Contemporary population genetic structure and phylogeography of pink salmon

Thesis (Master's)--University of Washington, 2016-06

Nonparametric Evaluation of Quantitative Traits in Population-Based Association Studies when the Genetic Model is Unknown

Statistical association between a single nucleotide polymorphism (SNP) genotype and a quantitative trait in genome-wide association studies is usually assessed using a linear regression model, or, in the case of non-normally distributed trait values, using the Kruskal-Wallis test. While linear regression models assume an additive mode of inheritance via equi-distant genotype scores, Kruskal-Wallis test merely tests global differences in trait values associated with the three genotype groups. Both approaches thus exhibit suboptimal power when the underlying inheritance mode is dominant or recessive. Furthermore, these tests do not perform well in the common situations when only a few trait values are available in a rare genotype category (disbalance), or when the values associated with the three genotype categories exhibit unequal variance (variance heterogeneity). We propose a maximum test based on Marcus-type multiple contrast test for relative effect sizes. This test allows model-specific testing of either dominant, additive or recessive mode of inheritance, and it is robust against variance heterogeneity. We show how to obtain mode-specific simultaneous confidence intervals for the relative effect sizes to aid in interpreting the biological relevance of the results. Further, we discuss the use of a related all-pairwise comparisons contrast test with range preserving confidence intervals as an alternative to Kruskal-Wallis heterogeneity test. We applied the proposed maximum test to the Bogalusa Heart Study dataset, and gained a remarkable increase in the power to detect association, particularly for rare genotypes. Our simulation study also demonstrated that the proposed non-parametric tests control family-wise error rate in the presence of non-normality and variance heterogeneity contrary to the standard parametric approaches. We provide a publicly available R library nparcomp that can be used to estimate simultaneous confidence intervals or compatible multiplicity-adjusted p-values associated with the proposed maximum test.

Perception of health benefits of dietary fibre among the Portuguese population

Introduction: Dietary iber (DF) has been part of human diet since ever, and its beneits for the human health have been well estab-lished and scientiically conirmed. Among these stand improved gastrointestinal functions, prevent cholesterol, diabetes or CVD. Objectives: To study the level of knowledge of people residing in Portugal about the health effects related to an adequate ingestion of DF. Methods: This is a descriptive cross-sectional study carried out on a non-probabilistic sample of 382 adults residing in Portugal. The questionnaire included a section about the socio-demographic characteristics (age, gender, level of education and living environ- ment) and another about the relation between dietary iber and possible beneicial effects to treat and prevent diseases. The data was treated using the SPSS software (V22). Results: The results allowed concluding that people were dif- ferently informed about the effects of DF in preventing and/or treating different diseases, being constipation the most recog- nized, followed in decreasing order by obesity, bowel cancer, cholesterol, cardiovascular diseases, diabetes and breast can- cer. The results also showed that signiicant differences were encountered between age groups for most of the diseases evalu- ated, but not between genders, levels of education or living en- vironments. Conclusions: Generally, it was concluded that the participants in this study were relatively well informed about the roles of DF in preventing and/or treating various diseases.

Relationship between menopause and periodontal disease: a cross-sectional study in a Portuguese population

Article published under a “Creative Commons Attribution Noncommercial License”, enabling the unrestricted non-commercial use, distribution, and reproduction of the published article in any medium, provided that the original work is properly cited.

Prevalence of Mental Health Problems in Children and Its Associated Socio-Familial Factors in Urban Population of Semnan, Iran (2012)

Background: The World Health Organization (WHO) defines mental health as “a state of well-being in which every individual realizes own potential, can cope with the normal pressures of life, is able to work effectively, and can make a contribution to community”. Objectives: Mental Health Problems (MHP) is a great concern for all societies in terms of its burden and impact. This survey screened MHP and its impact in an Iranian urban population aged 6 - 12 years old, and explored its associated socio-familial factors. Patients and Methods: The survey was conducted in the elementary schools of Semnan, using random cluster sampling. Collection and analysis of data was performed using the parent version of the “Strengths and Difficulties Questionnaire (SDQ)” and survey commands of Stata-nine, taking into account cluster effect and population weights. Associations were assessed by fitting simple and multiple logistic regression models. P < 0.05 was considered significant. Results: With regard to the SDQ total score, 19.3% (95% CI: 8.6, 30.1) scored above the normal threshold (9.6% abnormal, 9.7% borderline). The frequency of problems ranged between 16.1% (peer problems) and 8.4% (emotional symptoms), and in all subscales boys were affected more than girls. The impact score was abnormal in 68.4% of all children, and was greater in girls than in boys. “A previously diagnosed mental health disorder” (OR = 11.11, 95% CI: 5.55, 25.00), “male gender” (OR = 1.43, 95% CI: 1.10, 1.87 and “less time spent with the child by father” (OR = 1.61, 95% CI: 1.20, 2.17) were significantly associated with an abnormal SDQ. Conclusions: The high rate of MHP in 6 - 12 year-old children and the lack of any significant correlation with their age, underpins the importance of early screening for MHP in schools, with particular focus on high risk groups.

Évaluation de l’impact des services en téléobstétrique du RUIS McGill offerts à une population de femmes inuites avec grossesse à risque élevé habitant sur la côte de la baie d’Hudson au Nunavik

L’accessibilité à des soins de santé pour une population habitant une région éloignée au Québec représente un défi de taille pour le Ministère de la santé et des services sociaux. Des solutions, telles que la télésanté, ont été présentées afin de pallier ce problème. Le RUIS McGill a ainsi développé un programme de téléobstétrique afin de desservir une population de femmes inuites à grossesse à risque élevé (GARE) habitant le Nunavik. L’objectif de ce mémoire fut de comprendre l’impact du service de téléobstétrique du RUIS McGill sur la santé des femmes et de leur nouveau-né ainsi que sur les coûts de santé et l’utilisation des services suite à son implantation au Centre de santé et de services sociaux Inuulitsivik sur la côte de la baie d’Hudson. Les femmes inuites à grossesse à risque élevé et leurs enfants de la région de la baie d’Hudson du Nunavik, éloignés des services obstétriques spécialisés, sont visés. Le service de téléobstétrique permet un accès aux obstétriciens du RUIS McGill localisés à Montréal. Un devis quasi-expérimental est utilisé pour examiner trois hypothèses portant sur l’état de santé des mères et des enfants, sur l’utilisation des services de santé et sur leurs coûts. Le service de téléobstétrique est devenu fonctionnel en 2006, offrant la possibilité de constituer une étude avant-après à deux groupes de femmes, soit celles ayant accouché avant 2006 (prétest) et celle ayant accouché après 2012 (post-test). La collecte de donnée se fit, dans son intégralité, par l’entremise des dossiers médicaux papier des participantes permettant l’analyse de 47 dossiers pour le prétest et de 81 dossiers pour le post-test. L’exécution d’analyse de covariance, de régression logistique et du test non paramétrique de Mann-Witney permit de conclure que le prétest et le post-test ne différent que sur deux variables, soient le poids à la naissance, plus faible dans le post-test et la pression artérielle de la mère à la naissance, plus élevée dans le post-test. Pour l’ensemble des autres variables portant sur les trois hypothèses à l’étude, les résultats de ce mémoire ne démontrent aucune différence significative entre les deux groupes démontrant ainsi qu’une même qualité de soins a été conservée suite à l’implantation du programme de téléobstétrique. Sur la base des résultats, ce mémoire recommande de revoir et modifier les objectifs du programme; de partager les bornes de communication de télésanté avec d’autres spécialités; d’entreprendre une évaluation du programme axée sur les coûts; de suivre rigoureusement l’utilisation du programme pour en maximiser l’efficacité et le potentiel; d’établir un tableau de bord; et d’entreprendre une étude évaluative comparative dans un service de téléobstétrique comparable.

Évaluation de l’impact des services en téléobstétrique du RUIS McGill offerts à une population de femmes inuites avec grossesse à risque élevé habitant sur la côte de la baie d’Hudson au Nunavik

L’accessibilité à des soins de santé pour une population habitant une région éloignée au Québec représente un défi de taille pour le Ministère de la santé et des services sociaux. Des solutions, telles que la télésanté, ont été présentées afin de pallier ce problème. Le RUIS McGill a ainsi développé un programme de téléobstétrique afin de desservir une population de femmes inuites à grossesse à risque élevé (GARE) habitant le Nunavik. L’objectif de ce mémoire fut de comprendre l’impact du service de téléobstétrique du RUIS McGill sur la santé des femmes et de leur nouveau-né ainsi que sur les coûts de santé et l’utilisation des services suite à son implantation au Centre de santé et de services sociaux Inuulitsivik sur la côte de la baie d’Hudson. Les femmes inuites à grossesse à risque élevé et leurs enfants de la région de la baie d’Hudson du Nunavik, éloignés des services obstétriques spécialisés, sont visés. Le service de téléobstétrique permet un accès aux obstétriciens du RUIS McGill localisés à Montréal. Un devis quasi-expérimental est utilisé pour examiner trois hypothèses portant sur l’état de santé des mères et des enfants, sur l’utilisation des services de santé et sur leurs coûts. Le service de téléobstétrique est devenu fonctionnel en 2006, offrant la possibilité de constituer une étude avant-après à deux groupes de femmes, soit celles ayant accouché avant 2006 (prétest) et celle ayant accouché après 2012 (post-test). La collecte de donnée se fit, dans son intégralité, par l’entremise des dossiers médicaux papier des participantes permettant l’analyse de 47 dossiers pour le prétest et de 81 dossiers pour le post-test. L’exécution d’analyse de covariance, de régression logistique et du test non paramétrique de Mann-Witney permit de conclure que le prétest et le post-test ne différent que sur deux variables, soient le poids à la naissance, plus faible dans le post-test et la pression artérielle de la mère à la naissance, plus élevée dans le post-test. Pour l’ensemble des autres variables portant sur les trois hypothèses à l’étude, les résultats de ce mémoire ne démontrent aucune différence significative entre les deux groupes démontrant ainsi qu’une même qualité de soins a été conservée suite à l’implantation du programme de téléobstétrique. Sur la base des résultats, ce mémoire recommande de revoir et modifier les objectifs du programme; de partager les bornes de communication de télésanté avec d’autres spécialités; d’entreprendre une évaluation du programme axée sur les coûts; de suivre rigoureusement l’utilisation du programme pour en maximiser l’efficacité et le potentiel; d’établir un tableau de bord; et d’entreprendre une étude évaluative comparative dans un service de téléobstétrique comparable.

The role of area-level deprivation and gender in participation in population-based faecal immunochemical test (FIT) colorectal cancer screening

This study aimed to investigate the effects of sex and deprivation on participation in a population-based faecal immunochemical test (FIT) colorectal cancer screening programme. The study population included 9785 individuals invited to participate in two rounds of a population-based biennial FIT-based screening programme, in a relatively deprived area of Dublin, Ireland. Explanatory variables included in the analysis were sex, deprivation category of area of residence and age (at end of screening). The primary outcome variable modelled was participation status in both rounds combined (with “participation” defined as having taken part in either or both rounds of screening). Poisson regression with a log link and robust error variance was used to estimate relative risks (RR) for participation. As a sensitivity analysis, data were stratified by screening round. In both the univariable and multivariable models deprivation was strongly associated with participation. Increasing affluence was associated with higher participation; participation was 26% higher in people resident in the most affluent compared to the most deprived areas (multivariable RR = 1.26: 95% CI 1.21–1.30). Participation was significantly lower in males (multivariable RR = 0.96: 95%CI 0.95–0.97) and generally increased with increasing age (trend per age group, multivariable RR = 1.02: 95%CI, 1.01–1.02). No significant interactions between the explanatory variables were found. The effects of deprivation and sex were similar by screening round. Deprivation and male gender are independently associated with lower uptake of population-based FIT colorectal cancer screening, even in a relatively deprived setting. Development of evidence-based interventions to increase uptake in these disadvantaged groups is urgently required.

Metabolic syndrome and associated factors in a population-based sample of schoolchildren in Colombia: The FUPRECOL Study

In contrast to the definition of metabolic syndrome (MetS) in adults, there is no standard definition of MetS in pediatric populations. We aimed to assess the differences in the prevalence of MetS in children and adolescents aged 9–17 years in the city of Bogota (Colombia) using four different operational definitions for these age groups and to examine the associated variables. A total of 673 children and 1,247 adolescents attending public schools in Bogota (54.4% girls; age range 9–17.9 years) were included. The prevalence of MetS was determined by the definitions provided by the International Diabetes Federation (IDF) and three published studies by Cook et al., de Ferranti et al., and Ford et al. The prevalence of MetS was 0.3%, 6.3%, 7.8%, and 11.0% according to the IDF, Cook et al., Ford et al., and de Ferranti et al. definitions, respectively. The most prevalent components were low high-density lipoprotein cholesterol and high triglyceride levels, whereas the least prevalent components were abdominal obesity and hyperglycemia. Overall, the prevalence of MetS was higher in obese than in non-obese schoolchildren. In conclusion, MetS diagnoses in schoolchildren strongly depend on the definition chosen. These findings may be relevant to health promotion efforts for Colombian youth to develop prospective studies and to define which cut-offs are the best indicators of future morbidity.

Is the human population a large-scale indicator of the species richness of ground beetles?

Aim Positive regional correlations between biodiversity and human population have been detected for several taxonomic groups and geographical regions. Such correlations could have important conservation implications and have been mainly attributed to ecological factors, with little testing for an artefactual explanation: more populated regions may show higher biodiversity because they are more thoroughly surveyed. We tested the hypothesis that the correlation between people and herptile diversity in Europe is influenced by survey effort

Genetic diversity and population structure of the sea lamprey (Petromyzon marinus L.) across its distributional range

Lampreys are a group of ancient vertebrates with 360 million years of existence. Throughout their evolution, they have acquired local adaptations to the colonized habitats, showing high plasticity and adaptive capacities. The sea lamprey (Petromyzon marinus L.) is a parasitic and anadromous species that occurs in both sides of the North Atlantic. The aims of this study were to analyse, using microsatellite markers, the genetic diversity and population structure of sea lamprey throughout its distributional range. Analyses demonstrated consistent signs of high population differentiation between European and North American samples (two-groups structure), most probably due to isolation by distance, but low differentiation among populations from the same coast. The apparent lack of homing in this species is in line with its high evolutive success, as homing may bring adults back to natal habitats that have changed, or that are intermittently unfavourable. Analyses also demonstrated higher levels of genetic diversity in North American samples; DIVERSIDADE GENÉTICA E ESTRUTURA POPULACIONAL DA LAMPREIA-MARINHA (PETROMYZON MARINUS L.) AO LONGO DA SUA ÁREA DE DISTRIBUIÇÃO Resumo: As lampreias são organismos ancestrais com cerca de 360 milhões de anos de existência. No decorrer da longa escala evolutiva têm vindo a adquirir adaptações aos locais que colonizaram, tendo uma forte capacidade evolutiva e adaptativa. A lampreia-marinha (Petromyzon marinus L.) é uma espécie parasita e anádroma que ocorre em ambas as costas do Atlântico Norte. Este estudo teve como principal objetivo estudar a diversidade genética e a estrutura populacional desta espécie ao longo da sua área de distribuição, através do uso de microssatélites. Os resultados demonstraram forte divergência entre populações das costas Este e Oeste do Atlântico Norte, provavelmente devido à elevada distância entre populações, mas pouca diferenciação entre populações da mesma costa. A ausência de homing nesta espécie terá contribuído para o seu sucesso evolutivo, uma vez que o homing pode levar indivíduos a reproduzirem-se em habitats que se tornaram desfavoráveis ou intermitentemente inapropriados. Os resultados demonstraram também uma maior variabilidade genética nas populações americanas.

Genetic structure and mating type analysis of the Pyricularia oryzae population causing widespread epidemics in southern Brazil.

Blast is a major disease of rice in Brazil, the largest rice-producing country outside Asia. This study aimed to assess the genetic structure and mating-type frequency in a contemporary Pyricularia oryzae population, which caused widespread epidemics during the 2012/13 season in the Brazilian lowland subtropical region. Symptomatic leaves and panicles were sampled at flooded rice fields in the states of Rio Grande do Sul (RS, 34 fields) and Santa Catarina (SC, 21 fields). The polymorphism at ten simple sequence repeats (SSR or microsatellite) loci and the presence of MAT1-1 or MAT1-2 idiomorphs were assessed in a population comprised of 187 isolates. Only the MAT1-2 idiomorph was found and 162 genotypes were identified by the SSR analysis. A discriminant analysis of principal components (DAPC) of SSR data resolved four genetic groups, which were strongly associated with the cultivar of origin of the isolates. There was high level of genotypic diversity and moderate level of gene diversity regardless whether isolates were grouped in subpopulations based on geographic region, cultivar host or cultivar within region. While regional subpopulations were weakly differentiated, high genetic differentiation was found among subpopulations comprised of isolates from different cultivars. The data suggest that the rice blast pathogen population in southern Brazil is comprised of clonal lineages that are adapting to specific cultivar hosts. Farmers should avoid the use of susceptible cultivars over large areas and breeders should focus at enlarging the genetic basis of new cultivars.

Adapting The Sniffin' Sticks Olfactory Test To Diagnose Parkinson's Disease In Estonia.

The aim of the study was to develop a culturally adapted translation of the 12-item smell identification test from Sniffin' Sticks (SS-12) for the Estonian population in order to help diagnose Parkinson's disease (PD). A standard translation of the SS-12 was created and 150 healthy Estonians were questioned about the smells used as response options in the test. Unfamiliar smells were replaced by culturally familiar options. The adapted SS-12 was applied to 70 controls in all age groups, and thereafter to 50 PD patients and 50 age- and sex-matched controls. 14 response options from 48 used in the SS-12 were replaced with familiar smells in an adapted version, in which the mean rate of correct response was 87% (range 73-99) compared to 83% with the literal translation (range 50-98). In PD patients, the average adapted SS-12 score (5.4/12) was significantly lower than in controls (average score 8.9/12), p < 0.0001. A multiple linear regression using the score in the SS-12 as the outcome measure showed that diagnosis and age independently influenced the result of the SS-12. A logistic regression using the SS-12 and age as covariates showed that the SS-12 (but not age) correctly classified 79.0% of subjects into the PD and control category, using a cut-off of <7 gave a sensitivity of 76% and specificity of 86% for the diagnosis of PD. The developed SS-12 cultural adaption is appropriate for testing olfaction in Estonia for the purpose of PD diagnosis.

One Step Forward: Contrasting The Effects Of Toe Clipping And Pit Tagging On Frog Survival And Recapture Probability.

Amphibians have been declining worldwide and the comprehension of the threats that they face could be improved by using mark-recapture models to estimate vital rates of natural populations. Recently, the consequences of marking amphibians have been under discussion and the effects of toe clipping on survival are debatable, although it is still the most common technique for individually identifying amphibians. The passive integrated transponder (PIT tag) is an alternative technique, but comparisons among marking techniques in free-ranging populations are still lacking. We compared these two marking techniques using mark-recapture models to estimate apparent survival and recapture probability of a neotropical population of the blacksmith tree frog, Hypsiboas faber. We tested the effects of marking technique and number of toe pads removed while controlling for sex. Survival was similar among groups, although slightly decreased from individuals with one toe pad removed, to individuals with two and three toe pads removed, and finally to PIT-tagged individuals. No sex differences were detected. Recapture probability slightly increased with the number of toe pads removed and was the lowest for PIT-tagged individuals. Sex was an important predictor for recapture probability, with males being nearly five times more likely to be recaptured. Potential negative effects of both techniques may include reduced locomotion and high stress levels. We recommend the use of covariates in models to better understand the effects of marking techniques on frogs. Accounting for the effect of the technique on the results should be considered, because most techniques may reduce survival. Based on our results, but also on logistical and cost issues associated with PIT tagging, we suggest the use of toe clipping with anurans like the blacksmith tree frog.

Design, Synthesis And Biological Evaluation Of Hybrid Bioisoster Derivatives Of N-acylhydrazone And Furoxan Groups With Potential And Selective Anti-trypanosoma Cruzi Activity.

Hybrid bioisoster derivatives from N-acylhydrazones and furoxan groups were designed with the objective of obtaining at least a dual mechanism of action: cruzain inhibition and nitric oxide (NO) releasing activity. Fifteen designed compounds were synthesized varying the substitution in N-acylhydrazone and in furoxan group as well. They had its anti-Trypanosoma cruzi activity in amastigotes forms, NO releasing potential and inhibitory cruzain activity evaluated. The two most active compounds (6, 14) both in the parasite amastigotes and in the enzyme contain the nitro group in para position of the aromatic ring. The permeability screening in Caco-2 cell and cytotoxicity assay in human cells were performed for those most active compounds and both showed to be less cytotoxic than the reference drug, benznidazole. Compound 6 was the most promising, since besides activity it showed good permeability and selectivity index, higher than the reference drug. Thereby the compound 6 was considered as a possible candidate for additional studies.