Du paysage génomique à la gestion des pêches chez le homard d'Amérique : structure des stocks à haute résolution et développement d'outils avancés en génomique marine appliqué aux enjeux de la pêche

Les ressources halieutiques représentent un enjeu majeur pour le Canada. Le homard d'Amérique (Homarus americanus) est l'espèce marine exploitée de plus grande valeur commerciale au Canada, ce qui rend essentielle la gestion durable de cette espèce. Ainsi, une gestion efficace nécessite la définition d'unités de gestion biologiquement significatives, ce qui requiert notamment une connaissance rigoureuse de la structure biologique des stocks. L'objectif général de cette thèse de doctorat consiste à documenter la variation génomique neutre et potentiellement adaptative à différentes échelles spatiales en vue de vérifier la concordance entre la structure génétique naturelle des populations et la délimitation des régions administratives sur lesquelles repose la gestion de la pêche du homard au Canada. Ce travail de recherche se base sur un large plan d'échantillonnage impliquant plus de 4 000 échantillons collectés dans 35 des 41 unités administratives de pêche pour cette espèce. Les analyses génomiques ont confirmé la présence d'une structure génétique hiérarchique dominée par deux grandes unités génétiques à large échelle spatiale, séparant les populations sur un axe latitudinal en deux régions Nord et Sud. La délimitation entre ces deux grandes régions a été identifiée avec précision au centre de l'unité de gestion 32. A l'intérieur des deux grandes régions, nos résultats basés sur la variation génétique neutre ont démontré un très faible degré de différenciation génétique et soutiennent une connectivité biologique importante entre les unités de gestion. L'étude de la variation génétique associée aux variables environnementales a révélé la présence d'une sous-structure au sein des régions Nord et Sud. En outre, des efforts considérables ont été déployés pour innover et identifier des nouveaux types de variants (i.e. variants structuraux) chez cette espèce pourtant dépourvue de ressources génomiques (i.e génome de référence). L'étude de ces nouveaux variants à mis en évidence des patrons de structure notamment dans le sud du Golfe du St-Laurent, suggérant un signal d'adaptation locale en lien avec la température. D'un point de vue global, l'ensemble des résultats soulignent l'intérêt d'étudier les diverses composantes du paysage génomique afin de saisir les différents axes de diversité et de différenciation génétique distribués au sein et entre les stocks. La recherche conduite durant cette thèse constitue la plus grande étude de la structure génomique des populations menée à ce jour chez les crustacés marins. Cet ensemble de données exceptionnelles nous a permis de développer de nouveaux outils avancés en génomique marine appliquée aux enjeux de la gestion des pêches. Finalement, considérant les nouvelles connaissances apportées par ce travail, nous proposons quelques éléments de réflexion ainsi que des nouvelles pistes de recherche afin d'aider à l'amélioration future du cadre de gestion de la pêche du homard au Canada.Fisheries resources are a major issue for Canada. The American lobster (Homarus americanus) is the most commercially valuable exploited marine species in Canada, which makes sustainable management of this species essential. Thus, effective management requires the definition of biologically significant management units, which requires a rigorous knowledge of the biological structure of the stocks. The general objective of this doctoral thesis is to document the neutral and putative adaptive genomic variation at different spatial scales in order to assess the concordance between the natural genetic structure of populations and the delineation of administrative regions on which the management of the lobster fishery in Canada is based. This research is based on a large sampling design involving more than 4,000 samples collected from 35 of the 41 administrative fishing units. Genomic analyses confirmed the presence of a hierarchical genetic structure dominated by two large genetic units at broad spatial scale, separating the populations on a latitudinal axis into two regions, North and South. The delineation between these two large regions has been accurately identified in the center of Management Unit 32. Within these two large regions, our results based on neutral genetic variation demonstrated a very low degree of genetic differentiation and support significant biological connectivity between the management units. The study of genetic variation associated with environmental variables revealed the presence of substructure within each of the northern and southern regions. Further, considerable efforts were made to develop innovative approaches to identify new types of variants (i.e. structural variants) in this species, which lacks genomic resources (i.e. reference genome). The study of these new variants has highlighted structural patterns, particularly in the southern Gulf of St. Lawrence, suggesting a signal of local adaptation related to temperature. Together, all of the results underline the importance of studying the various components of the genomic landscape in order to understand the different axes of genetic diversity and differentiation distributed within and between stocks. There search conducted during this thesis constitutes the largest study of population genomic structure in marine crustaceans to date. This exceptional data set has allowed us to develop new advanced tools in marine genomics applied to fisheries management issues. Finally, considering the new knowledge brought by this work, we propose a few elements for reflection as well as new avenues of research to help improve the future management framework of the lobster fishery in Canada

Garlic and its significance for the prevention of cancer in humans: a critical view.

Recently published results of epidemiologic case-control studies in China and Italy on gastric carcinoma in relation to diet suggest that consuming garlic may reduce the risk of gastric cancer. Chemical constituents of garlic have been tested for their inhibiting effect on carcinogenesis, using in vitro and in vivo models. In most experiments inhibition of tumour growth was established using fresh garlic extract, garlic compounds or synthetically prepared analogs. In this review the strengths and weaknesses of the experiments are discussed and the outcomes are evaluated to assess the possible significance of garlic or garlic compounds for the prevention of cancer in humans. It is concluded that evidence from laboratory experiments and epidemiologic studies is presently not conclusive as to the preventive activity of garlic. However, the available evidence warrants further research into the possible role of garlic in the prevention of cancer in humans

A prospective cohort study on Allium vegetable consumption, garlic supplement use, and the risk of lung carcinoma in The Netherlands

The association between the consumption of onions and leeks (vegetables belonging to the Allium genus), garlic supplements, and the risk of lung carcinoma was investigated in a large-scale prospective cohort study on diet and cancer in the Netherlands. The Netherlands Cohort Study was started in 1986 among 120,852 men and women, ages 55-69 years, by collecting information on usual diet and important life-style characteristics. After 3.3 years of follow-up, 550 incident lung carcinoma cases were observed. Information on Allium vegetable consumption was available for 484 lung carcinoma cases and 3123 members of a randomly sampled subcohort. In stratified analysis, a lower lung carcinoma risk was observed in the highest onion intake category [rate ratio (RR) = 0.65; 95% confidence interval, 0.45-0.95] compared to the lowest consumption category. After including other, dietary and nondietary, determinants of lung carcinoma in the multivariable models and using pack years for past and current smoking, instead of using smoking status categorized as never, ex-, and current smoking, the rate ratio in the highest intake category increased to 0.80 and was no longer significantly different from unity (95% confidence interval, 0.52-1.24). Leek consumption was not associated with risk for lung carcinoma (RR = 1.08; 95% confidence interval 0.80-1.45 in the highest intake category, compared to the lowest). No statistically significant trends in the rate ratios associated with increasing consumption of these vegetables were detected for lung carcinoma or the four histological subtypes. A higher lung carcinoma risk was observed for those subjects who used exclusively garlic supplements (RR = 1.78; 95% confidence interval, 1.08-2.92), compared to those not taking dietary supplements. A lower lung carcinoma risk was seen for those using garlic supplements together with any other supplement (RR = 0.93; 95% confidence interval 0.46-1.86) compared to those using any other supplement. In conclusion, we found no evidence of a relation between the consumption of onions or leeks and the risk of lung carcinoma or any of the histological subtypes. Garlic supplement use seems not associated with a lower risk of lung carcinoma

Anthropometry in relation to prostate cancer risk in the Netherlands Cohort Study

In the Netherlands Cohort Study, the authors investigated whether anthropometry is associated with prostate cancer risk. At baseline in 1986, 58,279 men aged 55-69 years completed a self- administered questionnaire on diet, anthropometry, and other risk factors for cancer. After 6.3 years of follow-up, 681 cases were available with complete data on height and weight at baseline, and for 523 cases, there were data for weight at age 20 years. In both age-adjusted and multivariate case-cohort analyses (adjusted for age, family history of prostate cancer, and socioeconomic status), height, body mass index (BMI; kg/m2), and lean body mass (kg) at baseline were not associated with prostate cancer risk. The rate ratios of prostate cancer for men with a BMI at age 20 of less than 19, 19-20.9, 21-22.9, 23-24.9, and 25 or greater were 1.00 (reference), 1.06, 1.09, 1.39, and 1.33, respectively (p for trend = 0.02). For gain in BMI from age 20 years to age of the cohort at baseline, an inverse trend in risk was found (p for trend = 0.01), which did not persist after additional adjustment for BMI at age 20 (p for trend = 0.07). In subgroup analyses, no clear associations between anthropometry and advanced prostate cancer were found. Our findings suggest that body composition in young adulthood may already exert an effect on later risk of prostate cancer

The role of diet and other environmental factors in the causation of gastric cancer in Iran—A population based study

Despite a declining trend in the incidence of gastric cancer (GC), it is still a major global public health concern of the 21st century. The rates of GC reported from Ardabil Province, Iran, are among the highest in the world. To investigate risk factors for GC in Ardabil, we undertook a population-based case-control study. The study aimed to recruit all Ardabil residents newly diagnosed with GC in the time period of 2004–2005, and 2 controls per case. Participants were interviewed using a structured questionnaire. Ten milliliters of blood was collected for blood grouping and investigating the presence of IgG antibodies against Helicobacter pylori. During the study period, 217 people with GC and 394 controls were recruited. In multivariate analysis, diet and Helicobacter pylori infection (OR 5 2.41; 95% CI: 1.35–4.32) were found to be the factors that were most strongly related to GC. High intake of Allium vegetables (OR 5 0.35) and fruit, especially citrus fruit (OR 5 0.31) and consumption of fresh fish (OR 5 0.37) were significantly protective. On the other hand, consumption of red meat (OR 5 3.40) and dairy products (OR 5 2.28) were positively associated with the risk of GC. People who had a preference for higher salt intake (OR 5 3.10) and drinking strong and hot tea (OR 5 2.64 and 2.85, respectively) were at higher risk. In conclusion, Helicobacter pylori infection as measured by serum IgG as well as the consumption of red meat and dairy products increases the risk of GC in Ardabil, while the intake of fresh fruit and fresh fish decrease the risk