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Babic, Ana [Verfasser]. "Profiling of synaptic transcriptome / Ana Babic." Berlin : Freie Universität Berlin, 2017. http://d-nb.info/1122586566/34.
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Perera, Surangi Nalika. "Olfactory ensheathing cell development : a transcriptome profiling approach." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/288787.
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Olfactory ensheathing cells (OECs), the glia of the olfactory nerve, are promising candidates for patient-specific cell-mediated repair of both peripheral nerves and the spinal cord. The recent discovery that OECs originate from the neural crest, rather than the olfactory epithelium as previously thought, potentially means that homogeneous populations of OECs for repair could be expanded in culture from neural crest stem cells persisting in the patient's own skin and hair follicles. The first step towards this long-term goal is to understand the molecular mechanisms underlying neural crest differentiation into OECs, as opposed to Schwann cells (the glia of all other peripheral nerves), which are less effective in spinal cord repair. To identify transcription factors and signalling pathways that might be involved in OEC versus Schwann cell differentiation, I took an unbiased transcriptome profiling approach. Taking advantage of Sox10 expression throughout both OEC and Schwann cell development, I used laser-capture microdissection on cryosections of mouse embryos carrying a Sox10:H2BVenus transgene, to isolate OEC subpopulations (olfactory mucosal OECs, from the olfactory nerve, and olfactory nerve layer OECs, from the olfactory nerve layer surrounding the olfactory bulb) at different stages of development, and Schwann cells from trigeminal nerve branches on the same sections, for RNA-seq and cross-wise comparison of transcriptomes. Validation of candidate genes by in situ hybridisation revealed some contamination with adjacent cells from mesenchyme, olfactory epithelium or olfactory bulb, but also identified the expression in developing OECs of various genes previously reported to be expressed in adult OECs, and of over 20 genes previously unknown in OECs. Some of these genes are expressed by OECs but not Schwann cells; some are expressed by olfactory nerve layer OECs but not olfactory mucosal OECs, while some are expressed by olfactory mucosal OECs and Schwann cells but not olfactory nerve layer OECs. For a subset of the genes, I was also able to analyse OEC differentiation in mouse mutants. I also collected transcriptome data from neural crest-derived cells that persist on the olfactory nerve in Sox10-null embryos (in which neural crest-derived cells colonise the olfactory nerve, but normal OEC differentiation is disrupted). Comparison with wild-type OEC transcriptome data from the same embryonic stage identified genes whose expression is likely either downregulated or up-regulated in the absence of Sox10, supporting a role in normal OEC differentiation. Overall, these various transcriptomic comparisons (between OECs at different developmental stages, different OEC subpopulations, OECs versus Schwann cells, and OECs versus Sox10-null neural crest-derived cells on the olfactory nerve) have identified multiple transcription factor and signalling pathway genes, amongst others, that are expressed during OEC development in vivo (including some specific to different OEC subpopulations) and that may be important for OEC differentiation. Furthermore, some of these genes are not expressed by embryonic Schwann cells. This work provides a foundation for understanding how to promote OEC rather than Schwann cell differentiation from neural crest stem cells in culture, with the potential for clinical application in the future.
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Pinal, Fernández Iago. "Transcriptome profiling and longitudinal cohort studies of myositis subsets." Doctoral thesis, Universitat Oberta de Catalunya, 2020. http://hdl.handle.net/10803/673293.
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Inflammatory myopathies are a heterogeneous family of rare autoimmune diseases affecting multiple organs and systems, including the skin, the lungs, the muscles and/or the joints. Accurately defining their pathogenesis and classifying them correctly are key for understanding and managing these diseases. In this doctoral thesis we explored specific autoantibody-defined myositis subsets and quantitatively compared the ability of autoantibodies to the 2017 EULAR/ACR classification standard to predict the phenotype of patients with myositis. We also performed RNA sequencing on 119 muscle biopsies of patients with different types of myositis and 20 controls. We studied the differential expression, performed pathway analysis and developed exploratory machine learning pipelines to define the specific expression profiles and pathogenic pathways in each disease subgroup. With these studies we determined that the autoantibodies outperform current clinical criteria to predict the phenotype of myositis patients and discovered unique expression profiles in the muscle tissue of patients with different types of myositis.Las miopatías inflamatorias son una familia heterogénea de enfermedades autoinmunes raras que afectan a múltiples órganos y sistemas, incluidos los músculos, la piel, los pulmones y/o las articulaciones. Definir con precisión su patogenia y clasificarlas correctamente es clave para comprender y manejar estas enfermedades. En esta tesis doctoral exploramos subconjuntos específicos de miositis definidas por autoanticuerpos y comparamos cuantitativamente la capacidad de los autoanticuerpos con la clasificación EULAR/ACR de 2017 para predecir el fenotipo de pacientes con miositis. Además, realizamos la secuenciación de ARN en 119 biopsias musculares de pacientes con diferentes tipos de miositis y 20 controles. Estudiamos la expresión diferencial, realizamos análisis de vías y desarrollamos procesos de aprendizaje automático exploratorios para definir los perfiles de expresión específicos y las vías patogénicas en cada subgrupo de enfermedades. Con estos estudios determinamos que los autoanticuerpos superan los criterios clínicos actuales para predecir el fenotipo de los pacientes con miositis y descubrimos perfiles de expresión únicos en el tejido muscular de pacientes con diferentes tipos de miositis.
Les miopaties inflamatòries són una família heterogènia de malalties autoimmunes rares que afecten múltiples òrgans i sistemes, inclosos els músculs, la pell, els pulmons i/o les articulacions. Definir-ne amb precisió la patogènia i classificar-les correctament és clau per comprendre i manejar aquestes malalties. En aquesta tesi doctoral explorem subconjunts específics de miositis definides per autoanticossos i comparem quantitativament la capacitat dels autoanticossos amb la classificació EULAR/ACR de 2017 per predir el fenotip de pacients amb miositis. A més, realitzem la seqüenciació d'ARN en 119 biòpsies musculars de pacients amb diferents tipus de miositis i 20 controls. Estudiem l'expressió diferencial, fem anàlisis de vies i desenvolupem processos d'aprenentatge automàtic exploratoris per definir els perfils específics d'expressió i les vies patogèniques a cada subgrup de malalties. Amb aquests estudis determinem que els autoanticossos superen els criteris clínics actuals per predir el fenotip dels pacients amb miositis i descobrim perfils d'expressió únics al teixit muscular de pacients amb diferents tipus de miositis.
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Werne, Solnestam Beata. "Interpreting the human transcriptome." Doctoral thesis, KTH, Genteknologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-158320.
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The human body is made of billions of cells and nearly all have the same genome. However, there is a high diversity of cells, resulted from what part of the genome the cells use, i.e. which RNA molecules are expressed. Rapid advances within the field of sequencing allow us to determine the RNA molecules expressed in a specific cell at a certain time. The use of the new technologies has expanded our view of the human transcriptome and increased our understanding of when, where, and how each RNA molecule is expressed. The work presented in this thesis focuses on analysis of the human transcriptome. In Paper I, we describe an automated approach for sample preparation. This protocol was compared with the standard manual protocol, and we demonstrated that the automated version outperformed the manual process in terms of sample throughput while maintaining high reproducibility. Paper II addresses the impact of nuclear transcripts on gene expression. We compared total RNA from whole cells and from cytoplasm, showing that transcripts with long, structured 3’- and 5’-untranslated regions and transcripts with long protein coding sequences tended to be retained in the nucleus. This resulted in increased complexity of the total RNA fraction and fewer reads per unique transcript. Papers III and IV describe dynamics of the human muscle transcriptome. For Paper III, we systematically investigated the transcriptome and found remarkably high tissue homogeneity, however a large number of genes and isoforms were differentially expressed between genders. Paper IV describes transcriptome differences in response to repeated training. No transcriptome-based memory was observed, however a large number of isoforms and genes were affected by training. Paper V describes a transcript profiling protocol based on the method Reverse Transcriptase Multiplex Ligation-dependent Probe Amplification. We designed the method for a few selected transcripts whose expression patterns are important for detecting breast cancer cells, and optimized the method for single cell analysis. We successfully detected cells in human blood samples and applied the method to single cells, confirming the heterogeneity of a cell population.Människokroppen är uppbyggd av miljarder celler och nästan alla innehåller samma arvsmassa. Trots detta finns det många olika celler med olika funktioner vilket är en följd av vilken del av arvsmassan som cellerna använder, dvs vilka RNA-molekyler som finns i varje cell. Den snabba utvecklingen av sekvenseringstekniker har gjort det möjligt att studera när, var och hur varje RNA-molekyl är uttryckt och att få en djupare förståelse för hur människans celler fungerar. Arbetet som presenteras i denna avhandling fokuserar på analys av RNA-molekyler i människans celler. I artikel I beskriver vi en automatiserad metod för att förbereda cellprov för RNA-sekvensering. Det automatiserade protokollet jämfördes med det manuella protokollet, och vi visade att det automatiserade protokollet överträffade det manuella när det gällde provkapacitet samtidigt som en höga reproducerbarheten behölls. I artikel II undersökte vi effekterna som RNA-molekyler från en del av cellen (cellkärnan) har på den totala mängden uttryckta RNA-molekyler. Vi jämförde RNA från hela cellen och från en del av cellen (cytoplasman) och visade att RNA-molekyler med långa och strukturerade 3'- och 5'-otranslaterade regioner och RNA-molekyler med långa proteinkodande sekvenser tenderade att hållas kvar i cellkärnan till en högre grad. Detta resulterade i en ökad komplexitet av RNA-molekylerna i hela cellen, medan vi i cytoplasma-fraktionen lättare kunde hitta de korta och svagt uttryckta RNA-molekyler. I Artikel III och IV studerar vi RNA-molekyler i människans skelettmuskler. I artikel III visar vi att andelen RNA-molekyler uttryckta i skelettmuskler är väldigt lika mellan muskler och mellan olika personer, men att ett stort antal RNA-molekyler var uttryckta i olika nivåer hos kvinnor och män. Artikel IV beskriver RNA-nivåer som svar på upprepade perioder av uthållighetsträning. Artikel V beskriver en metod för att studera ett fåtal utvalda RNA-molekyler. Vi valde RNA-molekyler vars uttryck är viktigt vid analys av bröstcancerceller, och optimerade metoden för analys av enskilda celler. Vi analyserade cancerceller från blodprov och använde metoden för att titta på RNA-nivåer i enskilda celler från en grupp av celler och visade på skillnader i RNA-nivåer inom gruppen.
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Mitko, Katrin Gabriele. "Dynamic transcriptome profiling of bovine endometrium during the oestrous cycle." Diss., lmu, 2008. http://nbn-resolving.de/urn:nbn:de:bvb:19-95112.
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Vickovic, Sanja. "Transcriptome-wide analysis in cells and tissues." Doctoral thesis, KTH, Genteknologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-199447.
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High-throughput sequencing has greatly influenced the amount of data produced and biological questions asked and answered. Sequencing approaches have also enabled rapid development of related technological fields such as single-cell and spatially resolved expression profiling. The introductory parts of this thesis give an overview of the basic molecular and technological apparatus needed to analyse the transcriptome in cells and tissues. This is succeeded by a summary of present investigations that report recent advancements in RNA profiling. RNA integrity needs to be preserved for accurate gene expression analysis. A method providing a low-cost alternative for RNA preservation was reported. Namely, a low concentration of buffered formaldehyde was used for fixation of human cell lines and peripheral blood cells (Paper I). The results from bulk RNA sequencing confirmed gene expression was not negatively impacted with the preservation procedure (r2>0.88) and that long-term storage of such samples was possible (r2=0.95). However, it is important to note that a small population of cells overexpressing a limited amount of genes can skew bulk gene expression analyses making them sufficient only in carefully designed studies. Therefore, gene expression should be investigated at the single cell resolution when possible. A method for high-throughput single cell expression profiling termed microarrayed single-cell sequencing was developed (Paper II). The method incorporated fluorescence-activated cell sorting, sample deposition and profiling of thousands of barcoded single cells in one reaction. After sample attachment to a barcoded array, a high-resolution image was taken which linked the position of each array barcode sequence to each individual deposited cell. The cDNA synthesis efficiency was estimated at 17.3% while detecting 27,427 transcripts per cell on average. Additionally, spatially resolved analysis is important in cell differentiation, organ development and pathological changes. Current methods are limited in terms of throughput, cost and time. For that reason, the spatial transcriptomics method was developed (Paper III). Here, the barcoded microarray was used to obtain spatially resolved expression profiles from tissue sections using the same imaging principle. The mouse olfactory bulb was profiled on a whole-transcriptome scale and the results showed that the expression correlated well (r2=0.94-0.97) as compared to bulk RNA sequencing. The method was 6.9% efficient, reported signal diffusion at ~2 μm and accurately deconvoluted layer-specific transcripts in an unbiased manner. Lastly, the spatial transcriptomics concept was applied to profile human breast tumours in three dimensions (Paper IV). Unbiased clustering revealed previously un-annotated regions and classified them as parts of the immune system, providing a detailed view into complex interactions and crosstalk in the whole tissue volume. Spatial tumour classification divulged that certain parts of the tumour clearly classified as other subtypes as compared to bulk analysis providing useful data for current practice diagnostics. The last part of the thesis discusses a look towards the future, how the presented methods could be used, improved upon or combined in translational research.QC 20170109
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Saal, Lena [Verfasser], and Michael [Gutachter] Sendtner. "Whole transcriptome profiling of compartmentalized motoneurons / Lena Saal ; Gutachter: Michael Sendtner." Würzburg : Universität Würzburg, 2016. http://d-nb.info/1144862051/34.
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Bergthold, Guillaume. "Genomic Profiling of Pediatric Low-Grade Gliomas." Thesis, Paris 11, 2015. http://www.theses.fr/2015PA11T053/document.
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Les gliomes de bas-grade représentent la tumeur cérébrale la plus fréquente chez l’enfant. Elles sont caractérisées par un large spectre de sous-types tumoraux, très hétérogènes. Leur définition actuelle est principalement basée sur des critères histologiques ce qui représente une limite importante car ces classifications souffrent d’un manque de précision. Les progrès récents de la génomique nous permettent d’approfondir considérablement les connaissances sur la biologie de ces tumeurs afin d’enrichir leur classification actuelle. Ce travail présente une analyse approfondie des altérations génomiques de l’ADN et l’ARN des gliomes de bas-grade pédiatriques. Le premier niveau d’analyse se base sur l’analyse du séquençage à haut débit de 169 gliomes de bas-grade de l’enfant. Bien que les mutations des gènes BRAF et FGFR1 sont les plus fréquemment décrites dans ces tumeurs, nous avons identifié pour la première fois le réarrangement chromosomique MYB-QKI majoritairement associé aux gliomes angiocentriques. Dans un deuxième temps ce travail décrit l’analyse du transcriptome de 151 gliomes de bas grade extraits à partir de tissu conservé en paraffine. Nous avons observé des différences moléculaires en fonction de leur sous-type histologique, de la localisation tumorale et de leur statut BRAF. Dans le dernier volet de ce travail, nous avons testé la faisabilité d’isoler par cytométrie en flux une cellule unique en les distinguant selon un marqueur de différenciation glial (A2B5+ et A2B5-) et d’effectuer une analyse transcriptomique à haut-débit en séquençant l’ARN à l’échelle d’une cellule unique. Cette technique nous a permis de décrire des différences moléculaires intéressantes entre des cellules A2B5+ et A2B5-. Ces résultats soulignent l’intérêt d’exploiter des nouvelles technologies de pointe pour servir de base à l’étude des caractéristiques biologiques des cellules tumoralesLow-grade gliomas represent the most frequent brain tumor arising during childhood. They are characterized by a broad spectrum of tumor types.The definition of low-grade gliomas has been mainly based on morphology. This histological classification of pediatric low-grade gliomas (PLGG), suffers from the lack of reproducibility. The recent progress in molecular biology and genetics has brought new insights in the biology of those tumors and allows better understanding of their biology. This work provides a comprehensive analysis of two different genetic approaches in PLGGs. The first part is based on the description of somatic genetic alterations of the DNA. Using a large PLGG cohort, we have dissect the genome of those tumors and draw the landscape of their genetic alteration. Although BRAF and FGFR1 alterations are predominantly altered, we have discovered a new translocation, MYB-QKI, that is almost exclusively present in a specific histological subgroup; angiocentric gliomasThe second part of the thesis describes transcriptomic analysis of bulk PLGGs. This work describes molecular differences between PLGGs from distinct histologies and arising from different locations in the brain as well as different BRAF mutation status.We were also able to test single-cell expression analyses in three pilocytic astrocytomas (PAs) using RNA-sequencing. In this experimental work we have successfully tested the hypothesis that we can isolate single-cells from fresh PLGG tumors in order to analyze the trasncriptome at a large scale. We observed that single-cells expressing A2B5, a glial progenitor marker, isolated in pediatric PAs are characterized as a distinct biological population. These results underline the importance to improve the precision of the transcriptomic studies to capture the molecular signal of tumor cells and further understand the different pattern between normal cells and tumor cells
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Klevebring, Daniel. "On Transcriptome Sequencing." Doctoral thesis, KTH, Genteknologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-11446.
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This thesis is about the use of massive DNA sequencing to investigate the transcriptome. During recent decades, several studies have made it clear that the transcriptome comprises a more complex set of biochemical machinery than was previously believed. The majority of the genome can be expressed as transcripts; and overlapping and antisense transcription is widespread. New technologies for the interroga- tion of nucleic acids have made it possible to investigate such cellular phenomena in much greater detail than ever before. For each application, special requirements need to be met. The work presented in this thesis focuses on the transcrip- tome and the development of technology for its analysis. In paper I, we report our development of an automated approach for sample preparation. The procedure was benchmarked against a publicly available reference data set, and we note that our approach outperformed similar manual procedures in terms of reproducibility. In the work reported in papers II-IV, we used different massive sequencing technologies to investigate the transcriptome. In paper II we describe a concatemerization approach that increased throughput by 65% using 454 sequencing,and we identify classes of transcripts not previously described in Populus. Papers III and IV both report studies based on SOLiD sequencing. In the former, we investigated transcripts and proteins for 13% of the human gene and detected a massive overlap for the upper 50% transcriptional levels. In the work described in paper IV, we investigated transcription in non-genic regions of the genome and detected expression from a high number of previ- ously unknown loci.QC 20100723
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Ha, Kevin C. H. "Characterization of alternative splicing and gene fusions using current transcriptome profiling technologies." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=103747.
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The study of the transcriptome, which consists of all RNA molecules in a cell, has been important for elucidating the underlying mechanisms involved in the regulation and expression of genes. Here we describe two studies that apply current high-throughput techniques to investigate two genetic phenomena at the transcriptome level in humans: alternative splicing using whole-transcript gene expression microarrays, and gene fusions using massively parallel transcriptome sequencing (RNA-Seq). Alternative splicing is a post-transcriptional mechanism that allows for the production of multiple transcript isoforms of the same gene, resulting in increased transcriptome diversity. Recently, the global analysis of AS has been facilitated by the Exon Array, which feature oligonucleotide probes that target individual exons across the length of the gene. A similarly designed array, the Gene Array, was later released for measuring whole gene expression. In our first study, we questioned whether it could be used to study AS. We analyzed previously published data to show that expression profiling at both the gene and exon level was highly concordant between both platforms. This suggests that the Gene Array is capable of making AS observations like the Exon Array. Another profiling tool that has emerged is RNA-Seq, which enables the profiling of the entire transcriptome at single-base resolution. In the second study, we describe an RNA-Seq approach to detect gene fusions, which have been frequently implicated in cancer. The role of gene fusions in BRCA1-mutated breast cancers has not been well explored. BRCA1 is involved in tumour suppression by regulating DNA repair pathways and thus mutations in this gene can lead to increased chromosomal instability. While we hypothesized that this may lead to the creation of gene fusions, we did not find them to be significantly enriched. We identified, however, one novel gene fusion that was non-recurrent. With these two studies, we demonstrate how the continued advancement of investigative tools can aid in making biological discoveries.L'étude du transcriptome, composé de toutes les molécules d'ARN dans la cellule, a été très importante pour élucider les mécanismes impliqués dans la régulation et l'expression des gènes. Dans les travaux présentés ici, nous décrivons deux stratégies appliquant des technologies à haut débit afin d'étudier deux phénomènes à l'échelle du transcriptome humain : l'épissage alternatif en utilisant des puces à ADN, et les fusions de gènes en utilisant le séquençage d'ARN de nouvelle génération (RNA-Seq). L'épissage alternatif est un mécanisme post-transcriptionnel qui permet la production de plusieurs transcrits à partir d'un seul gène, permettant ainsi d'augmenter la diversité du transcriptome. Récemment, l'analyse globale de l'épissage alternatif a été grandement facilitée par une micropuce à ADN « Exon Array », qui possède des sondes ciblant des exons individuels tout au long des gènes. Un autre type de micropuce à ADN, la « Gene Array », a ensuite été développée pour quantifier l'expression génique seulement, au niveau du génome complet. Dans la première étude présentée dans cette thèse, nous vérifions la possibilité d'utiliser ce dernier type de micropuces afin d'étudier l'épissage alternatif. Nous avons analysé des données publiées dans le passé afin de montrer que le profil d'expression obtenu tant au niveau de gènes complets qu'au niveau des exons est très concordant entre les deux plateformes. Ceci suggère que la micropuce de gènes permette d'étudier l'épissage alternatif tout comme la micropuce à exons. Ultérieurement, une nouvelle technologie a émergé : le RNA-Seq. Cette technologie permet d'obtenir le profil du transcriptome au complet avec une résolution d'une seule base. Dans la deuxième partie de cette thèse, nous présentons une approche basée sur le RNA-Seq pour détecter des fusions de gènes, fréquemment impliquées dans le cancer. Le rôle des fusions de gènes dans les cancers qui possèdent des mutations dans le gène BRCA1, n'a pas été exploré en détail jusqu'à présent. BRCA1 est impliquée dans la suppression de tumeurs par l'entremise de la régulation des voies de réparation d'ADN. Des mutations dans ce gène pourraient donc produire une augmentation de l'instabilité des chromosomes, ce qui entraînerait des fusions de gènes. Cependant, nous n'avons trouvé aucune augmentation significative de fusions en présence de mutations de BRCA1. Nous avons néanmoins identifié une nouvelle fusion de gènes qui a été non récurrente. Grâce à ces deux études, nous démontrons comment l'avancement continu des technologies de recherche peut contribuer aux découvertes biologiques.
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Gräns, Hanna. "Transcriptome analysis of patients with chronic fatigue syndrome /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-448-1/.
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Ockendon, Nina Frances. "Comparative transcriptome profiling in wild species : uncovering gene expression signatures of mating systems." Thesis, University of Bath, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.646142.
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Understanding the molecular processes underlying adaptation of complex phenotypes presents major challenges in evolutionary biology. An important question currently is how to accurately use the plethora of ‘omics data to better understand ecological variation. Using RNA-seq transcriptome data from many lineages, I demonstrate the power of this data type when studying the molecular basis of complex phenotypes. My work has produced three major results. Firstly, I have integrated bacterial RNA-seq data with high throughput phenotype microarrays, providing the first indication of functional pathways implicated at genomic and phenotypic levels in trait evolution related to host switching and proliferation in Photorhabdus species. Secondly, since genome sequence data are currently unavailable for most species, I present an optimised methodology for RNA-seq transcriptome annotation for species with no sequenced genome. This shows that direct mapping of RNA-seq short reads to a reference genome – from the same species or a closely-related species – is the most effective, accurate and least functionally biased strategy for annotating transcriptomes compared to currently popular transcriptome assembly methods. Thirdly, I have contributed genomic resources to the scientific community by obtaining brain transcriptomes from two non-sequenced songbird species that represent interesting ecological models of mating behaviour. Applying my direct genome mapping annotation strategy to the novel data, I have described the transcriptomes via gene expression profiling and functional characterisation, amongst others methods. I have provided a first indication of genes differentially regulated during the breeding seasons of typically monogamous and polygamous songbirds. Overall, I have provided insight into the performance of state-of-the-art high throughput genomic and phenotypic analyses, identifying genes and functional pathways potentially important in the evolution and development of specific complex phenotypes across a variety of taxa. Thus, my work provides an excellent basis for further studies to disentangle how these phenotypes evolved and dissect the mechanisms by which they operate.
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Cruz, Pulido Diana Patricia. "Comparative transcriptome profiling of human and pig intestinal epithelial cells after Deltacoronavirus infection." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1587711071257247.
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De, Luca Amalia. "Transcriptome-profiling in porcine arteries to identify shear-responsive regulators of endothelial apoptosis." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/40902.
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Atherosclerosis develops predominantly at regions of the arterial tree exposed to disturbed blood flow, which generates low, oscillatory shear stress (WSS) at the lumen. Of note, endothelial cells (EC) at lesion-prone regions are characterised by an increased rate of apoptosis, thus providing a potential explanation for the distinct spatial localisation of atherosclerosis. To understand the interaction between flow and apoptosis we used microarray technology coupled to computational fluid dynamics (CFD) to identify genes differentially expressed at high or low WSS regions of the porcine aorta. We examined whether putative regulators of apoptosis can be activated by flow in vitro and studied their function using cultured EC. In this study, we employed magnetic resonance imaging and CFD to model blood flow in the porcine aortic arch and generate WSS maps that served as guidelines for the isolation of EC for subsequent transcriptional analysis. Furthermore we characterised the flow in stenosed carotid arteries where a constrictive extravascular device was surgically applied. The influence of WSS on the expression of putative regulators of apoptosis was studied using in vitro flow assays and gene function was analysed using siRNA-based approaches. Computed WSS maps revealed great spatial heterogeneity and challenged common assumptions about the mechanical conditions at susceptible and protected regions. In addition, microarray analysis of ECs isolated from the aortic arches of 5 pigs identified 764 differentially expressed genes that influence diverse physiological activities. Functional annotation of these transcripts highlighted the presence of 41 molecules with an inferred or known role in the regulation of apoptosis. We selected two candidates for functional screening in vitro: PERP and PDCD2L. Staining for active caspase-3 and DNA fragmentation revealed that EC apoptosis was significantly enhanced in EC exposed to oscillatory shear stress compared to cells exposed to uniform flow. Silencing of PERP reduced apoptosis in EC exposed to oscillatory shear stress, while silencing PDCD2L did not have a significant effect. We conclude that shear stress influences EC viability through transcriptional mechanisms that might involve the novel apoptosis regulator PERP. Our observations illuminate the molecular mechanisms that regulate the focal nature of vascular injury and atherosclerosis and provide a large genetic dataset to use in future studies.
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Wirta, Valtteri. "Mining the transcriptome - methods and applications." Doctoral thesis, Stockholm : School of Biotechnology, Royal Institute of Technology, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4115.
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Hoover, Cindi A. "Transcriptome and secondary metabolite profiling of the soft corals, Sinularia polydactyla and Sinularia maxima." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 2.51 Mb., 169 p, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:3221084.
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Dhoogra, Minishca. "Gene expression profiling of polyamine-depleted Plasmodium falciparum." Diss., Pretoria : [s.n.], 2007. http://upetd.up.ac.za/thesis/available/etd-12132007-103643/.
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Chou, Hsin-Jung. "Transcriptome-Wide Analysis of Roles for Transfer RNA Modifications in Translational Regulation." eScholarship@UMMS, 2017. https://escholarship.umassmed.edu/gsbs_diss/943.
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Covalent nucleotide modifications in RNAs affect numerous biological processes, and novel functions are continually being revealed even for well-known modifications. Among all RNA species, transfer RNAs (tRNAs) are highly enriched with diverse modifications, which are known to play roles in decoding and tRNA stability, charging, and cellular trafficking. However, studies of tRNA modifications have been limited in a small scale and performed by groups with different methodologies. To systematically compare the functions of a large set of noncoding RNA modifications in translational regulation, I carried out ribosome profiling in 57 budding yeast mutants lacking nonessential genes involved in tRNA modifications. Deletion mutants with enzymes known to modify the anticodon loop or non-tRNA substrates such as rRNA exhibited the most dramatic translational perturbations, including altered dwell time of ribosomes on relevant codons, and altered ribosome density in protein-coding regions or untranslated regions of specific genes. Several mutants that result in loss of tRNA modifications in locations away from the anticodon loop also exhibited altered dwell time of ribosomes on relevant codons. Translational upregulation of the nutrient-responsive transcription factor Gcn4 was observed in roughly half of the mutants, consistent with the previous studies of Gcn4 in response to numerous tRNA perturbations. This work also discovered unexpected roles for tRNA modifying enzymes in rRNA 2’-O-methylation, and in transcriptional regulation of TY retroelements. Taken together, this work revealed the importance and novel functions of tRNA modifications, and provides a rich resource for discovery of additional links between tRNA modifications and gene regulation.
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Larsson, Ola. "Transcriptome studies of cell-fate and aging /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-296-9/.
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Linley, A. J. "A dynamic transcriptome technique for transcriptional profiling and gene regulatory network involving the helicase antigen (HAGE)." Thesis, Nottingham Trent University, 2010. http://irep.ntu.ac.uk/id/eprint/243/.
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Increased knowledge into the molecular pathways disrupted in tumours has led to the development of various therapies that can target specific mediators of these cascades. Such therapies have proven successful in patients or demonstrate significant potential for clinical use. However, this better understanding is undermined by the continued prevalence of cancer and the limitations of these drugs. Therefore, it is possible signalling networks could be influenced by as yet unknown molecules or known mediators with function that have not yet been described. As a result of this, work must continue to improve knowledge yet further to allow the design of novel therapies to aid in the treatment of cancer patients. In the present study, work was performed on the helicase antigen (HAGE), a cancer/testis (CT) antigen and DEAD-box protein found to be present in numerous types of malignancy. As with the majority of CT antigens, the role of HAGE remains unclear. In this instance, studies were carried to discover the function of HAGE in malignant cells. Preliminary in vitro proliferation studies following HAGE gene knockdown or cDNA transfection strongly indicated an association between HAGE expression and increased tumour cell proliferation. This was supported by results gained from in vivo work performed within an immuno-compromised murine model. Expression profiling analysis of data gained from using the Genechip oligonucleotide microarray platform found significant changes to genes linked not only with proliferation but other cell processes altered during tumorigenesis. Confirmation using real-time qPCR suggested change in expression of certain genes could be recognised in other HAGE-expressing tumour cell lines. This analysis also indicated a possible interaction between HAGE and the oncogene N-RAS. Subsequent genetic and protein studies implicated HAGE acting upstream of N-RAS, markedly increasing the N-RAS level in cells. Very preliminary work has begun to demonstrate a role not just in proliferation, but in immune escape, apoptosis inhibition and metastasis, all processes potentially influenced by the RAS oncogenes. The data presented here strongly supports the hypothesis of HAGE having a significant role in malignant biology and warrant continued investigation to further confirm its role in cancer and possibly use as a target for malignancy in the future.
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Gad, Ahmed [Verfasser]. "Transcriptome profiling of bovine blastocysts developed under alternative culture conditions during specific stages of development / Ahmed Gad." Bonn : Universitäts- und Landesbibliothek Bonn, 2012. http://d-nb.info/1043054731/34.
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Wang, Zhongyi [Verfasser], and Henrik [Akademischer Betreuer] Kaessmann. "Ribosome profiling reveals principles of translatome and transcriptome evolution in mammalian organs / Zhongyi Wang ; Betreuer: Henrik Kaessmann." Heidelberg : Universitätsbibliothek Heidelberg, 2019. http://d-nb.info/1200636376/34.
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Stafslien, Shane J. "Preliminary Investigation of Escherichia Coli K12 Biofilm Inhibition on an Antimicrobial Polysiloxane Coating using Whole Transcriptome Profiling." Thesis, North Dakota State University, 2012. https://hdl.handle.net/10365/26642.
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Whole transcriptome profiling was examined in E. coli K12 when cultured on the surface of a pure polysiloxane coating (Sil) and a polysiloxane coating containing a tethered quaternary ammonium compound (QSil) shown to inhibit biofilm formation. An optimized protocol was developed for isolating high quality RNA from the surface of these coatings prepared in multi-well plates. DNA microarray data obtained from the Sil and QSil coatings revealed that 222 genes were differentially expressed between these two surfaces by a factor of at least 2-fold and with a 90% level of confidence. Several genes of the lsr operon, which encode the various components of the AI-2 based quorum sensing system, were repressed on the QSil coating surface. The QSil coatings ability to effectively interfere with the AI-2 based quorum sensing system was most likely the primary factor that contributed to the impairment of E. coli K12 biofilm formation on that surface.
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Galata, Mariana. "Transcriptome profiling, and the cloning and characterization of a monoterpene synthase from the seeds of Coriandrum sativum L." Thesis, University of British Columbia, 2013. http://hdl.handle.net/2429/45688.
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Plant terpenes are a large and diverse class of naturally-derived compounds, valuable in the medicinal, perfume and culinary industries. The seeds of Coriandrum sativum (coriander) produce essential oil (EO) rich in monoterpenes, volatile C₁₀ terpenes. In this study the coriander seeds were viewed under a scanning electron microscope and stomata as well as vittae structures were observed on the seed surface and in cross-section, respectively. The EO of C. sativum seeds was extracted and qualitatively and quantitatively analyzed using gas chromatography-mass spectrometry. The EO terpene content findings agreed with previous literature, with linalool being the most abundant monoterpene in coriander EO.
The transcriptome of coriander seeds, at three developmental stages (early, mid and late) was sequenced via Illumina technology. Analysis of the differential transcript abundance of select terpene biosynthetic genes between these stages revealed that two terpene production pathways are constitutively active in the seeds, with slight upregulation in the mid-developmental stage. All the genes involved with active photosynthesis and fatty acid biosynthesis and metabolism were also identified from the coriander transcript library.
To validate the usability of the transcriptome sequence data, a terpene synthase candidate gene, CsγTRPS, encoding a 611 amino acid protein was expressed in bacteria and the recombinant protein purified by Ni-NTA affinity chromatography. Enzymatic assays with geranyl diphosphate (GPP), the precursor to monoterpenes, revealed that this 65.86 kDa recombinant protein catalyzed the conversion of GPP to γ-terpinene, with apparent Vmax, Km, and kcat values of 2.2 ± 0.2 pkat/mg, 66 ± 13 µM and 1.476 × 10-⁴ s-¹, respectively. Knowledge gained from these experiments will facilitate future studies concerning essential and fatty acid oil production in coriander. They will also enable efforts to improve the EO of coriander through metabolic engineering or plant breeding.
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Chen, Ru. "Promoter-level transcriptome identifies stemness associated with relatively high proliferation in pancreatic cancer cells." Kyoto University, 2020. http://hdl.handle.net/2433/259015.
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付記する学位プログラム名: 充実した健康長寿社会を築く総合医療開発リーダー育成プログラムKyoto University (京都大学)
0048
新制・課程博士
博士(医科学)
甲第22747号
医科博第116号
新制||医科||8(附属図書館)
京都大学大学院医学研究科医科学専攻
(主査)教授 長船 健二, 教授 武藤 学, 教授 小川 誠司
学位規則第4条第1項該当
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Choudry, Fizzah Aziz. "Novel insights into megakaryopoiesis, thrombopoiesis and acute coronary thrombosis : transcriptome profiling of the haematopoietic stem cell, megakaryocyte and platelet." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/283252.
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The aim of this project was to investigate the transcriptome of human haematopoietic stem cells (HSCs), megakaryocytes and platelets to gain insights into steady state and accelerated thrombopoiesis that occurs in states of haemostatic demand and in thrombosis by applying these findings to the pathological setting of acute coronary thrombosis. To investigate transcriptional heterogeneity within the human HSC population, single cell RNA sequencing was performed in human bone marrow HSCs. Transcriptionally distinct subpopulations were identified including two megakaryocyte biased subsets with potentially differing functional relevance. Both populations expressed megakaryocyte specific transcripts, one of which also co-expressed common myeloid and megakaryocyte-erythroid progenitor transcripts while the other did not. This study represents the first interrogation of the human bone marrow megakaryocyte transcriptome. Cells were collected from healthy human bone marrow and analysed by low input and single cell RNA sequencing. To identify novel drivers of megakaryocyte maturation, the human bone marrow megakaryocyte transcriptome was compared to that of megakaryocytes cultured from human CD34+ cells, a process known to generate immature megakaryocytes. Transcriptional signatures associated with increasing megakaryocyte ploidy were then investigated. Increasing megakaryocyte ploidy level was found to be associated with an upregulation of transcripts involved in translation and protein processing as well as expression of a number of transmembrane receptors which might have functional relevance. Finally, the pathological setting of acute coronary thrombosis was used as a model for accelerated thrombopoiesis. Megakaryocyte and platelet transcriptomes were compared between patients with acute myocardial infarction (AMI) as well as severe coronary disease and a control group. The transcriptional signature relating to disease compared to control in megakaryocytes included upregulation of platelet activation related transcripts in megakaryocytes isolated from patients with AMI and severe coronary artery disease.
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Arce, Joann Diray. "The Path to Understanding Salt Tolerance: Global Profiling of Genes Using Transcriptomics of the Halophyte Suaeda fruticosa." BYU ScholarsArchive, 2016. https://scholarsarchive.byu.edu/etd/6355.
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Salinity is a major abiotic stress in plants that causes significant reductions in crop yield. The need for improvement of food production has driven research to understand factors underlying plant responses to salt and mechanisms of salt tolerance. The aim of improving tolerance in traditional crops has been initiated but most crops can only tolerate a limited amount of salt in their systems to survive and produce biomass. Studies of naturally occurring high salt-tolerant plants (halophytes) are now being promoted for economic interests such as food, fodder or ecological reasons. Suaeda fruticosa, a member of the family Chenopodiaceae, belongs to a potential model halophyte genus for studying salt tolerance. However, published reports on the identification of genes, expression patterns and mechanisms of salinity tolerance in succulent halophytes are very limited. Next generation RNA-sequencing techniques are now available to help characterize genes involved in salinity response, along with expression patterns and functions of responsive genes. In this study, we have optimized the assembly of the transcriptome of S. fruticosa. We have annotated the genes based on their gene ontology characteristics and analyzed differential expression to identify genes that are up- and down-regulated in the presence of salt and have grouped the genes based on their putative functions. We also have provided evidence for groups of transcription factors that are involved in salt tolerance of this species and have identified those that may affect the regulation of salt tolerance. This work elucidates the characterization of genes involved in salinity tolerance to increase our understanding of the regulation of salt in a succulent halophyte.
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Stewart, Caitlin. "Stage-specific profiling of the transcriptome during oogenesis and identification of a novel type of small RNA within the zebrafish Danio rerio." Thesis, University of Cambridge, 2016. https://www.repository.cam.ac.uk/handle/1810/262168.
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Developmental biology is an important field of study, as breakthroughs in this field can be used to understand aspects of evolution, more complex biological processes, and even diseases, such as cancer. Pathways and developmental programs are often highly conserved between organisms, especially vertebrates, allowing for studies within model organisms to have implications in humans. Zebrafish have long been used in the study of developmental biology due to their fast replication times, translucent embryos and relatively low cost. Much is known about early zebrafish embryology due to results from mutagenesis studies, however some aspects of development continue to remain unclear. It is known that maternal products control early development, including setting up the axes and providing the transcripts required prior to zygotic genome activation, but the timing of the production of these transcripts is unknown. To be accurately localized within the embryo, these transcripts are deposited prior to fertilization, during egg development (oogenesis). The oocyte goes through many important changes in gene expression, chromatin conformations, meiotic stages and maturation processes during oogenesis, all of which are essential for normal embryonic development. In this thesis, I have used next generation sequencing techniques to profile and characterize the rapidly changing transcriptome during each stage of oogenesis, using the zebrafish as a model organism. Specifically, a method for accurate staging and collection of high quality oocytes was developed based on previous work on zebrafish and Xenopus oogenesis. Once separated into stages the small RNA content of stage I oocytes was closely examined and profiled using RNA-Seq. Following this, the transcriptomes of each stage of oogenesis were characterized using whole molecule polyA RNA-Seq. An in depth analysis of the transcriptomes elucidated the timings of important oogenic events and identified specific expression patterns within each stage. Finally, I compared the small RNA of stage I oocytes with polyA RNA to examine and identify common features.
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Kwenda, Stanford. "Transcriptome profiling of potato plant stems challenged with Pectobacterium carotovorum subsp. brasiliense and elucidation of the role of small RNAs in Pectobacterium survival mechanisms." Thesis, University of Pretoria, 2016. http://hdl.handle.net/2263/60818.
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Pectobacterium carotovorum subsp. brasiliense, a necrotrophic phytopathogen belonging to the soft rot Enterobacteriaceae (SRE) family is responsible for causing tuber soft rot and blackleg diseases of stems in potato plants. In recent years, P. c. brasiliense, has emerged as a soft rot pathogen of significance, potentially threatening potato production globally. To date, P. c. brasiliense is the most aggressive soft rot phytopathogen isolated from potato in South Africa. Currently effective chemical control measures are unavailable once soft rot pathogens have established disease in potato plants and/or harvested tubers. Therefore, this study sought to determine the molecular basis of quantitative resistance in potato stems challenged with P. c. brasiliense. In addition, this thesis explores some of the regulatory mechanisms important in the adaptation of Pectobacterium species to harsh nutrient-deficient environments such as plant xylem vessels. Determining the activated defense responses in potato stems is key in deciphering potential control approaches against pectobacteria as these soft rot pathogens colonize vascular tissues during infection of plants. Currently, no transcriptome-wide studies have been applied in the P. c. brasiliense and potato stem interaction to understand inducible defense responses within potato stems.
In chapter 2, by implementing a time-course RNA-seq analysis, our study revealed important signaling pathways suggested to contribute to the potato defense transcriptome against P. c. brasiliense infection. Comparison of transcriptomes between a susceptible potato cultivar (Solanum tuberosum cv Valor) and tolerant cultivar (S. tuberosum cv BP1) following P. c. brasiliense inoculation revealed that the MAPK signaling cascades and ethylene hormonal pathway are central to potato defense responses against this pathogen. Specifically, genes encoding MPK3 protein kinase, and MKS1; ethylene biosynthetic and signaling pathways such as ACC, ERF2 and EIN3 genes were up-regulated in the tolerant cultivar within the time-course. Furthermore, expression of downstream defense-related genes was enhanced in S. tuberosum cv BP1, including transcription factors such WRKY33, MYB83, and several ethylene-responsive binding factors (ERFs); as well as various secondary wall biosynthetic genes for lignification and cellulose biosynthesis, for example, IRX9 and CESA8, respectively.
In chapter 3, a bioinformatics analysis using strand-specific RNA sequencing allowed the identification of 1113 potato long intergenic noncoding RNA (lincRNAs) from stem tissues. Long noncoding RNAs (lncRNAs) have been implicated in diverse regulatory roles in eukaryotes. Recently, defense-related lncRNAs have been identified in Arabidopsis and wheat. In this thesis we identified 559 potato lincRNAs that were differentially expressed (DE) in both cultivars compared to mock-inoculated controls, following inoculation by P. c. brasiliense. Furthermore, co-expression analysis associated 17 of these lincRNAs with 12 potato defense-related genes. These results suggest that lincRNAs possibly have functional roles in potato defence responses. Future work will focus on characterization of these lincRNAs in order to understand their specific functional roles, particularly in potato defense mechanisms.
In chapter 4, regarding potential regulatory mechanisms employed by Pectobacterium species during survival under nutrient-limiting conditions, we described 137 sRNA transcripts in P. atrosepticum genome. About 62% of the identified sRNAs are conserved within the SRE. Furthermore, 68 sRNAs were differentially expressed when comparing P. atrosepticum cells under growth-promoting and starvation conditions; with 47 sRNAs up-regulated under nutrient-deficient conditions. Thus, since many starvation-induced sRNAs were identified, these findings highlighted that sRNAs play key roles in adaptive responses in the genus Pectobacterium.Thesis (PhD)--University of Pretoria, 2016.
Microbiology and Plant Pathology
PhD
Unrestricted
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Islam, Md Aminul [Verfasser]. "Global mRNA and miRNA transcriptome profiling of peripheral blood mononuclear cells to investigate the host immunogenetic response to PRRSV vaccination in pigs / Md. Aminul Islam." Bonn : Universitäts- und Landesbibliothek Bonn, 2017. http://d-nb.info/1124590781/34.
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Hamasaki, Mike Yoshio. "Análise transcriptômica em estruturas encefálicas de ratos jovens e idosos submetidos ao modelo de ligadura e perfuração cecal." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/5/5164/tde-11092018-154135/.
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Dentre as manifestações clínicas observadas em pacientes sépticos, as disfunções neurológicas são, provavelmente, as de fisiopatologia mais obscura e pobremente explorada, o que consequentemente as torna de difícil entendimento e tratamento médico. Adicionalmente, estudos epidemiológicos indicam que a síndrome séptica é mais frequente e mais letal em pacientes idosos. Nesse contexto, este trabalho objetivou comparar os efeitos da sepse, induzida pelo modelo de ligadura e perfuração cecal, no encéfalo de ratos jovens e idosos por meio da análise da expressão gênica de larga escala (transcriptoma), a fim de averiguar como as alterações no padrão de expressão podem estar relacionadas a disfunções neurológicas. Os resultados deste estudo indicaram a diminuição da expressão dos genes Bcl-3, S100A8 e uridina fosforilase 1, bem como o aumento da expressão de Stefin A3, sendo tais efeitos característicos das manifestações comuns da sepse no sistema nervoso central, independentemente da idade dos animais; por outro lado, a diminuição da expressão do gene da haptoglobina foi observada apenas nos animais idosos com sepse. De forma geral, na comparação entre animais idosos e jovens, os resultados desta pesquisa apontaram que animais idosos apresentam uma quantidade menor de genes modificados pela sepse, o que sugere menor capacidade de ativar mecanismos neuroprotetoresAmong the clinical manifestations observed in septic patients, the neurological dysfunctions are probably the most obscure and poorly explored pathophysiology, which consequently makes them difficult to understand and to treat. Additionally, epidemiological studies indicate that septic syndrome is more frequent and more lethal in elderly patients. In this context, this article is aimed at comparing the effects of sepsis, induced by the ligature model and cecal perforation, on the brain of young and elderly rats by means of the analysis of the large scale gene expression (transcriptome), in order to investigate how the changes in this expression may be related to neurological dysfunctions. The results of this study indicated decreased expression of the Bcl-3, S100A8 and uridine phosphorylase 1 genes, as well as increased expression of Stefin A3, these effects being characteristic of the common manifestations of central nervous system sepsis regardless of the age of the animals; on the other hand, decreased haptoglobin gene expression was observed only in the elderly animals with sepsis. In general, in the comparison between old and young animals, the results of this research indicated that elderly animals present a smaller amount of genes modified by sepsis, which suggests a smaller capacity to activate neuroprotective mechanisms
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Nahle, Sara. "Réponse macrophagique aux nanomatériaux carbonés : effets de leur caractéristiques physiques et chimiques sur le transcriptome Carbon-based nanomaterials induce inflammation and autophagy in rat alveolar macrophages Single wall and multiwall carbon nanotubes induce different toxicological responses in rat alveolar macrophages Gene expression profiling of alveolar macrophages exposed to non-functionalized, anionic or cationic multi-walled carbon nanotubes shows three different mechanisms of toxicity Cytotoxicity and global transcriptional responses induced by zinc oxide nanoparticles NM 110 in PMA-differentiated THP-1 cells Protein and lipid homeostasis altered in rat macrophages after exposure to metallic oxide nanoparticles." Thesis, Université de Lorraine, 2019. http://www.theses.fr/2019LORR0142.
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Les nanomatériaux carbonés (NMC) sont très utilisés dans le monde industriel et leurs applications, nombreuses, sont en plein développement. L’absence de réglementation pour leur préparation et leur emploi fait qu’il est nécessaire comme pour tous les nano-objets, de déterminer le risque qu’une exposition fait courir à l’Homme et d’adapter la législation en conséquence. Une meilleure connaissance de leur potentiel toxique est donc nécessaire. Les difficultés de plus en plus grandes pour utiliser les modèles animaux, rend nécessaire le développement d’études avec des lignées cellulaires au sein desquelles les macrophages ont une place prépondérante. Ces NMC sont très légers et forment facilement des aérosols et les modèles préférés sont les macrophages alvéolaires. Cependant il n’existe pas à l’heure actuelle de lignées de macrophages alvéolaires humains à la différence de cellules de rat. Le sujet de ma thèse porte sur l’étude de la réponse macrophagique aux NMC et la compréhension des effets de leurs caractéristiques physiques et chimiques sur leur transcriptome. Les NMC étudiés sont les nanotubes de carbone (NTC) multi feuillets, les NTC mono feuillets, le noir de carbone et l’oxyde de graphène. Nos résultats montrent que tous les NMC étudiés déclenchent une réaction inflammatoire dans les cellules NR8383 et les cellules THP-1 différenciées, et certains d’entre eux induisent une cytotoxicité importante. La taille, la fonctionnalisation et la forme contrôlent les mécanismes de toxicité induits par les NMC. Des NTC de tailles similaires altèrent des voies de signalisation identiques, une fonctionnalisation par des groupements amines produit un stress des lysosomes tandis que la fonctionnalisation par des groupements carboxyle entraine un stress du réticulum endoplasmique (RE). Les nanotubes induisent une désorganisation du cytosquelette plus importante que les nanoparticules sphériques. Nous avons également mis en évidence une accumulation de lipides chez les cellules NR8383 suite à un stress du RE induit par le Mitsui-7, un NTC multi feuillet. Le même NTC induit aussi une fusion de ces macrophages. La formation de ces cellules spumeuses et des cellules géantes à multi-noyaux sont des évènements clés entrainant la formation de granulomes. Les résultats obtenus présentent un support important pour la compréhension des effets des NMC montrant une certaine toxicité non négligeable de point de vue moléculaire. Cette toxicité est dépendante des caractéristiques physiques et chimiques de ces nanomatériaux. Ainsi, en se basant sur ce type de données, on pourra s’orienter vers une fabrication safe-by-design pour limiter les risques liés à leur expositionCarbon nanomaterials (CNM) are widely used in the industrial world and they have many applications. The absence of legislation controlling their preparation and uses makes necessary, as for all nano-objects, the study of their toxicity in order to determine the risk of human exposure and to adapt legislation accordingly. Therefore, a better knowledge of their toxic potential is necessary. The increasing difficulties in using animal models make necessary the development of studies using cell lines especially macrophages that play a predominant role. These CNM are very light and form easily aerosols, reason why the preferred models for toxicity studies are alveolar macrophages. However, there are no human alveolar macrophage lines currently but rat cells exist. The subject of my thesis is to study macrophages response to CNM and the understanding of the effect of their physical and chemical characteristics on the transcriptome. The CNM studied are multiwall carbon nanotubes (CNT), single wall CNT, carbon black and graphene oxide. Our results show that all CNM studied trigger an inflammatory reaction in NR8383 and differentiated THP-1 cells, also some of them induce cytotoxicity. Size, functionalization and form control CNM toxicity mechanisms: CNT with similar size alter identical signaling pathways, amino group functionalization produces lysosomal stress, whereas functionalization with carboxyl groups causes reticulum endoplasmic (RE) stress, nanotubes induce cytoskeleton disorganization more than spherical nanoparticles. Otherwise, we identified lipid accumulation in NR8383 cells due to RE stress induced by Mitsui-7, a multiwall CNT. There was also a fusion of these macrophages. The formation of these foam cells and giant multi-nucleus cells are key events leading to granulomas formation. The results obtained are an important support for understanding CNM effects, showing some significant toxicity at molecular level. This toxicity is dependent on the physical and chemical characteristics of these nanomaterials. Thus, based on this type of data, we can move towards a safer manufacture to avoid the risks associated with their exposure
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Roy, Christian K. "Putting the Pieces Together: Exons and piRNAs: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/726.
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Analysis of gene expression has undergone a technological revolution. What was impossible 6 years ago is now routine. High-throughput DNA sequencing machines capable of generating hundreds of millions of reads allow, indeed force, a major revision toward the study of the genome’s functional output—the transcriptome. This thesis examines the history of DNA sequencing, measurement of gene expression by sequencing, isoform complexity driven by alternative splicing and mammalian piRNA precursor biogenesis. Examination of these topics is framed around development of a novel RNA-templated DNA-DNA ligation assay (SeqZip) that allows for efficient analysis of abundant, complex, and functional long RNAs. The discussion focuses on the future of transcriptome analysis, development and applications of SeqZip, and challenges presented to biomedical researchers by extremely large and rich datasets.
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Roy, Christian K. "Putting the Pieces Together: Exons and piRNAs: A Dissertation." eScholarship@UMMS, 2005. http://escholarship.umassmed.edu/gsbs_diss/726.
Full textAbstract:
Analysis of gene expression has undergone a technological revolution. What was impossible 6 years ago is now routine. High-throughput DNA sequencing machines capable of generating hundreds of millions of reads allow, indeed force, a major revision toward the study of the genome’s functional output—the transcriptome. This thesis examines the history of DNA sequencing, measurement of gene expression by sequencing, isoform complexity driven by alternative splicing and mammalian piRNA precursor biogenesis. Examination of these topics is framed around development of a novel RNA-templated DNA-DNA ligation assay (SeqZip) that allows for efficient analysis of abundant, complex, and functional long RNAs. The discussion focuses on the future of transcriptome analysis, development and applications of SeqZip, and challenges presented to biomedical researchers by extremely large and rich datasets.
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Bürfent, Benedikt [Verfasser]. "The immunomodulatory capacity of helminths on inflammation: Impact of eosinophils on E. coli-induced sepsis and genome-wide transcriptome profiling of human monocytes stimulated with helminth extract and LPS implicate immune functions and diseases / Benedikt Bürfent." Bonn : Universitäts- und Landesbibliothek Bonn, 2017. http://d-nb.info/1149154284/34.
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Rubanova, Natalia. "MasterPATH : network analysis of functional genomics screening data." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC109/document.
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Dans ce travail nous avons élaboré une nouvelle méthode de l'analyse de réseau à définir des membres possibles des voies moléculaires qui sont important pour ce phénotype en utilisant la « hit-liste » des expériences « omics » qui travaille dans le réseau intégré (le réseau comprend des interactions protéine-protéine, de transcription, l’acide ribonucléique micro-l’acide ribonucléique messager et celles métaboliques). La méthode tire des sous-réseaux qui sont construit des voies de quatre types les plus courtes (qui ne se composent des interactions protéine-protéine, ayant au minimum une interaction de transcription, ayant au minimum une interaction l’acide ribonucléique micro-l’acide ribonucléique messager, ayant au minimum une interaction métabolique) entre des hit –gènes et des soi-disant « exécuteurs terminaux » - les composants biologiques qui participent à la réalisation du phénotype finale (s’ils sont connus) ou entre les hit-gènes (si « des exécuteurs terminaux » sont inconnus). La méthode calcule la valeur de la centralité de chaque point culminant et de chaque voie dans le sous-réseau comme la quantité des voies les plus courtes trouvées sur la route précédente et passant à travers le point culminant et la voie. L'importance statistique des valeurs de la centralité est estimée en comparaison avec des valeurs de la centralité dans les sous-réseaux construit des voies les plus courtes pour les hit-listes choisi occasionnellement. Il est supposé que les points culminant et les voies avec les valeurs de la centralité statistiquement signifiantes peuvent être examinés comme les membres possibles des voies moléculaires menant à ce phénotype. S’il y a des valeurs expérimentales et la P-valeur pour un grand nombre des points culminant dans le réseau, la méthode fait possible de calculer les valeurs expérimentales pour les voies (comme le moyen des valeurs expérimentales des points culminant sur la route) et les P-valeurs expérimentales (en utilisant la méthode de Fischer et des transpositions multiples).A l'aide de la méthode masterPATH on a analysé les données de la perte de fonction criblage de l’acide ribonucléique micro et l'analyse de transcription de la différenciation terminal musculaire et les données de la perte de fonction criblage du procès de la réparation de l'ADN. On peut trouver le code initial de la méthode si l’on suit le lien https://github.com/daggoo/masterPATHIn this work we developed a new exploratory network analysis method, that works on an integrated network (the network consists of protein-protein, transcriptional, miRNA-mRNA, metabolic interactions) and aims at uncovering potential members of molecular pathways important for a given phenotype using hit list dataset from “omics” experiments. The method extracts subnetwork built from the shortest paths of 4 different types (with only protein-protein interactions, with at least one transcription interaction, with at least one miRNA-mRNA interaction, with at least one metabolic interaction) between hit genes and so called “final implementers” – biological components that are involved in molecular events responsible for final phenotypical realization (if known) or between hit genes (if “final implementers” are not known). The method calculates centrality score for each node and each path in the subnetwork as a number of the shortest paths found in the previous step that pass through the node and the path. Then, the statistical significance of each centrality score is assessed by comparing it with centrality scores in subnetworks built from the shortest paths for randomly sampled hit lists. It is hypothesized that the nodes and the paths with statistically significant centrality score can be considered as putative members of molecular pathways leading to the studied phenotype. In case experimental scores and p-values are available for a large number of nodes in the network, the method can also calculate paths’ experiment-based scores (as an average of the experimental scores of the nodes in the path) and experiment-based p-values (by aggregating p-values of the nodes in the path using Fisher’s combined probability test and permutation approach). The method is illustrated by analyzing the results of miRNA loss-of-function screening and transcriptomic profiling of terminal muscle differentiation and of ‘druggable’ loss-of-function screening of the DNA repair process. The Java source code is available on GitHub page https://github.com/daggoo/masterPATH
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Huet, Sarah. "Caractérisation moléculaire des cellules de lymphome folliculaire et de leur micro-environnement et incidence clinique." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10305.
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Le lymphome folliculaire (LF) représente le 2ème lymphome par ordre de fréquence et reste considéré à l’heure actuelle comme incurable. De nombreuses questions sur le processus de lymphomagénèse sont encore non résolues et il n’existe aucun marqueur génomique ou moléculaire unanimement reconnu permettant de prédire l’évolution des patients. Nos travaux de recherche s’inscrivent dans l’objectif de mieux comprendre l’impact des altérations moléculaires identifiées dans ces tumeurs, grâce à une approche intégrative visant à combiner des données génomiques, transcriptomiques et mutationnelles. Ce travail a permis de construire un score, basé sur l’expression d’un panel de gènes, prédictif du risque de progression de la maladie. Ce score a été confirmé sur une seconde cohorte de patients, validant son utilité potentielle en pratique clinique. Par ailleurs, nos résultats suggèrent que les cellules tumorales peuvent acquérir des propriétés évocatrices d’un profil de cellules souches et associées à un pronostic particulièrement défavorable. Une 2ème partie de notre travail a porté sur les altérations touchant le gène EZH2, muté chez 25% des patients. Nous avons démontré qu’un gain génomique au niveau du locus EZH2 pouvait également avoir des conséquences sur le profil transcriptomique et un impact pronostique, soulignant l’importance de prendre en compte l’ensemble des anomalies touchant ce gène. Enfin, nous rapportons qu’un polymorphisme constitutionnel situé dans ce gène est associé au risque de progression des patients traités par un anticorps anti-CD20. L’ensemble de ces résultats apporte un éclairage nouveau sur la biologie du LF et peut contribuer à améliorer la prise en charge des patientsFollicular Lymphoma (FL) is the 2nd most frequent lymphoma subtype and is usually considered incurable with current strategies. Several questions regarding the lymphomagenesis process are still pending, and no molecular or genomic marker has been unanimously recognized yet to predict outcome. We performed an integrative analysis combining genomic, transcriptomic and mutational data in the view to bringing new highlights in the molecular alterations acting in FL. Based on gene-expression profiling data we developed a model able to predict progression-free survival in FL patients. We confirmed its predictive value in another cohort of patients, thereby allowing its potential use in clinical practice. Furthermore, our results highlight that some tumors show a stem-cell-like gene-expression profile that was associated with highly unfavorable outcome. In the second part of our work, we focused on alterations of the gene EZH2. Although mutations have been reported in 25% of FL patients, we questioned whether genomic gains at EZH2 locus could also contribute to lymphomagenesis. We showed that such gain may impact the transcriptional profile and have a prognostic significance, thus highlighting the crucial interest of determining both kinds of alterations. Finally, we report that a germ-line polyporphism in the EZH2 gene was significantly associated with progression-free survival in patients treated by anti-CD20 therapy. Taken together, these results bring new highlights on FL biology and may help to improve the clinical management of FL patients
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Qi, Qin. "An integrative approach to understanding the fitness cost of rifampicin resistance in Pseudomonas aeruginosa." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:6a82bd64-3b3f-444b-b379-62f01f681594.
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Antibiotic resistance in bacteria is acquired through spontaneous chromosomal mutations or horizontal gene transfer. In the absence of antibiotics, resistant mutants generally show reduced fitness due to compromised growth rate, competitive ability and virulence compared to their antibiotic-sensitive ancestors. The focus of my research is to dissect the molecular underpinnings of the variations in the fitness cost of chromosomal antibiotic resistance using a systems-level approach. From an evolutionary perspective, my research aims are to understand how the fitness cost influences adaptation in resistant populations in an antibiotic-free environment. Using rifampicin resistance in Pseudomonas aeruginosa as a model, my work shows that most of the variation in the fitness cost of rifampicin resistance can be attributed to the direct effect of rifampicin resistance mutations on transcriptional efficiency. Through RNA-Seq transcriptome profiling, I demonstrate that global changes in gene expression levels associated with resistance mutations are surprisingly subtle, suggesting that the transcriptional regulatory network of P. aeruginosa is robust against compromised transcriptional efficiency. Using experimental evolution and whole-genome sequencing, my work reveals a systematic difference in the genetic basis of adaptation in mutants that were propagated in the absence of antibiotics. During compensatory adaptation, resistant mutants can recover the fitness cost of resistance by fixing second-site mutations that directly offset the deleterious effects of resistance mutations. Amongst resistant mutant populations with low fitness costs, general adaptation limits compensatory adaptation, which is most likely to be due to the rarity of compensatory mutations and clonal interference. Far from being the most ubiquitous mechanism in the evolution of resistance, compensatory adaptation is the exception that is more likely to be observed in resistant mutants with high fitness costs. In addition, I applied key elements of the integrative experimental approach developed in this work to dissect the molecular basis of the fitness cost associated with carriage of the pNUK73 small plasmid in P. aeruginosa, which carries the rep gene encoding a plasmid replication protein. My results confirmed that rep expression generates a significant fitness cost in P. aeruginosa and demonstrate how the molecular origins of the fitness cost of resistance can be dissected in a different biological context.
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Viana, Joana Fortio Fernandes Pacheco. "Methylomic and transcriptomic profiling of the schizophrenia brain." Thesis, University of Exeter, 2016. http://hdl.handle.net/10871/24774.
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Schizophrenia is a severe psychiatric disorder that affects more than twenty-one million people worldwide, contributing significantly to the global burden of disease. A growing body of genetic, epigenetic and epidemiological evidence suggests that schizophrenia has its origins during neurodevelopment and that dysregulation of the immune system and infection may play a role in disease etiology. Twin and family studies have highlighted a considerable heritable component to schizophrenia; however the role of genetic variation in the etiology of the disorder is complex. In the majority of cases, susceptibility is attributed to the combined action of multiple common genetic risk variants of low penetrance. Improved understanding about the biology of the genome has led to increased interest in the role of non-sequence-based variation in the etiology of neurodevelopmental phenotypes, including schizophrenia. The notion that epigenetic processes and gene expression dysregulation are involved in the onset of schizophrenia is supported by recent studies of disease-discordant monozygotic twins, clinical sample cohorts, and post-mortem brain tissue. To date, however, studies characterizing schizophrenia-associated methylomic and transcriptomic variation in the brain have been limited by small sample number or the assessment of a single brain region. The main aim of this thesis was to undertake a comprehensive study of genomic variation across four brain regions in schizophrenia. The results provide further support for a neurodevelopmental origin to schizophrenia, as well as a role of the immune system on schizophrenia etiology. My analyses also suggest that epigenetic variation associated with polygenic burden for schizophrenia might play a role in the disease. In summary, the work presented in this thesis represents the first analysis of epigenetic and gene expression variation associated with schizophrenia across multiple brain regions and highlights the utility of polygenic risk scores for identifying molecular pathways associated with etiological variation in complex disease.
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Bou, Samra Elias. "Recherche et caractérisation de biomarqueurs pronostiques dans les leucémies myélomonocytaires chroniques et aiguës myéloïdes par exploration des transcriptomes." Thesis, Montpellier 2, 2012. http://www.theses.fr/2012MON20057/document.
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Un défi de la transcriptomique est d'explorer l'intégralité du répertoire des transcrits normaux et anormaux. Les analyses de GEP (Gene Expression Profiling) basées sur la technologie des puces à ADN sont largement exploitées en cancérologie depuis plusieurs années. Parallèlement, les nouvelles méthodes basées sur le séquençage à haut débit offrent désormais la possibilité de réaliser des analyses précises et sensibles nécessaires à l'étude des cellules normales et cancéreuses. Quelle que soit la méthode, la caractérisation de l'ensemble des transcrits codants et non-codants représente un réel défi biologique pour la recherche de nouveaux marqueurs de diagnostic et de pronostic, et pour la bonne prise en charge des patients. Dans ce travail, j'ai eu l'occasion de traiter deux aspects différents de la biologie qui convergent vers l'identification de transcrits exprimés de manière aberrante dans les leucémies myéloïdes. Le premier aspect a consisté à proposer une sélection de biomarqueurs moléculaires pour la caractérisation de la leucémie myélomonocytaire chronique (LMMC). A partir de l'expression de ces gènes, nous avons développé un score de pronostic qui a permis de définir deux groupes de patients cliniquement distincts. Nous avons ensuite complété notre étude par une caractérisation phénotypique par cytométrie en flux des sous-populations cellulaires aberrantes constituant les lignages mono- et granulocytaires. Une partie de ce travail a été étendue aux leucémies aiguës myéloïdes (LAM) à caryotype normal (CN). L'autre aspect a consisté à participer à la mise en place d'une approche computationnelle intégrée pour caractériser de nouveaux ARNs non annotés et fort probablement non-codants. En explorant des données de Digital Gene Expression (DGE), nous avons quantifié et caractérisé la fraction de ces transcrits dans les régions intergéniques. Nous avons vérifié l'expression de ces nouveaux transcrits dans les tissus normaux et cancéreux en croisant avec d'autres données d'expression, telles que le RNA-Sequencing, et regarder leur conservation et leur expression dans d'autres espècesA challenge of transcriptomics is to explore the full repertoire of normal and abnormal transcripts. Gene expression profiling analyses based on microarray technology are widely used in cancer research since many years. Meanwhile, new methods based on high-throughput sequencing methods offers henceforth the possibility to undergo accurate and sensitive analyses necessary for studying normal and cancer cells. Despite the method, the characterization of all coding and non-coding transcripts is a real biological challenge in identifying novel diagnostic and prognostic markers, and for the proper care of patients. In the present work, I had the opportunity to address two different aspects of biology, both convergent toward the identification of aberrantly expressed transcripts in myeloid leukemia. The first aspect was to provide a selection of molecular biomarkers for the characterization of chronic myelomonocytic leukemia (CMML). We developed a gene expression-based prognostic score which identified two clinically distinct groups of patients. We then completed our study with a phenotypic characterization by flow cytometry of aberrant subpopulations constituting the myeloid and granulocytic lineages. A part of this work has been extended to acute myeloid leukemia (AML) patients with normal karyotype. The other aspect was to participate in the implementation of an integrated computational approach in order to characterize novel non annotated RNAs, more likely non-coding. We quantified and characterized the proportion of these transcripts in intergenic regions by exploring Digital Gene Expression (DGE) data. We checked their expression in normal and cancer tissues by crossing with RNA-Seq data, and their conservation and expression in other species
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He, Liqun. "Analysis of kidney glomerular and microvascular transcriptomes /." Stockholm : Karolinska institutet, 2007. http://diss.kib.ki.se/2007/978-91-7357-300-9/.
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Xu, Binjie. "Investigating AmrZ-mediated activation of Pseudomonas aeruginosa twitching motility and alginate production." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1447348689.
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Törne, von Christine. "Transcriptomic profiling and regulatory pathway modeling in a renal allograft transplantation model." Diss., lmu, 2009. http://nbn-resolving.de/urn:nbn:de:bvb:19-108524.
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Chtanova, Tatyana Biotechnology & Biomolecular Sciences Faculty of Science UNSW. "T cell transcriptomes: uncovering the mechanisms for T cell effector function through gene profiling." Awarded by:University of New South Wales. Biotechnology and Biomolecular Sciences, 2005. http://handle.unsw.edu.au/1959.4/22029.
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T cells are at the heart of the adaptive immune response. They mediate many important immunological processes that provide protection against viruses, bacteria and other pathogens. The aim of the work described in this thesis was to use gene expression profiling to gain insights into different aspects of T cell biology. In particular we wanted to examine the mechanisms and identify the genes that underlie T cell effector function. IFN-g-producing Th1 cells are a major effector subset that protects against intracellular pathogens, while Th2 cells produce IL-4, IL-5 and IL-13 and mediate protection against large extracellular pathogens. Microarray profiling of gene expression in mouse and human Th1 and Th2 cells, as well as mouse Tc1 and Tc2 cells, identified a number of novel markers of these T cells which may have important roles in T cell differentiation/function. We found that T cell type, host species and differentiation conditions significantly influenced gene expression profiles generated during T cell polarization. Providing help to B cells for antibody production is the major function of the third effector subset of CD4+ T cells termed T follicular homing or TFH cells. Relatively little is known about the generation of these cells, and the mechanisms of their effector function. Using oligonucleotide microarrays we identified a TFH-specific gene expression signature, which included many novel genes which will undoubtedly enable better identification and characterization of this novel subset. A comprehensive study profiling all the major leukocyte subsets revealed their distinct gene expression signatures and numerous leukocyte subset specific genes. A detailed examination of most major T cell subsets identified distinguishing features of each subset together with gene expression changes associated with T cell activation and exposure to cell culture conditions. In addition, we described a distinctive transcriptional profile for gd T cells and examined the differences between central and effector memory T cells. We also showed that specific gene expression signatures provide a powerful tool for subset classification. Taken together this work provides important insights into T cell differentiation and effector function, and presents a basis for future work examining numerous novel genes relevant to T cell biology.
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Goya, Rodrigo. "Bioinformatic approaches for identifying single nucleotide variants and profiling alternative expression in cancer transcriptomes." Thesis, University of British Columbia, 2017. http://hdl.handle.net/2429/64070.
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Over the last decade, the advent of high-throughput sequencing (HTS) has given us the ability to study DNA and RNA sequences at nucleotide resolution at an unprecedented speed and at a relatively low cost. This has been an invaluable tool in the study of cancer, allowing projects such as The Cancer Genome Atlas and the International Cancer Genome Consortium to sequence thousands of tumours from multiple cancer types. The ever-increasing amounts of data created by these projects demanded new analysis methods: in the first part of this thesis, I focus on method development for mutation calling in genome and transcriptome data. I present SNVMix, a single nucleotide variant (SNV) caller based on a set of probabilistic models created to adapt to variations in allele representation in a tumour. Differential allele representation in DNA can occur when multiple clones are present in the sequenced tumour, and in RNA can occur due to differences in gene expression or allele bias. These situations are nearly ubiquitously encountered in cancer sequencing studies, and thus need to be accounted for. I demonstrate that SNVMix was able to outperform another contemporary SNV caller that does not account for variations in allele representation. I also present BWA-R, an adaptation of the Burrows Wheeler Aligner, that can properly align RNA-Seq paired-end reads to a genome reference extended with exon-exon junction sequences formed through splicing. I show that BWA-R provides better alignments for SNV calling in transcriptomes, resulting in an increase in the proportion of true positive calls obtained. In the second part of this thesis, I analyze RNA-Seq data from a triple negative breast cancer (TNBC) cohort and describe the alternative splicing profiles of the previously defined Basal and NonBasal subgroups. TNBC is characterized by the absence of estrogen and progesterone receptors and human epidermal growth factor receptor 2 (HER2), which precludes the use of currently available targeted therapies. TNBC patients are thus treated with chemotherapy, and outcomes are generally poor. I identify alternatively expressed genes that may be relevant to the biology of these two subgroups and that could provide clues for further studies or treatment options.Science, Faculty of
Graduate
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Yarra, Tejaswi. "Transcriptional profiling of shell calcification in bivalves." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31408.
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Mollusc shells are unique adaptations that serve to protect the organisms that make them, and are a defining feature of the phylum. However the molecular underpinnings of shell forming processes are still largely unexplored. To further understand mollusc shell formation, I studied three bivalve species in this project: the blue mussel Mytilus edulis, the Pacific oyster Crassostrea gigas, and the king scallop Pecten maximus. While previous analyses of the shell proteomes showed species specificity, transcriptomes of the mantle tissues revealed more commonalities. To reconcile these differences, I studied differential gene expression in shell damage-repair experiments and during the formation of the first larval shell, to produce a comprehensive overview of shell formation processes. Expression data showed large biological variability between individuals, requiring matched-pair experimental designs to detect differential gene expression during shell repair. Loci differentially expressed during shell repair and in the larvae encoded shell matrix proteins, transmembrane transporters, and novel transcripts. A large number of shell matrix proteins, encoded in differentially expressed loci, were common in all three species during shell formation, indicating that shell forming proteins between different species may be more common than previously thought. Differential expression of transmembrane transporters during shell repair indicated that the animals may be regulating bicarbonate ions during shell formation. Finally, the experiments revealed novel transcripts, with unknown annotations to public datasets, that may putatively be involved in shell formation.
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Amnebrink, Dennis. "Transcriptomic profiling of marine bacteria between development and senescence phases of a phytoplankton bloom." Thesis, Linnéuniversitetet, Institutionen för biologi och miljö (BOM), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-79200.
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Bacterioplankton provide important ecosystem functions by carrying out biogeochemical cycling of organic matter. Playing an important role in the microbial loop they help remineralize carbon and nutrients. Bacteria also interact with phytoplankton during phytoplankton blooms. However, fundamental understanding on the underlying molecular mechanisms involved in the degradation of phytoplankton-derived organic matter is still in its infancy. Therefore, we analysed data from a mesocosm experiment following a natural phytoplankton-bloom from an upwelling system in the North- East Atlantic Ocean. The purpose was to contribute a mechanistic understanding based on functional gene expression analysis of natural microbial assemblages. Our results show the difference in functional gene expression within a bacterial metacommunity and how this functional response drastically switches between bloom build up and senescence. Transcripts showed a broad change in gene expression involving major SEED categories, with the bloom senescence phase exhibiting a higher relative abundance in major categories such as Carbohydrates, Protein Metabolism and Amino Acids and Derivatives. Within these categories genes connected to carbon utilization and transport systems (Ton and Tol) as well as chemotaxis showed a higher abundance during bloom senescence. The change in functionality based on transcripts showed a different bacterial community composition appearing over a very short time. We thus conclude that the bacterial functional gene expression response between build-up and degradation bloom phases is remarkably different and associated with a change in the identity of bacteria with active expression. Our findings highlight the importance of bacterial substrate specialists with different functional roles during different time points of phytoplankton blooms.
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Howland, Matthew. "Transcriptomic and Secretomic Profiling of Isolated Leukocytes Exposed to Alpha-Particle and Photon Radiation - Applications in Biodosimetry." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/26081.
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The general public is at risk of ionising-radiation exposure. The development of high-throughput methods to triage exposures is warranted. Current biodosimetry techniques are low-throughput and encumbered by time and technical expertise. Although there has been an emergence of gene-profiling tools for the purpose of photon biodosimetry, similar capacities do not exist for alpha-particle radiation. Herein is the first genomic study useful for alpha-particle radiation biodosimetric triage. This work has identified robust alpha-particle induced gene-based biomarkers in isolated, ex-vivo irradiated leukocytes from multiple donors. It was found that alpha-particle and photon radiation elicited similar transcriptional responses, which could potentially be distinguished by aggregate-signature analysis. Although no distinct genes were sole indicators of exposure type, clustering algorithms and principal component analysis were able to demarcate radiation type with some success. By comparing the biological effects elicited by photon and alpha-particle radiation, significant contributions have been made to the field of radiation biodosimetry.
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Marquez-Quinones, Adriana. "Reactive oxygen species, hepatitis and carcinogenesis initiation : an integrative approach combining transcriptomic and metabonomic profilings." Toulouse, INSA, 2007. http://eprint.insa-toulouse.fr/archive/00000181/.
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Le stress oxydant et l’inflammation jouent un rôle important dans le développement du cancer. Les modèles animaux, comme le rat LEC, qui est muté sur un gène en relation avec l’excrétion hépatique du cuivre et qui développe spontanément une hépatite puis un carcinome hépatocellulaire, sont des outils intéressants pour comprendre la relation existant entre inflammation, stress oxydant et initiation du cancer. L’expression des gènes et les profils métaboliques des rats LEC à différentes étapes de l’hépatite ont donc été comparés à ceux de rats LEC contrôles, traités par un chélateur du cuivre, de façon à pouvoir mettre en évidence les familles de gènes et les ensembles métaboliques impliqués dans l’inflammation et l’initiation de la cancérogenèse hépatiques. Les analyses statistiques multivariées, couplées à l’utilisation des bases de données d’ontologie des gènes a permis de mettre en évidence une sur-représentation et une augmentation de l’expression des gènes impliqués dans le protéasome avec l’hépatite. Cependant, certaines activités du protéasome ont été parallèlement diminuées. L’hypothèse de l’intervention du protéasome dans la pathogenèse de l’hépatite est nouvelle. Les analyses métabonomiques réalisées à partir des profils 1H-RMN urinaires et hépatiques ont permis d’identifier des métabolites associés au développement de l’hépatite. De plus, grâce à une régression PLS2, nous avons établi une relation canonique entre les données transcriptomiques et métabonomiques du foie. La relation linéaire obtenue entre les deux jeux de données a montré que l’expression des gènes et les perturbations métaboliques pouvaient être corrélées en fonction du développement de l’hépatite. Ces données corrélées pourront servir à formuler d’autres hypothèses concernant les mécanismes impliqués dans le développement de l’hépatite et du cancer du foie. Ce travail constitue une approche originale et fonctionnelle qui illustre la puissance des analyses statistiques multivariées pour analyser les données provenant des technologies en omique et qui permet de formuler des hypothèses rationnellesOxidative stress and inflammation play an important role in the development of cancer. Animal models, such as LEC rats, which have a mutation related to hepatic copper excretion and develop spontaneously an hepatitis and a subsequent hepatocellular carcinoma, are useful tools to study the relationship between oxidative stress, inflammation and initiation of cancer. Gene expression and metabolic profiles of LEC rats at different stages of hepatitis were compared to those of control LEC rats treated with a copper chelating agent, to evaluate the different gene families and metabolic networks involved in liver inflammation and carcinogenesis initiation. Multivariate statistical analyses coupled to gene ontology classification of transcriptomic data revealed an overrepresentation and an increase in the expression of genes involved in protein metabolism-related functions, mainly proteasome genes, with hepatitis. However, some proteasome activities were decreased at the same time. Involvement of proteasome in hepatitis pathogenesis is a new hypothesis. Metabonomic analyses done on 1H NMR profiles from urine and liver samples allowed to identify some metabolites related to hepatitis development. PLS2 regression was made to determine a canonical relationship between liver metabonomic and transcriptomic data. The linear correlation obtained indicated that both gene expression and metabolic perturbations are closely related face to hepatitis development. These correlated data will help making new hypotheses for mechanisms involved in liver inflammation and cancer. We present here an integrative analysis of hepatitis development and cellular responses due to oxidative stress. Our work shows an original and functional way of analysis that illustrates the power of multivariate statistical tools to explore omic data and to raise rational biological hypothesis
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Fan, Ben. "Plant colonization by GFP-labeled Bacillus amyloliquefaciens FZB42 and transcriptomic profiling of its response to plant root exudates." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2011. http://dx.doi.org/10.18452/16267.
Full textAbstract:
In dieser Arbeit wurden zunächst die Kolonisationen von drei verschiedenen Pflanzengattungen durch den GFP-markierten Bacillus amyloliquefaciens FZB42 mittels confocaler Lasermikroskopie und Elektronmikroskopie verfolgt. Hier konnte gezeigt werden, dass FZB42 alle ausgewählten Pflanzen besiedeln konnte. Bei Arabidopsis- und Maiskeimlingen wurden die Wurzelhaare und Verbindungen, an denen laterale Wurzeln entstehen, durch FZB42 bevorzugt besiedelt. Weiterhin wurden bei Arabidopsis die Spitzen der Primärwurzeln, und bei Mais die Wurzelkerben bevorzugt besiedelt. Bei Lemna wurden FZB42 Zellansammlungen entlang der Furchen, die zwischen den Epidermiszellen der Wurzel liegen, sowie den intrazellulären Hohlräumen an der Blattunterfläche gefunden. Anschließend wurden die Transkriptome von FZB42, der mit Maiswurzelexudat angezogen wurde, mittels Microarray analysiert. Insgesamt wurden 302 Gene, die 8,2 % des Transkriptoms ausmachen, signifikant durch das Wurzelexudat beeinflusst, wobei die Mehrzahl (260 Gene) hochreguliert wurde. Die induzierten Gene, dessen Funktion bereits bekannt ist, sind hauptsächlich an dem Nährstoffwechsel, Chemotaxis und Beweglichkeit, sowie an der Produktion von Antibiotika beteiligt. Auch wurden die Trankriptome von sieben FZB42-Muatnten durch Microarray analysiert. Diese hatten jeweils eine Deletionen in fünf Sigmafaktor-Genen (sigB, sigD, sigM, sigV,and sigX) und zwei globalen Transkriptionsregulator-Genen (degU und abrB). Die Expression vieler Genen wird durch diese Genprodukte beeinflusst. Mögliche Mechanismen, wie diese Faktoren die bakterielle Reaktion auf Wurzelexsudaten beeinflüssen, wurden vorgeschlagen. Schließlich wurden Northernblott-Untersuchungen an möglichen sRNA-Kandidaten durchgeführt, dessen Expression signifikant durch Wurzelexudate beeinflusst wurde. Dabei konnten 6 von 20 vermeintlichen sRNA-Kandidaten betätigt werden. Dies weist auf eine noch unbekannte Rolle der sRNAs bei der Pflanzen-Mikroben-Wechselwirkung.In this work colonization of three different plants genera, maize, Arabidopsis, and Lemna, by GFP-labeled Bacillus amyloliquefaciens FZB42 in a gnotobiotic system was firtly studied using confocal laser scanning microscopy and electron microscopy. It was shown that FZB42 is able to colonize all these three plants with a specific pattern. Root hairs and the junctions where lateral roots occurred were a preferred area of FZB42 on both maize and Arabidopsis seedlings. On Arabidopsis, tips of primary roots were another favored site of FZB42; while, on maize, the concavities in root surfaces were preferred. FZB42 cells were also able to colonize Lemna, preferably accumulating along the grooves between epidermis cells on roots and the concaved intercellular space on fronds. Secondly, microarray experiments were performed concerning the transcriptomic response of FZB42 to maize root exudates. A total of 302 genes representing 8.2% of FZB42 transcriptome were significantly altered in transcription by the presence of root exudates, the majority of them (260) were up-regulated in expression. The induced genes with known function were mainly involved in nutrition utilization, chemotaxis and motility, and antibiotic production. The transcriptome of seven FZB42 mutants, defective in five sigma factor genes (sigB, sigD, sigM, sigV, and sigX) and two global transcriptional regulator genes (degU and abrB), were also investigated through microarray experiments. A vast number of genes were indentified to be controlled by the protein factors respectively. Possible mechanisms were proposed of how these protein factors are involved in the response to root exudates. Finally, by northern blot existence of six out of 20 small RNA (sRNA) candidates was identified, which were significantly altered in expression by root exudates. This suggests that sRNA may play a hitherto unrecognized role in plant-microbe interaction.