A alimentação diferencial durante o desenvolvimento das abelhas Apis mellifera desencadeia respostas endógenas em vias de sinalização e sistema endócrino, que promovem o desenvolvimento de fenótipos alternativos nas castas femininas. Rainhas e operárias diferem em sua fisiologia, morfologia, longevidade, função na colônia, comportamento, e principalmente, na ativação do sistema reprodutivo. Em relação aos ovários, resultados prévios baseados em ensaios de microarranjos revelaram um conjunto de genes como diferencialmente expressos (DEGs) em larvas de rainhas e operárias. Esse trabalho teve como objetivo analisar os padrões de expressão desses DEGs em mais detalhe em ovários larvais de rainhas e operárias. Com esse objetivo, foram selecionados 18 DEGs para validação por RTqPCR. Estas análises foram realizadas em ovários dissecados de rainhas e operárias em quatro estágios larvais que representam fases críticas no desenvolvimento ovariano (L4, L5F1, L5F2 e L5F3). Dentre os 18 DEGs candidatos, 11 foram confirmados como de fato diferencialmente expressos. Entre esses, quatro genes que codificam enzimas: short chain dehydrogenase reductase (GB54419), 15-hydroxyprostaglandin dehydrogenase (GB18737), SCPEP1-like gene (GB11273) e glycerol-3-phosphate dehydrogenase (GB50902), exibiram um pico de expressão em L5F1 em ovários de operárias. Dentre os dois genes relacionados à estocagem ou transporte de proteínas, o gene apolipoprotein III (GB20117) encontrou-se mais expresso em operárias enquanto que hexamerin 70b (GB10869) se mostrou superexpresso em ovários de rainhas. Os genes relacionados à tradução de mRNA e vias de sinalização: elongation factor 1? (GB52028), heat shock protein 60 (GB18969), heat shock protein 90 (GB40976) e mitogen-activated protein kinase 3 (GB41845) estavam significativamente superexpressos em ovários de rainhas. O gene OCLP-1 (GB19297), que possui uma função hipotética como inibidor de cistina foi encontrado como superexpresso em ovários de operárias. A fim de avaliar a modulação desses genes por hormônio juvenil, foi realizado o tratamento in vivo de larvas de operárias com aplicação tópica do hormônio. Após seis horas de tratamento, os ovários foram dissecados e as amostras analisadas por RT-qPCR. Dos onze DEGs testados para resposta a HJ, seis se mostraram significativamente modulados pelo hormônio Dois genes, short chain dehydrogenase reductase e heat shock protein 90, que também respondem a ecdisona, são up-regulados por HJ, enquanto os genes OCLP-1, hexamerin 70b, 15-hydroxyprostaglandin dehydrogenase e apolipoprotein III eram downregulados. A expressão diferencial desses genes que codificam enzimas, proteínas de transporte/estocagem e fatores de vias de sinalização, indica que estes genes são importantes no desenvolvimento casta-especifíco dos ovários, uma vez que sua expressão está fortemente modulada durante os estágios em que ocorre a morte celular programada em ovários de operárias. / Differential feeding during larval development of the honey bee (Apis mellifera) triggers endogenous responses in signaling pathways and the endocrine system which promote the development of alternative phenotypes in the female castes. Queens and workers differ in physiology, morphology, longevity, function in the colony, behavior, and, especially so, the activation of the reproductive system. Concerning the ovaries, previous results based on microarray assays revealed a set of differentially expressed genes (DEGs) in queen and worker larvae.This project now aimed to further analyze the expression patterns of DEGs in the ovaries of larval workers and queens. From the microarray assays we selected a set of 18 DEGs for validation by qPCR. These analyses were performed on ovaries dissected from queens and workers of four larval stages representing critical phases of ovary development (L4, L5F1, L5F2, L5F3). Among the 18 DEG candidates, 11 were confirmed as differentially expressed. Four genes that code for enzymes: a short chain dehydrogenase reductase (GB54419), a 15-hydroxyprostaglandin dehydrogenase (GB18737), an SCPEP1-like gene (GB11273) and glycerol-3-phosphate dehydrogenase (GB50902) exhibited an expression peak at L5F1 in worker ovaries. Among the two genes encoding storage or transport proteins, apolipoprotein III (GB20117) was more expressed in workers and hexamerin 70b (GB10869) was overexpressed in queen ovaries. Among the genes related to mRNA translation and signaling pathways: elongation fator 1? (GB52028), heat shock protein 60 (GB18969), heat shock protein 90 (GB40976) and a mitogen-activated protein kinase 3 (GB41845) were found significantly overexpressed in queen ovaries. The gene OCLP-1 (GB19297), which has a hypothetical function as an inhibitor cystine knot peptide, was found higher expressed in worker ovaries. So as to evaluate the modulation of these genes by juvenile hormone, an in vivo treatment of workers larvae was performed with cuticular application of the hormone. After six hours of treatment, the ovaries were dissected and the samples analyzed by RTqPCR. Of the eleven DEGs tested for response to JH, six were significantly modulated by the hormone. Two genes, short chain dehydrogenase reductase and heat shock protein 90, which also respond to ecdysone, were up-regulated by JH, while OCLP-1 hexamerin 70b, 15- hydroxyprostaglandin dehydrogenase and apolipoprotein III were down-regulated.The differential expression of these genes encoding enzymes, storage/transport and signaling pathway proteins indicates that they are important in caste-specific ovary development, as their expression is strongly modulated during stages when programmed cell death takes place.

Abstract: Recent advances in Next-Generation Sequencing protocols have opened a variety of ways to generate data. However, each newly developed methodology is most suited to represent a certain phenomenon or molecule. The object of this analysis is to identify the most appropriate way to generate and process data to study the snoRNAs, or small nucleolar RNA. Recently, snoRNAs have been revealed as taking part in a variety of unexpected alternative functions such as splicing, resistance to oxidative shock and chromatin unwinding. Finding a method to generate and treat a large quantity of data containing snoRNAs and their potential interactors could highlight some of their unexplored roles within the cell. To tackle the problem, a new protocol was put forward. This new pipeline relies on a reverse transcriptase isolated from a bacterial group II intron which boasts a better representation of structured small RNAs such as tRNAs and snoRNAs. Indeed, when compared to data created by using the standard small RNA preparation protocol, the sequencing data generated through the group II intron retrotranscriptase gives a much fairer representation. These improvements are also present in the bioinformatics pipeline. The workflow was changed to facilitate the detection of ncRNAs. These modifications rescue millions of reads, further increasing the power of the analysis. Ultimately, such corrections increase the predictive power of sequencing data. / Des avancées récentes dans le domaine du séquençage de prochaine génération ont ouvert une panoplie de façons de générer des données. Toutefois, chaque nouvelle méthode dévelopée est souvent appropriée à la caractérisation d’un seul type de phénomène ou de molécules. L’objectif de cette analyse est d’identifier la manière la plus appropriée de générer et traiter les données pour étudier les petits ARNs nucléolaires, snoRNAs. Récemment, ceux-ci ont été révélés comme des acteurs dans une variété de fonctions alternatives comme l’épissage alternatif, la résistance au choc oxidatif et l’état de la chromatine. Il est donc impératif de trouver une méthode qui puisse traiter une large quantité de données contenant les snoRNAs et leurs intéracteurs pour découvrir les rôles encore inexplorés des snoRNAs. Dans cette optique, un nouveau protocole a été élaboré. Cette nouvelle suite d’analyses s’appuie sur une reverse transcriptase isolée d’un intron de groupe II bactérien qui affiche une meilleure représentation des petits ARNs structurés comme les tRNAs et les snoRNAs. En effet, quand les données générées à travers la méthode de préparation des libraries pour petits ARNs standard est comparée à celle basée sur la reverse transcriptase bactérienne, cette dernière donne une meilleure représentation du compte des espèces. Ces avancées sont aussi présentes dans la méthode d’analyse informatique. La suite d’outils a été modifiée afin de permettre une meilleure détection des petits ARN non-codants. Ces modifications permettent de récupérer des millions de lectures par ensemble de données ce qui augmente le pouvoir prédictif de l’analyse.

La production de lavande concoure au rayonnement de la région Rhône-Alpes. Les applications de l’huile essentielle (HE) de lavande reposent sur la culture de 3 espèces (L. aangustifolia, L. latifolia et L. stoechas et d’un hybride L. x intermedia) aux chémotypes marqués. Le genre Lavandula est un modèle idéal pour comprendre la structuration et l’origine de la diversité des composés organiques volatils (COV) en particulier des terpènes. Les lavandes ont l’avantage d’avoir une aire de distribution large avec des régions bioclimatiques différentes, un nombre d’espèces limité (39) ayant des caractéristiques morphologiques et écologiques variées. Pour caractériser la diversité des COV accumulés dans les espèces du genre et envisager leur évolution, nous avons analysé (GC-MS) les COV de 29 espèces (certaines pour la première fois). Comme souvent chez les plantes, la production de COV dans les inflorescences de lavande est soumise à une régulation spatio-temporelle. L'émission différentielle de COV au cours du temps chez L. angustifolia a été relevée par les agriculteurs qui ont observé une qualité d’HE différente suivant la maturité des inflorescences au moment de la récolte. Pour modéliser ces variations et les corréler avec des étapes du développement de la plante, nous avons analysé, au niveau chimique (GC-FID) et moléculaire (qPCR), les variations temporelles des principaux COV dans les feuilles et les inflorescences (plusieurs années et cultivars). En amont de ces recherches sur les COV du genre Lavandula, différent outils de bioinformatique ont été développés. En particulier, le module « MSeasy » qui permet d’automatiser le rapatriement de données de GC-MS. Ceci constitue un pré-requis pour utiliser la lavande comme modèle d’étude des COV chez les Lamiacées / The lavender production is of significant importance for the international visibility of the french Rhône-Alpes region. Uses of lavender essential oil (EO) are based on the growing of 3 species (L. angustifolia, L. latifolia, L. stoechas and an hybride L. x intermedia) with marked. The genus Lavandula is an ideal model for understanding the origin of the diversity of volatile organic compounds (VOCs), especially terpenes. Lavenders have the advantage of having a wide range of distribution areas with different bioclimatic regions, a limited number of species (39) with diverse morphological and ecological caracteristics. In order to characterize the diversity of the VOCs accumulated in the genus and consider their evolution, we have analyzed (GC-MS) the VOCS accumulated by 29 species (some for the first time). As often, in plants, the production of VOCs in the inflorescences of lavender is subject to spatial and temporal regulation. The differential emission of VOCs over time in L. angustifolia is a well known phenomenon for farmers who have observed a different quality of EO depending on the maturity of the inflorescences at harvest. To correlate these variations with stages of plant development, we have analysed the temporal variations of the main VOCs in leaves and inflorescences (several years and cultivars) at the chemical level (GC-FID) and the molecular level (qPCR). Upstream of this research on the genus Lavandula different bioinformatic tools have been developed. In particular, the module “MSeasy " which can automate GC-MS data retrieval. This is a prerequisite for using lavender in the future as a model study of VOCS in Lamiaceae

O relógio biológico de plantas é uma rede regulatória de grande relevância para a adaptação dos organismos ao ambiente. Essa rede é composta por diversas vias de controle transcricional e pós-transcricional que se retroalimentam e geram ritmos biológicos. O controle exercido pelo relógio pode ser observado nos mais diversos aspectos da fisiologia e desenvolvimento de plantas. No presente projeto de pesquisa foi investigada a relação entre o relógio biológico e a sinalização por auxinas, uma classe de fitohormônios, em cana-de-açúcar. Foram utilizadas técnicas de expressão gênica, como RT-qPCR, para definição de um protocolo robusto de avaliação de respostas transcricionais a auxinas em plântulas de cana-de-açúcar geradas por organogênese direta. Após 1h da aplicação de 80 µM auxina sintética ácido 1-naftalenoacético, foi possível observar controle transcricional evidente exercido pela aplicação de auxina sobre alguns genes. Também foi observado variação na resposta obtida, dependendo do horário do ciclo circadiano em que o estímulo era oferecido. Esse fenômeno de controle temporal sobre a resposta a um estímulo é chamado gating, sendo de grande relevância para a atuação do relógio biológico de plantas. A partir dessas observações foram realizadas análises de expressão gênica em larga escala, usando oligoarranjos, para compreensão mais aprofundada da conexão entre o relógio biológico e a sinalização por auxinas em cana-de-açúcar. Entre os genes diferencialmente expressos após estímulo com auxina, foi verificado grande presença de genes relacionados a respostas contraestresse biótico. Além disso, as respostas observadas devem estar sobre o controle do relógio biológico de cana-de-açúcar. Diversos genes relacionados a combate a infecções, como quitinases e taumatinas, tiveram sua expressão alterada após aplicação de auxinas, sendo possível observar diferenças no padrão de expressão dos genes dependendo do horário em que auxina era aplicada. Dessa forma, o relógio biológico de cana-de-açúcar, a partir da sinalização por auxinas, deve exercer controle sobre as respostas a estresses bióticos nesse organismo. Os dados obtidos são inéditos e podem contribuir para o aumento da produtividade de cana-de-açúcar assim como para o desenvolvimento de novas ferramentas biotecnológicas focadas nesse cultivar, o qual apresenta grande relevância econômica / The circadian clock is a regulatory network with great relevance to fitness of plants. This network creates biological rhythms, influencing plants metabolism and their interaction with the environment. The clock is composed of interlocking feedback transcriptional and post-transcriptional pathways. In the presente study, we investigated the interconnection between circadian clock and signaling through auxins, a group of phytohormones with great impact to plant biology. Using RT-qPCR, it was established a protocol to measure transcriptional responses after synthetic auxin 1-naphtalenacetic acid (NAA) treatment. The biological material used was leaves of sugarcane plantlets generated by direct organogenesis. After 1h treatment with 80 µM NAA, we observed obvious transcriptional responses in sugarcane plantlets. It was also possible to detect alterations of transcriptional responses according to the moment when the stimulus was offered. This temporal control is called gating and is of great relevance to plant circadian clocks. We then performed transcriptomic analysis, using oligoarrays, to get a deeper understanding of the results obtained. Indeed, it was verified that auxin stimulus is connected to biotic stress transcriptional responses and that these responses are clock-controlled. Transcripts coding for proteins like chitinases and thaumatins, which are related to biotic stress responses, were differentially expressed after auxin treatment. Also, the response of most genes was daytime-dependent. We conclude that sugarcane circadian clock, through auxin signaling, might exert control under biotic stressresponses in sugarcane. The data obtained are novelty and may contribute to increase sugarcane productivity and/or to development of new biotechnological tools dedicated to this cultivar.

Blood vessel mimics (BVMs) are simple tissue engineered blood vessel constructs intended for preclinical testing of vascular devices. This thesis developed and implemented methods to characterize two of these components. The first aim of this thesis investigated the effect of cell culture duration and flow conditions on endothelial cell gene expression, especially regarding endothelial-to-mesenchymal transition (EndMT). A trend of decreased endothelial marker gene expression and increased mesenchymal marker gene expression would indicate EndMT. qPCR analysis revealed that increased cell culture duration did not result in EndMT, and in fact increased endothelial marker expression as cell culture duration increased. Disturbed flow conditions decreased endothelial marker and increased mesenchymal marker expression relative to static culture. The second aim of this thesis developed methods to determine cytotoxicity of, and endothelial cell adhesion to, novel BTEAC salt scaffolds. Immunostaining was used to visualize these scaffold effects. The cytotoxicity elution assay showed that BTEAC salt scaffolds were not more cytotoxic than the standard PLGA scaffold. Direct contact assays spanning several timepoints also found that BTEAC salt scaffolds were not more cytotoxic than standard scaffolds but had higher endothelial cell adhesion and coverage than standard scaffolds. Overall, this thesis developed and implemented methods to characterize the endothelial cells used in the BVM model.

This diploma thesis focuses on the molecular characterization of selected PHA producers. Within this work, the PHA producing thermophilic isolates originating from the samples of activated sludge and compost were identified and characterized using molecular biological methods. By sequencing the 16S rRNA gene, the thermophilic isolates were identified and taxonomically classified into the Firmicutes bacterial phylum. In these bacterial isolates, the ability to produce PHA at the genotype level was determined by conventional PCR detection of the phaC gene encoding PHA synthase, which is a key enzyme in PHA biosynthesis. Class I, II and IV PHA synthases were detected in most of the isolated bacteria, wherein class I and II PHA synthases are not characteristic for these bacterial genera. The largest proportion of isolates was identified for the species of thermophilic bacterium Aneurinibacillus thermoaerophilus, in which class IV PHA synthase was detected. In the second part of the diploma thesis, the RT-qPCR method was implemented to study the expression of selected genes of the bacterium Cupriavidus necator H16 involved in PHA metabolism. As part of the implementation of this method, PCR-based detection of selected genes was optimized and quantification of genes using real-time PCR was performed. The tested method included steps of RNA isolation, cDNA synthesis and quantification of gene segments for which the critical points of the method were determined based on the obtained data.

Nitrogen cycling processes can be tracked using quantitative Polymerase Chain Reaction (qPCR) to determine the presence and qReverse Transcriptase-PCR (qRT-PCR) to determine expression of key genes, or ‘biological markers’, for nitrogen metabolism. Nitrification is catalyzed in part, by two enzymes: ammonia monooxygenase (AMO; NH3 NH2OH) and nitrite oxidoreductase (NXR; NO2- NO3-). For denitrification, four enzymes act sequentially: nitrate reductase (NAR/NAP; NO3- NO2-), nitrite reductase (NIR; NO2- NO), nitric oxide reductase (NOR; NO  N2O), and nitrous oxide reductase (NOS; N2O  N2). A principle of wastewater treatment (WWT) is to remove excess nitrogen by taking advantage of natural nitrogen cycling or biological nitrogen removal (BNR). This process involves using microorganisms to bring influent ammonia through nitrification and denitrification to release nitrogen gas, which does not contribute to eutrophication. A novel shortcut nitrogen removal configuration could increase nitrogen removal efficiency by promoting nitritation/denitritation, reducing the classic nitrogen cycle by removing the redundant oxidation/reduction step to nitrate (NO3-). Here, three nitrogen transformations were used to track the three main phases in the nitrogen cycle; ammonia monooxygenase for nitrification, nitrite oxidoreductase for shortcut, and nitrous oxide reductase for denitrification. Primers for qPCR and qRT-PCR were designed to capture as much sequence diversity as possible for each step. Genes from bacteria known to perform the nitrogen transformations of interest (amoA, nxrB, nosZ) were used to BLAST-query the Integrated Microbial Genomes & Microbiomes database (img.jgi.doe.gov) to find homologs from organisms commonly found in WWT. These sequences were then aligned to find regions sufficiently conserved for primer design. These PCR primers were tested against standards for each gene and used to track nitrogen transformation potential and expression in a novel lab-scale algal photo-sequencing batch reactor which promotes shortcut nitrogen removal from wastewater across three solids retention times (SRT, or mean cell residence time); 5, 10 and 15 days. SRT 15 had the greatest total nitrogen removal with nitritation and denitritation observed. Nitrate was not detected in the first cycle and shortcut nitrogen removal was supported by low levels of nxrB genes and transcripts. Simultaneous nitrification/denitrification was supported by elevated concentrations of nosZ during the light period and less nitrite produced than ammonium consumed. Nitritation was predominantly performed by Betaproteobacteria amoA and nitrous oxide reduction was predominantly from nosZ group I (Proteobacteria-type).

Brucellosis is an economically important bacterial disease of both animals and humans. In sub-Saharan Africa, the diagnosis of the disease remains a challenge. Brucellosis is underreported in South Africa, due to inconsistency in reports of bacteriological and serological tests, which lack adequate sensitivity and specificity in the diagnosis of the disease. They also are ineffective in confirming brucellosis during early stages of the disease. The aim of this study was to develop a 16S-23S ribosomal deoxyribonucleic acid (rDNA) internal transcribed spacer (ITS) quantitative polymerase chain reaction (qPCR) assay for early diagnosis of brucellosis and as a rapid screening tool. To achieve this, blood, milk and tissue samples were spiked with B. abortus biovar (bv.) 1 (B01988-18 strain) to determine the analytical sensitivity and specificity of the assay. The efficiency was 105% in tissue, 99% in blood, and 93% in milk. The 95% limit of detection (LOD) of the ITS qPCR assay was highest in tissue, followed by blood, then milk; thus (1.45, 13.30 and 45.54 bacterial genome copies/PCR reaction). Furthermore, the diagnostic performance of the assay was compared to the Brucella cell surface protein real time polymerase chain reaction (BCSP31 qPCR) assay. Out of 56 aborted foetal tissue samples from bovine, ovine and caprine, 33% (19/56) were positive for Brucella spp. The sensitivity and specificity of the ITS qPCR assay were 87% and 95% respectively, compared to the 92% and 89% for the BCSP31 qPCR assay and 47% and 55% for bacterial culture, respectively. The ITS qPCR gave earlier CT’s with a difference in CT (ΔCT) between ITS and BCSP31 ranging between 7.1 and 3.24. The assay was efficient, sensitive and specific. It detected as little as 1.45 bacterial genome copies/PCR reaction in tissue, making this assay a valuable tool in early detection of the presence of the Brucella pathogen. It is sensitive and specific in the diagnosis of brucellosis. / Dissertation (MSc)--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc / Unrestricted

Overweight (BMI 25–29) or obese (BMI over 30) pregnant women have an increased risk of complications during pregnancy and childbirth that can harm both women and their children.Due to increased risk for several complications such as of giving birth to large children, malformations or still births, the children have higher risk of obesity, blood pressure diseases and diabetes in childhood and later in life compared with children of normal weight. Various factors affect nutrient supply to the fetus such as activity of transport proteins, maternal and fetal blood flow to and from the placenta and placental metabolism. X-box-binding protein1 (XBP-1) is an important transcription factor that is part of the endoplasmic reticulum (ER)and facilitates the breakdown of misfolded proteins and gives ER good quality control over proteins. The purpose of this work was to study the XBP-1 protein in the placenta and see if the cells are stressed in women with obesity and compare levels of this protein with women who are normal weight. Placental expression of XBP-1 was analyzed by use of two different methods western blot including 36 women in three different groups, 12 women who were normal weight, 12 women who were obese and 12 women who were overweight. The second method was real- time polymerase chain reaction (RT- PCR) including 20 women in two different groups, 10 women who were normal weight and 10 women who were obese. The result showed that there was no protein detected in the placenta but there were bands in positive control. XBP-1 mRNA expression did not differ between study groups but there was a tendency towards a significant correlation mRNA and birth weight of the children. This indicate that it may a correlation between them, but our results should be confirmed with larger studies.

Campylobacteriosis is a leading foodborne illness worldwide, primarily caused by Campylobacter jejuni (C. jejuni) which is associated with poultry consumption. The emergence of antibiotic resistance has emphasized the need for alternative strategies to control C. jejuni colonization in poultry. To assess the prevalence of C. jejuni in poultry, 270 cloacal swab samples were collected from broilers raised under No-Antibiotics Ever system. Among these samples, 16.3% were identified as C. jejuni positive. Notably, these isolates exhibited a diverse range of virulence factors and antimicrobial resistance genes, with 61.36% of isolates showing hyper-motile and 20.45% demonstrating multidrug resistance. Following isolation, whole genome sequencing was conducted on four selected strains using a hybrid sequencing approach. Subsequently, the complete genomes of these C. jejuni strains were analyzed to identify vaccine candidates using reverse vaccinology. Three conserved potential vaccine candidates were identified as suitable targets for vaccine development, namely phospholipase A (PldA), TonB dependent transporter (ChuA), and cytolethal distending toxin (CdtB). Furthermore, the gene expression of these candidates was examined in four C. jejuni strains during host-pathogen interactions using avian macrophage cell line HD11. Significant upregulation of all three candidate genes were observed in the four tested C. jejuni strains during interaction with host cells, indicating their crucial role in C. jejuni infection. Additionally, the expression of immune genes was evaluated in avian macrophage cells to understand the immune responses during C. jejuni infection. The infection resulted in the upregulation of toll-like receptor genes (TLR-4), pro-inflammatory genes (IL-1β, IFN-γ, IL-6, IL-8L1), anti-inflammatory gene (IL-10), and iNOS2 gene expression. The observed immune response demonstrates the potential of C. jejuni to induce host immunity for protection. In conclusion, our study identifies three conserved potential vaccine candidates and provides insights into the immune responses induced by C. jejuni infection in avian macrophage cells. These findings are crucial for the development of an effective vaccine against C. jejuni, aiming to reduce C. jejuni transmission through poultry consumption and the risk of human infection.