi.org/10.1109/mlsd.2019.8910975.
Full textReports on the topic "MLSA"
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Kang, Myong H., Judith N. Froscher, and Ira S. Moskowitz. A Framework for MLS Interoperability. Fort Belvoir, VA: Defense Technical Information Center, January 1996. http://dx.doi.org/10.21236/ada465306.
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Sleefe, G., B. Engler, P. Drozda, R. Franco, and J. Morgan. Development of the Multi-Level Seismic Receiver (MLSR). Office of Scientific and Technical Information (OSTI), February 1995. http://dx.doi.org/10.2172/54277.
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Keim, Paul. Quarterly Report for MLVA Development for Bacterial Pathogens. Office of Scientific and Technical Information (OSTI), April 2000. http://dx.doi.org/10.2172/761601.
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Kang, Myong H., Judith N. Froscher, and Brian J. Eppinger. Towards an Infrastructure for MLS Distributed Computing. Fort Belvoir, VA: Defense Technical Information Center, January 1998. http://dx.doi.org/10.21236/ada465483.
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Kang, Myong H., Judith N. Froscher, Brian J. Eppinger, and Ira S. Moskowitz. A Strategy for an MLS Workflow Management System. Fort Belvoir, VA: Defense Technical Information Center, January 1999. http://dx.doi.org/10.21236/ada465482.
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Froscher, J. N., and M. H. Kang. A Client-Server Architecture Supporting MLS Interoperability with COTS Components. Fort Belvoir, VA: Defense Technical Information Center, January 1997. http://dx.doi.org/10.21236/ada465304.
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Costich, Oliver, and Sushil Jajodia. Maintaining Multilevel Transaction Atomicity in MLS Database Systems with Kernelized Architecture. Fort Belvoir, VA: Defense Technical Information Center, January 1993. http://dx.doi.org/10.21236/ada465420.
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Hendel, Igal, Aviv Nevo, and François Ortalo-Magné. The Relative Performance of Real Estate Marketing Platforms: MLS versus FSBOMadison.com. Cambridge, MA: National Bureau of Economic Research, September 2007. http://dx.doi.org/10.3386/w13360.
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McCarthy, Noel, Eileen Taylor, Martin Maiden, Alison Cody, Melissa Jansen van Rensburg, Margaret Varga, Sophie Hedges, et al. Enhanced molecular-based (MLST/whole genome) surveillance and source attribution of Campylobacter infections in the UK. Food Standards Agency, July 2021. http://dx.doi.org/10.46756/sci.fsa.ksj135.
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This human campylobacteriosis sentinel surveillance project was based at two sites in Oxfordshire and North East England chosen (i) to be representative of the English population on the Office for National Statistics urban-rural classification and (ii) to provide continuity with genetic surveillance started in Oxfordshire in October 2003. Between October 2015 and September 2018 epidemiological questionnaires and genome sequencing of isolates from human cases was accompanied by sampling and genome sequencing of isolates from possible food animal sources. The principal aim was to estimate the contributions of the main sources of human infection and to identify any changes over time. An extension to the project focussed on antimicrobial resistance in study isolates and older archived isolates. These older isolates were from earlier years at the Oxfordshire site and the earliest available coherent set of isolates from the national archive at Public Health England (1997/8). The aim of this additional work was to analyse the emergence of the antimicrobial resistance that is now present among human isolates and to describe and compare antimicrobial resistance in recent food animal isolates. Having identified the presence of bias in population genetic attribution, and that this was not addressed in the published literature, this study developed an approach to adjust for bias in population genetic attribution, and an alternative approach to attribution using sentinel types. Using these approaches the study estimated that approximately 70% of Campylobacter jejuni and just under 50% of C. coli infection in our sample was linked to the chicken source and that this was relatively stable over time. Ruminants were identified as the second most common source for C. jejuni and the most common for C. coli where there was also some evidence for pig as a source although less common than ruminant or chicken. These genomic attributions of themselves make no inference on routes of transmission. However, those infected with isolates genetically typical of chicken origin were substantially more likely to have eaten chicken than those infected with ruminant types. Consumption of lamb’s liver was very strongly associated with infection by a strain genetically typical of a ruminant source. These findings support consumption of these foods as being important in the transmission of these infections and highlight a potentially important role for lamb’s liver consumption as a source of Campylobacter infection. Antimicrobial resistance was predicted from genomic data using a pipeline validated by Public Health England and using BIGSdb software. In C. jejuni this showed a nine-fold increase in resistance to fluoroquinolones from 1997 to 2018. Tetracycline resistance was also common, with higher initial resistance (1997) and less substantial change over time. Resistance to aminoglycosides or macrolides remained low in human cases across all time periods. Among C. jejuni food animal isolates, fluoroquinolone resistance was common among isolates from chicken and substantially less common among ruminants, ducks or pigs. Tetracycline resistance was common across chicken, duck and pig but lower among ruminant origin isolates. In C. coli resistance to all four antimicrobial classes rose from low levels in 1997. The fluoroquinolone rise appears to have levelled off earlier and among animals, levels are high in duck as well as chicken isolates, although based on small sample sizes, macrolide and aminoglycoside resistance, was substantially higher than for C. jejuni among humans and highest among pig origin isolates. Tetracycline resistance is high in isolates from pigs and the very small sample from ducks. Antibiotic use following diagnosis was relatively high (43.4%) among respondents in the human surveillance study. Moreover, it varied substantially across sites and was highest among non-elderly adults compared to older adults or children suggesting opportunities for improved antimicrobial stewardship. The study also found evidence for stable lineages over time across human and source animal species as well as some tighter genomic clusters that may represent outbreaks. The genomic dataset will allow extensive further work beyond the specific goals of the study. This has been made accessible on the web, with access supported by data visualisation tools.
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Rosseel, T. M. Heavy-Section Steel Irradiation (HSSI) Program (W6953) Monthly Letter Status Report - February 2001 - ORNL/HSSI (6953) MLSR-2001/5. Office of Scientific and Technical Information (OSTI), March 2001. http://dx.doi.org/10.2172/814111.
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