Rozprawy doktorskie na temat „Phenotype Microarry”
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Wennmalm, Kristian. "Analytical strategies for identifying relevant phenotypes in microarray data /". Stockholm, 2007. http://diss.kib.ki.se/2007/978-91-7357-401-3/.
Pełny tekst źródłaSjödin, Andreas. "Populus transcriptomics : from noise to biology /". Umeå : Department of Plant Physiology, Umeå University, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1423.
Pełny tekst źródłaTurton, Nicola. "Association of gene expression and genomic change, analysed using microarrays, with phenotype in breast carcinoma". Thesis, University of Leicester, 2003. http://hdl.handle.net/2381/30770.
Pełny tekst źródłaYahaya, Badrul H. "Analysis of time-dependent transcriptomic and phenotypic changes associated with repair and regeneration in the airway epithelium". Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4800.
Pełny tekst źródłaShaffer, Justin P., Jana M. U'Ren, Rachel E. Gallery, David A. Baltrus i A. Elizabeth Arnold. "An Endohyphal Bacterium (Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae)". FRONTIERS MEDIA SA, 2017. http://hdl.handle.net/10150/623193.
Pełny tekst źródłaGhadiali, Alifiya H. "Studies on Mycobacterium avium subsp. paratuberculosis genotypic and phenotypic variations /". Connect to this title online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1110229469.
Pełny tekst źródłaDocument formatted into pages; contains xxi, 216 p. Includes bibliographical references. Abstract available online via OhioLINK's ETD Center; full text release delayed at author's request until 2006 March 9.
Roberge, Christopher (Christopher M. ). "Design, manufacture, and application of DNA microarrays to study gene expression phenotypes of lysine-producing Corynebacterium glutamicum". Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/32322.
Pełny tekst źródłaIncludes bibliographical references (leaves 197-213).
Corynebacterium glutamicum partial genome DNA microarrays were constructed that were capable of assaying the transcriptional profile of the genes of pathways involved in central carbon metabolism and lysine biosynthesis. It was found that to ensure arrays of high quality, protocols applying the arrays should include DNase treatment of RNA samples. additional RNA filtration purification steps, and the use of gene specific primers in the formation of labeled cDNA through reverse transcription. After implementing these procedures, the accuracy and reproducibility of the array data were validated. The microarrays were used to explore the effects of the over-expression of the key anaplerotic enzyme pyruvate carboxylase and the use of different medium carbon source compositions, both of which have been shown to influence the yields of biomass on carbon and of lysine on biomass. Three different strains of C. glutamicum that were grown on six different minimal medium formulations that varied in their balance of glucose and lactate were assayed by isolating total mRNA samples from cultures in three different phases of growth and lysine production. Genes associated with glycolysis and the pentose phosphate pathway showed decreased transcript concentrations as the available carbon source was shifted from glucose to lactate, while those associated with the TCA cycle and the glyoxylate bypass demonstrated increased transcription. As the cultures stopped generating biomass and began generating lysine, mRNA of genes associated with lysine synthesis and export was measured at elevated concentrations.
(cont.) Reduced gene expression trends seen for aspartokinase and aspartate semialdehyde dehydrogenase suggest that the enzymes are bottlenecks to lysine production, particularly when pyruvate carboxylase is over-expressed and lactate is the available carbon source. This over-expressing strain also had higher transcription levels of the genes of biotin synthesis. and lower transcription levels of the acyl-coA carboxylases dtsRl, dtsR2, accC, and accD. Other results implied that malic enzyme is co-expressed with pyruvate carboxylase to better allow cultures grown on lactate to produce NADPH in the absence of significant pentose phosphate pathway flux. Also, the transcriptional and flux profiles of a pair of C. glutamicum strains grown on two different medium compositions of isotopically labeled glucose and lactate were determined simultaneously from the same set of actively growing and lysine-producing cultures. Flux maps for each of the four combinations of strain and medium were constructed using calculations derived from metabolite balances and GC-MS measurements of the isotopic distributions within biomass hydrolysates of the pseudo-steady-state cultures. Comparisons of the two sets of data showed that 19 of 28 pairs of flux and transcription measurements had trends with good agreement with one another. Different pathways of the metabolic network were found to be controlled via transcription in varying degrees. On average, the Embden- Meyerhof-Parnas pathway was shown to be less likely to be regulated though transcription than the pathways of the tricarboxylic acid cycle and central carbon anaplerosis.
(cont.) In the split pathway available to the cells for producing lysine, the succinylation branch showed an increase in flux for only the case of a pyruvate carboxylase over-expressing strain that was grown on lactate, while the alternate dehydrogenation branch showed a complementary decrease in flux. These flux changes were matched by changes in transcription that only occurred for the same culture and growth medium. Through these findings we have demonstrated the application of C. glutamicum DNA microarrays to the determination of how the cells regulate their responses at the transcriptional level to changes in both gene over-expression and medium composition.
by Christopher Roberge.
Ph.D.
Wong, Chieh Lee. "Identification of unique genetic and epigenetic signatures in myeloproliferative neoplasms using microarray and next generation sequencing : association with MPN-related mutations and clinical phenotypes". Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/52714.
Pełny tekst źródłaMok, Bobo. "Genomic and transcriptomic variation in blood stage Plasmodium falciparum /". Stockholm : Karolinska institutet, 2007. http://diss.kib.ki.se/2007/978-91-7357-291-0/.
Pełny tekst źródłaMartínez, Enguita David. "Identification of personalized multi-omic disease modules in asthma". Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-15987.
Pełny tekst źródłaRösel, Anja [Verfasser], i Frank [Akademischer Betreuer] Pessler. "Application of the Biolog Phenotype MicroArray TM to study changes in host cell metabolism during influenza A virus infection / Anja Rösel ; Akademischer Betreuer: Frank Peßler ; Institut für Experimentelle Infektionsforschung des Twincore Zentrum für Experimentelle und Klinische Infektionsforschung". Hannover : Bibliothek der Medizinischen Hochschule Hannover, 2017. http://nbn-resolving.de/urn:nbn:de:gbv:354-2017061613.
Pełny tekst źródłaRösel, Anja [Verfasser], i Frank [Akademischer Betreuer] Peßler. "Application of the Biolog Phenotype MicroArray TM to study changes in host cell metabolism during influenza A virus infection / Anja Rösel ; Akademischer Betreuer: Frank Peßler ; Institut für Experimentelle Infektionsforschung des Twincore Zentrum für Experimentelle und Klinische Infektionsforschung". Hannover : Bibliothek der Medizinischen Hochschule Hannover, 2017. http://d-nb.info/1135490783/34.
Pełny tekst źródłaBouchiat, Coralie. "Facteurs bactériens impliqués dans la survenue de l’endocardite infectieuse au cours d’une bactériémie à Staphylococcus aureus". Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10187.
Pełny tekst źródłaInfective endocarditis (IE) is a severe condition complicating 10-25% of Staphylococcus aureus bacteremia. Although host-related IE risk factors have been identified, the involvement of bacterial features in IE complication is still unclear. This PhD work aimed to characterize strictly defined IE and bacteremia isolates and searched for discriminant features. Phenotypic traits previously reported or hypothesized to be involved in staphylococcal IE pathogenesis were tested. In parallel, the genotypic profiles of all isolates, obtained by microarray, were analyzed. No significant difference was observed between IE and bacteremia strains, regarding either phenotypic or genotypic univariate analyses, suggesting a multifactorial process. However, the discriminant analysis of principal components (DAPC), applied on microarray data, segregated IE and bacteremia isolates. The performance of this model was confirmed with an independent collection of IE and bacteremia isolates. Finally, a simple linear discriminant function based on a subset of 8 genetic markers retained valuable performance both in study collection and in the independent validation collection. At last, IE and bacteremia isolates were compared based on whole genome sequence data from a subset of 40 isolates. When applied to this dataset, DAPC confirmed a possible segregation between the two groups of isolates. All in all, this PhD work provides the proof of concept that bacterial characteristics may contribute to the occurrence of IE in patients with S. aureus bacteremia
Hebrant, Aline. "Pathologies thyroïdiennes et modèles in vitro: profils d'expression génique et phénotypes moléculaires". Doctoral thesis, Universite Libre de Bruxelles, 2010. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210139.
Pełny tekst źródłaLa première partie du travail a consisté à réaliser un modèle d’étude in vitro pour caractériser les PTC au niveau moléculaire. A cet effet, des cultures primaires de thyrocytes ont été traitées avec de l’EGF et du sérum pendant différents temps (1,5h, 3h, 16h, 24h et 48h) ce qui stimule la cascade des MAPK, activée constitutivement dans les PTC. Nous avons hybridé sur des lames microarrays maison les différents échantillons et nous avons montré que les cultures primaires stimulées pendant des temps longs (24h et 48h) ont des profils d’expression génique qui ressemblent à ceux des PTC et constituent donc un bon modèle d’étude de cette tumeur.
La seconde partie a pour objectif de définir les phénotypes moléculaires et fonctionnels des FNAH et de les comparer aux AA. Ces deux pathologies résultent d’une mutation dans le récepteur de la TSH (TSHR) activant de manière constitutive la cascade de l’AMPc. Dans le cas des FNAH, la mutation est héréditaire et toute la glande est affectée contrairement aux AA où la mutation survient plus tard, généralement à l’âge adulte, et où seule une partie de la glande est affectée. Nous avons comparé le profil d’expression génique des FNAH avec celui des AA, par hybridation sur des lames microarrays HEEBO. L’intégration de ces différentes données montre que les AA et les FNAH sont deux sous-types différents de la même maladie: l’hyperthyroïdie génétique. Les caractéristiques de chacun de ces sous-types dépendent de l’intensité de la mutation, du nombre de cellules initialement affectées et du stade de développement au moment duquel la mutation survient.
Dans la dernière partie de ce travail, nous avons caractérisé les ATC au niveau du profil d’expression des ARNm et des miRNA par hybridation respectivement sur lames Affymetrix ou sur lames miRNA maison et au niveau de leur état mutationnel du gène p53. Le profil d’expression génique des ATC a été comparé avec celui des PTC afin de mettre en évidence des gènes différentiellement exprimés entre les 2 types de cancers, que nous avons ensuite tenté d’invalider par siRNA, dans un modèle in vitro de lignée cellulaire thyroïdienne dérivée d’un ATC (8505C). Les résultats obtenus jusqu’ici ne sont malheureusement pas prometteurs. Le profil d’expression des miRNA nous a permis d’identifier une signature de 34 miRNA caractéristique des ATC.
Doctorat en Sciences biomédicales et pharmaceutiques
info:eu-repo/semantics/nonPublished
Gupta, Kuldeepkumar Ramnaresh. "(p)ppGpp and c-di-GMP : A Tale of Two Second Messengers in Mycobacterium smegmatis". Thesis, 2015. http://etd.iisc.ac.in/handle/2005/4117.
Pełny tekst źródłaNarayanaswamy, Rammohan 1978. "Genome-wide analyses of single cell phenotypes using cell microarrays". Thesis, 2008. http://hdl.handle.net/2152/3967.
Pełny tekst źródłatext
Lin, Wen-Ting. "Systematic data preprocess procedures and factor extraction of multiple phenotypes for one-color microarray". 2004. http://www.cetd.com.tw/ec/thesisdetail.aspx?etdun=U0001-1607200415331300.
Pełny tekst źródłaLin, Wen-Ting, i 林雯婷. "Systematic data preprocess procedures and factor extraction of multiple phenotypes for one-color microarray". Thesis, 2004. http://ndltd.ncl.edu.tw/handle/22547434483964753647.
Pełny tekst źródła國立臺灣大學
工業工程學研究所
92
Microarrays are widely used to monitor gene expressions to yield information for genomes. Though there are many methods and mechanisms proposed to extract information from microarray data, the preprocess of raw expression data determine the accuracy and reliability of the extracted information. The first objective of this research is to implement a systematic procedure to preprocess the raw intensity reading. The proposed data preprocess procedure has 3 steps: rectification of intensity reading, signal normalization and bad spots screening. The rectification of intensity uses coefficient of variation (CV) to assess the consistencies of mean intensity and median intensity from raw intensity readings to decide which one to employ and then test the correlations between foreground intensity and background intensity to correct background intensity effects. Signal normalization transforms the rectified data to remove the chip-to-chip brightness variation and contrast variation by logarithm transformation, median subtraction and deviation division. After signal normalization, the hypothesis T-test is used to screen out bad expressions in replicated spots. More recently, microarrays have been conducted not only to relate genes with one phenotype, but also inquire relations between gene expression levels and multiple phenotypes. The second objective of this research is to apply Factor Analysis (FA) to extraction of the underlying co-regulating and independent factors of the multiple phenotypes. And then the treated factors can be taken as an individual phenotype for testing differentially expressed genes. Both of the objectives are to prepare experimental readings for accurate, effective biological information mining procedure. Finally, a real case of microarray experiment investigating gene expressions in 24 human blood samples with 19 phenotypes is provided to demonstrate and test the proposed preprocessing procedures.
Stojakovic, Milica. "Role of the CD40 receptor/CD154 ligand dyad in the control of smooth muscle cells phenotype". Doctoral thesis, 2003. http://hdl.handle.net/11858/00-1735-0000-0006-AB93-0.
Pełny tekst źródłaNiu, Wei. "Development of imaging-based high-throughput genetic assays and genomic evaluation of yeast gene function in cell cycle progression". Thesis, 2007. http://hdl.handle.net/2152/3606.
Pełny tekst źródłaYip, Cindy Ying Yin. "Pathology of Calcific Aortic Valve Disease: The Role of Mechanical and Biochemical Stimuli in Modulating the Phenotype of and Calcification by Valvular Interstitial Cells". Thesis, 2010. http://hdl.handle.net/1807/26520.
Pełny tekst źródłaBellabarba, Agnese. "Into the wild: how rhizobia compete and survive in the early stage of symbiosis". Doctoral thesis, 2022. http://hdl.handle.net/2158/1280999.
Pełny tekst źródłaBrito, Lauro David Silva de. "Determining the functional interactions of inducers/inhibitor compounds in controlling the ramA locus in Klebsiella pneumoniae". Master's thesis, 2012. http://hdl.handle.net/10400.1/11028.
Pełny tekst źródłaΣυμεωνίδη, Διονυσία. "Βιοπληροφορική ανάλυση και χαρακτηρισμός γονιδίων που εμπλέκονται στη φαινοτυπική πλαστικότητα του zebrafish (Danio rerio, Hamilton 1822)". Thesis, 2011. http://hdl.handle.net/10889/5366.
Pełny tekst źródłaDevelopmental temperature plays a principal role in the ontogeny of fish. It is known that developmental temperature may shift the initiation time of the ontogenetic stages and induce plasticity in morphological and physiological characters e.g. the musculoskeletal and the cardiovascular system. However, its effect on the gene expression pattern has not previously been attempted for zebrafish. In the present study, zebrafish Affymetrix microarrays of 15,509 probe sets were used to map the transcriptome profile of: a) 20 dpf* old zebrafish larvae at three developmental temperatures, i.e. 22oC, 28oC and 32oC (1st experiment) and b) 20 dpf old zebrafish larvae, which were all grown at 28oC for the first 10 days and subsequently divided into three groups, which were grown at 22oC, 28oC and 32oC, respectively; the profile of 10 dpf old larvae was also measured (2nd experiment). We have isolated total RNA from the above populations and then, hybridization of RNA samples has been done on oligonucleotide Affymetrix microarrays of 15,509 probe sets. All 21 profiles were normalized and filtered (dChip software), and multivariate statistical analysis techniques were used on the normalized 9,488 probe set expression profiles (TM4 MeV software). Hierarchical Clustering (HCL) and Principal Component Analysis (PCA) on expression profiles indicated: a) clear separation of the two experiments based on their transcriptomic patterns, b) clustering of the 28oC and 32oC profiles of the 20 dpf old larvae separately from those at 22oC in both experiments and c) clear separation of the 28oC profiles based on the developmental stage. We would expect expression profiles of 28oC to be clustered together, though this was not observed because of experimental parameters during the hybridization, as the two experiments were carried out independently on different dates. So the normalization of “28” profiles took place, in order to eliminate the experimental noise. HCL and PCA, then, indicated: a) clustering of the 28oC and 32oC profiles of the 20 dpf old larvae separately from those at 22oC, as the effect of developmental temperature, b) clear separation of 22oC profiles of the two experiments, based on the effect of the period and duration of thermal conditions and c) clear separation of the 28oC profiles based on the developmental stage. Then, Significant Analysis of Microarrays (SAM) and Functional Genomic Classification Analysis (DAVID software) of statistically significant genes was carried out. Analysis of genes based on tissue-specific expression indicated characteristic genes for the development of the eye, pectoral fins and brain in 22oC profiles versus 28oC and 32oC profiles. The present study has proved that thermal effect is determinative among the early ontogenetic stage, especially in the case of longer cold thermal period, and developmental temperature may induce plastic response of gene expression, that could affect the fate of fish. *dpf: days post fertilization
(10725786), James Michael Amstutz. "Cluster-Based Analysis Of Retinitis Pigmentosa Candidate Modifiers Using Drosophila Eye Size And Gene Expression Data". Thesis, 2021.
Znajdź pełny tekst źródłaThe goal of this thesis is to algorithmically identify candidate modifiers for retinitis pigmentosa (RP) to help improve therapy and predictions for this genetic disorder that may lead to a complete loss of vision. A current research by (Chow et al., 2016) focused on the genetic contributors to RP by trying to recognize a correlation between genetic modifiers and phenotypic variation in female Drosophila melanogaster, or fruit flies. In comparison to the genome-wide association analysis carried out in Chow et al.’s research, this study proposes using a K-Means clustering algorithm on RNA expression data to better understand which genes best exhibit characteristics of the RP degenerative model. Validating this algorithm’s effectiveness in identifying suspected genes takes priority over their classification.
This study investigates the linear relationship between Drosophila eye size and genetic expression to gather statistically significant, strongly correlated genes from the clusters with abnormally high or low eye sizes. The clustering algorithm is implemented in the R scripting language, and supplemental information details the steps of this computational process. Running the mean eye size and genetic expression data of 18,140 female Drosophila genes and 171 strains through the proposed algorithm in its four variations helped identify 140 suspected candidate modifiers for retinal degeneration. Although none of the top candidate genes found in this study matched Chow’s candidates, they were all statistically significant and strongly correlated, with several showing links to RP. These results may continue to improve as more of the 140 suspected genes are annotated using identical or comparative approaches.