E. coli is the most frequently isolated Gram negative pathogen from bacteremia in cancer patients and is repeatedly recovered from many other extraintestinal illnesses. These infections are commonly endogenous in nature and interfere with the treatment of cancer resulting in increased healthcare costs, morbidity, and mortality rates. Cancer and the treatments related to cancer cause alterations in the microbiome of the gut and other organs. Despite this point, there is a serious lack of knowledge about the genetic types of E. coli infecting cancer patients. This gap results in vague prevention strategies and limited treatment options for cancer patients. Multi Locus Sequence Typing (MLST) was used to successfully genotype 105 sequentially collected E. coli isolates from patients admitted to H. Lee Moffitt Cancer Center (HLMCC, Tampa, FL) with confirmed extraintestinal infections between 2010 and 2012. In total, 24 distinct genotypes (STs) have been identified in this dataset using EcMLST (STEC Reference Center). Of these, ST34 constituted 39% of the isolates and may represent a disseminating clone at HLMCC. Furthermore, 17 isolates not found in the EcMLST database have been identified. Importantly, phylogenetic analysis of DNA sequence data for MLMCC E. coli revealed only 22% of HLMCC E. coli clustered with ECOR reference strains commonly attributed to the B2 phylogroup of extraintestinal pathogenic E. coli (ExPEC). Four HLMCC E. coli belonging to ST171 and attributed to life-threatening blood infections clustered with Shiga toxin (Stx) producing E. coli (STEC) strain TW06296. HLMCC E. coli belonging to ST34 clustered with enteroaggregative E. coli (EAEC) strain TW10263. Importantly, these non-B2 phylogroup strains demonstrated more pathogenic potential than HLMCC E. coli clustered with B2 ExPEC,which included a higher incidence of bacteremia and sepsis, as well as resistance to first-line antibiotics. Upon further investigation, ST34 may equate to ST131 by another MLST database. These findings suggest that isolates previously characterized as commensal and intestinal pathogenic E. coli have an increased ability to cause infection outside of the gastrointestinal tract in cancer patients and that selective pressures are contributing to increased antibiotic resistance. These findings may change the approach to clinical management of E. coli infections at cancer centers.

Pennisetum Rich, is one of the most important genera in the family Poaceae because it includes forage and crop species such as Pennisetum purpureum Schumach. and Pennisetum glaucum (L.) R. Br. Both P. purpureum and P. glaucum have a number of cultivars and varieties arising due to natural crossing which are very difficult to distinguish morphologically. P. purpureum and P. glaucum also hybridize naturally because they are protogynous and cross pollinated. The resulting hybrids are highly sterile and resemble P. purpureum. Lepidopteran stem borers cause great yield loss in maize produced by resource-poor farmers in Africa and are managed by habitat management or push-pull strategies, in which P. purpureum cultivars and hybrids are used as a trap crop. The aims of this project were to genotype different P. purpureum cultivars and hybrids using Amplified Fragment Length Polymorphism (AFLP) as well as Random Amplified Polymorphic DNA (RAPD) in order to identify cultivars and hybrids and possible misidentifications, assess the congruency of results between AFLPs and RAPDs and to attempt to relate these results to the oviposition preference of Chilo partellus for different P. purpureum cultivars. The individuals to be fingerprinted were collected from several countries in sub-Saharan Africa, a few from the USA and one from China. The AFLP analysis of these individuals were done with primer combinations EcoRI/MseI and Mlul/Msel on polyacrylamide gels and an ABI 3130 xl Genetic Analyzer respectively. The automated sequencer visualized more bands than the polyacrylamide gels. The RAPD technology was not developed any further after 17 primers were tested and no polymorphic bands detected. Overall results indicated that cultivars did not cluster according to geographical origin, and cultivars known by popular names did not always cluster together, indicating diversity within the cultivar or misidentifications. An example of a misidentification is the cultivar Green Gold being no other than cultivar Harare, or cultivar Swaziland 3 being cultivar Sanitas. Proper management by nursery managers cannot be stressed enough, as this will prevent plants getting mixed up, causing confusion. There was no relationship between the relatedness of cultivars and moth oviposition preference. The AFLP technology could be a powerful tool for the DNA fingerprinting and molecular characterization of this grass species, but poor germ plasm management negates its application. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2008.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Soybean (Glycine max) is an important crop in the world in terms of total production and usage. It is also among the least diverse species. The main objectives of the present study were 1) to determine differences between ISSR and RAPD marker systems in detecting genetic variation in soybeans and 2) to identify and characterize accession- diagnostic molecular markers in G. max accessions. Genomic DNAs from 108 G. max accessions from 11 different gene pools were analyzed using several ISSR and RAPD primers. The levels of polymorphic loci detected with the two marker systems were in general moderate and similar.. Overall, 82% of genetic distance values were above 0.40 based on ISSR analysis. However, RAPD data revealed that the accessions from different countries are closely related with 64% genetic distance values below 0.40. The dendrograms constructed with ISSR data revealed that the South Korean accessions formed an out-group while the RAPD analysis showed that accessions from Sweden were separate from the other 10 gene pools. One variety-diagnostic marker generated with ISSR 5 primer was identified in the accession Kao Chien Tao from China. This marker was cloned, and sequenced. Although RAPD and ISSR marker systems detected similar levels of genetic variability, they target different regions of the soybean genome, resulting in different clustering of the 11 gene pools indicating different genetic relatedness among them. This finding demonstrates the usefulness of both marker systems in assessing diversity and relatedness among Glycine max gene pools.

Pennisetum Rich, is one of the most important genera in the family Poaceae because it includes forage and crop species such as Pennisetum purpureum Schumach. and Pennisetum glaucum (L.) R. Br. Both P. purpureum and P. glaucum have a number of cultivars and varieties arising due to natural crossing which are very difficult to distinguish morphologically. P. purpureum and P. glaucum also hybridize naturally because they are protogynous and cross pollinated. The resulting hybrids are highly sterile and resemble P. purpureum. Lepidopteran stem borers cause great yield loss in maize produced by resource-poor farmers in Africa and are managed by habitat management or push-pull strategies, in which P. purpureum cultivars and hybrids are used as a trap crop. The aims of this project were to genotype different P. purpureum cultivars and hybrids using Amplified Fragment Length Polymorphism (AFLP) as well as Random Amplified Polymorphic DNA (RAPD) in order to identify cultivars and hybrids and possible misidentifications, assess the congruency of results between AFLPs and RAPDs and to attempt to relate these results to the oviposition preference of Chilo partellus for different P. purpureum cultivars. The individuals to be fingerprinted were collected from several countries in sub-Saharan Africa, a few from the USA and one from China. The AFLP analysis of these individuals were done with primer combinations EcoRI/MseI and Mlul/Msel on polyacrylamide gels and an ABI 3130 xl Genetic Analyzer respectively. The automated sequencer visualized more bands than the polyacrylamide gels. The RAPD technology was not developed any further after 17 primers were tested and no polymorphic bands detected. Overall results indicated that cultivars did not cluster according to geographical origin, and cultivars known by popular names did not always cluster together, indicating diversity within the cultivar or misidentifications. An example of a misidentification is the cultivar Green Gold being no other than cultivar Harare, or cultivar Swaziland 3 being cultivar Sanitas. Proper management by nursery managers cannot be stressed enough, as this will prevent plants getting mixed up, causing confusion. There was no relationship between the relatedness of cultivars and moth oviposition preference. The AFLP technology could be a powerful tool for the DNA fingerprinting and molecular characterization of this grass species, but poor germ plasm management negates its application. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2008.

Pennisetum Rich, is one of the most important genera in the family Poaceae because it includes forage and crop species such as Pennisetum purpureum Schumach. and Pennisetum glaucum (L.) R. Br. Both P. purpureum and P. glaucum have a number of cultivars and varieties arising due to natural crossing which are very difficult to distinguish morphologically. P. purpureum and P. glaucum also hybridize naturally because they are protogynous and cross pollinated. The resulting hybrids are highly sterile and resemble P. purpureum. Lepidopteran stem borers cause great yield loss in maize produced by resource-poor farmers in Africa and are managed by habitat management or push-pull strategies, in which P. purpureum cultivars and hybrids are used as a trap crop. The aims of this project were to genotype different P. purpureum cultivars and hybrids using Amplified Fragment Length Polymorphism (AFLP) as well as Random Amplified Polymorphic DNA (RAPD) in order to identify cultivars and hybrids and possible misidentifications, assess the congruency of results between AFLPs and RAPDs and to attempt to relate these results to the oviposition preference of Chilo partellus for different P. purpureum cultivars. The individuals to be fingerprinted were collected from several countries in sub-Saharan Africa, a few from the USA and one from China. The AFLP analysis of these individuals were done with primer combinations EcoRI/MseI and Mlul/Msel on polyacrylamide gels and an ABI 3130 xl Genetic Analyzer respectively. The automated sequencer visualized more bands than the polyacrylamide gels. The RAPD technology was not developed any further after 17 primers were tested and no polymorphic bands detected. Overall results indicated that cultivars did not cluster according to geographical origin, and cultivars known by popular names did not always cluster together, indicating diversity within the cultivar or misidentifications. An example of a misidentification is the cultivar Green Gold being no other than cultivar Harare, or cultivar Swaziland 3 being cultivar Sanitas. Proper management by nursery managers cannot be stressed enough, as this will prevent plants getting mixed up, causing confusion. There was no relationship between the relatedness of cultivars and moth oviposition preference. The AFLP technology could be a powerful tool for the DNA fingerprinting and molecular characterization of this grass species, but poor germ plasm management negates its application. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2008.

Made available in DSpace on 2014-06-11T19:30:28Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-03-23Bitstream added on 2014-06-13T20:00:43Z : No. of bitstreams: 1 tashima_nt_dr_arafcf.pdf: 1639832 bytes, checksum: 4ebbfa8c2c4802ba76fbdfe822f9a1f3 (MD5) / Universidade Estadual Paulista (UNESP) / O estudo epidemiológico da giardíase empregando técnicas moleculares, como o RAPD (Randomly Amplified Polimorphic DNA), fornece subsídio para identificação dos fatores de transmissão da G. lamblia. Este trabalho teve como objetivo estudar a epidemiologia da G. lamblia em uma creche infantil de Presidente Bernardes, SP, Brasil, no ano de 2006, por meio de um inquérito epidemiológico e tipagem molecular das cepas isoladas empregando a técnica de RAPD. A análise dos perfis genéticos obtidos foi realizada com auxílio de um dendrograma de similaridade obtido pelo programa Gel Compar II versão 2.0 para Windows (Applied MATHS). Foram realizados exames parasitológicos de fezes de 101 crianças freqüentadoras da creche infantil. A partir desses exames, 15 amostras que apresentavam cistos de G. lamblia foram purificadas para posterior extração do DNA. Os pais e irmãos das 15 crianças parasitadas, assim como os cães de estimação e também dos funcionários da creche tiveram suas fezes coletadas para posterior exame parasitológico. Das mesmas extraíram-se DNA das amostras que apresentavam cistos de G. lamblia. Entre as 31 amostras positivas para G. lamblia obtida entre as crianças e seus respectivos pais e irmãos, concluiu-se que a transmissão do parasita ocorreu entre as crianças provavelmente no convívio da creche, mas não no convívio familiar. / Epidemiological studies on giardiasis by using molecular techniques such as RAPD (Randomly Amplified Polymorphic DNA) give information on factors related to the transmission of G. lamblia. The aim of this work was to assess the G. lamblia epidemiology in a day care center in Presidente Bernardes, SP, Brazil, in 2006, by means of an epidemiological inquiry and molecular typing of the isolated strains by using the RAPD technique. The genetic profiles were analyzed by means of a dendrogram of similarity obtained with the software Gel Compar II v. 2.0 for Windows (Applied MATHS). Parasitological examinations were made on feces samples taken from 101 children attended in the day care center. After examinations, 15 samples that presented G. lamblia cysts were purified for further DNA extraction. The respective relatives and brothers of the 15 children, in addition to their pets and the day care center s workers had their feces collected for further parasitological examination. Samples in which G. lamblia cysts were found were also submitted to DNA extraction. Among the 31 samples positive for G. lamblia obtained from the children and their respective parents and brothers, it was concluded that the transmission of the parasite occurred between children probably during the cohabitation in the day care center, but not inside the family.

Made available in DSpace on 2014-06-11T19:32:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-12-10Bitstream added on 2014-06-13T20:24:20Z : No. of bitstreams: 1 fabiano_tlt_dr_jabo.pdf: 373992 bytes, checksum: 54cb0750ac5f6c1287f8733a4da8a103 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Foram coletadas 143 amostras de mãos de humanos e camas hospitalares, através de suabes em caldo BHI (Brain Heart Infusion), em um Hospital Escola de Ribeirão Preto, SP. Este trabalho teve como objetivo caracterizar as cepas de Staphylococcus sp e verificar o grau de similaridade genética entre as cepas pelo RAPD-PCR e analisar o perfil de resistência a diversos antimicrobianos. As amostras coletadas foram incubadas a 37º C por 24 horas e após este período as culturas foram semeadas em placas de Petri contendo agar “Staphylococcus Médium 110”. As colônias típicas do gênero Staphylococcus foram coletadas e estocadas a 4º C até o momento de elaboração das provas de produção de catalase e coagulase, fermentação do manitol, DNAse e hemólise. As cepas isoladas foram analisadas através da técnica de RAPD-PCR para verificar o grau de similaridade. A sensibilidade das cepas isoladas foi testada frente a 11 diferentes antibióticos. Foram isoladas 92 cepas de Staphylococcus sp sendo 67 (72,8%) cepas de Staphylococcus coagulase negativas e 25 (27,2%) cepas de Staphylococcus coagulase positivas. A análise de similaridade mostrou heterogeneidade genética entre as cepas. Foram encontradas oito (8.7%) cepas de Staphylococcus sp resistentes à vancomicina, sendo uma multirresistente a todos os antibióticos. Introduzir medidas de assepsia nas mãos de pessoal e leitos hospitalares e a racionalização do uso indiscriminado de antibióticos muito contribuirá para diminuição das infecções nosocomiais. / A total of 143 samples were analyzed in this study. These included samples from human hands and hospital beds at a Medical Teaching Hospital of Ribeirão Preto, SP. This study aimed to characterize the strains of Staphylococcus sp and verify the degree of genetic similarity between the strains by RAPD-PCR and analyse the profile of the various antimicrobial resistance. Swabs samples were collected and cultured in brain heart infusion medium at 37o C for 24 h. Further cultivation was performed on Staphylococcus medium 110 agar plates. Typical colonies representing Staphylococcus genus were collected and stored at 4º C until it was used for identification tests, which included catalase, coagulase and mannitol production, hemolysis and Dnase. Isolates were analyzed by RAPD-PCR to verify similarity level. Antibiotic susceptibility was determined using 11 different antibiotics. A total of 92 Staphylococcus sp strains were isolated, whereas 67 (72.8%) were coagulase-negative Staphylococcus strains and 25 (27,2%) were coagulase-positive Staphylococcus strains. Similarity analysis revealed a great dissimilarity among isolates. High percentage of beta-lactams resistant Staphylococcus sp was found. Eight strains (8.7%) were vancomycin-resistant. A high percentage of multiresistant strains were found. Introduce of good hygiene practices for hands and hospital beds and adequate antibiotic use, may contribute to reduction of nosocomial infection and consequently improved antibiotic treatment response.

Submitted by Marco Antônio de Ramos Chagas (mchagas@ufv.br) on 2017-05-10T11:24:39Z No. of bitstreams: 1 texto completo.pdf: 1458718 bytes, checksum: 848cff4ffab0a6124463173e706a2f70 (MD5) / Made available in DSpace on 2017-05-10T11:24:39Z (GMT). No. of bitstreams: 1 texto completo.pdf: 1458718 bytes, checksum: 848cff4ffab0a6124463173e706a2f70 (MD5) Previous issue date: 2002-07-08 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A mancha-angular, causada pelo fungo Phaeoisariopsis griseola, é uma das principais doenças do feijoeiro, provocando perdas que podem chegar a 70% da produção no Brasil. Para o controle da doença, o uso de cultivares resistentes é uma medida eficiente, prática e econômica, no entanto, a alta variabilidade patogênica de P. griseola dificulta o trabalho dos melhoristas. Neste caso, a estratégia de piramidação de genes de resistência, pode ser utilizada, buscando-se uma resistência mais duradoura. Este trabalho teve como principais objetivos, a obtenção de linhagens de feijoeiro com grãos tipo carioca e resistentes à mancha- angular, além da caracterização de 58 cultivares de feijoeiro quanto a esta doença. Na geração RC 2 F 2 do cruzamento Rudá x México 54, procedeu-se a seleção de plantas resistentes por meio de inoculação com a raça 63.19 de P. griseola, bem como pelo uso do marcador SCAR OPN02 890 . Estas, geraram 15 famílias RC 2 F 2:3 com grãos tipo carioca, as quais foram avaliadas em teste de progênie, identificando-se duas famílias como homozigotas para o gene de resistência. A partir da análise das distâncias genéticas por marcadores RAPD, foram selecionadas quatro linhagens RC 2 F 3 com distâncias genéticas relativas em relação ao genitor Rudá variando de 8,38 a 11,26%. Para o cruzamento Rudá x MAR-2, utilizou-se a raça 63.39 de P. griseola e o marcador RAPD OPE04 500 na geração RC 1 F 2 , para seleção de plantas resistentes. Foram selecionadas dezenove famílias RC 1 F 2:3 com grãos tipo carioca, para o teste de progênie. Destas, foram selecionadas duas como resistentes homozigotas. Quatro linhagens RC 1 F 3 foram selecionadas com auxílio de marcadores RAPD, com distâncias genéticas relativas variando de 11,73 a 14,17% em relação à cultivar Rudá. Na geração RC 1 F 2 do cruzamento entre Rudá x BAT 332, plantas resistentes foram selecionadas, por meio do marcador RAPD OPAO12 950 . Selecionaram-se dezessete famílias RC 1 F 2:3 que possuíam grãos do tipo carioca para o teste de progênie. Por este teste, foram selecionadas 5 famílias como homozigotas resistentes. Seis linhagens RC 1 F 3 foram selecionados pela análise por RAPD, com distâncias genéticas relativas variando de 13,94 a 14,14% em relação ao Rudá. Na caracterização de 58 cultivares de feijoeiro quanto à reação às raças 63.19, 31.15, 63.55 e 63.23 de P. griseola, as cultivares Antioquia 8 e CAL 143, ambas de origem andina e Equador 299 e México 235, de origem mesoamericana, apresentaram resistência às quatro raças testadas. O uso de cultivares andinas e mesoamericanas em programas de melhoramento visando resistência à mancha- angular é importante, devido às evidências de coevolução patógeno-hospedeiro. Desta forma, Antioquia 8, CAL 143, Equador 299 e México 235 podem ser úteis em tais programas. Todos as outras cultivares possuem algum nível de suscetibilidade às quatro raças de P. griseola estudadas. Os mais suscetíveis foram: AB 7419, AN 9022180, Aporé, Bambuí, Carioca 80, CNC, CNF 9287, Diamante Negro, Earlly Gallatin, Jamapa e KW 780. / Angular leaf spot caused by the fungus Phaeoisariopsis griseola is a major common bean disease, and may cause yield losses up to 70% in Brazil. An effective, practical and economic way to control the angular leaf spot is to use resistant cultivars, however, high P. griseola pathogenic variability makes the development of such resistant cultivars a difficult task. In this case, pyramiding of resistance genes may be used if a longer lasting resistance is to sought. This work aimed at obtaining common bean lines with “carioca” grain type and resistant to the angular leaf spot, as well as the characterization of 58 common bean cultivars to this disease. In generation BC 2 F 2 of Ruda x Mexico 54 cross the selection of resistant plants was proceeded by inoculation of race 63.19 of P. griseola, as well as by the use of the SCAR OPN02 890 marker. Those plants bred 15 BC 2 F 2:3 families with “carioca” grain type, which were used in the progeny test, and two families were identified as resistant and homozygous. From the analyses of genetic distances by RAPD markers, four BC 2 F 3 plants were selected with relative genetic distances to the recurrent parent Ruda ranging from 8.38 to 11.26%. In the Ruda x MAR-2 cross, race 63.39 of P. griseola and the RAPD OPE04 500 were used in generation BC 1 F 2 to select resistant plants. Nineteen BC 1 F 2 plants were selected for progeny test which bred BC 1 F 2:3 families with “carioca” grain type, From those 19 families, 2 were selected as homozygous resistant. Through the analysis of BC 1 F 3 plants by RAPD markers, four were selected with relative genetic distances to Ruda ranging from 11.73 to 14.17%. In generation BC 1 F 2 of Ruda x BAT 332 cross, resistant plants were selected using the RAPD OPAO12 950 marker. Those plants bred 17 BC 1 F 2:3 families with “carioca” grain type, which were used in the progeny test, and 5 families were identified as resistant homozygous. Six BC 1 F 3 individuals were selected through the RAPD analysis, with relative genetic distances, ranging from 13.94 to 14.14% to Ruda. In the characterization of 58 common bean cultivars, for their reaction to the races 63.19, 31.15, 63.55 and 63.23 of P. griseola, the cultivars Antioquia 8 and CAL143, both of Andean, and Equador 299 and México 235, of Mesoamerican common bean groups, showed resistance to the four tested races. The use of Andean and Mesoamerican common beans in breeding programs aiming angular leaf spot resistance is an important strategy due to the evidences of pathogen-host coevolution. Thus, Antioquia 8, CAL 143, Equador 299 and México 235 may be good choices in such programs. All the other cultivars were susceptible to at least one of the four races tested. Amongst the most susceptible ones were: AB 7419, AN 9022180, Aporé, Bambuí, Carioca 80, CNC, CNF 9287, Diamante Negro, Earlly Gallatin, Jamapa and KW 780. / Dissertação importada do Alexandria

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