In killer whales, fish- versus mammal-eating ecological differences are regarded as key ecological drivers of sociality, but the potential influence of specific target prey characteristics remains unclear. This thesis aimed to study the social patterns and dynamics of Icelandic killer whales feeding upon herring, a schooling prey that undergoes frequent changes in distribution and school size. I used a multi-disciplinary approach combining photo-identification and genetic data to understand the sociality, role of kinship and genetic differentiation within the population. Individuals sighted in summer-spawning and overwintering herring grounds during at least five separate days (N = 198) were considered associated if photographed within 20 seconds of each other. Photo-identified individuals were genotyped (N = 61) for 22 microsatellites and mitochondrial DNA control region (611 bp). The population had weak but non-random associations, fission-fusion dynamics at the individual level and seasonal patterns of preferred associations. The society was significantly structured but not hierarchically. Social clusters were highly diverse and, whilst kinship was correlated with association, it was not a prerequisite for social membership. Indeed, some cluster members had different mitochondrial haplotypes, representing separate maternal lineages. Individuals with different observed movement patterns were genetically distinct, but associated with each other. No sex-biased dispersal or inbreeding was detected. This study revealed that the Icelandic population has a multilevel society without clear hierarchical tiers or nested coherent social units, different from the well-studied salmon- (‘residents') and seal-eating populations in the Northeast Pacific. In the Icelandic population kinship drives social structure less strongly than in residents. These findings suggest effective foraging on schooling herring in seasonal grounds promotes the formation of flexible social groupings which can include non-kin. Killer whale sociality may be strongly influenced by local ecological context, such as the characteristics of the specific target prey (e.g., predictability, biomass, and density) and subsequent foraging strategies of the population.

Suspeita-se da Síndrome de Lynch (SL) a partir da história pessoal e familial do indivíduo. Posteriormente, os dados histopatológicos, imuno-histoquímicos e moleculares podem ser utilizados para aprimorar o diagnóstico da doença. Entretanto, um grande desafio no diagnóstico da Síndrome de Lynch é a baixa acurácia dos critérios clínicos utilizados. OBJETIVOS: Avaliar a frequência de SL em pacientes submetidos a tratamento cirúrgico por câncer colorretal e com história familial de câncer. Avaliar quais dos critérios clínicos e/ou moleculares seriam mais informativos no diagnóstico desta Síndrome na população brasileira. PACIENTES E MÉTODOS: Estudaram-se 458 casos de câncer colorretal (CCR), do Serviço de Coloproctologia do Departamento de Gastroenterologia do Hospital das Clínicas - FMUSP, de janeiro de 2005 a dezembro de 2008. História familial (HF) positiva para CCR ocorreu em 118 pacientes. Promoveu-se a revisão das lâminas para critérios histopatológicos de MSI (diretrizes de Bethesda), avaliação imuno-histoquímica (IHC) para as proteínas MLH1, MSH2, MSH6, PMS2, através do complexo avidina-biotina-peroxidase e instabilidade de microssatélites (MSI) (BAT-25, BAT-26, NR-21, NR-24 e MONO-27). Realizada a análise da mutação somática para o BRAF em todos os casos com MSI positiva. RESULTADOS: Dos 118 pacientes com HF, 61 (51,69%) preencheram pelo menos um dos critérios de Bethesda revisados. 36 eram do sexo feminino (59%), média de idade de 53,2 anos. Nove (14,7%) pacientes apresentaram todos os critérios de Amsterdam I. Cinquenta e dois tumores localizaram-se no cólon esquerdo. Os componentes histopatológicos de MSI incluíram: linfócitos intratumoral (47,5%), característica expansiva do tumor (29,5%) e o componente mucinoso (27,8%) (componentes histopatológicos de MSI instável) em 44 (72%). A IHC estava alterada em oito (13%) e a MSI em 12 pacientes (20%). Houve associação entre os critérios de Amsterdam I e MSI e na IHC com MLH1 e PMS2. Houve associação entre os critérios de Bethesda revisados com o sexo, na histopatologia com o componente mucinoso e a reação Crohn like; com a MSI e na IHC com o MLH1 e PMS2. O BRAF foi realizado nos 12 casos com MSI positiva e em todos os casos foram negativos. Os indivíduos que apresentaram o critério 4 de Bethesda revisado (CCR ou câncer associado a SL, diagnosticado em um ou mais parentes de primeiro grau, desde que uma das neoplasias tenha ocorrido antes dos 50 anos de idade), tiveram uma chance 10,6 vezes maior de apresentar MSI positiva. Propôs-se um escore para caracterizar pacientes com SL baseado nas variáveis estudadas nesta pesquisa. CONCLUSÕES: A frequência de Síndrome de Lynch nos pacientes submetidos a ressecção por câncer e com história familial foi de 20%. O critério 4 de Bethesda revisado associou-se mais fortemente à presença de instabilidade de microssatélites na população estudada. O escore desenvolvido neste estudo contribui como uma ferramenta prática na ampliação diagnóstica da Síndrome de Lynch / Lynch Syndrome is suspected due to the personal and familial history of the individual. Subsequently, histopathological, immunohistochemical and molecular data can be used to improve diagnosis of the disease. However, a major challenge in the diagnosis of Lynch Syndrome is the low accuracy of clinical criteria. OBJECTIVES: To assess the frequency of Lynch Syndrome in patients with familial cancer history submitted to colorectal cancer resection. To assess what clinical and / or molecular criteria would be the most informative in the diagnosis of this syndrome in Brazilian population. PATIENTS AND METHODS: 458 colorectal cancer (CRC) cases were studied, from the Coloproctology Unit of the Department of Gastroenterology, Hospital das Clinicas - USP, from January 2005 to December 2008. Positive family history (FH) for CRC occurred in 118 patients. The pathologic slides were reviewed for histological criteria for MSI (Bethesda guidelines), immunohistochemical analysis (IHC) for MLH1, MSH2, MSH6, PMS2 proteins, through the avidin-biotin-peroxidase complex, and microsatellite instability (MSI) (BAT-25, BAT-26, NR-21, NR-24 and MONO-27). BRAF somatic mutation was analyzed in all cases with positive MSI. RESULTS: Of the 118 patients with HF, 61 (51.69%) met at least one of the revised Bethesda criteria. Thirty-six were female (59%), and the mean age was 53.2 years. Nine (14.7%) patients presented all Amsterdam criteria I. Fifty-two tumors were located in the left colon. MSI histopathological components included: intratumoral lymphocytes (47.5%), expansive characteristics of the tumor (29.5%) and mucinous component (27.8%) (Histological unstable components of MSI) in 44 (72%). IHC was abnormal in eight (13%) and MSI in 12 patients (20%). There was an association between the Amsterdam criteria I and MSI; and between IHC with MLH1 and PMS2. There was an association with the revised Bethesda criteria with: sex, mucinous histology and Crohn\'s like reaction; with MSI and IHC with PMS2 and MLH1. BRAF was performed in 12 patients with MSI positive, and all were negative. Patients who presented the revised Bethesda criteria 4 (CRC or cancer associated with SL, diagnosed in one or more first-degree relatives, with one of the neoplasms occurred before 50 years of age), had a 10.6 increased chance to display positive MSI. Based on the studied variables, we proposed a score to characterize the Lynch Syndrome. CONCLUSIONS: The frequence of Lynch Syndrome in patients who were submitted to cancer resection, and had a cancer familial history was 20%. The criterion 4 Revised Bethesda was associated more strongly with the presence of microsatellite instability in the studied population. The developed score contributes as a practical tool in the diagnosis of Lynch Syndrome

INTRODUÇÃO: O câncer colorretal metastático (CCRm) é uma doença clinicamente e molecularmente heterogênea. Os pacientes apresentam diferentes prognósticos e respostas variáveis às terapias direcionadas contra o tumor. Alterações na função do sistema de reparo do DNA (deficiency mismatch repair - dMMR) estão associadas com o fenótipo de instabilidade de microssatélites e bom prognóstico em tumores de estádio inicial. No entanto, dMMR é raro no CCRm e pouco se sabe sobre sua influência na taxa de resposta (TR) ao tratamento. Nosso objetivo primário foi comparar a TR, de acordo com o status dMMR, nos pacientes com CCRm. Os desfechos secundários foram TR, conforme RAS e BRAF mutados, e a sobrevida global (SG), de acordo com dMMR. MÉTODOS: Estudo retrospectivo com grupo controle que comparou a TR por RECIST 1.1 em pacientes com CCRm, tratados com quimioterapia (QT) sistêmica, de acordo com o status dMMR. Os dados clínicos foram coletados, retrospectivamente, dos prontuários médicos. Todas as imagens foram digitais e recuperadas para avaliação de resposta por um único radiologista, cego quanto ao status dMMR. dMMR foi definido como a perda de expressão imuno-histoquímica em pelo menos um dos genes MMR (MLH1, MSH2, MSH6 e PMS2). Mutações em RAS e BRAF foram investigadas por meio de sequenciamento gênico. Os casos foram os pacientes com dMMR, e os controles, com MMR proficiente (pMMR), selecionados de forma consecutiva, em proporção de 1:2. Com base em características clínicas e moleculares, os indivíduos dMMR foram classificados como provável Lynch ou dMMR esporádico. Estatística descritiva foi usada para resumir os resultados. A associação entre dMMR e os resultados específicos de cada grupo foram analisados pelo teste do qui-quadrado, e para a avaliação de SG mediana, curvas de Kaplan-Meier e teste log-rank foram utilizados. Valores bicaudados de p < 0.05 foram considerados significativos. RESULTADOS: Entre janeiro de 2009 e janeiro de 2013, de 1270 pacientes, 762 foram elegíveis e rastreados para dMMR: N = 27 (3,5%) tiveram dMMR e N = 735 (96,5%) tiveram pMMR. Dada a raridade, foram incluídos 14 indivíduos com dMMR fora do período de inclusão, totalizando 41 casos (pacientes dMMR) e 84 controles (pacientes pMMR). Em análise por intenção de tratamento, considerando os pacientes que receberam pelo menos uma dose de QT baseada em oxaliplatina (N dMMR = 34), aqueles com dMMR apresentaram TR numericamente menor, comparados aos pMMR (11.7% vs 28.6%, OR: 0.33, IC 95%: 0.08-1.40, p = 0.088). Em análise por protocolo, incluindo apenas os pacientes que preencheram os critérios de inclusão (N dMMR = 33), aqueles com dMMR mantiveram TR menor à QT baseada em oxaliplatina em primeira linha, em comparação aos doentes pMMR, embora estatisticamente não significante (12.1% vs 28.6 %, OR: 0.34, IC 95%: 0.09-1.18, p = 0.102). Ainda neste contexto, os pacientes com possível Lynch apresentaram maior TR do que os indivíduos com provável dMMR esporádico (16% vs 0). Mutações em RAS ou BRAF não influenciaram na TR ou sobrevida. O status \"provável dMMR esporádico\" foi fator de pior prognóstico, quando todos os pacientes da amostra (N dMMR = 41) foram considerados. CONCLUSÃO: Este estudo sugere que dMMR é preditivo de resistência à quimioterapia baseada em oxaliplatina, como mostrado por outros estudos. Aparentemente, essa resistência é mais acentuada nos pacientes dMMR esporádicos, sugerindo heterogeneidade biológica nos doentes com CCRm e dMMR / BACKGROUND: Metastatic colorectal cancer (mCRC) is a clinically and molecularly heterogeneous disease, where patients present different prognosis and variable responses to cancer-directed therapies. Alterations in the function of DNA deficiency mismatch repair (dMMR) genes are associated with microsatellite instability and good prognosis in early stage tumors. However dMMR dysfunction is rare in mCRC and little is known about its influence on treatment response rate (RR). Our primary endpoint was to compare the RR of mCRC patients according to dMMR status and to explore differences between patients with likely sporadic versus likely Lynch-related tumors. Secondary endpoints were RR according to RAS and BRAF mutation status, and survival times as per dMMR status. METHODS: Retrospective study with control group that compared the RR by RECIST 1.1 in patients with mCRC treated with systemic chemotherapy according to dMMR status. Clinical data were collected retrospectively from medical charts. All images were digital and were retrieved for response evaluation by a single radiologist blinded to dMMR results. dMMR status was defined as loss of immunohistochemistry expression in at least one of the MMR genes (MLH1, MSH2, MSH6 e PMS2). RAS and BRAF mutations were investigated through next generation sequencing. Cases were defined as dMMR and controls, as proficient MMR (pMMR) patients, in a 1:2 fashion. Based on clinical and molecular features, dMMR patients were classified as likely Lynch or sporadic. Descriptive statistics was used to summarize the results. The association between dMMR and outcomes of each group were analyzed by chi-square test; estimates of median overall survival were done by the Kaplan-Meier method and comparisons, by the log-rank test. Two-tailed p values < 0.05 were considered significant. RESULTS: From January 2009 to January 2013, out of 1270 patients, 762 were eligible and screened for dMMR: N = 27 (3.5%) had dMMR and N = 735 (96.5%) had pMMR. Given the rarity, 14 dMMR cases outside the inclusion period were included, with a total of 41 cases (dMMR patients) and 84 controls (pMMR patients). By intention-to-treat analysis, considering all patients who received at least one dose of oxaliplatin-based chemotherapy (N dMMR = 34), those with dMMR had numerically lower RR, compared with pMMR (RR = 11.7% vs 28.6%, OR: 0.33, 95% CI: 0.08-1.40, p = 0.088). As per protocol analysis, considering only the patients who met inclusion criteria (N dMMR = 33), those with dMMR status persisted with numerically, but non-significant, lower RR to first-line oxaliplatin-based chemotherapy compared with pMMR (12.1% vs 28.6%, OR: 0.34, 95% CI: 0.09-1.18, p = 0.102); also, patients with likely Lynch-related mCRC presented higher RR than subjects with probable sporadic dMMR (16% vs 0). Either survival or RR was influenced by RAS or BRAF mutations. Probable sporadic dMMR status was a poor prognostic factor when all patients in the sample (N dMMR = 41) were analyzed. CONCLUSION: This study suggests that the dMMR phenotype is predictive of resistance to oxaliplatin-based chemotherapy, as shown by other studies. Apparently, such resistance is more pronounced in the sporadic dMMR patients, suggesting biological heterogeinity within the dMMR mCRC patients

Suspeita-se da Síndrome de Lynch (SL) a partir da história pessoal e familial do indivíduo. Posteriormente, os dados histopatológicos, imuno-histoquímicos e moleculares podem ser utilizados para aprimorar o diagnóstico da doença. Entretanto, um grande desafio no diagnóstico da Síndrome de Lynch é a baixa acurácia dos critérios clínicos utilizados. OBJETIVOS: Avaliar a frequência de SL em pacientes submetidos a tratamento cirúrgico por câncer colorretal e com história familial de câncer. Avaliar quais dos critérios clínicos e/ou moleculares seriam mais informativos no diagnóstico desta Síndrome na população brasileira. PACIENTES E MÉTODOS: Estudaram-se 458 casos de câncer colorretal (CCR), do Serviço de Coloproctologia do Departamento de Gastroenterologia do Hospital das Clínicas - FMUSP, de janeiro de 2005 a dezembro de 2008. História familial (HF) positiva para CCR ocorreu em 118 pacientes. Promoveu-se a revisão das lâminas para critérios histopatológicos de MSI (diretrizes de Bethesda), avaliação imuno-histoquímica (IHC) para as proteínas MLH1, MSH2, MSH6, PMS2, através do complexo avidina-biotina-peroxidase e instabilidade de microssatélites (MSI) (BAT-25, BAT-26, NR-21, NR-24 e MONO-27). Realizada a análise da mutação somática para o BRAF em todos os casos com MSI positiva. RESULTADOS: Dos 118 pacientes com HF, 61 (51,69%) preencheram pelo menos um dos critérios de Bethesda revisados. 36 eram do sexo feminino (59%), média de idade de 53,2 anos. Nove (14,7%) pacientes apresentaram todos os critérios de Amsterdam I. Cinquenta e dois tumores localizaram-se no cólon esquerdo. Os componentes histopatológicos de MSI incluíram: linfócitos intratumoral (47,5%), característica expansiva do tumor (29,5%) e o componente mucinoso (27,8%) (componentes histopatológicos de MSI instável) em 44 (72%). A IHC estava alterada em oito (13%) e a MSI em 12 pacientes (20%). Houve associação entre os critérios de Amsterdam I e MSI e na IHC com MLH1 e PMS2. Houve associação entre os critérios de Bethesda revisados com o sexo, na histopatologia com o componente mucinoso e a reação Crohn like; com a MSI e na IHC com o MLH1 e PMS2. O BRAF foi realizado nos 12 casos com MSI positiva e em todos os casos foram negativos. Os indivíduos que apresentaram o critério 4 de Bethesda revisado (CCR ou câncer associado a SL, diagnosticado em um ou mais parentes de primeiro grau, desde que uma das neoplasias tenha ocorrido antes dos 50 anos de idade), tiveram uma chance 10,6 vezes maior de apresentar MSI positiva. Propôs-se um escore para caracterizar pacientes com SL baseado nas variáveis estudadas nesta pesquisa. CONCLUSÕES: A frequência de Síndrome de Lynch nos pacientes submetidos a ressecção por câncer e com história familial foi de 20%. O critério 4 de Bethesda revisado associou-se mais fortemente à presença de instabilidade de microssatélites na população estudada. O escore desenvolvido neste estudo contribui como uma ferramenta prática na ampliação diagnóstica da Síndrome de Lynch / Lynch Syndrome is suspected due to the personal and familial history of the individual. Subsequently, histopathological, immunohistochemical and molecular data can be used to improve diagnosis of the disease. However, a major challenge in the diagnosis of Lynch Syndrome is the low accuracy of clinical criteria. OBJECTIVES: To assess the frequency of Lynch Syndrome in patients with familial cancer history submitted to colorectal cancer resection. To assess what clinical and / or molecular criteria would be the most informative in the diagnosis of this syndrome in Brazilian population. PATIENTS AND METHODS: 458 colorectal cancer (CRC) cases were studied, from the Coloproctology Unit of the Department of Gastroenterology, Hospital das Clinicas - USP, from January 2005 to December 2008. Positive family history (FH) for CRC occurred in 118 patients. The pathologic slides were reviewed for histological criteria for MSI (Bethesda guidelines), immunohistochemical analysis (IHC) for MLH1, MSH2, MSH6, PMS2 proteins, through the avidin-biotin-peroxidase complex, and microsatellite instability (MSI) (BAT-25, BAT-26, NR-21, NR-24 and MONO-27). BRAF somatic mutation was analyzed in all cases with positive MSI. RESULTS: Of the 118 patients with HF, 61 (51.69%) met at least one of the revised Bethesda criteria. Thirty-six were female (59%), and the mean age was 53.2 years. Nine (14.7%) patients presented all Amsterdam criteria I. Fifty-two tumors were located in the left colon. MSI histopathological components included: intratumoral lymphocytes (47.5%), expansive characteristics of the tumor (29.5%) and mucinous component (27.8%) (Histological unstable components of MSI) in 44 (72%). IHC was abnormal in eight (13%) and MSI in 12 patients (20%). There was an association between the Amsterdam criteria I and MSI; and between IHC with MLH1 and PMS2. There was an association with the revised Bethesda criteria with: sex, mucinous histology and Crohn\'s like reaction; with MSI and IHC with PMS2 and MLH1. BRAF was performed in 12 patients with MSI positive, and all were negative. Patients who presented the revised Bethesda criteria 4 (CRC or cancer associated with SL, diagnosed in one or more first-degree relatives, with one of the neoplasms occurred before 50 years of age), had a 10.6 increased chance to display positive MSI. Based on the studied variables, we proposed a score to characterize the Lynch Syndrome. CONCLUSIONS: The frequence of Lynch Syndrome in patients who were submitted to cancer resection, and had a cancer familial history was 20%. The criterion 4 Revised Bethesda was associated more strongly with the presence of microsatellite instability in the studied population. The developed score contributes as a practical tool in the diagnosis of Lynch Syndrome

La compréhension de la connectivité entre les nourriceries estuariennes et les habitats marins est fondamentale pour l'étude de la dynamique des peuplements et des populations de poissons et pour la conception de stratégies efficaces de conservation et de gestion des pêches. Le but de ce travail était donc de fournir une première référence faunistique et écologique des poissons des estuaires et du lagon de l'île de Socotra (Nord-Ouest de l'Océan Indien) pour les gestionnaires de la zone côtière, avec un accent particulier sur le fonctionnement des populations d'une espèce sentinelle: Terapon jarbua. Dans cette étude, une approche multidisciplinaire a été développée afin de comprendre le fonctionnement et l'importance des estuaires (TOCE's : Temporarily Open / Closed Estuaries) et du lagon de l'île de Socotra pour les poissons marins. Différents outils de la biologie et de la chimie (taxonomie, écologie, phylogéographie, génétique des populations, microstructure et microchimie des otolithes) ont été utilisés et les principales conclusions de ce travail sont les suivantes: 1) Les estuaires de Socotra sont composés de 64 espèces dans 30 familles, un chiffre élevé par rapport aux normes régionales. La comparaison avec les inventaires faunistiques d'Afrique du Sud et du Yémen suggère que Socotra joue le rôle de tremplin biogéographique, en permettant la connexion d'une grande variété de groupes taxonomiques provenant de différentes unités biogéographiques. De plus 33 des 64 espèces recensées sont considérées comme importantes pour l'économie locale, soulignant l'importance primordiale des estuaires comme sites de fraie et nourriceries, pour le fonctionnement durable des services écosystémiques. 2) La phylogéographie et la structure génétique des populations de T. jarbua ont été analysées considérant des marqueurs de type Cytochrome c Oxydase sous-unité I et microsatellites. Une différenciation génétique élevée et significative a été observée à l'échelle de l'Indo-Ouest Pacifique. Trois groupes de populations ont pu être identifiés, le groupe du Nord-Ouest de l'Océan Indien (Socotra, Yémen et Iran), le groupe de l'Ouest de l'Inde et le groupe de la Mer de Chine. Cependant, les grandes différences nucléotidiques observées soulèvent certaines questions concernant l'identification de l'espèce et suggèrent que T. jarbua pourrait être en réalité un complexe d'espèces, en dépit du fait que la coloration caractéristique de T. jarbua facilite son identification. A l'échelle plus restreinte du Nord-Ouest de l'Océan Indien, une expansion récente de la population de T. jarbua après des extinctions locales au cours des glaciations du Pléistocène pourrait expliquer la faible mais significative différenciation génétique. Le génotypage des marqueurs microsatellites souligne une différenciation génétique relativement élevée et significative entre les estuaires, sur le secteur Socotra-Yémen. Si la distance géographique n'est pas un facteur structurant majeur des populations de T. jarbua dans la région du Golfe d'Aden, le lien étroit entre les juvéniles T. jarbua et les TOCE, ainsi que les phénomènes d'ouverture associés à de possibles goulots d'étranglement démographiques dans ces systèmes côtiers, peuvent expliquer la mise en place d'une différenciation génétique locale significative entre les estuaires. Bien que l'environnement dynamique de la région puisse limiter la différenciation génétique, la courte durée du stade larvaire de cette espèce (25 jours estimés par la lecture des microstructures de l'otolithe) et la possible rétention des larves dans certains secteurs peuvent réduire l'homogénéisation à plus grande échelle géographique. 3) Les analyses de la composition élémentaire des nucleus d'otolithes suggèrent l'existence de plusieurs zones de fraie marines; ces données confrontées aux résultats des investigations en génétique des populations suggèrent un modèle régional de métapopulation composée de sous-populations ouvertes (sources multiples et mélange plus ou moins marqué des flux larvaires présentant une variabilité spatio-temporelle). De plus, les analyses des ratios Sr:Ba le long de l'axe de croissance des otolithes ont clairement montré des patrons de migrations des post-larves dans les estuaires où les juvéniles resteront deux ans. Enfin, les tests d'assignation d'empreintes géochimiques en bordure d'otolithe à des nourriceries spécifiques se sont avérés être très précis et pourraient conduire à terme à estimer la contribution d'une nourricerie à une population adulte de T. jarbua ainsi que d'autres espèces d'importance écologiques et économiques.

European hazelnut is a significant crop in the Pacific Northwest, and the US ranks 4th internationally for hazelnut production. Production in the Pacific Northwest is threatened, however, by the disease eastern filbert blight (EFB) caused by the fungus Anisogramma anomala (Peck) E. Müller. To meet the challenges faced by the hazelnut industry in Oregon and Washington, the breeding program at Oregon State University has focused on developing DNA marker technology and producing EFB resistant cultivars. This study focused on developing new microsatellite markers from hazelnut transcriptome sequences and on disease resistance from three accessions ('Culpla,' 'Crvenje,' and OSU 495.072) which showed no disease symptoms following a series of inoculations. DNA markers have been useful in hazelnut breeding for marker-assisted selection, construction of genetic linkage maps, cultivar fingerprinting, and phylogeny studies. Previously developed markers include AFLP, RAPD, ISSR, and microsatellite (SSR) markers developed from enriched libraries and ISSR fragments. This study utilized the transcriptome sequence from 'Jefferson' hazelnut to mine for microsatellites, align with the genomic sequence, design primers, screen for polymorphism, and characterize and map polymorphic markers. A total of 1432 microsatellites were mined from the transcriptome sequence, and the most frequently found motifs were AG (35.8%), AT (13.3%), and AAG (12.7%), and 382 primer pairs were designed. Screening showed that 119 markers were polymorphic, and these were characterized on sets of 50 and 14 accessions. Fifty-three markers that segregated in the mapping population or in three alternate populations were mapped and assigned to linkage groups. A dendrogram showed that accessions clustered mostly according to geographic origin. These results confirm the high level of diversity present in hazelnut, and the markers developed in this study will be useful for further genetics studies in hazelnut. The three EFB resistant parents 'Culpla,' 'Crvenje,' and OSU 495.072 were subjected to two inoculation treatments: greenhouse inoculations and exposure under an inoculation structure. The accessions remained free of disease after both treatments. Progeny segregating for resistance were produced. The progeny were inoculated either in the greenhouse or under the structure, and disease response recorded for each individual. DNA was extracted from seedlings, and sets of 32 seedlings from each resistant parent were screened with previously mapped markers using PCR and capillary electrophoresis. All three resistance sources were correlated with marker A614, allowing the resistance loci to be assigned to linkage group (LG) 6. The progeny were then screened with all known microsatellite markers on LG 6, and linkage maps constructed of the marker loci and resistance loci. Markers KG821, LG628, and LG696 are especially close to the resistance loci and will be useful for marker-assisted selection. Although these resistance loci are located in the same region of LG 6 as the 'Gasaway' resistance gene, they are different from 'Gasaway,' and markers linked to resistance will be useful for introgressing and pyramiding resistance in new cultivars. / Graduation date: 2013

Predators can have large effects on prey populations and on the structure and function of communities. In addition to direct consumption of prey, predators often cause prey to alter their foraging behavior, habitat selection, and morphology. These non-lethal effects of predators can propagate to multiple trophic levels and often exert equal or larger effects upon communities than those of direct consumption. For non-lethal predatory effects to occur, prey must detect and respond to predation risk. While the importance of information transfer in this process has been realized, few studies explore how prey responses are influenced by predator characteristics and environmental conditions that influence the transmission of cues indicative of predation risk. In this dissertation I investigate factors that influence how a single prey species evaluates and responds to predation risk. Here, I examined: 1) the type and nature of cues prey use to evaluate predator risk; 2) how predator identity, predator diet, and the relative risk of predators influence prey response to predation risk; 3) how hydrodynamic conditions influence the delivery of predator cues; 4) how biogeographic trends in predator distribution influence prey response to predation risk; and 5) how genetic structure might vary according to prey geographic location and habitat. To address these questions, I used a common intertidal model system consisting of the rocky intertidal whelk Nucella lapillus (Linnaeus, 1758) and a suite of its predators, the native rock crab Cancer irroratus (Say, 1817), Jonah crab Cancer borealis (Stimpson, 1859), and the invasive green crab Carcinus maenas (Linnaeus, 1758). Nucella use chemical cues emanating from their most common predator (Carcinus maenas) and crushed conspecifics to evaluate predation risk. Nucella from different habitats experience different levels of predation risk, and Nucella from habitats with high levels of predation had larger antipredatory responses to predator risk cues than Nucella that experienced less predation. These chemical cues indicative of predation risk are influenced by hydrodynamic conditions, and Nucella have the strongest anti-predatory response in flow velocities of u= ~4- 8 cm s^-1. Furthermore, Nucella from geographic regions where green crabs are historically absent did not elicit anti-predatory responses, while Nucella from regions where green crabs are common frequently responded. Findings from my dissertation research demonstrate that prey detection and response to predation risk is highly dependent upon predator identity, predator diet, environmental forces, and biogeographic patterns in predator and prey distributions.

Triops cancriformis (Crustacea: Notostraca) occurs in ephemeral habitats like rain pools or floodplain pools distributed over a large geographical range. The named habitats are disturbed by human impacts and, consequently, T. cancriformis is endangered throughout its distribution range. In the present thesis the populated habitats and threats are characterised and further morphological and genetic variations detected among and within European populations are reported. On the basis of recent investigations it is shown that T. cancriformis subspecies separation is hampered by an individual variability which points to the necessity of species revision. The analysis of mitochondrial gene sequence data suggests that the species has colonised most of Europe very recently. The advantage of a complex reproductive strategy in T. cancriformis in this process is discussed. The population structure resolved with nuclear DNA markers highlights that there is low allelic diversity among and within populations compared to other Branchiopoda (Daphnia). By means of the present study it can be shown that habitat conservation is most important to protect T. cancriformis.

Effects of man made pollutants on an ecosystem are initiated at the cellular level where a prime determinant for survival of an organism is its ability to metabolise and excrete toxic chemicals or their metabolites, thereby preventing cellular toxicity or damage to germ cell DNA. Cytochrome P450 (CYP) enzymes are responsible (in concert with the remainder of the Ah battery enzymes) for the metabolism of numerous xenobiotics and endogenous compounds, including the metabolic activation of most environmental toxic chemicals and carcinogens. Genetic polymorphisms which affect performance of these enzymatic detoxification systems may alter tolerance to pollutants and thus survival in polluted environments. Alterations in the susceptibility of individuals and the development of resistant populations has arisen by forced selection of populations with variant genes, resulting in increased detoxification capacity. There is evidence for such scenarios of variations in activities of pollutant biotransforming enzymes of fish contributing to survival in polluted estuarine environments and several chemically resistant populations have been identified in the USA and Europe. In fish it has been demonstrated that CYP1A enzyme activity is required to activate some carcinogenic xenobiotics to a metabolic state in which they can form DNA adducts. The mechanism of reduced CYP1A expression in highly contaminated populations may therefore represent resistance to chemical stressors. European flounder (Platichthys flesus) from some waterways which have a long history of severe sedimentary contamination do not show elevated levels of CYP1A. The aim of the current study was to investigate whether any heritable differences were apparent between offspring from parents inhabiting long-term polluted and pristine areas. Flounder were obtained from a highly polluted estuary in the UK and crossed with fish from a relatively pristine environment. Offspring were raised in communal tanks in order to standardise environmental conditions, and allow investigations into the genetic variation of CYP1A. To allow identification of offspring to parental fish, polymorphic microsatellite loci were isolated and characterised for the flounder. Novel cDNA probes to transcription factors in the detoxification pathway (AhR2 and ARNT2) were cloned for flounder, and RT-PCR / Southern blot methods were developed for quantitation of gene transcript levels. A novel method of CYP1A quantification using real-time PCR was developed. PAH and PCB exposure trials were carried out on mixed batch offspring, and CYP1A gene transcript levels assessed using Northern blot and real-time PCR techniques. Offspring were genotyped to their parents using the microsatellites obtained, and CYP1A transcript levels were correlated with clean and polluted areas. CYP1A was further correlated to transcription factor expression, and data are presented. Following exposure to the commercial PCB mixture, Aroclor 1254, CYP1A transcript levels were found to be significantly lower in families whose parents originated from a polluted area. This observation indicates that there is a possible genetic component to variation in CYP1A levels, and that these fish may have acquired a heritable tolerance to polluted areas. The lack of induction, or correlation with CYP1A levels, of AhR2 and ARNT2 expression indicates a possible AhR independent pathway for the metabolism of PCBs in the flounder. © Tom Dixon 2003 http://www.tomdixon.org

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