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Análise do perfil de resistência a antibióticos e detecção dos genes de virulência e resistência em Aeromonas provenientes de amostras ambientais / Analysis of antibiotic resistance profile and detection of virulence and resistance genes in Aeromonas from environmental samples.Moura, Elisabeth Mendes Martins de 30 August 2010 (has links)
INTRODUÇÃO: As Aeromonas são bactérias distribuídas predominantemente em meio aquático. São consideradas patógeno emergente, podendo causar doenças em peixes como também no homem. Os problemas mais comuns são a gastrenterite no homem e morte em peixes. OBJETIVO: Este estudo foi desenvolvido para comparar a identificação fenotípica com a genotípica, e também para conhecer o perfil de resistência aos antibióticos em Aeromonas caviae, A. aquariorum, e A. sanarellii isoladas do ambiente aquático e a presença de genes de virulência e resistência. MATERIAL E MÉTODOS: O DNA das 24 cepas em estudo foi extraído por choque térmico e purificado utilizando CTAB. Foram realizadas as PCRs para a detecção dos genes de virulência e dos genes de resistência, após a realização do antibiograma. RESULTADOS: Foram identificadas 4 A. caviae das quais 3(75,0 por cento) apresentaram pelo menos um dos genes act, ast ou alt. Das 3 A. aquariorum, 1(33,3 por cento) apresentaram positividade para os genes act e ast. Entre os 5 isolados de A. sanarellii 1(50,0 por cento) possuíam os genes alt e ast. Seis isolados não foram posicionados taxonomicamente entre as espécies descritas de Aeromonas, e dentre essas um exemplar apresentou o gene alt. Em relação às enzimas MBL e AmpC foram obtidos respectivamente: 3(100 por cento) e 3(100 por cento) em A. aquariorum; 2(50,0 por cento) e 4(100 por cento) em A. caviae; 3(75,0 por cento) e 5(100 por cento) em Aeromonas spp.; 1(20 por cento) e 5(100 por cento) A. sanarellii; Nenhum isolado apresentou resultado positivo, no teste fenotípico, para a produção de ESBL. Com a realização da PCR foi detectada a presença de 5 amostras com gene tipo blaMOX, 21blaCPHA , 17 tipo blaTEM e 2 cepH. CONCLUSÃO: Os resultados sugerem que os isolados podem servir potencialmente como reservatórios de resistência aos antimicrobianos e ainda, que os isolados podem ser considerados patógeno emergentes e significativos para a saúde pública / INTRODUCTION: Aeromonas spp. is predominantly distributed in the aquatic environment. They are regarded as emerging pathogen, causing disease in fish but also in man. The most common problems are gastroenteritis in humans and death in fish. OBJECTIVE: This study was designed to compare phenotypic with genotypic identification, and also to know the profile of antibiotic resistance in Aeromonas caviae, A. aquariorum, and A. sanarellii isolated from aquatic environment and the presence of virulence genes and resistance. MATERIAL AND METHODS: DNA from 24 strains under study was extracted by thermal shock and purified using CTAB. PCR reactions were performed for the detection of virulence and resistance genes, after the completion of the antibiotic resistance test. RESULTS: We identified four A. caviae from which 3(75.0per cent) had at least one of the genes act, ast or alt. From 3 A. aquariorum, 1(33.3per cent) was positive for the genes act and ast. Among the five isolated A. sanarellii, 1(50.0per cent) had the alt and ast genes Six isolates were not positioned within taxonomically described species of Aeromonas, and among these only one strain presented the alt gene. Regarding the MBL and AmpC it was obtained respectively: 3(100per cent) and 3(100per cent) isolates from A. aquariorum; 2(50.0per cent) and 4(100per cent) isolates from A. caviae; 4(66.7per cent) and 3(50.0per cent) isolates from Aeromonas spp.; and 1(20per cent) and 5 (100per cent) isolates from A. sanarellii. None of the isolates showed positive results in the phenotypic test for ESBL production. The PCR reaction detected the presence of 5 strains with blaMOX-like gene; 21 with blaCPHA gene; 17 with blaTEM-like gene and 2 with cepH gene. CONCLUSION: These findings suggest that the isolates may serve as potential reservoirs of antimicrobial resistance and also that the isolates could be considered emerging pathogens of public health significance
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Caracterização da frequência de resistência antimicrobiana de Campylobacter jejuni isolados de frangos de corteParavisi, Mariana January 2017 (has links)
O uso de antimicrobianos de forma terapêutica, preventiva e promotora de crescimento trouxe inúmeras vantagens para a avicultura mundial, entretanto a utilização excessiva dos antimicrobianos e de maneira indevida tem estimulado um aumento no número de micro-organismos resistentes. Entre eles, destaca-se o Campylobacter jejuni, bactéria frequentemente associada a enterites em humanos, sendo o frango a principal reservatório e fonte de transmissão deste patógeno para o homem. A transmissão de bactérias resistentes entre animais e seres humanos pode resultar em infecções multirresistentes e insucesso no tratamento terapêutico, sendo a exposição continua destes micro-organismos a esses medicamentos o fator mais importante na origem da resistência. Diante desse cenário, objetivou-se nesse trabalho investigar e caracterizar, através de métodos fenotípico e genotípico, a susceptibilidade antimicrobiana de 54 isolados de C. jejuni coletados em diferentes etapas do processamento da carne de frango de matadouro-frigoríficos da região do Rio Grande do Sul. Para a determinação do MIC, os isolados foram testados frente aos seguintes antimicrobianos: ácido nalidíxico, ciprofloxacina, cloranfenicol, eritromicina, gentamicina e tetraciclina. Dos 54 isolados de C. jejuni, 94,4% foram resistentes a ciprofloxacina, 83,3% ao ácido nalidíxico, 51,8% a tetraciclina e 48% a eritromicina. Todos os isolados foram sensíveis a gentamicina e ao cloranfenicol. Doze isolados foram resistentes a três classes diferentes de antibióticos, sendo assim considerados multi-resistentes. Para verificar a presença da mutação gênica da Região Determinante de Resistência à Quinolona (RDRQ) no gene gyrA, foi realizado sequenciamento gênico de 31 isolados considerados resistentes por métodos fenotípicos. Todos os isolados possuíam a mutação Tre-86-Ile na RDRQ do gene gyrA, que confere resistência às fluoroquinolonas, confirmando a predominância dessa mutação em Campylobacter spp. resistentes a esses antimicrobianos. A ocorrência do gene de resistência à tetraciclina foi verificada por PCR. Dos 28 isolados considerados resistentes por métodos fenotípicos, 42,8% possuíam o gene tet(O), que confere resistência as tetraciclinas. Os resultados mostram um alto nível de resistência antimicrobiana em C. jejuni evidenciando a necessidade da implementação de políticas de uso prudente de antimicrobianos na medicina veterinária. / The use of antimicrobials in a therapeutic, preventive and growth promoting way has brought numerous advantages to the world poultry industry; however, the excessive and undue use of antimicrobials has stimulated an increase in the number of resistant microorganisms. Among them, we highlight Campylobacter jejuni, a bacterium frequently associated with enteritis in humans, with chicken being the main reservoir and source of transmission of this pathogen to man. The transmission of resistant bacteria between animals and humans can result in multi resistant infections and failure in therapeutic treatment, and the continued exposure of these microorganisms to these drugs is the most important factor in the source of resistance. Therefore, the aim of this study was to investigate and characterize, through phenotypic and genotypic methods, the antimicrobial susceptibility of 54 C. jejuni isolates collected at different stages of the processing of chicken meat from slaughterhouse in Rio Grande do Sul. For MIC determination, strains were tested against the following antimicrobials: nalidixic acid, ciprofloxacin, chloramphenicol, erythromycin, gentamicin and tetracycline. Of the 54 isolates of C. jejuni, 94.4% were resistant to ciprofloxacin, 83.3% to nalidixic acid, 51.8% to tetracycline and 48% to erythromycin. All isolates were sensitive to gentamicin and chloramphenicol. Twelve strains were resistant to three different classes of antibiotics, thus being considered multi resistant. To verify the presence of the gene mutation of the Quinolone Resistance Determinant Region (QRDR) in the gene gyrA, gene sequencing of 31 strains considered resistant by phenotypic methods was performed. All strains had the Tre-86-Ile mutation in the QRDR of the gyrA gene, which confers resistance to fluoroquinolones, confirming the predominance of this mutation in Campylobacter spp. resistant to these antimicrobials. The occurrence of tetracycline resistance gene was verified by PCR. Of the 28 strains considered resistant by phenotypic methods, 42.8% had the tet(O) gene. The results show a high level of antimicrobial resistance in C. jejuni that evidences the need for implementation of policies in the prudent use of antimicrobials in veterinary medicine.
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Análise do perfil de resistência a antibióticos e detecção dos genes de virulência e resistência em Aeromonas provenientes de amostras ambientais / Analysis of antibiotic resistance profile and detection of virulence and resistance genes in Aeromonas from environmental samples.Elisabeth Mendes Martins de Moura 30 August 2010 (has links)
INTRODUÇÃO: As Aeromonas são bactérias distribuídas predominantemente em meio aquático. São consideradas patógeno emergente, podendo causar doenças em peixes como também no homem. Os problemas mais comuns são a gastrenterite no homem e morte em peixes. OBJETIVO: Este estudo foi desenvolvido para comparar a identificação fenotípica com a genotípica, e também para conhecer o perfil de resistência aos antibióticos em Aeromonas caviae, A. aquariorum, e A. sanarellii isoladas do ambiente aquático e a presença de genes de virulência e resistência. MATERIAL E MÉTODOS: O DNA das 24 cepas em estudo foi extraído por choque térmico e purificado utilizando CTAB. Foram realizadas as PCRs para a detecção dos genes de virulência e dos genes de resistência, após a realização do antibiograma. RESULTADOS: Foram identificadas 4 A. caviae das quais 3(75,0 por cento) apresentaram pelo menos um dos genes act, ast ou alt. Das 3 A. aquariorum, 1(33,3 por cento) apresentaram positividade para os genes act e ast. Entre os 5 isolados de A. sanarellii 1(50,0 por cento) possuíam os genes alt e ast. Seis isolados não foram posicionados taxonomicamente entre as espécies descritas de Aeromonas, e dentre essas um exemplar apresentou o gene alt. Em relação às enzimas MBL e AmpC foram obtidos respectivamente: 3(100 por cento) e 3(100 por cento) em A. aquariorum; 2(50,0 por cento) e 4(100 por cento) em A. caviae; 3(75,0 por cento) e 5(100 por cento) em Aeromonas spp.; 1(20 por cento) e 5(100 por cento) A. sanarellii; Nenhum isolado apresentou resultado positivo, no teste fenotípico, para a produção de ESBL. Com a realização da PCR foi detectada a presença de 5 amostras com gene tipo blaMOX, 21blaCPHA , 17 tipo blaTEM e 2 cepH. CONCLUSÃO: Os resultados sugerem que os isolados podem servir potencialmente como reservatórios de resistência aos antimicrobianos e ainda, que os isolados podem ser considerados patógeno emergentes e significativos para a saúde pública / INTRODUCTION: Aeromonas spp. is predominantly distributed in the aquatic environment. They are regarded as emerging pathogen, causing disease in fish but also in man. The most common problems are gastroenteritis in humans and death in fish. OBJECTIVE: This study was designed to compare phenotypic with genotypic identification, and also to know the profile of antibiotic resistance in Aeromonas caviae, A. aquariorum, and A. sanarellii isolated from aquatic environment and the presence of virulence genes and resistance. MATERIAL AND METHODS: DNA from 24 strains under study was extracted by thermal shock and purified using CTAB. PCR reactions were performed for the detection of virulence and resistance genes, after the completion of the antibiotic resistance test. RESULTS: We identified four A. caviae from which 3(75.0per cent) had at least one of the genes act, ast or alt. From 3 A. aquariorum, 1(33.3per cent) was positive for the genes act and ast. Among the five isolated A. sanarellii, 1(50.0per cent) had the alt and ast genes Six isolates were not positioned within taxonomically described species of Aeromonas, and among these only one strain presented the alt gene. Regarding the MBL and AmpC it was obtained respectively: 3(100per cent) and 3(100per cent) isolates from A. aquariorum; 2(50.0per cent) and 4(100per cent) isolates from A. caviae; 4(66.7per cent) and 3(50.0per cent) isolates from Aeromonas spp.; and 1(20per cent) and 5 (100per cent) isolates from A. sanarellii. None of the isolates showed positive results in the phenotypic test for ESBL production. The PCR reaction detected the presence of 5 strains with blaMOX-like gene; 21 with blaCPHA gene; 17 with blaTEM-like gene and 2 with cepH gene. CONCLUSION: These findings suggest that the isolates may serve as potential reservoirs of antimicrobial resistance and also that the isolates could be considered emerging pathogens of public health significance
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Pesquisa de genes de resistência a antimicrobianos em filés de tilápia comercializados no município de São Paulo-SP / Search for antimicrobial resistance genes in tilapia fillets commercialized in São Paulo city SPVanessa Fernandes Bordon 27 August 2014 (has links)
IIntrodução A utilização excessiva de antimicrobianos na medicina humana, veterinária e agricultura resultou no aparecimento da resistência bacteriana. Este fenômeno gera problemas de saúde pública que podem resultar na reemergência de doenças infecciosas. O uso de antibióticos, principalmente de forma profilática, tornou-se prática na aquicultura, como ocorre no Brasil, onde a regulamentação para o uso de medicamentos veterinários é ineficiente. Além disso, há evidências da transferência de organismos resistentes para humanos por meio do consumo de produtos de origem animal, quando, durante a fase de criação e produção destes foram administrados antibióticos. Objetivo Pesquisar a ocorrência de genes de resistência a antibióticos em filés de tilápia comercializados em supermercados do município de São Paulo SP. Material e Métodos Foram coletadas 10 amostras de filé de tilápia e realizada a pesquisa de coliformes termotolerantes como indicadores das condições higiênico-sanitárias do alimento. Em seguida, as amostras foram inoculadas em Caldo Lúria 0,5 por cento e o DNA total das bactérias cultivadas nesse meio foi extraído por meio de choque térmico para pesquisa de genes de resistência aos antibióticos -lactâmicos e tetraciclinas pela PCR. Os genes identificados pela PCR foram confirmados pelo sequenciamento. Resultados Em 100 por cento das amostras analisadas o resultado para coliformes termotolerantes foi < 3 NMP.g-1. Na pesquisa de genes de resistência a -lactâmicos, o gene blaOXY-5 foi detectado em 90 por cento das amostras, blaTEM-1b em 20 por cento , blaLEN-16 em 10 por cento , blaSHV-28 em 10 por cento , blaKPC-2 em 20 por cento , blaMOX-6 em 10 por cento e blaCphA em 60 por cento . Os genes de resistência a tetraciclinas identificados foram tetB em 10 por cento das amostras, tetC em 20 por cento , tetD em 80 por cento , tetE em 50 por cento , tetG em 60 por cento , tetO e tetS em 10 por cento cada e tetW em 20 por cento . Conclusões Em 90 por cento das amostras foi identificada a presença de genes de resistência aos antibióticos -lactâmicos e tetraciclinas, demonstrando uma grande circulação de resistência bacteriana na aquicultura e verificando a necessidade de legislação e fiscalização mais atuantes no controle do uso de antibióticos na aquicultura / IIntroduction The excessive use of antimicrobials in human medicine, veterinary medicine and agriculture has resulted in the emergence of bacterial resistance. This phenomenon creates public health problems that may result in the re-emergence of infectious diseases. The use of antibiotics, mainly prophylactically, has become a practice in aquaculture, including Brazil, where the legislation for the use of veterinary drugs is inefficient. Furthermore, there is evidence of transmission of resistant organisms to humans through consumption of animal products, especially when the antibiotics have been administered during the raising and production of these animals. Objective To search for the occurrence of antibiotics resistance genes in tilapia fillets commercialized in supermarkets in São Paulo city - SP. Material and Methods 10 tilapia fillet samples were collected and submitted to fecal coliform search as an indicator of the sanitary conditions of the food. Then, the samples were inoculated into Luria broth 0,5 per cent and the total DNA was extracted from growing bacteria by thermal shock for the search of resistance genes to -lactam and tetracyclines antibiotics by PCR. The genes identified by PCR were confirmed by sequencing. Results In 100 per cent of samples the result was < 3 NMP.g-1 for fecal coliform organisms. In the study of -lactam resistance genes, blaOXY-5 gene was detected in 90 per cent of samples, blaTEM-1b in 20 per cent , blaLEN-16 in 10 per cent , blaSHV-28 in 10 per cent , blaKPC-2 in 20 per cent , blaMOX-6 in 10 per cent and blaCphA in 60 per cent . The tetracyclines resistance genes identified were tetB in 10 per cent of samples, tetC in 20 per cent , tetD in 80 per cent , tetE in 50 per cent , tetG in 60 per cent , tetO and tetS in 10 per cent each and tetW in 20 per cent . Conclusions 90 per cent of the samples showed the presence of -lactam and tetracyclines resistance genes, demonstrating a high circulation of bacterial resistance in aquaculture and verifying the need for more active law and surveillance in controlling the use of antibiotics in aquaculture.
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Caratterizzazione molecolare di geni per l'antibiotico resistenza in Streptococcus Thermophilus / Molecular Characterization of Antibiotic Resistant Genes in Streptococcus ThermophilusBERRUTI, GIANGIACOMO 15 February 2007 (has links)
Obiettivo di questo lavoro è stato valutare la diffusione di AR in differenti ceppi di S. thermophilus isolati tra il 1947 e il 2004 e provenienti da differenti ambienti, in modo da avere un chiaro andamento del fenomeno; questo è stato possibile analizzando un numero significativo di ceppi isolati in un periodo di tempo che va da prima dell'utilizzo degli antibiotici fino ai giorni nostri. L'espressione fenotipica è stata valutata con tre differenti metodi (microdiluizioni in brodo, E-test e Disk Diffusion), in accordo con gli standard NCCLS, per la determinazione delle MICs (Minimum Inhibitory Concentration, ovvero Concentrazioni Minime Inibenti). Per la valutazione genetica è stata impiegata la tecnica dei microarrays a DNA utilizzando oligonucleotidi da 50 e 60-mer, per un totale di 300, appartenenti a 10 diverse classi di antibiotici. La conferma dei risultati è stata ottenuta mediante PCR e sequenziamento. In 9 ceppi di S. thermophilus è stato possibile mettere in evidenza la presenza di almeno uno dei geni tetS ed ermB responsabili della resistenza agli antibiotici Tetraciclina e Eritromicina rispettivamente. / The aim of the present work was to assess the AR diffusion in a total of 70 different strains of Streptococcus thermophilus, collected between 1950 and 2004 and from different environments; in this way we had the possibility to obtain a clear overview of the response of these bacteria to a large variety of antibiotics, having been able to analyze a significant number of different strains, originated from different areas and distributed over a wide time period, since before the use of antibiotics up to the present day. The phenotypic expression has been evaluated by using three different methods: microdilution, E-test and disk diffusion. The genetic analysis was performed using 50 and 60-mer oligonucleotides DNA based micro array for the identification of AR genes; the AR genes represented by the oligonucleotides on the micro array belong to: Aminoglycoside, Extended Spectrum ?-lactamase (ESBL), Chloramphenicol, Macrolide Lincosamides and Streptogramin (MLS) group, Sulfonamide, Tetracycline, Trimethoprim and Vancomycin.
tetS and ermB genes were found and sequenced in 4 out of the total of the S. thermophilus investigated. Furthermore we have wanted to establish the genetic location of above-mentioned genes and assess their transfer intra and inter species adopting the conjugation technique in plate.
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Identification And Cloning Of Genes Induced And / Or Repressed Upon Treatments Of Wheat Plants (avocet S) With Bth, Baba And Trichoderma Harzianum Raifi Krl-ag2Al-asbahi, Adnan Ali 01 October 2006 (has links) (PDF)
One of the major problems concerning the production of food crops is the controlling of plant diseases to maintain the high quality and yield. Wheat diseases are caused by parasitic bacteria, fungi and viruses that are a major hazard in wheat production. Therefore, understanding of any resistance mechanism is prerequisite for the successful utilization of wheat crop species in modern agriculture. The phenomenon of induced resistance by fungi, bacteria, microbial elicitors and chemicals has been investigated widely and resulted in many discoveries that conclude a general realization that the disease resistance signaling pathway in plants shares a number of common elements with those leading to innate immunity but a few of them have been characterized at the molecular level yet. Therefore our goal in this study is to identify genes activated or repressed after treatment of wheat plants with biological elicitor fungus, Trichoderma harzianum, and chemical inducers, benzo (1,2,3) thiadiazole-7-carbothioic acid S-methyl ester (BTH) and ß / -aminobutyric acid (BABA).
mRNA differential display technique, which is a powerful tool to identify those genes that are differentially expressed between the two cell types has been extensively used in this study. The variety ' / Avocet S' / is used to identify putative genes activated or repressed after treatment of wheat plants with biological elicitor fungus, Trichoderma harzianum, and chemical inducers, BTH and BABA comparing to untreated ' / Avocet S' / wheat plants. The differentially expressed cDNA bands were cloned and sequenced. Nucleotide sequences of differentially expressed cDNA bands were searched in the Genbank. Sequence alignments between the fragments that represent a certain gene were also searched in ClustalX-1.81 computer programs. The sequences of the differentially expressed fragments were also confirmed by real time PCR that verify the gene expression differences observed between the biologically or chemically treated and untreated plants as a result of defense induction. The confirmed genes were found to be involved directly or indirectly in the induced disease resistance. These genes are important in terms of understanding the mechanism of systemic acquired resistance (SAR) signalling defense and helpful in producing transgenic wheat.
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Development of An Antibiotic Marker-Free Gene Delivery System in Streptococcus gordoniiHulbah, Maram 11 April 2013 (has links)
Streptococcus gordonii, a commensal oral bacterium, is considered a good candidate to function as a live oral vaccine vector. The introduction of vaccine antigen genes into S. gordonii relies on the use of antibiotic resistance genes as selectable markers, which is undesirable. In this study, we used auxotrophic complementation (deletion of an essential gene from the chromosome and insertion into a plasmid) as a means to create an antibiotic marker-free gene delivery system in S. gordonii. S. gordonii ?thyA was created and complemented by an antibiotic marker-free expression plasmid containing the intact thyA gene, pDL276/thyAdelkan. Transformation of pDL276/thyAdelkan into the mutant gave an unexpected 100-fold increase in transformation efficiency as compared to pDL276. The transformants arose from both single and double crossing over. The increase in transformation efficiency suggests that a highly efficient antibiotic marker-free system to deliver genes to the chromosome has been created using thyA complementation.
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MOLECULAR, GENETIC AND BIOCHEMICAL CHARACTERIZATION OF OLEIC ACID- AND GLYCEROL-MEDIATED SIGNALING IN PLANT DEFENSEVenugopal, Srivathsa C. 01 January 2008 (has links)
Oleic acid (18:1) is one of the important monounsaturated fatty acids, which is synthesized upon desaturation of stearic acid and this reaction is catalyzed by the SSI2 encoded stearoyl-acyl-carrier-protein-desaturase. A mutation in SSI2 leads to constitutive activation of salicylic acid (SA)-mediated defense responses. Consequently, these plants accumulate high levels of SA and show enhanced resistance to bacterial and oomycete pathogens. Replenishing 18:1 levels in ssi2 plants, via a second site mutation in GLY1 encoded glycerol-3-phosphate (G3P) dehydrogenase, suppresses all the ssi2-triggered phenotypes. Study of mechanism(s) underlying gly1-mediated suppression of ssi2 phenotypes showed that 18:1 levels are regulated via acylation with G3P and a balance between G3P and 18:1 is critical for the regulation of defense signaling pathways. To establish a role for 18:1 and G3P during host defense, interaction between Colletotrichum higginsianum and Arabidopsis was studied. Resistance to C. higginsianum correlated with host G3P levels. The gly1 plants showed increased susceptibility while act1 plants, defective in utilization of G3P, showed enhanced resistance. Plant overexpessing GLY1 showed enhanced resistance in both wild type as well as camalexin deficient backgrounds. Together, these results suggested that G3P conferred resistance acted downstream or independent of camalexin.
Exogenous application of glycerol lowered 18:1 levels and produced ssi2-like phenotypes in wild-type plants. Furthermore, glycerol application or the ssi2 mutation produced similar phenotypes in fatty acid desaturation mutants and mutants defective in SA/resistance gene signaling. Expression studies showed that ssi2 phenotypes were likely due to increased expression of resistance genes. Epistatic analysis suggested that certain components of SA pathway had redundant function and were required for 18:1-regulated signaling.
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Characterization of antibiotic resistance genes abundance and diversity in soil bacteria by metagenomic approaches : what is the dissemination potential of the soil resistome?Nesme, Joseph 16 May 2014 (has links) (PDF)
Environmental bacteria and especially soil bacteria are active producers of antibiotic molecules and most drugs used nowadays are isolated from saprophytic soil bacteria and these microorganisms have also evolved numerous resistance pathways leading to an arsenal of Antibiotic Resistance Genes Determinants (ARGD) known as the environmental resistome. A survey of ARGD prevalence is required in order to characterize this natural phenomenon with critical implications in our current infectious diseases management. In order to perform such analysis we compiled a set of 71 metagenomic datasets from various environmental origins: soils, oceans, lakes, human feces, indoor air, etc., and compared their sequences with a database of known antibiotic resistance gene determinants (ARGD). ARGD-annotated reads are found in every environment analyzed confirming their ubiquity. Soil is found to be the richest and shares a large part of ARGD with the human gut microbiome, indicating ARGD transfers between these environments. Experiments using qPCR and metagenomic DNA sequencing on soil samples from two sites with known and distinct antibiotic pollution history were conducted to understand how ARGD abundance and diversity in soil are affected when impacted by antibiotic molecules. The first site is a reference soil from a long-term experiment without history of antibiotic pollution (Rothamsted Park Grass, UK). Soil microcosms are setup with addition of either antibiotic-containg animal manure or pure molecules and incubated for 6 months to monitor changes in ARGD concentration following these perturbations. Our second study-site is a very remote settlement in French Guiana where antibiotics are available since recently and may have impacted the local soil microbial community. Soil samples are taken following a line-transect going from the village (antibiotic source) to 3km deep in the forest in a gradient of human-impact. Our results all confirm prevalence of ARGD in soil at significant abundance but also that ARGD distribution is more correlated to environmental factors such as soil type, microbial taxonomy composition or microcosms incubation conditions than antibiotic molecules exposure in both sites. Pathogens ARGD diversity is far lower than ARGD diversity found in the environment and not all the soil resistome is readily accessible for transfer. In order to characterize the soil mobile gene pool, a strategy is proposed to isolate specifically mobile DNA directly from the environment for sequencing purposes. Better knowledge on the microbial ecology factors limiting ARGD transfers to pathogens may greatly help us reduce the current threat on our limited medical antibiotic molecules resource.
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Pyramiding of novel rust resistance genes in wheat, utilizing marker assisted selection and doubled haploid technologySmit, Corneli 12 1900 (has links)
Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Wheat rust, caused by the Puccinia spp., is a global biotic cause of wheat yield losses. This disease can effectively be combatted by implementing rust resistant wheat cultivars. The release of new resistant wheat cultivars is however prolonged due to the time needed to fix resistance genes in a good quality background and develop pure breeding wheat lines. The aim of this study was the pyramiding of novel species derived leaf and stripe rust resistance genes in bread wheat lines through the utilization of high throughput marker assisted selection and microspore derived doubled haploid technology. / AFRIKAANSE OPSOMMING: Koringroes het wêreldwyd verliese in koringopbrengste tot gevolg. Dit word veroorsaak deur die Puccinia fungi. Hierdie siekte kan effektief beveg word deur die verbouing van roesbestande kultivars. Die vrystel van nuwe weerstandbiedende kultivars is egter ‘n langdurige proses weens die tyd verbonde daaraan om weerstandsgene te fikseer in ‘n genetiese agtergrond met ‘n goeie kwaliteit en om dan suiwertelende lyne te ontwikkel. Die doelwit van hierdie studie was om nuwe spesie-verhaalde blaar- en streeproes weestandsgene in koringlyne te stapel met behulp van merker bemiddelde seleksie en mikrospoor geassosieerde verdubbelde haploïede tegnologie.
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