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).

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The ability of human pluripotent stem cells (hPSCs) to differentiate into different types of cells has been regarded as a significant discovery in the development of cell replacement therapy for type 1 diabetic patients. MicroRNAs can be transported to recipient cells via vesicles, so-called exosomes. Exosomal microRNA differ from those of the parent cells suggesting that cells possess an active selecting mechanism of exosomes and their contents. Therefore, microRNAs may directly or indirectly regulate the expression of pancreatic islet-specific transcription factors to control the differentiation and maturation of pancreatic islet cells. In this study, the dynamic expression of exosomal and intracellular microRNAs from human pancreatic islets were analyzed and were compared with that in stem cell-derived islet-like clusters. The study also aimed to analyze the expression levels of intracellular microRNA in human pancreatic islets and stem cell-derived islet-like clusters compared to exosomal microRNA extracted from human islet media and stem cell media, respectively. The primary method of exosome extraction was ultracentrifugation, followed by microRNA isolation using a kit. The exosomes were then characterized with NTA, and the isolated microRNAs were detected using RT-qPCR. The results showed that the expression of microRNAs was generally low in human islets compared to isolated exosomes. The microRNA expression levels in stem cell-derived islet-like clusters and their respective isolated exosomes were also analyzed and it showed that let-7a, miR-375 and miR-26a were more abundant in exosomes. The results can contribute to the generation of more functional stem cell-derived islet-like cell clusters prepared from hPSCs to some extent. However, continued research in this area is required.

L’utilisation de molécules stimulatrices des défenses des plantes (SDP), également appelées inducteurs de résistance, constitue une alternative potentielle aux traitements fongicides conventionnels pour combattre les maladies dues à des champignons phytopathogènes. Trois SDPs, le tréhalose (TR), l’acide salicylique (SA) et l’heptanoyl d’acide salicylique (HSA), un dérivé fonctionnel du SA, protègent le blé (Triticum aestivum L.) contre l’oïdium (Blumeria graminis f.sp. tritici), lorsqu’ils sont utilisés de façon préventive. La protection obtenue n’est pas liée à un effet fongistatique direct sur la germination des spores du champignon, mais à l’induction chez le blé de défenses qui diminuent le développement de la maladie. Notre travail consistait à caractériser les mécanismes de défense mis en jeu après applications foliaires de TR, de HSA et de SA chez un cultivar de blé sensible à l’oïdium. Un suivi de l’expression de gènes marqueurs de défense, réalisé par RTqPCR, a été mené en cinétique,depuis le traitement par les SDPs jusqu'à 4 jours après infection. Les activités enzymatiques correspondantes ont été également mesurées, et l’influence indirecte des SPDs sur le processus infectieux a été observé en microscopie in planta. Ainsi, les réactions de défense déclenchées par le TR, le SA et le HSA ralentissent l’évolution de l’infection, jouant respectivement sur la germination des conidies, structures infectieuses de Bgt, sur la germination du tube germinatif appressorial (AGT) et sur la proportion d’AGTs qui parviennent à pénétrer dans les tissus foliaires. Le TR est à l’origine d’une augmentation de l’expression des gènes codant pour une lipoxygénase, une protéine de transfert des lipides et une phospholipase C, impliquées dans le métabolisme lipidique et la signalisation, et de gènes codant pour des protéines PR comme les chitinases et PR1, tous connus comme marqueurs de défense. Ainsi, les réactions déclenchées par le TR correspondent à un effet inducteur de défenseplutôt qu’à une réaction de stress osmotique. Le HSA modifie particulièrement le métabolisme lipidique, en induisant fortement et pendant toute la cinétique, l’expression du gène codant pour la LOX et l’activité correspondante, aussi bien hors contexte infectieux qu’en contexte infectieux. Cette augmentation de l’activité LOX n’est pas retrouvée chez des feuilles traitées au SA et caractérise donc le HSA. L’importance des réactions observées avec le TR, le SA et le HSA, hors contexte infectieux et en présence de Bgt amène à discuter les effets éliciteurs et potentialisateurs de ces 3 SDPs. / The use of plant elicitors, also known as resistance inducers, is an alternative to conventional fungicides to control diseases caused by phytopathogenic fungi. Three resistance inducers, trehalose (TR), salicylic acid (SA) and heptanoyl salicylic acid (HSA), a functional derivative of SA, protect wheat (Triticum aestivum L.) against powdery mildew (Blumeria graminis f . sp. tritici) when applied prior to infection. The protection obtained is not linked to any direct fungistatic effect on the fungal spore germination, but to the induction of wheat defences that impair the development of the disease. Our work aimed at characterizing the defence mechanisms triggered after foliar applications of TR, HSA and SA in a wheat cultivar susceptible to powdery mildew. Monitoring of defence markers genes expression by RTqPCR was conducted during a time-course experiment from the treatment time until 4 days after infection. Corresponding enzyme activities were also measured, and the indirect influence of elicitors on the infectious process was observed by microscopy in planta. Thus, defence responses triggered by TR, SA and HSA slow the progression of the infection, respectively altering the germination of infectious structures such as conidia, the differentiation of appressorial germ tube (AGT) and the proportion of AGTs that manage to penetrate the epidermis. TR causes an increase in the expression of genes encoding a lipoxygenase, a lipid transfer protein and a phospholipase C, which are involved in lipid metabolism and signaling, and genes encoding for PR-proteins such as chitinases and PR1, all known as markers of defence. Thus, the reactions triggered by TR match with the ones triggered during induced defence rather than during osmotic stress response. HSA specifically targeted lipid metabolism, inducing strongly and throughout the time-course, the expression ofthe gene encoding LOX and the corresponding enzyme activity, both in infectious and non-infectious contexts. This increase in LOX activity was not found in leaves treated with SA and thus characterizes HSA mode of action. The importance of the reactions observed with TR, SA and HSA, in non-infectious conditions and in the presence of Bgt have to be considered regarding either elicitation or potentiation.

Accurate smoltification and disease management in Atlantic salmon (Salmo salar) are key issues for the aquaculture industry. Due to their anadromous lifecycle the transfer of salmon from fresh water (FW) to seawater (SW) is crucial to their survival; too early can cause mortality, too late can cause desmoltification and long-term health problems. Both scenarios can increase susceptibility to four viral diseases: Salmon alphavirus (SAV), Infectious salmon anemia virus (ISAV), orthoreovirus (PRV), and Piscine myocarditis virus (PMCV). They all show similar clinical and histopathological symptoms and can easily spread throughout farms. Understanding the initial innate immune response to these viruses may provide biomarkers that could help identify and monitor infections. An in house and onsite Na+/K+ ATPase (NKA) qRT-PCR assay was developed for the salmon biomarker ATPase to test smoltification readiness in salmon smolts. Tested against NKA enzymatic assays it showed a similar success rate over 3 years: NKA qRT-PCR (57%), NKA activity assay (60%). Onsite tests confirmed that the ATPase mRNA transcript is a useful biomarker for smoltification detection. An in-lab and mobile multiplex qRT-PCR assay was developed for detection of SAV, PRV and PMCV. The analytical sensitivity of the SAV (86.5% SE 0.11), PRV (90.94%, SE 0.09) and PMCV (100.46%, SE 0.19) assays was 102 copies for PMCV and 103 for SAV and PRV. Initial results suggest individual assays could be run on site at farms. Addition of an internal control, probit analysis and viral positive tests are still required for multiplex assay integration. Salmon erythrocytes were infected with ISAV, SAV and Poly I:C to investigate whether they induce and up-regulate innate immune response genes. All genes were expressed at low levels in all parameters investigated including non-infected control erythrocytes. These findings suggest erythrocytes act as an initial buffer to viral infections and may help stimulate the innate immune response.

Barley and wheat are the two most important crop species in Turkey. Molecular studies for increasing crop yield of these species are very important for the economic benefits of Turkey. Powdery mildew and yellow rust are the two main pathogens, infecting barley and wheat, respectively in our country and causing a great amount of yield loss each year. Till now, classical genetics studies were performed in order to develop resistant barley and wheat cultivars, but these studies have not been succesful. Therefore, molecular plant-pathogen interactions studies are starting to become the new tool to fight against pathogens. In this thesis, two important aspects of plant microbe interactions were investigated. In the first part, the role of microRNAs (miRNAs) in powdery mildew-barley pathosysytem, and yellow rust-wheat pathosystem were studied. The expression levels of miRNAs and their putative targets were investigated via miRNA microarray analysis and qRT-PCR, respectively, in response to virulent and avirulent pathogen infections. These data were used to establish a new model for powdery mildew-barley and yellow rust-wheat pathosystems. In the second part, functional analysis of a novel F-box gene, which was a ZTL-type F-box, was performed by using Barley Stripe Mosaic Virus mediated Virus Induced Gene Silencing. This F-box gene (HvDRF) (Hordeum vulgare Disease Related F-box) was induced upon yellow rust infection and we studied its role in powdery mildew infection. The results confirmed HvDRF as a positive regulator of race specific immunity and enlarged the roles of ZTL-type F-box proteins to biotic stress responses.

Immune systems are fundamentally based on the differentiation of self and non-self. Unlike mammals, plants have an innate immune system responding to the pathogen only at the site of attack. One of these pathogens is Blumeria graminis f. sp. hordei which is an obligate biotrophic pathogen causing powdery mildew disease and resulting in up to 30% yield loss for both cultivated and wild barley. In this study, Pallas-01 (P-01) and Pallas-03 (P-03) barley lines were inoculated with powdery mildew race Bgh103 (64/01) resulting incompatible and compatible interactions, respectively. 6, 12, 24, 48 and 72 hour-post-inoculation (hpi) samples were used in order to define the differential gene expression of NAD malic enzyme, chloroplast lipocalin, phosphoglyceromutase (PGM), Mg chelatase and 26S protease regulatory subunit 6B homolog. In the proteomics study previously conducted in the laboratory, except for the NAD-dependent malic enzyme, the other four proteins were shown to be involved in the incompatible interaction of P-01 and Bgh103 at protein level, whereas NAD-dependent malic enzyme was changing in the compatible interaction. The expression level for both proteomics and transcriptomics were assumed to be similar. However, the level of transcript would not always reflect its protein level or correlate with the level of proteins, due to complex cellular regulation processes. Post-transcriptional modifications such as synthesis, processing, degradation and post-translational modifications are changing the level of proteins expressed, thus a parallel correlation between the protein and mRNA levels can be lost. Other possible reasons for this variation can be changes in mRNA and protein stability, efficiency of translation and protein&rsquo / s turnover rate. The transcription level changes of the genes investigated in this study are found to be differentially expressed, supporting the proteomics data indicating that these genes are possibly involved in resistance. For further investigations, genetic tools such as gene silencing with RNAi and knockout experiments are required in order to elucidate the mechanism of these candidate genes in the plant-pathogen interaction.

Selon plusieurs évidences, la présence de cellules tumorales occultes dans la circulation sanguine aux premières étapes du cancer du sein pourrait être à l’origine des lésions métastasiques. Plusieurs études de recherche ont montré que l’utilisation de la RT-PCR en temps réel pour la détection des cellules tumorales circulantes CTC offre la meilleure sensibilité dans la quantification des marqueurs tumoraux. Présentement de routine, le suivi du cancer du sein est réalisé par le dosage immunologique des marqueurs sériques CA15-3 et CEA. Cependant, la faible sensibilité de ces marqueurs aux stades précoces de la maladie et leur manque de spécificité tissulaire ne permet pas leur utilisation pour le diagnostic et le pronostic du cancer du sein. Le diagnostic de la maladie est plutôt basé sur l’analyse d’une biopsie de la tumeur ou des ganglions lymphatiques, des méthodes invasives, coûteuses et peu adaptées pour un suivi de routine dans l’évaluation du risque de rechute et de la réponse au traitement. Malgré les études, la détection de ces cellules dans les laboratoires hospitaliers est rare. Nous avons envisagé de mettre en place un nouveau test RT-PCR pour la détection de cellules malignes du cancer du sein dans la circulation. La spécificité et la sensibilité de plusieurs marqueurs potentiels ont été comparées. Le but ultime de ce projet est d’offrir la détection d’un ou d’une combinaison de ces marqueurs de routine aux patientes. Nos résultats montrent une corrélation positive entre l’expression des ARNm des marqueurs CK19 et de HER2 avec les données cliniques des patientes. De plus, la sensibilité et la spécificité des tests RT-PCR sont comparables à la littérature récente. Finalement, la comparaison de notre test avec le dosage immunologique des marqueurs tumoraux sériques CA15.3 et CEA a montré que la détection de la CK19 et de HER2 par RT-PCR est plus sensible chez les patientes de cancer du sein métastatique. / According to several evidences, the presence of occult tumor cells in blood circulation in the early stages of breast cancer could be the origin of metastatic lesions. Recent research studies have shown that the use of qRT-PCR for the detection of circulating tumor cells CTC offers the best sensitivity in the quantification of tumor markers. Currently routine monitoring of breast cancer is performed by immunoassay of serum markers CA15.3 and CEA. However, the low sensitivity of these markers in the early stages of the disease and the lack of tissue specificity does not allow their use in diagnosis and prognosis of breast cancer. The diagnosis of the disease is rather based on the analysis of biopsies of the tumor or lymph nodes. This is an invasive procedure, expensive and not suitable for routine monitoring of the risk of relapse and response to treatment. Despite these studies, detection of these cells in hospital laboratories is rare. Our objective is to set up a new RT-PCR assay for the detection of malignant breast cancer cells in the circulation. The specificity and sensitivity of some potential markers will be compared. The ultimate goal of this project is to routinely offer the detection of one or of a combination of these markers routinely to patients with breast cancer. Our results show a positive correlation between the expression of CK19 and HER2 mRNA with clinical data of patients. Furthermore, the sensitivity and specificity of our RT-PCR tests are similar to the recent literature. Finally, the comparison of our test with the immunoassay of serum tumor markers CEA and CA15.3 showed that the detection of HER2 and CK19 by RT-PCR is more sensitive in patients with metastatic breast cancer

The genes that regulate pubertal timing in the general population are not well understood. Recently, genome-wide association studies have demonstrated that genetic variants near LIN28B associate with variation in pubertal timing in humans. To investigate where within the hypothalamic-pituitary-ovarian (HPO) axis Lin28b, and its homologue Lin28a, regulate pubertal timing, expression of these genes was assessed across the pubertal transition. The finding that Lin28a/b expression decreases only in the ovary suggests that the Lin28 pathway may exert its regulatory effects with respect to puberty in the ovary. Another aim of this thesis was to examine the effect of estrogen on Lin28b expression in immortalized GnRH neuronal cells, but the data remains equivocal and detailed future studies are needed to make definitive conclusions. The ovarian expression data lay the foundation for further studies using conditional knockout mice to verify the importance of the tissue and age specific developmental pattern that was identified.

The genes that regulate pubertal timing in the general population are not well understood. Recently, genome-wide association studies have demonstrated that genetic variants near LIN28B associate with variation in pubertal timing in humans. To investigate where within the hypothalamic-pituitary-ovarian (HPO) axis Lin28b, and its homologue Lin28a, regulate pubertal timing, expression of these genes was assessed across the pubertal transition. The finding that Lin28a/b expression decreases only in the ovary suggests that the Lin28 pathway may exert its regulatory effects with respect to puberty in the ovary. Another aim of this thesis was to examine the effect of estrogen on Lin28b expression in immortalized GnRH neuronal cells, but the data remains equivocal and detailed future studies are needed to make definitive conclusions. The ovarian expression data lay the foundation for further studies using conditional knockout mice to verify the importance of the tissue and age specific developmental pattern that was identified.