The propagation of contaminants in the environment continues to threaten public health and safety. Conventional analytical techniques for environmental detection require centralized facilities and intensive resources for operation. An effective implementation of a wide network of field deployable point-of-use (POU) sensors can potentially enable real-time monitoring of water quality parameters and inform decision making on public health outbreaks. The use of nanotechnology and field-deployable analytical tools can potentially advance the development of POU sensors for future field application. In this dissertation, we developed environmental sensing techniques that utilize nanocomposites made of low-cost, biocompatible, and sustainable nanomaterials combined with Raman spectroscopy. First, a technology pre-assessment was performed that included a comprehensive evaluation of cellulose-derived nanocomposites and nanobiotechnology enabled techniques for their sustainable long-term environmental application. Furthermore, to contribute to the better understanding of the potential environmental implications of nanomaterial production and application, life cycle assessment (LCA) was used to evaluate the environmental impacts of six iron precursors and seven iron oxide nanoparticle synthesis methods. Secondly, in the technology development step, gold (Au) and iron oxide (Fe3O4) nanoparticles were incorporated onto bacterial cellulose nanocrystals and nanoscale magnetite were synthesized. As proof-of-concept environmental applications, the Au@Fe3O4@BCNCs were applied for the magnetic separation and surface-enhanced Raman scattering (SERS) detection of malachite green isothiocyanate (MGITC), and nanoscale magnetite were applied for phosphate (PO43-) removal and recovery from synthetic urine matrices. Finally, in the technological application step, three environmental sensing applications are presented that use nanomaterial-based sensor platforms and/or Raman spectroscopic techniques. The first application involved using Lectin-modified BCNCs coupled SERS and machine learning for discrimination of bacterial strains. The second application presents a simple Raman-stable isotope labeling approach for the study of viral infection of bacteria. The third application involved use of SERS pH nanoprobes for measuring pH in droplets of complex matrices (e.g., DMEM cell culture media, human saliva). / Doctor of Philosophy / The current generation of analytical tools for environmental detection rely upon centralized facilities and intensive resources for operation. The combination of nanotechnology and field deployable analytical tools can aid in the development of point-of-use (POU) sensors for field monitoring of environmental contaminants. In this dissertation, we combined low-cost, biocompatible, and sustainable nanomaterials with Raman spectroscopy-based techniques to develop potentially field-deployable environmental sensing techniques. First, a technology pre-assessment was performed which involved a comprehensive evaluation of cellulose-derived nanocomposites and nanobiotechnology enabled techniques for their sustainable long-term environmental application. Furthermore, life cycle assessment (LCA) was used to evaluate the environmental impacts of iron oxide nanoparticle synthesis methods to better understand environmental impacts of nanoparticle production. Secondly, in the technology development step, we developed the nanocomposites: Au and Fe3O4 nanoparticles incorporated bacterial cellulose nanocrystals and nanoscale magnetite. As proof-of-concept environmental applications, the Au@Fe3O4@BCNCs were used for the detection of malachite green isothiocyanate (MGITC), and the nanoscale magnetite were used for phosphate (PO43-) removal and recovery from synthetic urine. Finally, in the technological application step, (1) selective detection of bacteria was performed using lectin-modified BCNCs as SERS biosensors coupled with SERS and machine learning. (2) Viral infection of bacteria was evaluated using Raman spectroscopy and Deuterium isotope labeling, and (3) pH in micro-droplets of DMEM cell culture media and human saliva were observed using SERS pH nanoprobes.

Les retardateurs de flamme (RF) sont des substances utilisées dans de nombreux produits synthétiques pour limiter la propagation du feu et ainsi améliorer la sécurité des habitations et des lieux publics. En raison de leur stabilité, de leur bioaccumulation et de leur toxicité, l’utilisation massive de certains RF, en particulier halogénés parmi lesquels la famille de Dechloranes, génère cependant un problème de contamination de l’environnement qui pose aujourd’hui la question d’éventuelles répercussions sur la santé humaine. Les Dechloranes ont été détectés pour la première fois dans l’environnement en 2006 et préoccupent, depuis, la communauté scientifique et les autorités sanitaires. Le présent travail avait pour objectif de contribuer à combler le manque manifeste de données sur les niveaux de prévalence en Dechloranes.Pour ce faire, une stratégie analytique ciblée, dédiée à l’identification et à la quantification des Dechloranes à l’état de traces (pg/g) dans des denrées alimentaires d’origine animale (DAOA) et des huiles végétales et basée sur un couplage GC-HRMS a été développé. Une attention particulière a été portée à la maîtrise des contaminations procédurales, eu égard au caractère ubiquitaire de certains composés. L’application de la méthode développée à 378 échantillons de poissons d’eaux douces de surface en France et de DAOA et huiles végétale collectées en France, au Liban et dans quatre pays d’Afrique subsaharienne a permis de brosser le premier état des lieux des niveaux de contamination environnementale et alimentaire dans ces pays, jusqu’à estimer l'exposition alimentaire de leurs populations à ces composés persistants et émergents. / Flame retardants (FR) are substances used in many synthetic products to limit the spread of fire and thus improve the safety of homes and public places. Due to their stability, bioaccumulation and toxicity, certain FRs, in particular halogenated ones among which the family of Dechloranes, are widely used, generating an issue of environmental contamination with potential repercussions on human health. Dechloranes were detected for the first time in the environment in 2006 and have since raised concerns to the scientific community and health authorities. The purpose of this paper is to help fill the obvious gap in data on prevalence levels of Dechloranes. To this end, a targeted analytical strategy dedicated to the identification and quantification of trace amounts of Dechloranes (pg/g) in animal foods (DAOA)and vegetable oils based on a GC-HRMS method has been developed. Particular attention has been paid to the control of procedural contaminations, given the ubiquitous nature of certain compounds. This method was applied to 378 samples of surface freshwater fish in France and DAOA and vegetable oils collected in France, Lebanon and four sub-Saharan African countries, and draw for the first time an inventory of levels of environmental and food contamination in these countries to estimate the dietary exposure of their populations to these persistent and emerging compounds

We eat foods not nutrients. What is more, we eat them in combinations. Consequently, capturing our complex food habits is likely an advantage in nutrition research. The overall aim of this doctoral thesis was therefore to investigate dietary patterns in the Swedish population –nutrient intakes, nutritional biomarkers and health aspects. Prostate cancer is the most common cancer among men in the developed world. However, the impact of dietary factors on disease risk is largely unknown. In Study I we investigated the association between a Mediterranean- and a Low-carbohydrate-high-protein dietary pattern and prostate cancer risk, in a cohort of elderly Swedish men. The latter (but not the former) was associated, inversely, with prostate cancer risk when taking validity in food records into account. Diet is one of our main exposure routes to environmental contaminants. Hence, such exposure could act as a mediating factor in the relation between diet and health. In Study II we investigated the association between; a Mediterranean- and a Low-carbohydrate-high-protein dietary pattern, as well as the official dietary recommendations, and circulating levels of environmental contaminants, in an elderly Swedish population. The first two patterns were positively related to levels of both persistent organic pollutants and heavy metals, whilst the dietary recommendations were inversely associated to dioxin and lead. Finally, although dietary patterns are likely to influence health, little is known about current dietary patterns in Sweden. In Study III we used a data-reduction method to identify dietary patterns in a nationwide sample of the Swedish population. Two major patterns were derived; a Healthy pattern of foods generally considered healthy (e.g. vegetables, fruits, fish and vegetable-oils) and a Swedish traditional pattern (with e.g. meats, potatoes, sauces, non-Keyhole milk-products, sweet-bakery products and margarine). Derived patterns were associated to population characteristics and the Healthy dietary pattern was inversely associated to anthropometric variables in Study IV. Dietary characteristics of the patterns were well reflected in correlations to nutrient intake and (to a lesser extent) in nutritional biomarkers. In conclusion dietary patterns for overall health should be considered, as well as other lifestyle-factors, when interpreting results in nutrition epidemiology and establishing dietary recommendations.

Dans le contexte libanais, les infrastructures de traitement et d’approvisionnement en eau potable ne sont pas optimales et il existe un manque de connaissances sur l’association entre la consommation d’eau et les niveaux d’exposition aux métaux et éléments traces. La présente étude est une première tentative faisant état de l'exposition aux métaux et aux éléments traces dans des sous-groupes de la population libanaise en utilisant une approche de biosurveillance multi-matrices. Les concentrations en 11 métaux et éléments traces (aluminium (Al), arsenic (As), cadmium (Cd), chrome (Cr), cuivre (Cu), fer (Fe), plomb (Pb), manganèse (Mn), sélénium (Se), uranium (U), zinc (Zn)) ont été mesurées dans des échantillons d'urine, de cheveux et d'ongles d’orteils d'un groupe de la population et les niveaux ont été comparés en fonction de l'âge, du sexe, du tabagisme, du statut économique, de la zone géographique et de la source d'eau potable. Alors que la plupart des concentrations urinaires et d'ongles n'étaient pas statistiquement différentes entre les hommes et les femmes, les concentrations mesurées d'éléments dans les cheveux étaient statistiquement plus élevées chez les femmes que chez les hommes. Les concentrations urinaires d'Al, Cu, Se et Zn étaient statistiquement plus élevées chez les enfants comparativement aux adolescents et aux adultes. Les concentrations de plusieurs éléments dans les cheveux et les ongles (As, Cd, Pb, Mn, Se dans les cheveux et les ongles plus Al, Fe dans les ongles d’orteils) étaient significativement plus élevées chez les enfants que chez les adolescents et/ou adultes (MG chez les enfants vs. les adolescents vs. les adultes dans les cheveux: 0,009 vs 0,009 vs. 0.005 µg As/g (p<0,01); 0,046 vs. 0,016 vs. 0,022 µg Cd/ g (p<0,05); 1,16 vs. 0,580 vs. 0,627 µg Pb/g (p<0,1); 0,305 vs. 0,168 vs. 0,275 µg Mn/g (p<0,1); 0,365 vs. 0,370 vs. 0,217 µg Se/g (p<0,05) et dans les ongles d’orteils : 17,0 vs. 14,3 vs. 7,31 µg Al/g et 56,9 vs. 46,0 vs. 23,8 µg Fe/g (p<0,05). Le statut tabagique n’a aucune influence sur les concentrations de As, cd et Pb. Les niveaux de Cd, Pb et Mn étaient également statistiquement plus élevés dans les échantillons des sous-groupes ayant un statut économique inférieur (Cd et Pb dans les 3 matrices urines, cheveux et ongles d’orteils respectivement de 0,223 µg Cd/L(p<0,1); 0,062 µg Cd/ g (p<0,05) et 0,038 µg Cd/ g (p<0,01); 1,16 µg Pb/L(p<0,05); 1,84 µg Pb/ g (p<0,01) et 0,840 µg Pb/ g (p<0,01) et Mn dans les cheveux et ongles d’orteils respectivement de 0,434 µg Mn/ g (p<0,05); 0,689 µg Mn/g (p<0,05). Les mêmes tendances ont été observées pour la stratification en fonction de la zone géographique, mais la différence n'était pas statistiquement significative, sauf pour le Pb dans l'urine où les participants de Beyrouth centre avaient des niveaux urinaires significativement moins élevés que les autres zones (0,560 µg Pb/L(p<0,01). Très peu de corrélations ont été identifiées entre les sources d’eau potable et les concentrations des métaux et éléments traces dans les urines, cheveux et ongles d’orteils. Cependant, une corrélation a été trouvée entre les niveaux d’As, Cd et Pb dans les cheveux et les ongles d’orteils respectivement (r = 0,4, p<0,05); (r = 0,310, p<0,05) et (r = 0.,270, p<0,1). Dans l’ensemble, les résultats ont montré que la population était exposée à des concentrations plus élevées de certains métaux que les autres populations, une attention particulière doit être accordée à l'exposition aux As, Cd et Pb, Mn et Se. Bien que la source d'eau n'ait pas contribué à la différence dans les niveaux d'exposition, les niveaux de certains métaux et éléments traces différaient selon l'âge, le sexe, les zones géographiques de résidence et le statut économique. Il pourrait être pertinent d'étendre ce type d'enquête à une initiative de biosurveillance humaine à grande échelle dans la population libanaise afin de valider et de généraliser les résultats et d'observer les tendances temporelles dans le temps. / In the Lebanese context, drinking water treatment and supply infrastructures are not optimal and it exists a lack of knowledge on the association between water consumption and levels of exposure to metals and trace elements. The present study is a first attempt reporting exposure to metals and trace elements in subgroups of the Lebanese population using a multi-matrix biomonitoring approach. Concentrations of 11 metals and trace elements (aluminum (Al), arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), lead (Pb), manganese (Mn), selenium (Se), uranium (U), zinc (Zn)) were measured in urine, hair and toenail samples from a population group and the levels were compared according to the age, gender, smoking status, economic status, geographic area, and source of drinking water. While most urinary and nail concentrations were not statistically different between men and women, measured element concentrations in hair were statistically higher in women than in men. Urinary concentrations of Al, Cu, Se and Zn were statistically higher in children compared to adolescents and adults. Concentrations of several elements in hair and nails (As, Cd, Pb, Mn, Se in hair and toenails plus Al, Fe in toenails) were significantly higher in children than in adolescents and/or adults (MG in children vs. adolescents vs. adults in hair: 0.009 vs. 0.009 vs. 0.005 µg As/g (p<0.01); 0.046 vs. 0.016 vs. 0.022 µg Cd/g (p< 0.05), 1.16 vs. 0.580 vs. 0.627 µg Pb/g (p<0.1), 0.305 vs. 0.168 vs. 0.275 µg Mn/g (p<0.1), 0.365 vs. 0.370 vs. 0.217 µg Se/g (p<0.05) and in the nails: 17.0 vs. 14.3 vs. 7.31 µg Al/g and 56.9 vs. 46.0 vs. 23.8 µg Fe/g. Smoking status has no influence on the concentrations of metals and trace elements. The levels of Cd, Pb and Mn were also statistically higher in the samples of the subgroups with a lower economic status (Cd and Pb in the 3 matrices urine, hair and toenails respectively of 0.223 µg Cd/L (p<0, 1);0.062 µg Cd/g (p<0.05) and 0.038 µg Cd/g (p<0.01);1.16 µg Pb/L(p<0.05);1.84 µg Pb/ g (p<0.01) and 0.840 µg Pb/g (p<0.01) and Mn in hair and toenails respectively 0.434 µg Mn/g (p<0.05), 0.689 µg Mn/g (p <0.05). The same trends were observed for stratification according to geographical area, but the difference was not statistically significant, except for Pb in urine where participants from central Beirut had significantly lower urinary levels than the others zones (0.560 µg Pb/L (p<0.01). Very few correlations have been identified between the sources of drinking water and the concentrations of metals and trace elements in urine, hair and toenails. However, a correlation was found between As, Cd and Pb levels in hair and toenails respectively r = 0.4, p<0.05), r = 0.310, p<0.05) and r = 0.270, p<0.1). Overall, the results showed that the population was exposed to higher concentrations of some metals than other populations, particular attention should be paid to exposure to As, Cd and Pb, Mn and Se. Although water source did not contribute to the difference in exposure levels, levels of some metals and trace elements differed by age, sex, smoking status, geographic areas of residence, and economic status. It might be relevant to extend this type of investigation to a large-scale human biomonitoring initiative in the Lebanese population in order to validate and generalize the results and to observe temporal trends over time.

The goal of this project was to develop novel bacterial biomarkers for use in an industrial context. These biomarkers would be used to determine aluminium industry activity impact on a local ecosystem. Sediment bacterial communities of the Saguenay River are subjected to industrial effluent produced by industry in Jonquière, QC. In-situ responses of these communities to effluent exposure were measured and evaluated as potential biomarker candidates for exposure to past and present effluent discharge. Bacterial community structure and composition between control and affected sites were investigated. Differences observed between the communities were used as indicators of a response to industrial activity through exposure to effluent by-products. Diversity indices were not significantly different between sites with increased effluent exposure. However, differences were observed with the inclusion of algae and cyanobacteria. UniFrac analyses indicated that a control (NNB) and an affected site (Site 2) were more similar to one another with regard to community structure than either was to a medially affected site (Site 5) (Figure 2.4). We did not observe a signature of the microbial community structure that could be predicted with effluent exposure. Microbial community function in relation to bacterial mercury resistance (HgR) was also evaluated as a specific response to the mercury component present in sediments. Novel PCR primers and amplification conditions were developed to amplify merP, merT and merA genes belonging to the mer-operon which confers HgR (Table 5.6). To our knowledge, the roles of merP and merT have not been explored as possible tools to confirm the presence of the operon. HgR gene abundance in sediment microbial communities was significantly correlated (p < 0.05) to total mercury levels (Figure 3.4) but gene expression was not measurable. We could not solely attribute the release of Hg0 from sediments in bioreactor experiments to a biogenic origin. However, there was a 1000 fold difference in measured Hg0 release between control and affected sites suggesting that processes of natural remediation may be taking place at contaminated sites (Figure 3.7). Abundance measurements of HgR related genes represent a strong response target to the mercury immobilized in sediments. Biomarkers built on this response can be used by industry to measure long term effects of industrially derived mercury on local ecosystems. The abundance of mer-operon genes in affected sites indicates the presence of a thriving bacterial community harbouring HgR potential. These communities have the capacity to naturally remediate the sites they occupy. This remediation could be further investigated. Additional studies will be required to develop biomarkers that are more responsive to contemporary industrial activity such as those based on the integrative oxidative stress response.

The goal of this project was to develop novel bacterial biomarkers for use in an industrial context. These biomarkers would be used to determine aluminium industry activity impact on a local ecosystem. Sediment bacterial communities of the Saguenay River are subjected to industrial effluent produced by industry in Jonquière, QC. In-situ responses of these communities to effluent exposure were measured and evaluated as potential biomarker candidates for exposure to past and present effluent discharge. Bacterial community structure and composition between control and affected sites were investigated. Differences observed between the communities were used as indicators of a response to industrial activity through exposure to effluent by-products. Diversity indices were not significantly different between sites with increased effluent exposure. However, differences were observed with the inclusion of algae and cyanobacteria. UniFrac analyses indicated that a control (NNB) and an affected site (Site 2) were more similar to one another with regard to community structure than either was to a medially affected site (Site 5) (Figure 2.4). We did not observe a signature of the microbial community structure that could be predicted with effluent exposure. Microbial community function in relation to bacterial mercury resistance (HgR) was also evaluated as a specific response to the mercury component present in sediments. Novel PCR primers and amplification conditions were developed to amplify merP, merT and merA genes belonging to the mer-operon which confers HgR (Table 5.6). To our knowledge, the roles of merP and merT have not been explored as possible tools to confirm the presence of the operon. HgR gene abundance in sediment microbial communities was significantly correlated (p < 0.05) to total mercury levels (Figure 3.4) but gene expression was not measurable. We could not solely attribute the release of Hg0 from sediments in bioreactor experiments to a biogenic origin. However, there was a 1000 fold difference in measured Hg0 release between control and affected sites suggesting that processes of natural remediation may be taking place at contaminated sites (Figure 3.7). Abundance measurements of HgR related genes represent a strong response target to the mercury immobilized in sediments. Biomarkers built on this response can be used by industry to measure long term effects of industrially derived mercury on local ecosystems. The abundance of mer-operon genes in affected sites indicates the presence of a thriving bacterial community harbouring HgR potential. These communities have the capacity to naturally remediate the sites they occupy. This remediation could be further investigated. Additional studies will be required to develop biomarkers that are more responsive to contemporary industrial activity such as those based on the integrative oxidative stress response.

The goal of this project was to develop novel bacterial biomarkers for use in an industrial context. These biomarkers would be used to determine aluminium industry activity impact on a local ecosystem. Sediment bacterial communities of the Saguenay River are subjected to industrial effluent produced by industry in Jonquière, QC. In-situ responses of these communities to effluent exposure were measured and evaluated as potential biomarker candidates for exposure to past and present effluent discharge. Bacterial community structure and composition between control and affected sites were investigated. Differences observed between the communities were used as indicators of a response to industrial activity through exposure to effluent by-products. Diversity indices were not significantly different between sites with increased effluent exposure. However, differences were observed with the inclusion of algae and cyanobacteria. UniFrac analyses indicated that a control (NNB) and an affected site (Site 2) were more similar to one another with regard to community structure than either was to a medially affected site (Site 5) (Figure 2.4). We did not observe a signature of the microbial community structure that could be predicted with effluent exposure. Microbial community function in relation to bacterial mercury resistance (HgR) was also evaluated as a specific response to the mercury component present in sediments. Novel PCR primers and amplification conditions were developed to amplify merP, merT and merA genes belonging to the mer-operon which confers HgR (Table 5.6). To our knowledge, the roles of merP and merT have not been explored as possible tools to confirm the presence of the operon. HgR gene abundance in sediment microbial communities was significantly correlated (p < 0.05) to total mercury levels (Figure 3.4) but gene expression was not measurable. We could not solely attribute the release of Hg0 from sediments in bioreactor experiments to a biogenic origin. However, there was a 1000 fold difference in measured Hg0 release between control and affected sites suggesting that processes of natural remediation may be taking place at contaminated sites (Figure 3.7). Abundance measurements of HgR related genes represent a strong response target to the mercury immobilized in sediments. Biomarkers built on this response can be used by industry to measure long term effects of industrially derived mercury on local ecosystems. The abundance of mer-operon genes in affected sites indicates the presence of a thriving bacterial community harbouring HgR potential. These communities have the capacity to naturally remediate the sites they occupy. This remediation could be further investigated. Additional studies will be required to develop biomarkers that are more responsive to contemporary industrial activity such as those based on the integrative oxidative stress response.