The pecan nut casebearer, Acrobasis nuxvorella Neunzig (Lepidoptera: Pyralidae) is the most damaging insect pest of pecan, Carya illinoinensis (Wang) K. Koch (Fagales: Juglandaceae). Two sex pheromones have been identified for this species and are currently being used to assist pecan growers in the timing of insecticide applications. The discovery that there are two pheromone types produced by A. nuxvorella has led to complications in the implementation of pheromone monitoring programs. One pheromone (referred to as standard) is attractive to moths in the southern US, but not in Mexico. The other pheromone (referred to as Mexican) is attractive to moths in the southern US and in Mexico. Because most male lepidopterans respond only to a specific pheromone, it was suspected that there were two pheromone strains of A. nuxvorella, one exclusively present in the northern distribution of A. nuxvorella (US strain) and the other widely distributed from Sonora, Chihuahua, and Durango in Northern Mexico to Texas, Georgia, and Oklahoma in the US (Mexican strain). In order to confirm the existence of the two alleged pheromone strains, AFLP markers were obtained and analyzed, male response to pheromones was observed and phenological differences were assessed. Additionally, the relative abundance of each of the two pherotypes was evaluated and the population structure of this pest across its geographic distribution was determined. Results of genetic analysis show that the genetic differentiation between these insects is not explained by pheromone type. This information is further supported by a pheromone assay in which a large proportion of US collected A. nuxvorella males and Mexican collected A. nuxvorella males chose both pheromones when tested multiple times. Furthermore, no phenological differences were detected between the two pherotypes in the US, although significantly more male A. nuxvorella in the US are attracted to field-deployed pheromone traps baited with the standard pheromone than the Mexican pheromone. Finally, population genetic analyses indicate a high degree of genetic structure in A. nuxvorella across its geographic distribution, with the genetically distinct populations occurring in areas where A. nuxvorella is not native, but has been introduced.

The presented thesis consists of three papers/manuscripts (one published, one under review, one manuscript) on population genetic aspects of a host-parasite model, caryophyllidean tapeworm Wenyonia virilis and mochokid catfish Synodontis schall, in recently separated drainage basins, Lake Turkana and the Nile River. Three main topics are addressed herein: (i) intra- and inter-population genetic variability in and among hosts and parasites, (ii) comprehensive assessment of host model taxonomic status using multiple approaches, (iii) comparison of parasite intraspecific phenotypic with population genetic pattern. Two different genetic markers were applied to address these topics mtDNA (coxI) and whole genome scanning method (AFLP).

Doctor of Philosophy / Department of Plant Pathology / William W. Bockus / Septoria tritici blotch caused by Mycosphaerella graminicola (anamorph Septoria tritici), is an important disease of wheat worldwide capable of reducing yields by as much as 30 to 40%. In Kansas, the disease is widespread and losses in individual fields can exceed 25%. This study examined the genetic structure of Kansas populations of M. graminicola at different spatial scales (micro-plot, macro-plot, and statewide) using amplified fragment length polymorphism (AFLP) markers. Three primer pairs were used to resolve 174 polymorphic loci from 476 isolates. The results indicated high levels of genotypic variability, which is consistent with a genetically diverse initial inoculum. Genetic identities among populations representing the three spatial scales were >98%. Tests for differentiation among populations due to population subdivision revealed that on average 97.5% of the genetic variability occurred within populations with a correspondingly high migration rate of 16 to 23 individuals per generation. We observed little evidence of linkage disequilibrium, on average, only 4.6% of locus pairs were in disequilibrium. Our results indicate that Kansas populations of M. graminicola are characterized by regular recombination, are genetically diverse, and appear to be homogenous across different spatial scales. These populations are probably components of a larger pathogen pool that is distributed at least across much of Kansas and probably the central Great Plains. Because of the frequent recombination, the risk of adaptation of Kansas populations of M. graminicola to fungicide treatments or resistance genes is high and could be dispersed very quickly, whether these new pathogenic traits occur locally through mutation or by migration from other areas.

No abstract available. / Dissertation (MSc)--University of Pretoria, 2011. / Genetics / unrestricted

[EN] In the last years, various genotyping techniques were developed for isolation of Mycobacterium tuberculosis complex (MTBC) that has demonstrated a high discriminatory power. In this study, after the identification of selected strains at level of species by Genotype MTBC technique, we evaluated the profit of the simplified amplified-fragment Length Polymorphism technique (AFLPs) and the Mycobacterial Interspersed Repetitive Units technique (MIRU-15). A total of 131 mycobacterium tuberculosis isolates were analyzed, 68 isolates were collected in Ecuador, from the Clinical Laboratory of Hospital Alli Causai located in city of Ambato, and the Laboratory of Bacteriology in Carlos Andrade Marín Hospital located in the capital city Quito. The remaining 63 isolates were harvested in Spain and belong to microorganism's collection of Microbiology Services of Consorcio Hospital General Universitario and Hospital Clínico Universitario of the city of Valencia. Among these isolates, 126 were identified by conventional methods such as molecular MTBC, corresponding to 106 patients. The Mycobacterium tuberculosis control strain ATCC 25177 was also identified as such by this method. The AFLPs technique allowed as to group the strains in twelve patterns (P1 to P8, P10, P12, P13, P14), of which the most prevalent were patterns P1 with 77 (61.1%) and P2 with 27 (21, 4%) isolates, representing 82.5% of the same. These were followed by the pattern P5 with 5 (3.9%) isolates, the patterns P3, P4 and P6 grouped 3 isolates each one (2.4%), the patterns P8 and P12 with 2 isolates (1.6% ) and finally the patterns P7, P10, P13 and P14 with 1 isolated each one (0.8%). The control strain M. tuberculosis ATCC 25177, showed a restriction profile that prevented their inclusion in any of the patterns described. The discriminatory power of the Hunter-Gaston discriminatory index (HGDI) method was 0.5812 against to 0.9843 of the MIRU-15 technique, which grouped 69 strains (54.8%) in 20 clonal complex and 57 unique patterns (45.2%). In the case of Spain, the strains were related mostly to the lineage 4 or Euro-American including: Cammeroon (1.59%), Haarlem (36.51%), S (31.75%), and LAM (19.05%); the lineage 6 or West Africa I (9.53%), the lineage 1 or EIA (1.59%) In the case of Ecuador the strains were related to the lineage 4: Haarlem (42.86%), S (33.33%) and LAM (22.22%) and Beijing lineage 2 (1.59%) from Asia. The MIRU-VNTR Variable-Number Tandem Repeats (15 loci) technique proved to be a stable system, reproducible and high discriminatory power in comparison with AFLPs system, allowing the use of it to conduct prospective population studies with the aim of contributing to the public health programs to control Tuberculosis (TB). / [ES] En los últimos años se han desarrollado diversas técnicas de genotipificación para aislados de Mycobacterium tuberculosis complex (MTBC) que han demostrado tener un alto poder discriminatorio. En este estudio, tras identificación de las cepas seleccionadas al nivel de especie mediante la técnica comercial GenoType MTBC, se ha evaluado la utilidad de la técnica simplificada del Polimorfismo de Longitud de Fragmentos Amplificados (AFLPs) y la técnica de Unidades Repetitivas Intercaladas Micobacterianas (MIRU-15). Se analizaron un total de 131 aislados clínicos de los cuales 68 aislados fueron recolectados en Ecuador, provenientes tanto del Laboratorio Clínico del Hospital Alli Causai ubicado en la ciudad de Ambato, provincia de Tungurahua como del Laboratorio de Bacteriología del Hospital Carlos Andrade Marín ubicado en la ciudad capital Quito, provincia de Pichincha. Los 63 aislados restantes fueron recolectados en España y pertenecían colección de microorganismos de los Servicios de Microbiología del Consorcio Hospital General Universitario y Hospital Clínico Universitario de la ciudad de Valencia, provincia de Valencia. De éstos aislados, 126 fueron identificados por métodos convencionales y moleculares como MTBC, correspondientes a 106 pacientes. La cepa control Mycobacterium tuberculosis ATCC 25177 también fue identificada como tal mediante este método. La técnica AFLPs permitió agrupar a las cepas en doce patrones (P1 a P8, P10, P12, P13, P14), de los cuales los más prevalentes fueron los patrones P1 y P2 con 77 (61,1%) y 27 (21,4%) aislados respectivamente, lo que supone el 82,5% del total de los mismos. Le siguieron en frecuencia el patrón P5 con 5 (3,9%) aislados, los patrones P3, P4 y P6 agruparon a 3 aislados cada uno (2,4%), los patrones P8 y P12 con 2 aislados (1,6%) y finalmente los patrones P7, P10, P13 y P14 con 1 aislado cada uno (0,8%). La cepa control M. tuberculosis ATCC 25177, mostró un perfil de restricción que no permitió su inclusión en ninguno de los patrones descritos. El poder discriminatorio del método (HGDI) fue de 0,5812 frente a 0.9843 de la técnica MIRU-15, que agrupó a 69 cepas (54,8%) en 20 complejos clonales y 57 patrones únicos (45,2%). Para el caso de España, las cepas estuvieron relacionadas en su mayoría con el linaje 4 o Euro-Americano que incluye: Cammeroon (1,59%), Haarlem (36,51%), S (31,75%), y LAM (19,05%); el linaje 6 o West Africa I (9,53%), el linaje 1 o EIA (1,59%), Para el caso de Ecuador las cepas estaban relacionadas con el linaje 4: Haarlem (42,86%), S (33,33%), y LAM (22,22%) y el linaje 2 Beijing (1,59%) originario de Asia. La técnica MIRU-VNTR (15 loci) demostró ser un sistema estable, reproducible y con un poder discriminatorio alto en comparación con AFLPs lo que permitiría emplearlo para realizar estudios poblacionales prospectivos con la finalidad de contribuir a los programas de Salud Pública para el control de la Tuberculosis (TB). / [CAT] En els últims anys s'han desenvolupat diverses tècniques de genotipificació per aïllats de Mycobacterium tuberculosis complex (MTBC) que han demostrat tenir un alt poder discriminatori. En aquest estudi, després de la identificació de les soques seleccionades al nivell d'espècie mitjançant la tècnica comercial GenoType MTBC, s'ha avaluat la utilitat de la tècnica simplificada del Polimorfisme de longitud de fragments amplificats (AFLPs) i la tècnica d'Unitats repetitives Intercalades micobacterianes (Miru-15). Es van analitzar un total de 131 aïllats clínics dels quals 68 aïllats van ser recollectats a Equador, provinents tant del Laboratori Clínic de l'Hospital Alli Causai situat a la ciutat d'Ambato, província de Tungurahua com del Laboratori de Bacteriologia de l'Hospital Carlos Andrade Marín ubicat a la ciutat cabdal Quito, província de Pichincha. Els 63 aïllats restants van ser recollectats a Espanya i pertanyien a la collecció de microorganismes dels Serveis de Microbiologia del Consorci Hospital General Universitari i Hospital Clínic Universitari de la ciutat de València, província de València. D'aquests aïllats, 126 van ser identificats per mètodes convencionals i moleculars com MTBC, corresponents a 106 pacients. La soca control Mycobacterium tuberculosi ATCC 25177 també va ser identificada com a tal mitjançant aquest mètode. La tècnica AFLPs va permetre agrupar les soques en dotze patrons (P1 a P8, P10, P12, P13, P14), dels quals els més prevalents van ser els patrons P1 i P2 amb 77 (61,1%) i 27 (21, 4%) aïllats respectivament, fet que suposa el 82,5% del total dels mateixos. El van seguir en freqüència el patró P5 amb 5 (3,9%) aïllats, els patrons P3, P4 i P6 van agrupar a 3 aïllats cadascun (2,4%), els patrons P8 i P12 amb 2 aïllats (1,6%) i finalment els patrons P7, P10, P13 i P14 amb 1 aïllat cadascun (0,8%). La soca control M. tuberculosis ATCC 25177, va mostrar un perfil de restricció que no va permetre la seva inclusió en cap dels patrons descrits. El poder discriminatori del mètode (HGDI) va ser de 0,5812 enfront de 0,9843 de la tècnica MIRU-15, que va agrupar a 69 soques (54,8%) en 20 complexos clonals i 57 patrons únics (45,2%). Per al cas d'Espanya, les soques van estar relacionades majoritàriament amb el llinatge 4 o Euro-Americà que inclou: Cammeroon (1,59%), Haarlem (36,51%), S (31,75%), i LAM (19,05%); el llinatge 6 o West Africa I (9,53%), el llinatge 1 o EIA (1,59%), Pel cas de l'Equador les soques estaven relacionades amb el llinatge 4: Haarlem (42,86%), S ( 33,33%), i LAM (22,22%) i el llinatge 2 Beijing (1,59%) originari d'Àsia. La tècnica Miru-VNTR (15 loci) va demostrar ser un sistema estable, reproduïble i amb un poder discriminatori alt en comparació amb AFLPs, el que permetria emprar-lo per realitzar estudis poblacionals prospectius amb la finalitat de contribuir als programes de salut pública per al control de la Tuberculosi (TB). / Jiménez Arias, AP. (2016). Genotipificación de Mycobacterium tuberculosis complex mediante herramientas moleculares [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/62681 / TESIS

Acer rubrum L. and Liriodendron tulipifera L. are prolific throughout their ranges in the Southeastern U.S. and also have increasingly important roles in forestry and wood products in this region. The relatively low density and intermediate strength of the wood makes them versatile for use in many different wood products. Exploring the genetic structure of these species could provide a foundation for further genetic and breeding exploration with these economically important trees. This study utilizes amplified fragment length polymorphism to determine the level of genetic diversity of these species in contrasting physiographic provinces. AFLP was performed using five primer combinations on samples collected from six unmanaged populations of each species in the Mountains and Coastal Plain of the Southeastern U.S. Wood density was determined using an X-ray densitometer. A. rubrum lacked strong genetic structure while L. tulipifera showed differentiation between physiographic provinces. Genetic diversity of A. rubrum was lower within the Mountain populations (He: 0.327) than the Coastal Plain populations (He: 0.365). The average wood density for A. rubrum is lower in the Mountains (539.00 kg/m^3) than in the Coastal Plain (575.43 kg/m^3). Genetic diversity of L. tulipifera was higher overall (He: 0.289) than within the Mountain populations (He: 0.281) or the Coastal Plain populations (He: 0.271). The average wood density for L. tulipifera is greater in the Mountains (445.45 kg/m^3) than in the Coastal Plain (441.67 kg/m^3). / Master of Science

Potato haploids have been recent components in protoplast fusion research, strategies to combine wild and cultivated potato germplasm and the generation of economically valuable mutant phenotypes. Additionally, most major genetic mapping and QTL analyses in potato have utilized haploid germplasm to simplify linkage-mapping computations. The accuracy of genetic assumptions concerning the randomness and genetic purity of haploid genomes may directly affect the statistical validity of many results in current potato research. In the present study, AFLP analysis was conducted on two sibling S. phureja "BARD 1-3" monoploid populations derived by androgenesis in anther culture, and gynogenesis through the use of a haploid-inducing pollinator, S. phureja "IVP 101." Little indication of somaclonal variation and haploid-inducer gene introgression was found in the monoploid band data suggesting genomic stability. Segregation of marker alleles that were heterozygous in the parent was distorted from the expected 1:1 ratio in both populations, ranging from 35% in the gynogenic monoploids (GM) to 46% in the androgenic monoploids (AM). Genetic diversity appeared more random among the monoploid populations after skewed marker data was removed from phylogenetic analyses. Bilateral and unilateral marker skewness in the monoploid populations may respectively indicate common and unique segregation distorting loci (SDL) present in the AM and GM genomes. Representatives of both SDL types were located on a partial linkage map created using androgenic monoploid data. / Master of Science

O Actinobaculum suis é um dos principais micro-organismos relacionados a infecções de trato urinário em fêmeas suínas. As características de crescimento deste agente dificultam o isolamento bacteriano tradicional, o que pode tornar a sua prevalência subestimada. Este estudo teve por objetivos desenvolver a reação em cadeia pela polimerase (PCR) para detecção do A. suis, avaliar a sensibilidade e especificidade desta técnica e comparar seu desempenho com o isolamento bacteriano. Além disso, as cepas isoladas foram caracterizadas através do polimorfismo de comprimento de fragmentos amplificados (AFLP) e submetidas à determinação da concentração inibitória mínima para caracterização dos perfis de susceptibilidade antimicrobiana. Foram analisados 45 suabes prepuciais de machos e 192 urinas de fêmeas suínas provenientes de três granjas. Os resultados indicaram que a PCR desenvolvida foi específica para o A. suis e apresentou limiar de detecção entre 1,0 X 101 UF/mL e 1,0 X 102 UFC/mL. A frequência de A. suis encontrada através da PCR foi de 82,2% (37/45) nos suabes prepuciais e de 8,9% (17/192) nas urinas de fêmeas. No que se refere ao isolamento, nenhuma das amostras de urina foi positiva para o agente, enquanto 31,1% (14/45) dos suabes foram positivos. A partir das amostras positivas isoladas dos suabes prepuciais foram selecionadas 20 cepas de A. suis. Os perfis de susceptibilidade entre estas cepas foram semelhantes, no entanto diferiram dos isolados utilizados como controle e provenientes de uma fêmea com infecção urinária. A técnica de PCR foi mais eficiente que o isolamento na identificação de amostras positivas para A. suis. Através do AFLP com uma única enzima foi possível caracterizar todos os isolados e relacionar os dados obtidos com a origem das cepas e o perfil de resistência. Até o presente não há relatos na literatura de caracterização genotípica de A. suis através do AFLP ou detecção do agente através da PCR. / Actinobaculum suis is an important agent related to urinary infection in swine females. The growth characteristics of this agent hamper the traditional bacterial isolation, which can make their prevalence underestimated. The purpose of this study was to develop the polymerase chain reaction (PCR) for Actinobaculum suis detection, to evaluate the sensitivity and specificity of this technique and compare the results with bacterial isolation. Moreover, the isolates were characterized by amplified fragment length polymorphism (AFLP) and subjected to determination of minimum inhibitory concentration for characterization of the antimicrobial susceptibility profiles. Forty-five preputial swabs from boars and a hundred and ninety-two urine samples from sows of three herds were analyzed. The results indicate that the developed PCR was specific for A. suis, presenting a limit detection between 1.0 X 101 UFC/ml and 1.0 X 102 UFC/ml. A.suis frequency by PCR was 82.2% (37/45) in male preputial swabs and 8.9% (17/192) in females urine. Through traditional isolation, none of the urine samples were positive, while A.suis growing was observed in 31.1% (14/45) of the swabs. From the positive samples of the preputial swabs were selected 20 A.suis strains. The susceptibility profiles among these strains were similar, but differed from the female isolates used as control. The PCR technique was more effective than isolation for the A.suis detection. The AFLP with a single enzyme was able to characterize all isolates and relate the data obtained with the strains origin and resistance profile. Until present, there are no reports of genotypic characterization of A. suis strains through AFLP or agent detection by PCR.

A infecção por Actinobacillus pleuropneumoniae, doença conhecida como pleuropneumonia suína, assumiu grande importância na suinocultura moderna devido à alta ocorrência observada nos rebanhos. O impacto da doença está relacionado à capacidade do agente em causar pneumonia severa, levando os animais a óbito ou doença crônica, resultando em graves prejuízos zootécnicos. Diante desse cenário, o controle e monitoramento do agente se faz importante por meio da identificação dos diferentes sorotipos, da análise genética e da determinação dos perfis de resistência aos antimicrobianos. O objetivo do presente estudo foi caracterizar fenotípica e genotípicamente estirpes de Actinobacillus pleuropneumoniae isoladas a partir de quadros de pneumonia em suínos. Um total de 85 estipes de A. pleuropneumoniae foram submetidas a reação em cadeia pela polimerase (PCR) para identificação e sorotipagem, determinação da concentração inibitória mínima de antimicrobianos, polimorfismo do comprimento de fragmentos amplificados (AFLP) e eletroforese em gel de campo pulsado (PFGE). Os sorotipos mais frequentes foram: 5 (38,8%), 10 (29,4%), 7 (5,9%), 8 (5,9%) e 6 (3,5%), sendo que 14 (16,5%) estirpes foram não tipáveis. Foi observada alta heterogeneidade de perfil genético entre as estirpes analisadas, tanto pelo AFLP quanto pelo PFGE, e o índice discriminatório para cada técnica foi 0,97 e 0,84, respectivamente. Todas as estirpes foram sensíveis ao ceftiofur, gentamicina, tulatromicina e tilmicosina, sendo que 98,8% das estirpes foram resistentes à tilosina e altas taxas de resistência foram observadas ainda para as tetraciclinas, clindamicina e sulfadimetoxina. / Infection by Actinobacillus pleuropneumoniae, a disease known as swine pleuropneumonia, has gained greater relevance to modern pig farming due to the high recurrence rate observed in herds. The impact of the disease relates to the capacity of the agent to cause severe pneumonia, leading to animal death or chronic conditions, thus resulting in severe zootechnical losses. In view thereof, the control and monitoring of the agent is key, being performed through the identification of different serotypes, genetic analysis and determination of antimicrobial resistance profiles. The objective of this study was to characterize phenotypically and genotypically Actinobacillus pleuropneumoniae strains isolated from swine with clinical presentation of pneumonia. A total of 85 strains of A. pleuropneumoniae were subject to polymerase chain reaction (PCR) for identification and serotyping, determination of the minimal inhibitory concentration, amplified fragment length polymorphism (AFLP) and pulsed field gel electrophoresis typing techniques (PFGE). Most recurring serotypes were: 5 (38.8%), 10 (29.4%), 7 (5.9%), 8 (5.9%) and 6 (3.5%), of which 14 (16.5%) strains were nontypeable. High genetic heterogeneity was observed for both AFLP and PFGE, and the discriminatory index for each technique was 0.97 and 0.84, respectively. All 85 strains were susceptible to ceftiofur, gentamicin, tulatromicin and tilmicosin, 84 of which were resistant to tylosin, and high resistance rates were also observed for clindamycin, tetracyclines and sulfadimethoxine.

A Bordetella avium é o agente etiológico da bordetelose aviária, uma doença altamente contagiosa que afeta o trato respiratório superior das aves. B. avium adere-se preferencialmente às células do epitélio ciliado traqueal, promovendo inflamação e deformação da mucosa respiratória. As infecções do trato respiratório das aves resultam em grandes prejuízos para toda indústria avícola, desta forma, o presente estudo teve como objetivo a caracterização genotípica e de sensibilidade a antimicrobianos de isolados de B. avium provenientes de perus com histórico de aerossaculite. Dentre os 300 animais examinados, isolou-se B. avium de 13 aves e foram selecionadas 20 cepas do agente para os estudos posteriores. Através do antibiograma realizado pela técnica de disco difusão observou-se um alto número de cepas resistentes aos antimicrobianos beta lactâmicos (amoxacilina, ampicilina, penicilina e ceftiofur), assim como para lincomicina, sulfonamidas e combinação sulfonamidas/trimetoprima (cotrimoxazol) e uma grande heterogeneidade resultando em 15 perfis distintos. Os antimicrobianos com maiores níveis de sensibilidade foram o florfenicol, seguidos pelas quinolonas, doxiciclina e pelas tetraciclinas. Todas as cepas foram caracterizadas através da PFGE e do AFLP, apresentando 15 pulsotipos e 16 perfis genotípicos respectivamente. Os métodos fenotípicos e genotípicos apresentaram capacidade discriminatória semelhante e revelaram uma grande diversidade dentre os isolados analisados. / Bordetella avium is the etiologic agent of avian bordetellosis, a highly contagious disease that affects the upper respiratory tract of birds. B. avium adheres preferentially to ciliated tracheal epithelial cells, promoting inflammation and deformation of the respiratory mucosa. Infections of the respiratory tract of birds resulting in large losses for the entire poultry industry in this way, this study aimed to characterize genotypic and antimicrobial susceptibility of isolates of B. avium from turkeys with a history of Airsacculitis. Among the 300 animals examined, B. avium was isolated from 13 turkeys and 20 strains were selected for further studies. Through the antibiogram performed by disk diffusion technique was observed a high number of strains resistant to beta-lactamic antibiotics (amoxicillin, ampicillin, penicillin and ceftiofur), as well as, lincomycin, sulfonamides and sulfonamide combination/ trimethoprim (cotrimoxazole) and a high level of heterogeneity resulting in 15 different profiles. The antimicrobials with higher levels of sensitivity were florfenicol, followed by quinolones, doxycycline and tetracycline. All strains were characterized through to PFGE and AFLP, presenting 15 pulsotypes and 16 genetic profiles, respectively. Phenotypic and genotypic methods showed similar discriminatory capacity and presented a high diversity among isolates examined.