Under covid-19-pandemin har avloppsvattenbaserad epidemiologi (WBE) använts i stor utsträckning som ett komplement till kliniska tester över många delar av världen. Detta projekt syftade till att detektera och kvantifiera belastningen av Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) i avloppsvattenprover med hjälp av Revers transkriptas kvantitativ polymeraskedjereaktion (RT-qPCR). De analyserade proverna kom från fyra olika avloppsreningsverk i Sverige, under perioden november 2022 till maj 2023. Studien omfattade en översikt över olika provtagnings- och analytiska tekniker och normaliseringsmetoder som används i WBE-studier, vilket betonade vikten av metodval. SARS-CoV-2-RNA upptäcktes i alla analyserade prover och infektionstrender kunde identifieras effektivt, inklusive COVID-19-vågen som observerades under semesterperioden. De dominerande varianterna som upptäcktes under denna övervakningsperiod var omikron variantens undergrupper, BA.2. och BA.2.75. Den veckovisa kvantifierade SARS-CoV-2-belastningen i avloppsvattenproverna visade en signifikant positiv korrelation till de kliniska fall som rapporterats i motsvarande avrinningsområden. Denna associering förstärktes ytterligare genom att normalisera SARS-CoV-2-innehållet med fekal biomarkör peppar milt fläckvirus (PMMoV). Dessutom har två metoder för tidig varning, nämligen medelvärdet plus två standardavvikelser (MSD) och positiv procentuell förändring (PPC), implementerats på avloppsvattendata, vilket pekar på vikten av att tillämpa sådana varningsmetoder för att ge förståeliga och tolkbara resultat. Denna studie ger värdefulla insikter om övervakning och analys av SARS-CoV-2 i avloppsvatten, vilket bidrar till utvecklingen av robusta system för tidig varning och folkhälsostrategier. / During the COVID-19 pandemic, wastewater-based epidemiology (WBE) has been applied extensively as a complementary tool to clinical testing across many parts of the globe. This project aimed to detect and measure the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) load in wastewater samples using Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). The analyzed samples were from four different wastewater treatment plants (WWTPs) in Sweden, covering the period from November 2022 through May 2023. The study encompassed an overview of various sampling and analytical techniques and normalization approaches employed in WBE studies, highlighting the importance of method selection. SARS-CoV-2 RNA was detected in all the samples analyzed, and infection trends could be identified effectively, including the COVID-19 peak observed during the holiday season. The dominant variants detected during this monitoring period were the omicron variants; omicron BA.2. and omicron BA.2.75. The weekly quantified SARS-CoV-2 load in the wastewater samples showed a significant positive correlation to the clinical cases reported in the corresponding catchment areas. This association was further enhanced by normalizing SARS-CoV-2 content with the fecal biomarker pepper mild mottle virus (PMMoV). Furthermore, two early warning methods, namely the mean plus two standard deviations (MSD) and positive percentage change (PPC), were implemented on the wastewater data pinpointing the importance of applying such warning methods to provide understandable and interpretable results. This study provides valuable insights into the monitoring and analysis of SARS-CoV-2 in wastewater, contributing to the development of robust early warning systems and public health strategies.

Les organismes unicellulaires sont très vulnérables aux changements rapides de leur environnement puisqu’ils sont en contact direct avec celui-ci. Les organismes unicellulaires utilisent plusieurs stratagèmes pour réguler l’expression génique et par conséquent, les diverses voies métaboliques nécessaires aux différentes conditions environnementales auxquelles ils sont confrontés. On sait maintenant que certains ARN, dont les riborégulateurs, ont également un grand rôle à jouer dans les processus de régulation de l’expression du génome. En général, les riborégulateurs sont des éléments génétiques situés dans les régions 5’ non traduites (5’ UTR) de l’ARN messager bactérien. Ces éléments possèdent une structure tertiaire bien définie qui est conservée à travers l'évolution. Les riborégulateurs subissent un changement de conformation en s’associant à un ligand spécifique et modulent l’expression des gènes qu’ils contrôlent en aval. Le rôle des riborégulateurs en relation avec le métabolisme des eubactéries peut être d’une grande importance. C’est le cas de Clostridium difficile qui voit son génome régulé par au moins une quarantaine de riborégulateurs. Étant un pathogène nosocomial, causant des infections contractées dans le milieu hospitalier, bien connu pour engendrer des complications au niveau de l’intestin, il est intéressant d’étudier la relation gène-riborégulateur-métabolisme chez C. difficile. De plus, les riborégulateurs ont montré un potentiel intéressant comme cible antibiotique pour combattre certaines infections. C. difficile possède quatre riborégulateurs guanine transcriptionnels qui contrôlent quatre gènes intervenant dans la voie de biosynthèse de la guanosine monophosphate (GMP). Deux de ces gènes interviennent directement dans la voie de synthèse du GMP soit une guanosine-monophosphate synthase (guaA) et une xanthine phosphoribosyltransférase (XPRTase) (xpt) ainsi que deux transporteurs de précurseur nommés CD630_21070 codant pour une perméase uracile/xanthine et CD630_ 27040 une perméase putative. Bien que quelques études ont démontré l’importance que pourrait avoir le gène guaA chez d’autres espèces bactériennes (Staphylococcus aureus, Escherichia coli, Streptococcus suis et, Salmonella thyphimurium), aucune étude de C. difficile n'a élucidé la relation entre les quatre riborégulateurs guanine et les gènes qu’ils contrôlent, de même que leur rôle au sein du métabolisme du GMP dans un contexte in vivo. Le présent mémoire porte sur l’étude de ces quatre riborégulateurs guanine chez C. difficile, les gènes régulés par ces riborégulateurs et leurs effets sur la biologie de C. difficile. Une fois que les recherches bio-informatiques ont été entreprises, le projet s’est divisé en deux grandes parties soit l’efficacité de régulation des riborégulateurs guanine et l’importance des quatre gènes qui sont sous le contrôle de ces riborégulateurs chez C. difficile 630. Afin de vérifier si les riborégulateurs guanine avaient une affinité acceptable pour leur ligand (guanine), des essais de cartographies chimiques ont été faits et des Kd ont été déterminés. Ces Kd se retrouvent tous dans le bas nanomolaire (nM) de 2,61 ± 1,29 nM pour le riborégulateur guaA et des Kd de 1,78 ± 0,95 nM, de 3,06 ± 0,29 nM et de 4,44 ± 2,75 nM pour les riborégulateurs xpt, CD_21070 et CD_27040 respectivement. Pour la deuxième partie du projet, quatre mutants d’inactivation de gène par insertion ont été conçus grâce à l’utilisation du système ClosTron. Ces quatre mutants, correspondant aux gènes guaA, xpt, CD630_21070 et CD630_27040, ont ensuite été analysés lors d’essais de croissance afin de vérifier les phénotypes associés aux inactivations de gènes. À la suite des résultats d’essais de croissance des divers mutants d’inactivation, une emphase a été mise sur le gène guaA et son riborégulateur puisque ce dernier montrait un phénotype d’inhibition de croissance. L’efficacité avec laquelle le riborégulateur guaA pouvait réprimer l’expression génique a été déterminée lors des essais de gène rapporteur gusA et de PCR quantitative en temps réel. Une baisse de l’expression ligand-dépendante a été observée dans des conditions variant en concentration de guanine. Le mutant de délétion par inactivation du gène guaA a aussi démontré une baisse dans sa capacité d’infecter un modèle murin. En effet, lors d’une étude d’infection en compétition avec le type sauvage, les décomptes cellulaires du mutant guaA étaient diminués de 4 logs. Ces résultats indiquent un rôle fondamental du gène guaA sur le pouvoir infectieux de C. difficile 630 et mettent en évidence l’importance du riborégulateur qui contrôle l’expression de ce gène. Toutes les expériences faites dans le cadre du projet ont été entreprises chez C. difficile 630 afin de garder un contexte plus naturel au cours des analyses. Les résultats présentés ici mettent en évidence le potentiel des riborégulateurs comme cibles antibiotiques. Des travaux futurs devront être effectués afin de vérifier l’effet que pourraient avoir certains analogues de ligands qui ciblent les riborégulateurs guanine sur la viabilité de C. difficile.

Le processus d'épileptogenèse, qui conduit à la production de décharges électro-encéphalographiques spontanées caractéristiques de la maladie épileptique, implique des mécanismes inconnus pour la plupart et probablement divers. Des études récentes soulignent le rôle potentiel de l'inflammation cérébrale dans les mécanismes précoces de l'épileptogenèse. Le syndrome d'épilepsie de la face mésiale du lobe temporal (EMLT) est souvent associé à une perte neuronale unilatérale et sélective dans l'hippocampe, suggérant que cette structure est particulièrement sensible. Notre travail a donc été consacré à l'étude de l'épileptogenèse faisant suite à l'injection intrahippocampique de toxiques chimiques capables d'entraîner des modifications tissulaires et cellulaires locales chez la souris C57BL/6. Le rôle potentiel de la neuro-inflammation a été plus particulièrement recherché. Dans notre premier modèle, un déséquilibre cholinergique est induit par l'injection de soman, un puissant inhibiteur des cholinestérases. Il est capable d'induire un processus d'épileptogenèse sans état de mal initial, associé à un déficit de la réponse émotionnelle conditionnée contextuelle mais en l'absence de remaniements tissulaires majeurs (neurodégénérescence, œdème et neuro-inflammation). En revanche, dans le modèle d'EMLT obtenu par l'injection de kaïnate, une forte activation microgliale est détectée précocement dans les zones de neurodégénérescence. Une astrogliose est également observée. Grâce à la technique quantitative de transcription inverse suivie de polymérisation en chaîne (RT-qPCR), nous avons également pu mettre en évidence que certains médiateurs moléculaires de l'inflammation sont également liés dans le temps et dans l'espace (particulièrement la transcription d'IL-1β) aux événements neurodégénératifs. Pour s'assurer de la fiabilité des données analytiques de RT-qPCR dans les régions cérébrales touchées par ces modifications, le choix des gènes de référence doit faire l'objet d'études spécifiques. Nous avons pu montrer qu'un ensemble de cinq gènes (Hprt1, Ppia, Tbp, Actb et Arbp) avait une forte stabilité dans la structure hippocampique dans ce modèle murin d'EMLT et pouvait être utilisé pour normaliser les données brutes de RT-qPCR dans ce modèle. Nos résultats indiquent que, chez la souris, des altérations neurochimiques sont capables d'initier l'épileptogenèse même en l'absence de lésions tissulaires notables et qu'une réponse neuro-inflammatoire massive n'est pas une condition sine qua non. Déterminer le caractère bénéfique ou délétère de la neuro-inflammation reste un enjeu majeur pour la découverte de nouvelles thérapeutiques anti-épileptogènes.

Staphylococcus aureus belongs to the normal flora. Many healthy people are colonized by the bacterium mainly in the nose but also on the skin and on other mucous membranes without showing symptoms. After damage to the skin, the bacterium can enter the wound and cause infections. Methicillin-resistant S. aureus (MRSA) is resistant to b-lactam antibiotics such as penicillin and methicillin. The gene that gives resistance characteristic of MRSA is the mecA-gene. MRSA strains are spread in both hospitals and in the community, and it is important to identify these bacteria with rapid and sensitive methods. In this study, Taq Man RT-qPCR was compared with SYBR Green RT-qPCR (LightCycler480, Roche) to explore which method had the best sensitivity with the least working hours. In addition, Bullet for automated DNA extraction and CAS 1200 ™ for automated pipetting of the samples were evaluated. Twelve patient isolates and 232 patient samples for MRSA screening were included in the study. The results showed that the primers were of major importance for the outcome of the amplification. It was also shown that the Ct-values were clearly lower when the Bullet, CAS 1200 ™ and LightCycler480 were combined compared with manual DNA extraction, manual pipetting and the Rotor-Gene 6000. In future, the former method will be used by the laboratory when screening patient samples for MRSA.

Tetrachloroethene (PCE) is a major groundwater contaminant that often persists as dense, nonaqueous phase liquids (DNAPLs) in subsurface environments. Dissolved-phase PCE plumes emanate from DNAPL source zones, which act as continuous sources of contamination for decades. Removal of DNAPL source zones is crucial to achieve lasting remedy of contaminated aquifers. This research explored the contributions of the microbial reductive dechlorination process (i.e., anaerobic bioremediation) to PCE-DNAPL source zone remediation, either in isolation or as a polishing step for the removal of residual DNAPL remaining after application of surfactant enhanced aquifer remediation (SEAR), an emerging physical-chemical source zone treatment. Specific objectives of this research were to: (1) evaluate the ability of microorganisms to dechlorinate in the presence of PCE-DNAPL and at high dissolved-phase PCE concentrations expected near/in DNAPL source zones, (2) assess the distribution and activity of key dechlorinating populations during bioenhanced PCE-DNAPL dissolution in continuous-flow column experiments, (3) determine the influence of Tween 80, a biodegradable surfactant commonly used in SEAR, on the microbial reductive dechlorination process, (4) design and optimize quantitative real-time PCR (qPCR) protocols to detect and enumerate key dechlorinating populations (e.g., Geobacter lovleyi, Sulfurospirillum multivorans), and (5) explore the effects of oxygen on Dehalococcoides viability and biomarker quantification. This research demonstrated that microbial dechlorinating activity within DNAPL source zones promotes bioenhanced dissolution although many dechlorinating isolates cannot tolerate saturated PCE concentrations. Application of newly designed qPCR protocols established a direct link between dissolution enhancement and the distribution of relevant dechlorinating populations in the vicinity of PCE-DNAPL. The limited and reversible impact of Tween 80 on key dechlorinators supported the feasibility of a treatment train approach of SEAR followed by microbial reductive dechlorination to remediate PCE-DNAPL source zones. Finally, experiments with oxygen-exposed, Dehalococcoides-containing cultures suggested limitations of using Dehalococcoides DNA and RNA biomarkers for monitoring bioremediation at field sites. These findings advance the scientific understanding of the microbial reductive dechlorination process and are relevant to environmental remediation practitioners. The advantages and current shortcomings of PCE-DNAPL source zone bioremediation, as well as recommendations for future research, are discussed.

Submitted by Hiolanda Rêgo (hiolandarego@gmail.com) on 2018-02-05T14:14:00Z No. of bitstreams: 1 Dissertação_ICS_ ROCHA, D. J. P. G..pdf: 4034030 bytes, checksum: 7085be9f2fda81bc8248196d4b4e6988 (MD5) / Made available in DSpace on 2018-02-05T14:14:00Z (GMT). No. of bitstreams: 1 Dissertação_ICS_ ROCHA, D. J. P. G..pdf: 4034030 bytes, checksum: 7085be9f2fda81bc8248196d4b4e6988 (MD5) / CNPQ / O método mais comum de normalização em ensaios de quantificação relativa da expressão gênica por PCR quantitativa em tempo real (qPCR) faz uso de um gene de referência, que deve manter sua expressão estável sob diferentes condições experimentais. Em uma meta-análise da literatura e banco de dados de experimentos de análise de expressão gênica em bactérias, os genes gyrA (DNA gyrase subunidade A), gyrB (DNA gyrase subunidade B), dnaG (DNA primase), era (GTPase era) e secA (translocase proteica subunidade secA), figuram entre os mais estáveis em diversas condições experimentais. Neste cenário, este estudo se propõe a desenvolver e construir um conjunto de primers universais para esses genes de referência a partir de organismos modelo de grupos bacterianos de interesse clínico e biotecnológico. As ferramentas de alinhamento, ClustalOmega e PCR virtual, Primer-Blast foram utilizadas para encontrar regiões conservadas entre os genes candidatos em diferentes organismos bacterianos. Dentro do complexo Mycobacterium tuberculosis, todos os genes apresentaram homologia suficiente para o desenho de primers universais, enquanto que em outros grupos bacterianos a homologia de sequência foi restrita a algumas espécies. Potenciais primers universais foram desenhados para diferentes grupos bacterianos e os primers para a família Enterobacteriaceae foram validados por RT-qPCR em Escherichia coli; os resultados foram comparados contra o gene comumente usado, 16S rRNA. Os primers testados apresentaram eficiências de amplificação dentro dos limites esperados e as expressões dos genes de referência foram estáveis nas condições estudadas, tendo sido o gene dnaG o mais estável, de acordo com os softwares NormFinder e RefFinder. Conclui-se que é possível desenhar primers universais funcionais para normalização de RT-qPCR em grupos bacterianos específicos, contudo o baixo nível de conservação gênica de determinados genes pode limitar suas utilizações.

Submitted by PABLO ACERA MATEOS null (pablo.acera@hotmail.com) on 2016-02-26T21:46:04Z No. of bitstreams: 1 Dissertação Pablo.pdf: 2305687 bytes, checksum: f2605afbab8d002e94ee276992365da9 (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-02-29T14:25:02Z (GMT) No. of bitstreams: 1 mateos_pa_me_araiq.pdf: 2305687 bytes, checksum: f2605afbab8d002e94ee276992365da9 (MD5) / Made available in DSpace on 2016-02-29T14:25:03Z (GMT). No. of bitstreams: 1 mateos_pa_me_araiq.pdf: 2305687 bytes, checksum: f2605afbab8d002e94ee276992365da9 (MD5) Previous issue date: 2016-02-18 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Neste trabalho foi realizado um estudo de caracterização das proteínas RUV-1 e RUV-2 de Neurospora crassa, as quais são proteínas ubiquamente encontradas e descritas estar envolvidas em diferentes processos celulares. Resultados anteriores obtidos pelo nosso grupo identificaram, através de espectrometria de massas, a proteína RUV-1 como uma proteína capaz de se ligar ao promotor do gene da glicogênio sintase (gsn) durante a resposta ao choque térmico. Mais tarde, foi demonstrado que a proteína foi capaz de se ligar in vitro, e de maneira especifica, ao motivo de DNA STRE, também presente no promotor gsn. Considerando que a proteína RUV-1 interage com a proteína parceira RUV-2 e, juntas, participam de grandes complexos proteicos que atuam na regulação de diferentes processos celulares, este trabalho teve como objetivo realizar estudos de caracterização das proteínas RUV-1 e RUV-2. Os resultados de expressão gênica mostraram que o gene ruv-1 foi superexpresso na condição de choque térmico e que o gene ruv-2 não mostrou alteração na expressão na mesma condição. Além disso, foi demonstrado que o transcrito do gene ruv-2 é parcialmente processado na situação de choque térmico, e não em outra condição indutora de estresse, através do processo conhecido como intron retention levando à síntese de uma proteína truncada. No entanto, os resultados mostraram que a proteína RUV-2 foi detectada em extratos celulares do fungo obtidos até 4 h de choque térmico. Os cDNAs (ruv-1 e ruv-2) foram inseridos no vetor pET28a e as proteínas expressas em E. coli. Entretanto, ainda não foi finalizada a expressão de ambas utilizando o plasmídeo bicistrônico pETDUET-1, para a análise de interação de ambas proteínas. Neste trabalho também foi construída uma linhagem do fungo modificada geneticamente, a qual produz a proteína RUV-1 fusionada ao tag V5 (RUV-1-V5) e será posteriormente utilizada em ensaio de imunoprecipitação para identificação de proteínas parceiras. Ensaios de imunoprecipatação de cromatina (ChIP) com esta linhagem foram realizados com o objetivo de analisar se a proteína RUV-1 se liga in vivo ao mesmo fragmento de DNA. Entretanto, os experimentos ainda não permitiram identificar a ligação proteína-DNA. Análises de modelagem e dinâmica molecular das proteínas RUV-1 e RUV-2 de N. crassa sugeriram interação entre elas e homologia estrutural a outras proteínas RUV conhecidas / In this work, we performed characterization studies of Neurospora crassa RUV-1 and RUV-2, which are ubiquitous protein and have been described to be involved in different cellular processes. Previous results obtained by our group identified, by mass spectrometry, RUV-1 as a protein able of binding to the glycogen synthase gene promoter (gsn) during heat shock response. Later, it was demonstrated that the protein was able to bind in vitro, and in a specific manner, to the STRE DNA motif, also present in gsn promoter. Since RUV-1 interacts with RUV- 2 protein, and together participate in large protein complexes that act in the regulation of different cellular processes, this study aimed to conduct characterization studies of RUV-1 and RUV- 2 proteins. Gene expression results showed that ruv-1 gene, but not ruv-2 gene was overexpressed under heat shock. Furthermore, it was shown that ruv-2 transcript was incompletely processed under heat shock through a process known as intron retention that leads to the production of a truncated protein. No other stress inducing conditions led to the same phenomenon. However, RUV-2 protein was detected in cell extracts of the fungus exposed to heat shock up to 4 h. The cDNAc (ruv-1 and ruv-2) were inserted into the pET28a vector and the proteins were expressed in E. coli. However, it has not yet been completed the molecular cloning in the bicistronic plasmid pETDUET-1, which allows the production of both proteins in the same cell, what is required for protein-protein interaction analysis. In this work, was also constructed a genetically modified strain, which produces the V5- tagged RUV-1 protein (V5-RUV-1), which that will be later used in immunoprecipitation assay for the identification of partner proteins. Chromatin immunoprecipitation (ChIP) assay using this strain was performed in order to investigate whether RUV-1 protein binds in vivo the DNA fragment from the gsn promoter. Experiments have not allowed the identification of protein-DNA binding yet. Analysis of molecular modelling and dynamics of RUV-1 and RUV-2 proteins suggested the existence of interaction between them and structural homology to other known RUV proteins.

Submitted by TALITA BARBAN BILHASSI null (talitabarban@yahoo.com.br) on 2016-04-26T17:24:25Z No. of bitstreams: 1 TESE TALITA BARBAN BILHASSI.pdf: 3215997 bytes, checksum: 07aede5d76602ed82d16385cc21986cf (MD5) / Approved for entry into archive by Felipe Augusto Arakaki (arakaki@reitoria.unesp.br) on 2016-04-28T18:47:32Z (GMT) No. of bitstreams: 1 bilhassi_tb_dr_jabo.pdf: 3215997 bytes, checksum: 07aede5d76602ed82d16385cc21986cf (MD5) / Made available in DSpace on 2016-04-28T18:47:32Z (GMT). No. of bitstreams: 1 bilhassi_tb_dr_jabo.pdf: 3215997 bytes, checksum: 07aede5d76602ed82d16385cc21986cf (MD5) Previous issue date: 2016-02-29 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Entre as principais causas de perdas produtivas em bovinos criados nos trópicos está a infestação pelo carrapato Rhipicephalus (Boophilus) microplus e, consequentemente, dos hemoparasitas transmitidos por ele. A resistência dos zebuínos e de animais cruzados com raças taurinas à infestação por esse ácaro é amplamente conhecida. Entretanto, no que se refere à suscetibilidade às babesioses bovinas, existem evidências de que o grupo genético também pode interferir na resistência, seguindo o mesmo padrão observado para o carrapato vetor, com os taurinos apresentando maior sensibilidade. Assim, este estudo teve por objetivo avaliar a parasitemia por Babesia bovis e Babesia bigemina em 50 novilhas da raça Canchim ( Charolês + Zebu) naturalmente infestadas pelo R. (B.) microplus nas quatro estações do ano durante 24 meses, além de caracterizar o perfil de citocinas que podem estar associados ao fenótipo de resistência e suscetibilidade aos hemoparasitas do gênero Babesia spp. Foram realizadas contagens de fêmeas adultas de carrapatos com tamanho igual ou superior a 4,5 mm de diâmetro, presentes no lado esquerdo de cada bovino. As amostras de DNA extraídas foram submetidas à amplificação por meio da Reação em Cadeia da Polimerase Quantitativa em Tempo Real (qPCR), utilizando iniciadores que flanqueiam fragmentos dos genes mitocondriais do citocromo b (mt-cyt B), específicos para B. bovis e B. bigemina. O RNA extraído do sangue, foi usado para sintetizar o DNA complementar (cDNA) para análise de expressão dos genes do IFN- , TNF- , IL-10 e IL-12B por meio da quantificação relativa (RTqPCR). Foram observadas diferenças significativas (P<0,05) entre os meses das avaliações para a contagem de carrapatos. Entretanto, não houve efeito significativo (P>0,05) nas colheitas realizadas entre novembro de 2013 a janeiro de 2014 e entre os meses janeiro e fevereiro de 2015. A frequência da parasitemia no rebanho foi de 98%. Dentre as amostras de DNA que puderam ser quantificadas pela qPCR, 98% e 95,4% foram positivas para B. bovis e B. bigemina, respectivamente. Com relação ao número de cópias (NC) dos fragmentos dos genes mt-cyt B específicos para B. bovis e B. bigemina foram observados efeitos significativos (P<0,05) para ambas as espécies e interação das mesmas com as colheitas realizadas nas diferentes estações do ano. A análise do nível de expressão de mRNA do IFN- , TNF- e IL-12B revelou que houve um efeito siginificativo (P<0,05) da interação entre animais dos extremos de resistência/suscetibilidade e estações do ano, exceto para IL-10. Conclui-se que, a qPCR apresenta alta sensibilidade e especificidade para o diagnóstico das babesioses bovinas em amostras de sangue e que a oscilação na carga parasitária nas diferentes estações do ano pode estar associada com o perfil de expressão de citocinas apresentada. / Among the main causes of production losses in cattle is in the tropics infestation by Rhipicephalus (Boophilus) microplus, and consequently the hemoparasites transmitted by it. The resistance of zebu and crossbred with European breeds to infestation by this mite is widely known. However, as regards susceptibility to bovine babesiosis, there is evidence that genetic group can also interfere in resistance following the same pattern observed in the tick vector, with the taurine presenting greater sensitivity. This study aimed to evaluate parasitaemia by Babesia bovis and Babesia bigemina in 50 heifers Canchim (⅝ Charolais + ⅜ Zebu) naturally infested by R. (B.) microplus in four seasons for 24 months, and characterize the profile of cytokines that may be associated with phenotype resistance and susceptibility by gender hemoparasites Babesia spp. Adult female ticks counts with size equal to or greater than 4.5 mm in diameter, present in the left side of each calf were performed. The extracted DNA samples were subjected to amplification by Reaction Polymerase Chain Quantitative Real Time (qPCR), using primers flanking fragments of mitochondrial gene cytochrome B (mt-cyt B) specific for B. bovis and B. bigemina. The RNA extracted from the blood was used to synthesize complementary DNA (cDNA) for expression analysis of genes IFN-γ, TNF-α, IL-10 and IL-12B by relative quantification (RT-qPCR). Significant differences were observed (P <0.05) between the months of reviews for the tick count. However, there was no significant effect (P>0.05) in samples taken between november 2013 and january 2014 and between the months january and february 2015. The frequency of parasitaemia in the herd was 98%. Among the samples of DNA that could be quantified by qPCR, 98% and 95.4% were positive for B. bovis and B. bigemina, respectively. Regarding the number of copies (NC) of fragments of genes mt-cyt B, specific to B. bovis and B. bigemina significant effects were observed (P<0.05) for both species and interaction between those harvests in different seasons. Analysis of the mRNA expression level of IFN-γ, TNF-α and IL-12B showed that there was a significant effect (P<0.05) interaction between the animal extreme resistance/susceptibility and seasons, except for IL-10. It is concluded that the qPCR has high sensitivity and specificity for the diagnosis of bovine babesiosis in blood samples and that the fluctuation in the parasitic load in the different seasons of the year may be associated with the profile of cytokine expression presented by herd animals Canchim during the experimental period. / FAPESP: 2013/16246-9

Submitted by Taiwany Oliveira (taiwanyrodriguess@gmail.com) on 2018-10-22T14:48:18Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) TESE DE DOUTORADO LIGIA FERNANDES ABDALLA.pdf: 4835970 bytes, checksum: 41de8abe90eea5b202c2800675761f12 (MD5) / Approved for entry into archive by Marcos Roberto Gomes (mrobertosg@gmail.com) on 2018-10-22T15:27:12Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) TESE DE DOUTORADO LIGIA FERNANDES ABDALLA.pdf: 4835970 bytes, checksum: 41de8abe90eea5b202c2800675761f12 (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2018-10-23T14:07:04Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) TESE DE DOUTORADO LIGIA FERNANDES ABDALLA.pdf: 4835970 bytes, checksum: 41de8abe90eea5b202c2800675761f12 (MD5) / Made available in DSpace on 2018-10-23T14:07:04Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) TESE DE DOUTORADO LIGIA FERNANDES ABDALLA.pdf: 4835970 bytes, checksum: 41de8abe90eea5b202c2800675761f12 (MD5) Previous issue date: 2018-09-26 / Zika virus (ZIKV) is an emergent arbovirus of the family Flaviviridae and the genus Flavivirus, which until 2007 was restricted to some cases of mild disease in Africa and Asia. In Brazil, it`s suspected that the entry of the virus occurred during the 2013 Confederations Cup and in the first half of 2015, there were already confirmed cases in states in all regions of the country. The Brazilian epidemic revealed that the usually mild and self-limiting infection could be related to neurological disorders. The objectives of this study were to clarify numerous questions regarding ZIKV infection, aiming to contribute to a better understanding of the mechanisms involved in the immunopathogenesis and course of the disease. As a result, the first report of atrial fibrillation in patients with Zika was described and could be considered an atypical manifestation during the virus infection; elevation of proinflammatory cytokines during ZIKV infection was observed; CXCL10 chemokine was identified as a potential biomarker for infection; saliva was characterized as the fluid of choice for the detection of Zika virus in the acute phase of the disease and a logistic regression model for the classification of cases of zika in relation to dengue was set up based on the clinical evaluation. / O Zika virus (ZIKV) é um arbovírus emergente da família Flaviviridae e do gênero Flavivirus, que até 2007 estava restrito a alguns casos de doença leve na África e na Ásia. No Brasil, suspeita-se que a entrada do vírus tenha se dado durante a Copa das Confederações de 2013 e no primeiro semestre de 2015, já havia casos confirmados em estados de todas as regiões do país. A epidemia brasileira revelou que a infecção geralmente leve e autolimitada poderia estar relacionada à distúrbios neurológicos. Os objetivos deste trabalho era esclarecer inúmeros questionamentos existentes em relação à infecção pelo ZIKV, visando contribuir com uma melhor compreensão dos mecanismos envolvidos na imunopatogênese e curso da doença. Como resultados, descreveu-se o primeiro relato de fibrilação atrial em pacientes com Zika, podendo ser considerado uma manifestação atípica durante a infecção pelo vírus; observou-se elevação de citocinas pró-inflamatórias durante a infecção ZIKV; identificou-se a quimiocina CXCL10 como um biomarcador potencial de infecção; caracterizou-se a saliva como fluído de escolha para o detecção do vírus Zika na fase aguda da doença e, montouse um modelo de regressão logística para a classificação de casos de zika em relação à dengue, com base na avaliação clínica.

Antimicrobial engineered nanomaterials (ENM) are increasingly incorporated into products despite limited understanding of the interactions between ENMs and bacteria that lead to toxic impacts. The hazard posed by increasing environmental release of antimicrobial ENMs is also poorly characterized. The overall objective of this thesis is to inform questions about the types of interactions that lead to an ENM inducing bacterial toxicity. Many antimicrobial ENMs are soluble, and the ion plays an important role in their toxicity. Some believe that, beyond release of ions, ENM toxicity is expected to derive from a nanoparticle (NP)-specific effect. This research compares bacterial responses to ENMs, their metal salts, and/or their transformed species within different experimental settings to improve our understanding of the interactions that enable ENM bacterial toxicity. The first objective is to characterize the potential hazard posed by pristine and transformed antimicrobial ENMs on microbial communities within a complex environmental system. One pair of ENMs (Ag0 and Ag2S) led to differential short-term impacts on surficial sediment microbial communities, while the other did not (CuO and CuS), showing that ENM transformation does not universally lead to distinct impacts. The metal ion (Cu2+) had a more profound microbial community impact than did any of the four ENMs. By 300 days the microbial community structure and composition re-converged, suggesting minimal long-term impacts of high pulse inputs of antimicrobial ENMs on microbial communities within complex environments. The second objective is to identify NP-specific effects of a common antimicrobial ENM on a model bacterium. Analysis of transcriptional responses identified NP-specific induction of a membrane stress responsive gene, providing evidence of a NP-specific effect. Otherwise, our results suggest that CuO NP toxicity triggers the same stress responses as does Cu2+, but at more moderate levels. Two ion treatments with the same total Cu input – one with pulse addition and one with gradual addition that was meant to better represent the slow dissolution of the CuO NP – led to temporally distinct responses. This calls for the use of more representative ion controls for comparison against soluble NP impacts in future nanotoxicity studies. The third objective is to investigate the potential use of CuO ENMs to reduce virulence and growth of an emerging bacterial pathogen. CuO NP exposure led to reduction in relative expression of three Staphylococcus aureus virulence factor genes, especially in methicillinresistant S. aureus (MRSA) clinical isolates. Growth was inhibited at high CuO NP concentrations for all four isolates, too. Comparison across all genes assayed showed isolatespecific transcriptional responses, but with NP- and ion-induced responses showing clear differences for each isolate, too. Altogether, this research contributes novel knowledge that will guide efforts to characterize potential hazard from release of ENMs into the environment and to apply ENMs for effective antibacterial treatment.