Les entérovirus (EV) sont des Picornavirus (virus nus à génome ARN positif), caractérisés par une grande diversité génétique et antigénique (116 types classés en 4 espèces taxonomiques EV-A à D) et une évolution rapide. Les infections humaines sont très fréquentes, hautement contagieuses à partir des selles et épidémiques. La plupart des infections sont asymptomatiques ou bénignes ; elles peuvent être graves voire mortelles, en particulier chez les jeunes enfants. La poliomyélite, modèle d’infection à EV, est en voie d’éradication grâce aux programmes de vaccination et de surveillance sous l’égide de l’OMS. La détection de poliovirus sauvages dans des pays déclarés exempts de polio depuis plusieurs années et l’émergence récente de plusieurs EV non poliomyélitiques (EV-A71, EV-D68) associés à des manifestations cliniques sévères dans plusieurs régions du monde montrent l’importance de surveiller la circulation des EV dans la population humaine. Le but de la thèse était de rechercher et caractériser les EV dans les eaux usées de l’agglomération de Clermont-Ferrand et de comparer les données à celles de la surveillance clinique pour avoir une image plus complète de la circulation virale dans la population générale. Une méthode de concentration virale à partir des eaux usées prélevées en entrée (eaux usées brutes) et sortie (eaux usées traitées) de station d’épuration a été mise au point, permettant la détection moléculaire des EV et de 6 autres virus entériques humains. La présence de génomes viraux a été détectée dans tous les échantillons d’octobre 2014 à octobre 2015, avec une médiane de 6 virus différents en entrée de station et de 4 virus en sortie. L’analyse phylogénétique des séquences d’EV et des virus des hépatites A et E présents dans les eaux usées et les prélèvements cliniques des patients hospitalisés au CHU de Clermont-Ferrand pendant la même période, a validé l’approche mise en place pour surveiller la circulation communautaire d’un virus entérique. La diversité des EV présents dans les eaux usées brutes a été analysée par séquençage d’amplicons avec une technique haut débit Illumina (metabarcoding). Les résultats montrent la présence d’une grande diversité d’EV et la circulation silencieuse de 25 types (notamment 9 EV-C, dont des séquences de poliovirus 1 vaccinal) dans la population générale. L’analyse phylogénétique des variants intra-typiques a mis en évidence plusieurs profils épidémiques parmi les principaux types ayant circulé pendant la période d’étude. Les données obtenues montrent la faisabilité et la sensibilité de la stratégie développée pour détecter et caractériser les EV présents dans les eaux usées. Ils permettent de discuter la place de la surveillance environnementale dans la surveillance des infections à EV non polio (études épidémiologiques, prévention des épidémies, alertes sanitaires). Surveiller conjointement les virus entériques dans l’environnement et chez les patients permet une meilleure compréhension de leur prévalence. Cette approche globale de la circulation virale et de l’écologie de la santé représente un engagement important de la part des laboratoires et nécessitera une intégration dans des réseaux structurés de collaboration nationales et internationales dépassant la seule surveillance des EV. / Enterovirus (EV) are Picornaviruses (non-enveloped, positive-sense RNA viruses), characterized by a large genetic and antigenic diversity (116 types classified within 4 taxonomic species EV-A to D) and rapid evolution. Human infections are frequent, highly contagious from stools and occur as outbreaks. The infections are mainly asymptomatic or benign but severe or fatal cases can be reported in young children. Poliomyelitis is the model EV infection. Combined with clinical and virological surveillance, mass vaccination is closer than ever to achieve the WHO program of the Global Polio Eradication Initiative. However, the detection of wild type polioviruses in polio-free countries and the recent worldwide emergence of non-polio enteroviruses (EV-A71, EV-D68) associated with severe clinical manifestations underscore the importance of surveilling EV circulation in the general population. The aim of the PhD thesis was the detection and identification of EV strains in wastewater treated in the sewage treatment plant at Clermont-Ferrand (France). The viral data were compared with those reported through clinical surveillance to obtain a comprehensive picture of the viral circulation in the local population. A method was developed to concentrate viruses from raw and treated wastewater and molecular assays were used to detect EVs and 6 other human enteric viruses. The viral genomes were detected in all samples from October 2014 to October 2015, with a median of 6 and 4 different viruses in raw and treated wastewater respectively. Phylogenetic analysis of viral sequences (EV, hepatitis A and E viruses) determined in wastewater and reported in patients during the sampling period, showed the efficiency of the method for surveilling enteric viruses in the community. The EV diversity in raw wastewater was analyzed by sequencing of amplicons with the Illumina high throughput technology (metabarcoding). The analysis revealed a large viral diversity and the silent circulation of 25 types not detected from hospital data (in particular 9 EV-C, of which sequences of vaccine poliovirus 1). The phylogenetic analyses of intra-typic variants showed different epidemic patterns in the predominant EV types circulating over the study period. The data demonstrate the feasibility and sensitivity of the strategy developed for the detection and characterization of EV in wastewater and provide a future prospect for the implementation of environmental surveillance of non-polio EV infections in epidemiological studies, epidemic prevention, and for health alert. Combining the surveillance of enteric viruses in the environment and in the clinical setting allows a better understanding of their prevalence. This global approach of virus circulation and ecological health represents an important investment for laboratories, which will require integration in national and international collaboration networks beyond the scope of enterovirus surveillance.

Humane Astroviren (HAstV) stellen wichtige Erreger kindlicher Gastroenteritiden dar, die in ihrer Bedeutung lange Zeit unterschätzt wurden. Sie werden in acht Serotypen klassifiziert, die nach dem bisherigen Kenntnisstand mit den Genotypen korrespondieren. Ziel dieser Arbeit war es, Einsicht in die molekulare Epidemiologie der in Deutschland zirkulierenden Astroviren zu vermitteln. Eine HAstV-spezifische RT-PCR bildete die Grundlage für die phylogenetische Analyse eines Genomabschnitts, der für die Kapsidproteine des Virus kodiert. Dazu wurden 16 deutsche Astrovirusisolate aus den Jahren 1997-1999 unter Einbeziehung bereits publizierter Sequenzdaten der Serotypen 1-8 untersucht. In Anlehnung an ein in der vorliegenden Literatur verwendetes Klassifizierungsschema erfolgte die Einteilung der deutschen Isolate in unterschiedliche Genotypen. Hierbei bildete eine Konvergenz von mindestens 85% das Kriterium für die Zuordnung differenter Isolate zum gleichen Genotyp. Es konnte gezeigt werden, dass in Deutschland wenigstens vier HAstV-Genotypen (1-4) kozirkulieren. Über dem betrachteten Genomabschnitt stimmten einige Isolate aus unterschiedlichen geografischen Regionen in ihrer Sequenz überein. Im Rahmen dieser Arbeit wurde erstmals die Totalsequenz eines humanen Astrovirus vom Serotyp 3 ermittelt. Während in der phylogenetischen Analyse des betreffenden Isolats nur ein Genomabschnitt betrachtet wurde, ließ sich an seiner Totalsequenz demonstrieren, dass die Einordnung in den Geno- bzw. Serotyp 3 auch in anderen Genomregionen Gültigkeit besitzt. Analog zu den bisher bekannten Gesamtgenomsequenzen der Serotypen 1, 2 und 8 lassen sich drei überlappende offene Leseraster (ORFs) identifizieren. In den beiden am 5'-Ende gelegenen ORFs 1a und 1b erweisen sich die putativen Motive der Protease und der RNA-Polymerase zwischen den vier Serotypen als hochkonserviert, ebenso wie vier potentielle Transmembrandomänen, ein ribosomales frameshift-Signal und ein nukleäres Lokalisationssignal. In dem am 3'-Ende gelegenen ORF 2 befinden sich drei hochkonservierte potentielle N-Glykosylierungs-Sites sowie ein hochkonserviertes Glykosaminoglykan-Attachment-Site. Ein wesentlicher Befund im Zusammenhang mit der Totalsequenz ist der Nachweis einer 45 Nukleotide umfassenden Deletion im ORF1a im Originalmaterial (Stuhl). Diese wurde bisher nur bei Astroviren gefunden, die in Zellen kultiviert wurden. Von Interesse und weiteren Untersuchungen vorbehalten ist ihre Nähe zur nukleären Lokalisationssequenz, die für die Beeinflussung des Zielzell-Tropismus von Astroviren verantwortlich sein könnte. / Human astroviruses (HastV) are an important cause of infantile gastroenteritis. To date, there are eight recognized serotypes which correlate with genotypes. The aim of this study was to investigate the molecular epidemiology of astroviruses circulating in Germany. Based on a HAstV-specific RT-PCR, phylogenetic analysis of a segment of the capsid protein gene was performed. The examination included sequence data of 16 German astrovirus isolates from the years 1997-1999 as well as published sequence information of the serotypes 1-8. Molecular typing was carried out following published classification strategies. The criterion for classification of isolates into one genotype was sequence identity of at least 85%. Astroviruses of at least four different genotypes (1-4) were found to cocirculate in Germany. The nucleotide sequences of several isolates from different geographical regions were identical. As part of this study, the complete genomic sequence of a type 3 human astrovirus was determined. The classification of the virus as a genotype 3 astrovirus as suggested by phylogenetic analysis over a limited genome section was supported by sequence comparison over two different genomic regions. Similar to the known total sequences of serotypes 1,2 and 8, three overlapping open reading frames (ORFs) were identified. The 5' end ORFs 1a and 1b contain the putative protease and polymerase motifs, which are highly conserved between the four serotypes. A high degree of sequence identity was also found for four potential transmembrane domains, a ribosomal frameshift signal and a nuclear localisation signal. The 3' end ORF 2 encodes three almost totally conserved potential N-glycosylation sites and one highly conserved putative glycosaminoglycan attachment site. As an outstanding feature, the virus, which was isolated and sequenced directly from diarrheal feces, presents a 45-nucleotide deletion in ORF 1 a. This deletion has previously only been found in cell cultured astroviruses. Further studies are needed to determine whether all viral genomes within the quasispecies carry the deletion.

Gonorrhea, caused by the human pathogen Neisseria gonorrhoeae, is a severe public health problem worldwide with more than 82 million new infections each year. N. gonorrhoeae is transmitted by sexual contact and primarily causes urogenital mucosal infections in men and women. Left untreated, this infection may cause severe complications, especially in females. Eye infections of the newborn can occur. Gonorrhea infections enhance HIV transmission. The highly prevalent antibiotic resistance and the emergence of new drug resistances render treatment of the infections increasingly difficult. Close monitoring of antimicrobial susceptibility of this pathogen is crucial, and enhanced knowledge of molecular mechanisms of gonococcal antimicrobial resistance is urgently needed. There are no vaccines available against N. gonorrhoeae. Control of gonorrhea relies on comprehensive strategies which can be better formulated by understanding, at molecular levels, how N. gonorrhoeae is transmitted in communities. My research aimed to illustrate the severe burden of antimicrobial resistance in N. gonorrhoeae temporally and geographically in China and to reveal the molecular mechanisms of antibiotic resistance particularly the development of reduced susceptibility to ceftriaxone in N. gonorrhoeae isolates. To determine specific strain distributions, N. gonorrhoeae isolates were characterized using molecular typing methods such as a modified porB-based typing scheme and the N. gonorrhoeae Multi-Antigen Typing (NG-MAST) method, compared to traditional epidemiological approaches. The ultimate goal was to provide information for better formulating disease control strategies for gonorrhea. In this research, male patients with gonorrhea and their sex partners were recruited in Shanghai (2005 and 2008) and in Urumchi (2007-2008), China. Epidemiological information pertaining to sexual contacts was collected. N. gonorrhoeae isolates were investigated for their antimicrobial susceptibility. Molecular mechanisms of antimicrobial resistance were explored by analysis of potential resistant determinants (gyrA, parC, porB, mtrR, ponA and penA). The molecular data were combined with bioinformatic analysis and traditional epidemiological data. High percentages of N. gonorrhoeae isolates (11% - 19% in Shanghai, 4.5% in Urumchi) exhibited reduced susceptibility to ceftriaxone (MICs = 0.125-0.25 mg/L), the first line drug recommended for the treatment of gonorrhea in China. The majority of isolates (>98%) were susceptible to spectinomycin, an alternative regimen for gonorrhea treatment; however, the proportion of isolates having intermediate levels of susceptibility increased from 1.9% in 2005 to 9.9% in 2008. The majority of isolates tested were resistant to penicillin (80% - 93%), tetracycline (56% - 65%) and ciprofloxacin (98% - 100%). Plasmid-mediated resistance in N. gonorrhoeae isolates were highly prevalent (51% - 79%) in Shanghai and Urumchi. Analysis of 60 clinical isolates revealed that reduced susceptibility to ceftriaxone is mediated by porB1b allele and is associated with specific mutations in penicillin binding protein 2 and in the DNA binding and dimerization domains of MtrR. Penicillin binding protein 1 is not involved in reduced susceptibility to ceftriaxone. Although mutation patterns in quinolone resistant determinant regions (QRDRs) varied, the majority of ciprofloxacin resistant isolates had double mutations in GyrA (S91F and D95G/A/N) and most isolates also carried a S87R/N mutation in ParC. The presence of mutations in the QRDR of ParC is correlated with elevated ciprofloxacin MICs. A modified porB-based molecular typing scheme was developed and involved ~82% of the DNA sequence of gonococcal porB. This typing method proved to have high discriminatory ability (index of discrimination = 0.93 0.96), and was cost effective and easy to perform as compared to the NG-MAST analysis. Using the modified porB-based typing method, N. gonorrhoeae isolates were reliably differentiated, and transmission clusters were identified. Molecular epidemiology using the porB-based method confirmed direct sexual connections and identified sexual networks otherwise unrevealed by the patient self-reporting or traditional case-tracing methods.

Gonorrhea, caused by the human pathogen Neisseria gonorrhoeae, is a severe public health problem worldwide with more than 82 million new infections each year. N. gonorrhoeae is transmitted by sexual contact and primarily causes urogenital mucosal infections in men and women. Left untreated, this infection may cause severe complications, especially in females. Eye infections of the newborn can occur. Gonorrhea infections enhance HIV transmission. The highly prevalent antibiotic resistance and the emergence of new drug resistances render treatment of the infections increasingly difficult. Close monitoring of antimicrobial susceptibility of this pathogen is crucial, and enhanced knowledge of molecular mechanisms of gonococcal antimicrobial resistance is urgently needed. There are no vaccines available against N. gonorrhoeae. Control of gonorrhea relies on comprehensive strategies which can be better formulated by understanding, at molecular levels, how N. gonorrhoeae is transmitted in communities. My research aimed to illustrate the severe burden of antimicrobial resistance in N. gonorrhoeae temporally and geographically in China and to reveal the molecular mechanisms of antibiotic resistance particularly the development of reduced susceptibility to ceftriaxone in N. gonorrhoeae isolates. To determine specific strain distributions, N. gonorrhoeae isolates were characterized using molecular typing methods such as a modified porB-based typing scheme and the N. gonorrhoeae Multi-Antigen Typing (NG-MAST) method, compared to traditional epidemiological approaches. The ultimate goal was to provide information for better formulating disease control strategies for gonorrhea. In this research, male patients with gonorrhea and their sex partners were recruited in Shanghai (2005 and 2008) and in Urumchi (2007-2008), China. Epidemiological information pertaining to sexual contacts was collected. N. gonorrhoeae isolates were investigated for their antimicrobial susceptibility. Molecular mechanisms of antimicrobial resistance were explored by analysis of potential resistant determinants (gyrA, parC, porB, mtrR, ponA and penA). The molecular data were combined with bioinformatic analysis and traditional epidemiological data. High percentages of N. gonorrhoeae isolates (11% - 19% in Shanghai, 4.5% in Urumchi) exhibited reduced susceptibility to ceftriaxone (MICs = 0.125-0.25 mg/L), the first line drug recommended for the treatment of gonorrhea in China. The majority of isolates (>98%) were susceptible to spectinomycin, an alternative regimen for gonorrhea treatment; however, the proportion of isolates having intermediate levels of susceptibility increased from 1.9% in 2005 to 9.9% in 2008. The majority of isolates tested were resistant to penicillin (80% - 93%), tetracycline (56% - 65%) and ciprofloxacin (98% - 100%). Plasmid-mediated resistance in N. gonorrhoeae isolates were highly prevalent (51% - 79%) in Shanghai and Urumchi. Analysis of 60 clinical isolates revealed that reduced susceptibility to ceftriaxone is mediated by porB1b allele and is associated with specific mutations in penicillin binding protein 2 and in the DNA binding and dimerization domains of MtrR. Penicillin binding protein 1 is not involved in reduced susceptibility to ceftriaxone. Although mutation patterns in quinolone resistant determinant regions (QRDRs) varied, the majority of ciprofloxacin resistant isolates had double mutations in GyrA (S91F and D95G/A/N) and most isolates also carried a S87R/N mutation in ParC. The presence of mutations in the QRDR of ParC is correlated with elevated ciprofloxacin MICs. A modified porB-based molecular typing scheme was developed and involved ~82% of the DNA sequence of gonococcal porB. This typing method proved to have high discriminatory ability (index of discrimination = 0.93 0.96), and was cost effective and easy to perform as compared to the NG-MAST analysis. Using the modified porB-based typing method, N. gonorrhoeae isolates were reliably differentiated, and transmission clusters were identified. Molecular epidemiology using the porB-based method confirmed direct sexual connections and identified sexual networks otherwise unrevealed by the patient self-reporting or traditional case-tracing methods.

Neisseria meningitidis is a gram negative, and sometimes encapsulated, diplococcus that causes devastating disease worldwide. For the worldwide genetic surveillance of N. meningitidis, the gold standard for profiling the bacterium uses genetic loci found around the genome. Unfortunately, the software for analyzing the data for these profiles is difficult to use for a variety of reasons. This thesis shows my suite of tools called the Meningococcus Genome Informatics Platform for the analysis of these profiling data. To better understand N. meningitidis, the CDC Meningitis Laboratory and other world class laboratories have adopted a whole genome approach. To facilitate this approach, I have developed a computational genomics assembly and annotation pipeline called the CG-Pipeline. It assembles a genome, predicts locations of various features, and then annotates those features. Next, I developed a comparative genomics browser and database called NBase. Using CG-Pipeline and NBase, I addressed two open questions in N. meningitidis research. First, there are N. meningitidis isolates that cause disease but many that do not cause disease. What is the genomic basis of disease associated versus asymptomatically carried isolates of N. meningitidis? Second, some isolates' capsule type cannot be easily determined. Since isolates are grouped into one of many serogroups based on this capsule, which aids in epidemiological studies and public health response to N. meningitidis, often an isolate cannot be grouped. Thus the question is what is the genomic basis of nongroupability? This thesis addresses both of these questions on a whole genome level.

Rotaviruses, members of the family Reoviridae, are the major etiologic agents of severe, acute dehydrating diarrhea in the young of many mammalian species, including humans, calves and foals. Recent estimates indicate an annual death toll of approximately 600,000 infants due to rotavirus, besides inflicting staggering economic burden worldwide. Most of these deaths occur in the developing countries and India is estimated to account for about a quarter of these deaths. Extensive molecular epidemiology studies carried out by our laboratory have revealed many interesting aspects about rotavirus diversity in this country. Molecular epidemiology of rotaviruses causing severe diarrhea in foals in two organized farms in northern India was carried out. These foal rotaviruses exhibited 5 different electropherotypes (E), E1-E5. Strains belonging to E1, E2 and E5 exhibited G10, P6[1]; G3 and G1 type specificities. Though the E1 strains possessed genes encoding G10 and P6[1] type outer capsid proteins, unlike the G10, P8[11] type strain I321, they exhibited high reactivity with the G6-specific MAb suggesting that the uncommon combination altered the specificity of the conformation-dependent antigenic epitopes on the surface proteins. Strains belonging to electropherotypes E3 and E4 were untypeable. Sequence analysis of the VP7 gene from E4 strains (Erv92 and Erv99), revealed that they represent a new VP7 genotype, G16. Nonstructural protein 4 (NSP4) of rotavirus is a multidomainal, multifunctional protein and is the first viral enterotoxin identified. We have recently reported that the diarrhea-inducing and double-layered particle (DLP)–binding properties of NSP4 are dependent on a structurally and functionally overlapping conformational domain that is conferred by cooperation between the N- and C-terminal regions of the cytoplasmic tail (Jagannath et al., J. Virol, pp 412-425, 2006). Further, a stretch of 40 amino acids (aa) from the C-terminus is predicted to be unstructured and highly susceptible to trypsin cleavage. We examined the role of this unstructured C-terminus of Hg18 NSP4 and SA11 NSP4 on the biological properties of NSP4 using a series of deletion and substitution mutants of the conserved proline and tyrosine residues in this region. Gel filtration, CD spectroscopy and Thioflavin T binding studies showed that these mutants have altered secondary structural contents and either failed to multimerize efficiently or multimerized with altered conformation. The C-terminal ten residues appear to play a regulatory role on multimerization. Proline 168, tyrosine 166 and methionine 175 appear to be critical determinants of DLP binding activity whereas, proline 165 and tyrosine 85 and 131 appears to determine the affinity of binding to DLP in the context of NSP4 ∆N72. Deletion and substitution mutants exhibited severely reduced diarrhea inducing ability and DLP binding property. Of great biological significance is the drastic decrease in the diarrhea inducing ability of the N- and C- terminal deletion mutant ∆N94 ∆C29 that exhibited about 11,000-fold increase in DD50 than the wild type (WT) ∆N72. These studies revealed that the predicted unstructured C-terminus is an important determinant of biological properties of NSP4. Extensive efforts to crystallize the complete cytoplasmic tail (CT) of NSP4 were unsuccessful and to date, the structure of only a synthetic peptide corresponding to aa 95-135 has been reported. Our recent studies indicate that the interspecies variable regions from aa 135-141 as well as the extreme C-terminus are critical determinants of virus virulence and diarrhea-inducing ability of the protein. Here, we examined the crystallization properties of several deletion mutants and report the structure of a mutant recombinant NSP4 from symptomatic (SA11) and asymptomatic (I321) strains that lacked the N-terminal 94 and C-terminal 29 aa (NSP4: 95-146) at 1.67 Å and 2.7Å, respectively. In spite of the high-resolution data, electron density for the stretch of 9 residues from the C-terminus could not be seen suggesting its highly flexible nature. The crystal packing showed a clear empty space for this region. Extension of the unstructured C-terminus beyond aa 146 hindered crystallization under the experimental conditions. The present structure revealed significant differences from that of the synthetic peptide in the conformation of amino acids at the end of the helix as well as crystal packing owing to the additional space required to accommodate the unstructured virulence-determining region. Conformational differences in this critical region effected by the presence or absence of proline or glycine at specific positions in the unstructured C-terminus, could form the basis for the wide range of variation seen in the diarrhea-inducing ability of NSP4 from different strains in newborn mouse pups. Although symptomatic and asymptomatic strains do not generally differ in the presence or absence of the conserved prolines or glycines, they contain a few additional changes that could alter the unique conformation required for optimal biological activity. In conclusion, we demonstrate that the predicted unstructured C-terminal region is indeed highly flexible and is an important determinant of biological functions of the NSP4, mutations in which probably correlates with the virulence properties of the virus.

This thesis is dedicated to developments and applications of metabolomics, exploiting high field NMR spectroscopy. The first part is dedicated to a general presentation of metabolomics. We also report results about the introduction of reduced dimensionality techniques for the characterization of complex mixtures, coined targeted projection NMR spectroscopy. The second part of this manuscript reports results about three different metabolomic studies carried out in human populations. The first analysis demonstrates the suitability for metabolomics of serum samples collected in the framework of the European Prospective Investigation into Cancer and Nutrition (EPIC) study. The second study investigates a serum metabolic signature of metastatic breast cancer. The last analysis establishes potential plasma metabolic signatures for different liver pathologies, like hepatocellular carcinoma. The third part of this thesis is dedicated to the characterization of various model organisms. The first study presents a characterization of plasma and urine metabolic differences between four rat strains commonly used as controls in genetic studies. In the second study, we investigate the effects of physiological aging in Caenorhabditis elegans (C. elegans) and observe that dietary restriction buffers metabolic changes associated with aging. We further identify that perturbations in phosphocholine metabolism correlate with life expectancy. The third analysis of this part characterizes the ahr-1 C. elegans mutant, showing strong metabolic changes in ahr-1 mutants, which suggest an involvement in development and aging processes. We finally investigate in the last study the effects at the metabolic level of the interaction between an endogenous protein E4F1 and a viral protein HBx in liver cells infected by hepatitis B virus.

<p>Härtill 5 uppsatser</p> / digitalisering@umu

Background: Meat consumption is associated with an elevated risk of colorectal cancer (CRC); exposure to heterocyclic aromatic amines (HAAs), carcinogens produced when meat is cooked at high temperatures, is one hypothesized explanation for this relationship. HAAs form adducts with DNA; left unrepaired, DNA adducts can induce mutations which may initiate and/or promote the development of colorectal adenomas, precursors to the vast majority of CRCs. Along this continuum, genetic differences in the ability to biotransform or metabolize HAAs and repair DNA is postulated to modify the HAA-CRC relationship. Methods: This thesis examined the HAA-CRC relationship in two studies (Phase 1 and 2). In a cross-sectional study of 99 healthy volunteers, Phase 1 investigated the relationship between dietary exposure to HAAs and the levels of bulky DNA adducts in blood leukocytes. In Phase 2, a cross-sectional study examined the relationships between dietary exposures to: a) HAAs and; b) meat mutagenicity, and the prevalence of colorectal adenomas among 342 patients undergoing a screening colonoscopy. Both Phase 1 and 2 examined potential gene-diet interactions between dietary HAAs and genetic factors relevant to the biotransformation of HAAs and DNA repair. Results: In Phase 1, an interaction was observed for dietary HAAs and NAT1 polymorphisms where a positive association between HAA intakes and bulky DNA adduct levels was found among those with the NAT1 slow acetylator genotype, hypothesized to confer a lower ability to biotransform HAAs. In Phase 2, polymorphisms in genes involved in the biotransformation of HAAs (CYP1B1 rs10012 and rs1056827) and DNA repair (XPC rs2228001) were found to determine colorectal adenoma risk. As well, gene-diet interactions were observed for dietary HAAs/meat mutagenicity exposures and polymorphisms in CYP1B1 and XPD (rs13181 and rs1799793). Overall, a higher risk of colorectal adenoma was observed with higher HAA and/or meat mutagenicity exposures among those with polymorphisms which confer a greater activity to biotransform HAAs and/or a lower ability to repair DNA. Conclusion: This research supports the contribution of dietary HAAs and genetic susceptibility to the risk of developing colorectal adenomas and highlighted bulky DNA adduct formation as a potential biologic pathway through which HAAs may influence cancer risk. / Thesis (Ph.D, Community Health & Epidemiology) -- Queen's University, 2014-04-25 11:32:30.392

Orientador: Maria de Lourdes Ribeiro de Souza da Cunha / Resumo: A origem racial representa um dos principais determinantes dos riscos de colonização e infecção por Staphylococcus aureus. Há algum tempo, comunidades indígenas têm se mostrado mais propensas em relação a tais riscos, apresentando linhagens de S. aureus com perfis distintos dos quais normalmente se encontram em populações não-nativas. Características peculiares entre diferentes populações, tais como viver em condições de superlotação, assistência em saúde prejudicada e condições precárias de higiene podem ser mais relevantes na patogênese de algumas formas de infecções por S. aureus. Deste modo, os indígenas inegavelmente se enquadram no grupo de risco para o carreamento de microrganismos resistentes, estando suscetíveis tanto à aquisição quanto à disseminação de infecções. O presente estudo objetivou a identificação da prevalência e de fatores de risco para carreamento nasal e oral de S. aureus sensíveis e resistentes à meticilina (Methicilinsensitive Staphylococcus aureus MSSA e Methicilin-resistant Staphylococcus aureus MRSA, respectivamente) em indígenas de comunidades do Norte e Sudeste do Brasil, avaliando a diversidade genética, disseminação, fatores de virulência e resistência antimicrobiana, associados às questões étnicas, demográficas, ambientais e comportamentais. Para tanto, foram coletadas amostras nasais e de orofaringe de 400 indígenas (116 da região sudeste e 284 da região norte) através de swabs estéreis e posteriormente elas foram semeadas em meio de cultura... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor