Tesi sul tema "Oligonucleotide microarray"
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Li, Xiaopeng. "Development of Oligonucleotide Microarray for High Throughput DNA Methylation Analysis". Cleveland State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1224605179.
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Van, Zuydam Natalie Rachel. "Identification of Leptographium species by oligonucleotide discrimination on a DNA microarray". Diss., University of Pretoria, 2009. http://hdl.handle.net/2263/28928.
Testo completoAbstract (sommario):
Leptographium is an anamorph genus within the Ophiostomatoid group of fungi and represents a unique case for molecular applications. The genus has a near complete sequence data available for three genes across all known species. This characteristic makes it a perfect test group for investigating applications of new diagnostic techniques within ascomycetes. Probes and primers, for microarrays, are designed from phylogenetically useful gene regions and are fabricated onto a solid substrate using printing technology. The sample is prepared using PCR and is hybridised to the probes under stringent conditions. The resulting fluorescent pattern is rigorously analysed to distinguish species from each other. Diagnostic PCR uses primers that are designed in similar way to the way probes are designed for microarrays and indicate the presence of a species through positive amplification. This research methodology will be applied to Leptographium to evaluate the efficacy of microarray technology for discriminating species within that genus. The data gained from this research study will be used in applications for other genera using microarray technology.Dissertation (MSc)--University of Pretoria, 2011.
Genetics
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Broto, Avilés Marta. "Universal diagnostic platforms based on oligonucleotide codified nanoparticles and DNA microarray devices". Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/462828.
Testo completoAbstract (sommario):
La medicina personalitzada esta prenent rellevància últimament. Aquesta es basa en la monitorització simultània de diferents biomarcadors, els biomarcadors poden ser molècules de diferent naturalesa química. Aquest fet fa palesa la necessitat de desenvolupar aproximacions tecnològiques universals per al diagnòstic capaces de detectar aquests biomarcadors independentment de la seva naturalesa química. En aquests context, la principal finalitat del projecte és el desenvolupament d’una plataforma bioanalítica per al diagnòstic in vitro que sigui multiplexada (per més de un biomarcador) i multimodal (per biomarcadors de diferent naturalesa química). L’aproximació proposada pretén traduir qualsevol interacció biomolecular (biomarcador- bioreceptor) en una senyal amplificada d’ADN que serà finalment detectada en un bioxip d’ADN. Aquesta estratègia s’anomena biobarcode.
Com a prova de concepte de l’aproximació proposada ens hem centrat en la detecció de biomarcadors relacionats amb les malalties cardiovasculars (CVDs) i, també, en fàrmacs relacionats amb el càncer. CVDs són la principal causa de mort al món i inclouen un grup de desordres dels vasos coronaris i sanguinis. La detecció multiplexada i multimodal d’aquests biomarcadors podria ser de gran ajuda en el monitoratge de l’estat del pacient. Per altra banda, la segona causa de mort al món és el càncer, els fàrmacs utilitzats per tractar-lo s’anomenen cytostatics. La proximitat de la dosi tòxica i terapèutica dels fàrmacs cytostatics fa el monitoratge terapèutic dels fàrmacs (TDM) la clau per la optimització del tractament del càncer. Podem assumir que la monitorització del fàrmac juntament amb certs metabòlits milloraria la eficàcia i tolerabilitat, reduint la toxicitat.Personalized therapy has become a crucial issue lately. It should be based on the simultaneous monitoring of different biomarkers which might include molecules of different chemical nature. This fact, calls for developing universal technological diagnostic approaches, able to determine these biomarkers, independently from their chemical nature, while modulating the necessary amplification factor. In this context, the aim of the project is to develop of a universal, multiplexed (for several biomarkers) and multimodal (biomarkers of different chemical nature) in vitro diagnostic bioanalytical platform. The proposed approach (Figure 1) pretends to translate any type of biomolecular interaction (bioreceptor-biomarker) into a PCR-less DNA amplification process that is finally detected on a DNA-microarray biosensor platform. This strategy is called biobarcode assay. As proof-of-concept of the proposed approach, we have focused on the detection of biomarkers related to cardiovascular diseases (CVDs) and, also, drugs related to cancer disease. CVDs are the main cause of death in the world and include a group of disorders of the heart and blood vessels, multimodal and multiplexed detection of CVDs-related biomarkers would help the monitoring of patient status. Otherwise, the second cause of death worldwide is cancer; drugs used to treat cancer are called cytostatics. Closely levels of therapeutic and toxic doses of cytostatics make therapeutic drug monitoring the milestone for the optimization of cancer treatment. It can be assumed that monitoring of drug concentration jointly with main metabolites should improve efficacy and tolerability and reduce toxicity. The main objective of the project will consist on demonstrating that it is possible to analyze targets of different chemical nature, and that the amplification can be modulated by varying the charge of oligonucleotides covalently attached to the nanoparticles.
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Black, Ryan Weldon. "Design and Evaluation of Oligonucleotide Microarrays for the Detection of Bovine Pathogens". DigitalCommons@USU, 2009. https://digitalcommons.usu.edu/etd/381.
Testo completoAbstract (sommario):
Two microarray designs were developed and produced to screen for multiple bovine pathogens commonly found in the cattle industry today. The first microarray was designed, built, and processed in-house using conventional material and equipment and targeted Pasteurella multocida, Manheimia haemolytica, Histophilus somni, and Arcanobacterium pyogenes. For each pathogen, 12 perfect-match oligonucleotide probes, which were also designed in-house, targeted different sections of the respective 16S ribosomal genes, and were coupled with 12 corresponding mismatched probes for background. These arrays were able to produce distinct hybridization patterns for each pathogen that were easily visible without the need for computer analysis. However, the need for PCR amplification of the 16S gene prior to hybridization motivated us to explore more efficient array options. The second designed microarray, a custom Affymetrix GeneChip, targeted Escherichia coli, Salmonella typhimurium, and Salmonella dublin in addition to the previously mentioned pathogens and was more successful in overall performance than the "in-house" arrays. In addition to the 16S gene, oligonucleotide probes targeted other genes (from 2 to >4500, depending on whether the genome was sequenced) that were unique to each pathogen. This array also differed from the "in-house" arrays in that mismatched probes were not designed. The different probe sets performed at different detection limits as P. multocida, A. pyogenes, S. typhimurium, and S. dublin were detected with as little as 250ng of hybridized genomic DNA (gDNA), while M. haemolytica, H. somni, and E. coli required as much as 1μg gDNA. These pathogens were also spiked into bovine tissue to simulate multiorgan infections in which they were individually detected with the microarray design.
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Nordberg, Eric Kinsley. "Creating Scientific Software, with Application to Phylogenetics and Oligonucleotide Probe Design". Diss., Virginia Tech, 2015. http://hdl.handle.net/10919/64366.
Testo completoAbstract (sommario):
The demands placed on scientific software are different from those placed on general purpose software, and as a result, creating software for science and for scientists requires a specialized approach. Much of software engineering practices have developed in situations in which a tool is desired to perform some definable task, with measurable and verifiable outcomes. The users and the developers know what the tool "should" do. Scientific software often uses unproven or experimental techniques to address unsolved problems. The software is often run on "experimental" High Performance Computing hardware, adding another layer of complexity. It may not be possible to say what the software should do, or what the results should be, as these may be connected to very scientific questions for which the software is being developed. Software development in this realm requires a deep understanding of the relevent scientific domain area. The present work describes applications resulting from a scientific software development process that builds upon detailed understanding of the scientific domain area.
YODA is an application primarily for selecting microarray probe sequences for measuring gene expression. At the time of its development, none of the existing programs for this task satisfied the best-known requirements for microarray probe selection. The question of what makes a good microarray probe was a research area at the time, and YODA was developed to incorporate the latest understanding of these requirements, drawn from the research literature, into a tool that can be used by a research biologist. An appendix examines the response and use in the years since YODA was released.
PEPR is a software system for inferring highly resolved whole-genome phylogenies for hundreds of genomes. It encodes a process developed through years of research and collaboration to produce some of the highest quality phylogenies available for large sets of bacterial genomes, with no manual intervention required. This process is described in detail, and results are compared with high quality results from the literature to show that the process is at least as successful as more labor-intensive manual efforts. An appendix presents additional results, including high quality phylogenies for many bacterial Orders.Ph. D.
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Benoit, Marie-Helene. "Oligonucleotide microarray analysis of chromosome-X gene expression in human epithelial ovarian cancer cell lines". Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=81597.
Testo completoAbstract (sommario):
Microarray expression analysis was applied as an approach for identifying cancer-related genes on chromosome-X (CHR-X) in epithelial ovarian cancer (EOC). The Hu6800 and U133A GeneChipsRTM were used to evaluate the expression of 446 CHR-X genes in an in vitro EOC model system comprising 4 EOC cell lines and 12 primary cultures of normal ovary surface epithelia. Fifty-one new candidate CHR-X genes were identified in addition to 49 genes previously implicated in cancer. Many genes map to regions with frequent genetic aberrations in EOC tumours, or interact with the known EOC tumour suppressors BRCA1 and BRCA2. Candidate genes described in this study may provide novel markers for histopathological subtypes, or the tumourigenic potential of EOC tumours. The X-inactive-specific-transcript (XIST) was absent in two highly tumourigenic EOC cell lines, TOV21G and TOV112D. XIST mRNA is important for the stability of X-chromosome-inactivation (XCI), as its absence destabilizes the silencing of genes on the inactive-X. Aberrant bi-allelic expression of FHL1, a gene subjected to XCI was detected in the cell line TOV21G but not in the cell line TOV112D. Genotyping assays using polymorphic microsattelite markers suggested that TOV21G has retained heterozygosity of CHR-X. The majority of alleles tested for TOV112D were consistent with loss of heterozygosity of CHR-X. Taken together these findings are consistent with two proposed mechanisms mediating XIST loss-of-expression in cancer: (1) Duplication of the active-X followed by loss of the inactive-X (TOV112D); or (2) Reactivation of the previously inactive-X (TOV21G).
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Jeong, Sooyoung. "A custom oligonucleotide microarray analysis as a tool for dissecting soybean-bradyrhizobium japonicum nodule senescence". Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/6266.
Testo completoAbstract (sommario):
Thesis (M.S.)--University of Missouri-Columbia, 2007.The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on May 27, 2009) Includes bibliographical references.
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Gusnanto, Arief. "Regression on high-dimensional predictor space : with application in chemometrics and microarray data /". Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-153-9/.
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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/.
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Xue-Franzén, Yongtao. "DNA microarray approaches to understanding the regulation and evolution of gene expression networks". Stockholm : Huddinge : Karolinska institutet ; Södertörns högskola, 2009. http://diss.kib.ki.se/2009/978-91-7409-554-8/.
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Taylor, G. Scott. "Design and Development of Oligonucleotide Microarrays and their Application in Diagnostic and Prognostic Estimation of Human Gliomas". VCU Scholars Compass, 2006. http://scholarscompass.vcu.edu/etd/1459.
Testo completoAbstract (sommario):
DNA microarrays represent an ultra-high throughput gene expression assay employed to study the transcriptomic profiles of biological tissues. These devices are increasingly being used to study many aspects of gene regulation, and there is growing interest in the biotechnology and pharmaceutical industries for developing such devices in efforts toward rational product/drug design. The DNA microarray also provides a unique and objective means for diagnosis and prognosis of human diseases based on patterns of gene expression. This is especially important in cancer research and the thrust toward personalized medicine. This dissertation details the design and development of oligonucleotide microarrays and the design and execution of a gene expression study conducted using human glioma specimines. Chapter 2 details the design and development a ~10,000 gene human oligonucleotide microarray. This device consisted of a 21,168 features, each composed of a particular human gene-probe and was applied to the challenge of diagnostic and prognostic estimation for human gliomas (chapter 3). Gliomas are the most frequent and deadly neoplasms of the human brain characterized by a high misdiagnosis rate and low survival. The study in chapter 3 demonstrated that the specified design and development parameters were appropriate for conducting gene expression analysis and that this platform can be used successfully to predict malignancy grade and survival for glioma patients.
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Burke, Natalie. "Genetic Imbalances in Endometriosis Detected by Oligonucleotide-Array Based Comparative Genomic Hybridization". Digital Commons @ East Tennessee State University, 2013. https://dc.etsu.edu/etd/1129.
Testo completoAbstract (sommario):
Endometriosis is one of the most common gynecological diseases as it is thought to affect up to 15% of the female population. Characterized by the growth and proliferation of endometrial tissue outside of the uterine cavity, it is a complex condition with varying degrees of severity and can affect multiple regions of the body with symptoms ranging from a total lack of symptoms to debilitating pain and infertility. The most accepted theory of how endometriosis initiates is that of retrograde menstruation; however, approximately 90% of women with unobstructed fallopian tubes are thought to have some menstrual debris in the peritoneal cavity. Therefore, this theory does not explain in full why endometriosis occurs in some but not all women who experience retrograde bleeding.
Genetic factors are thought to play a major role in the pathogenesis of endometriosis as women with a family history are 5 to 10 times more likely to develop the disease. The goal of this study was to determine if common chromosomal aberrations in the form of additions, deletions, or regions of loss of heterozygosity that may contribute to the establishment or progression of the disease are present in a population of endometriosis patients. DNA was isolated from the peripheral blood of endometriosis patients and endometriosis tissue biopsies, and it was analyzed using oligonucleotide based array comparative genomic hybridization. The results suggest that an addition on chromosome 17p13.3 may play a role in the biological mechanisms involved in endometriosis as it was identified in 75% of the DNA samples obtained from the peripheral blood and 100% of the DNA samples obtained from the tissue biopsies. This chromosomal imbalance is of particular interest as it is located in a region that harbors the tumor suppressor gene, hypermethylated in cancer-1 (HIC-1), whose aberrant expression has been reported in multiple cancers.
Endometriosis has long been thought of as a benign disease despite its malignant characteristics, and individuals with endometriosis have been demonstrated to have an increased chance of developing ovarian cancer. This was the first study to examine the DNA from endometriosis patients using oligonucleotide based array comparative genomic hybridization to investigate genetic abnormalities in endometriosis. The findings may provide a novel target for future therapeutic options as well as indicate a link between endometriosis and cancer that has not been previously reported.
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Martin, Mallory N. "Microduplication 22q syndrome : investigation of intergenerational change using microarray-based comparative genomic hybridization /". Oklahoma City : [s.n.], 2009.
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Bonner, Allison E. "Organ development and tumorigenesis: a molecular link". The Ohio State University, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=osu1073936508.
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Lindroos, Katarina. "Accessing Genetic Variation by Microarray Technology". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2002. http://publications.uu.se/theses/91-554-5251-5/.
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Fält, Susann. "Analysis of global gene expression in complex biological systems using microarray technology /". Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-612-3/.
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Wagner, Brandie D. "Permutation based microarray gene selection methods with covarience adjustment applicable to complex diseases /". Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2007.
Cerca il testo completoAbstract (sommario):
Thesis (Ph.D. in Analytic Health Sciences) -- University of Colorado Denver, 2007.Typescript. Includes bibliographical references (leaves 57-60). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;
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Rasiah, Krishan Kumar St Vincent's UNSW. "The identification of novel biomarkers in the development and progression of early prostate cancer". Awarded by:University of New South Wales. St Vincent's, 2006. http://handle.unsw.edu.au/1959.4/24187.
Testo completoAbstract (sommario):
ABSTRACT The morphological premalignant changes in prostate epithelium such as high grade prostatic intraepithelial neoplasia (HGPIN) precede invasive prostate cancer (PC) by several decades. The overall aim of this project was to identify patterns of gene expression in HGPIN and early PC which increase our understanding of the early biology of PC and identify genes and pathways that correlate with an aggressive phenotype. A comprehensive tissue cohort of premalignant prostate lesions was collected in a tissue microarray (TMA) platform that was utilised for high-throughput validation of target genes. Using this unique resource, the expression of the tumour suppressor gene PTEN was assessed using immunohistochemistry in an initial candidate gene approach based on mouse models implicating PTEN in carcinogenesis. No significant difference in expression of PTEN was detected in premalignant and benign epithelium. A transcript profiling approach was undertaken by integrating laser capture microdissection, linear RNA amplification and oligonucleotide microarrays to perform a screen of matched patient samples of normal, HGPIN and PC cells. The expression patterns of two genes encoding secreted proteins, neuropeptide Y (NPY) and macrophage inhibitory cytokine (MIC-1) were validated using immunohistochemistry on TMAs representing the progression model of early PC. Increased expression of these proteins in PC was confirmed to occur early in the disease process and altered expression of NPY and MIC-1 was associated with worse clinical outcome. Further analysis of global gene expression patterns using a structured network knowledge base identified a notable aberration in the expression of extracellular matrix and extracellular matrix associated proteins in HGPIN and provided novel evidence for the role of this class of molecules in the development of PC. In summary, contrary to current dogma based on work in animal models, altered PTEN expression is unlikely to represent an important event in the development of malignancy in the human prostate. In contrast, the expression patterns and prognostic value of NPY and MIC-1 in HGPIN support their further evaluation as biomarkers for the development and progression of PC. The aberrant expression of genes and networks of genes detected in HGPIN will assist in further identification of biological pathways which may be targeted in therapeutic strategies against the development and progression of PC.
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Breznan, Anna Devorah. "Oligonucleotide microarray analysis of chromosome 17 gene expression in a model human epithelial ovarian cancer cell line, TOV112D, and in epithelial ovarian tumors and ovarian malignant ascites". Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=97911.
Testo completoAbstract (sommario):
The importance of developing relevant ovarian cancer models led us to test the applicability of a system comprised of epithelial ovarian cancer cell lines. The high frequency of loss of heterozygosity (LOH) and rearrangements of chromosome 17 in ovarian tumors provide evidence of a role of chromosome 17 genes in ovarian tumorigenesis. Oligonucleotide microarray expression analysis was applied to assess the expression profiles of 864 probe sets that map to chromosome 17. The TOV112D ovarian cancer cell line, a spontaneously immortalized and tumorigenic ovarian cancer cell line derived from an endometrioid histopathological subtype, which has been shown to exhibit LOH of chromosome 17, was used as a model to identify candidate genes based on Affymetrix expression microarray analyses in comparative analysis with three primary cultures derived from normal ovarian surface epithelium (NOSE). Two-way comparative analyses identified 81 probe sets, representing 64 differentially expressed genes, which exhibited at least a three-fold difference in expression relative to the mean of NOSE samples. The expression of these 64 candidate genes was investigated by microarray analysis in 31 fresh solid malignant ovarian tumors of different histopathologies, six ovarian tumors of borderline pathology, 32 primary cultures of ovarian tumors, 28 primary cultures of malignant ovarian ascites, and 16 NOSE samples. The chromosome 17 expression profile of TOV112D monolayer was compared with this cell line grown as a three-dimensional spheroid, solid tumors and monolayer cultures of these tumors from intraperitoneal and subcutaneous injection into nude mice. The expression profiles of selected candidates were validated by RT-PCR. About 63% of the candidates overexpressed at least three-fold relative to TOV112D were also overexpressed in some of the solid malignant ovarian tumors, and about 91% of the candidates that were underexpressed at least three-fold in TOV112D were also underexpressed in some of these tumors. The same differential pattern of gene expression of candidates was also observed in primary cultures of ovarian tumors and ovarian ascites, however, the effect in primary cultures was reduced. These results indicate that TOV112D, representing a spontaneously immortalized long-term passage, was more representative of solid ovarian tumors compared with the primary cultures. Growth conditions showed little impact on the expression profile of candidates when TOV112D was grown in different culture environments such as in vitro monolayer or mouse tumor xenograft. The finding that TOV112D identified differentially expressed genes in ovarian tumor samples regardless of histopathological subtype indicates that it is a useful model, not only to study the endometrioid subtype, but also serous and clear cell subtypes of epithelial ovarian cancer. Comparison of the expression profiles of our candidate genes identified by microarray analysis with published reports revealed that eight genes (ACACA, SFRS2, CCL2, CSF3, IGFBP4, KRT19, ITGA3, and TIMP2) were previously implicated in ovarian cancer, and 23 including MAC30 and TBX2 were implicated in tumorigenesis of other types of cancers. The use of long-term ovarian cancer cultures provides scientists with a model to study candidate genes, some of which may prove important for early detection or represent targets for the development of new ovarian cancer treatments.
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Röpcke, Stefan. "Robuste Datenauswertung und Anwendungen von Oligonukleotid-Arrays in der Genexpressionsanalyse". Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2003. http://dx.doi.org/10.18452/14992.
Testo completoAbstract (sommario):
Die Technologie der Oligonukleotid-Arrays erlaubt es, tausende von Genen parallel auf ihre Expression hin zu untersuchen. Die Firma metaGen, bei der diese Doktorarbeit entstand, setzt die Genexpressionsanalyse zur Identifikation von Targetmolekülen für die Therapie solider Tumoren ein. Im Zuge dieser Arbeit gelang die Entwicklung eines robusten Verfahrens zur Datenanalyse für Oligonukleotid-Arrays. Gerade für die Untersuchung humaner Proben ist die Robustheit von großem Interesse, da das Gewebematerial oft nur in sehr begrenzten Mengen und mit Qualitätsschwankungen behaftet vorliegt. Anhand eines eingeschränkten Sets an Kontrollversuchen konnte gezeigt werden, dass die vorgeschlagene Methode besser die Erwartungen an das System erfüllt als herkömmliche Verfahren. Ein weiterer Teil der Arbeit bestand im Aufbau einer relationalen Datenbank und in der schrittweisen Automatisierung der Auswertung. Stellvertretend für andere Krebserkrankungen wurde eine detaillierte Analyse zweier publizierter Expressionsdatensätze zum Bronchialkarzinom vorgenommen. Es konnten zwar in beiden Datensätzen zwischen Tumor- und Normalgewebe differenziell exprimierte Gene identifiziert werden, aber die Gegenüberstellung der Ergebnisse zeigte auch einen deutlichen Einfluss der unterschiedlichen Array-Technologien auf die gemessenen Intensitäten. Der spezielle Aufbau des verwendeten Oligonukleotid-Arrays gestattete die Entdeckung putativer Antisense-Transkripte. Die Koexpression einiger Sense- und Antisense-Sonden ließen sich durch Northern-Blot-Experimente bestätigen. Das unterstreicht das Anwendungspotenzial dieser Technologie für die Genomannotation. In einer Untersuchung der Transkriptome der Bäckerhefe und der Fruchtfliege konnte darüber hinaus ein Zusammenhang zwischen den Längen von Introns und Exons und der mittleren Expression von Genen hergestellt werden. Die Vielfalt der Anwendungen und die Ausbaumöglichkeiten verdeutlichen die Bedeutung und das Potenzial der Array-Technologie für die Genexpressionsanalyse. Eine wichtige Aufgabe bleibt deshalb die weitere Verbesserung der Qualitätskontrolle der Experimente und der Datenanalyse.Oligonucleotide arrays represent a modern technology for the investigation of the expression of thounsands of genes in parallel. The theses were worked out at the company metaGen that uses gene expression analysis for the identification of target molecules for the therapy of solid tumors. One major achievement was the developement of a robust method for oligonucleotide array data analysis. It turned out that for the investigation of human tissue samples the robustness is crutial because the material is often very limited and of variing quality. Using a restricted set of control experiments the superiority of the method over standard procedures could be demonstrated. A further important part of the work was the construction of a relational database and the automation of the analysis process. To demonstrate the applicability of the methods in cancer research two publicly available lung cancer data sets were analysed. A list of differentially expressed genes was identified. But the comparison also revealed that the expression signals are strongly distorted by technical factors. The special array used at metaGen allowed the discorvery of putative antisense transcripts. Three of the candidates had been validated by Northern-blot analysis. This clearly shows the applicability of the array technology to genome annotations. An analysis of the transcriptoms of the bakers yeast and the fruit fly revealed a relationship between the average gene expression and the lengths of introns and exons. The manifold applications and extentions illustrate the inportance and the potential of the array technology. So that the improvement of the technology and of the data analysis will remain a major concern.
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Zhang, Lei [Verfasser], Barbara [Akademischer Betreuer] Reinhold-Hurek e Anke [Akademischer Betreuer] Becker. "Design and application of an oligonucleotide microarray (nifH-phylochip) for nifH gene-based detection of nitrogen-fixing prokaryotes / Lei Zhang. Gutachter: Barbara Reinhold-Hurek ; Anke Becker. Betreuer: Barbara Reinhold-Hurek". Bremen : Staats- und Universitätsbibliothek Bremen, 2005. http://d-nb.info/1072302217/34.
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Brunner, Thomas. "Designing oligonucleotides for DNA microarrays /". Zürich : ETH, Eidgenössische Technische Hochschule Zürich, Department of Computer Science, 2003. http://e-collection.ethbib.ethz.ch/show?type=dipl&nr=116.
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Arteaga-Salas, Jose Manuel. "Statistical treatment of spatial flaws in oligonucleotide microarrays". Thesis, University of Essex, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.510491.
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Tjaden, Brian C. "Computational methods for transcription anlysis using oligonucleotide microarrays /". Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/6907.
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Udall, Joshua, Lex Flagel, Foo Cheung, Andrew Woodward, Ran Hovav, Ryan Rapp, Jordan Swanson et al. "Spotted cotton oligonucleotide microarrays for gene expression analysis". BioMed Central, 2007. http://hdl.handle.net/10150/610000.
Testo completoAbstract (sommario):
BACKGROUND:Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species.RESULTS:Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the microarray has direct application for analysis of the fiber transcriptome. To illustrate the utility of the microarray, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results.CONCLUSION:The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info webcite.
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Bergemann, Tracy L. "Image analysis and signal extraction from cDNA microarrays /". Thesis, Connect to this title online; UW restricted, 2004. http://hdl.handle.net/1773/9603.
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Dabney, Alan R. "The normalization of two-channel microarrays /". Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/9537.
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Lindsay, Jennefer. "Identification of genes regulated during neuronal apoptosis using oligonucleotide microarrays". Thesis, University College London (University of London), 2005. http://discovery.ucl.ac.uk/1444984/.
Testo completoAbstract (sommario):
Neuronal apoptosis occurs extensively during the normal development of the mammalian nervous system and ensures that appropriate connections are made between neurons and their target cells. Developing sympathetic neurons and the PC6-3 cell line, a PC 12 sub-clone, are useful in vitro systems for studying neuronal apoptosis. Both sympathetic neurons and neuronally differentiated PC6-3 cells depend on nerve growth factor (NGF) for survival and die by apoptosis after NGF withdrawal in a transcription and translation-dependent manner. The c-Jun protein is known to be required for neuronal cell death following survival factor withdrawal, however the direct targets of this basic/leucine zipper transcription factor are unknown. The aim of this thesis was to identify and study c-Jun target genes involved in neuronal apoptosis. In experiments using Affymetrix GeneChip oligonucleotide microarrays, 78 genes were identified that had an altered pattern of expression after NGF withdrawal from neuronal PC6-3 cells. One of the induced genes, ATF-3, a basic/leucine zipper transcription factor that can dimerise with c-Jun, was confirmed as an up-regulated transcript during PC6-3 cell apoptosis and this occurred after the induction of c-Jun. In sympathetic neurons, atf-3 RNA and protein levels increase between 8 and 16 hours after NGF withdrawal and remain elevated at 24 hours. This protein induction occurs after that of c-Jun and is inhibited by the c-Jun N-terminal kinase inhibitor SP600125 and the mixed-lineage kinase (MLK) inhibitor CEP-11004. This suggests that induction of ATF-3 may require JNK activity in neurons and that the atf-3 gene might be a target of c-Jun. The function of ATF-3 in sympathetic neurons was investigated in microinjection experiments. Injection of expression vectors for c-Jun and ATF-3 decreased the survival of sympathetic neurons in the presence of NGF, as measured at 72 hours after injection. In contrast, overexpression of ATF-3 or the ATF-3 basic/leucine zipper domain in the absence of NGF increased the survival of sympathetic neurons. In addition, when ATF-3 expression was knocked down, using a pSUPER ATF-3 RNAi expression vector, the amount of cell death observed after 48 hours of NGF deprivation in neurons was increased.
29
Epstein, Jason R. "Fiber optic microsphere-based oligonucleotide arrays : new developments and applications /". Thesis, Connect to Dissertations & Theses @ Tufts University, 2004.
Cerca il testo completoAbstract (sommario):
Thesis (Ph.D.)--Tufts University, 2004.Adviser: David R. Walt. Submitted to the Dept. of Chemistry. Includes bibliographical references. Access restricted to members of the Tufts University community. Also available via the World Wide Web;
30
Butler, M. J. "Identification of region-specific targets of wingless signalling in Drosophila melanogaster using oligonucleotide microarrays". Thesis, University of Sussex, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.559237.
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Tomascik-Cheeseman, Lisa Marie. "Gene expression profiling in prepubertal and adult male mice using cDNA and oligonucleotide microarrays". Morgantown, W. Va. : [West Virginia University Libraries], 2003. http://etd.wvu.edu/templates/showETD.cfm?recnum=2813.
Testo completoAbstract (sommario):
Thesis (Ph. D.)--West Virginia University, 2003.Title from document title page. Document formatted into pages; contains xiii, 180 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 138-151).
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Franck, William L. Stacey Gary. "Development and validation of a DNA microarray for analysis of the Bradyrhizobium japonicum transcriptome". Diss., Columbia, Mo. : University of Missouri--Columbia, 2009. http://hdl.handle.net/10355/6884.
Testo completoAbstract (sommario):
Title from PDF of title page (University of Missouri--Columbia, viewed on Feb 24, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Dissertation advisor: Dr. Gary Stacey. Vita. Includes bibliographical references.
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Furtado, Linda Michelle. "Interfacial oligonucleotide chemistry studied by an on-line biosensor, radiochemical labelling and nucleic acid microarrays". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ63600.pdf.
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Rivera, Brugués Núria. "Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarrays". Doctoral thesis, Universitat de Barcelona, 2012. http://hdl.handle.net/10803/81745.
Testo completoAbstract (sommario):
Genomic microarray analysis is rapidly replacing conventional chromosome analysis by molecular karyotyping due to the significant increase in the power to detect causative CNVs. Here, we extensively validated the HumanHap550 and Human610-Quadv1_B Illumina platforms for potential diagnostic application by using patients with undiagnosed intellectual disability (ID). The first and foremost goal of our application study was to use these arrays for reliable genome wide detection of rare CNVs in patients of three different cohorts: 1) patients with unexplained intellectual disability 2) patients with unknown diffuse congenital hyperinsulinism (CHI) and 3) a family with a distinctive diagnosis of Holt-Oram syndrome (HOS).
We showed that SNP-based arrays allow the detection of intragenic deletions and duplications. The identification of a disease-CNV affecting only a single gene allowed us to consider that particular gene as a candidate for intellectual disability. This was the case for three unrelated patients with moderate intellectual disability, global developmental delay, and severe speech and language disorders in which a de novo deletion encompassing solely the FOXP1 gene was detected. To prove further the causality of the FOXP1 deletion following-up investigations were based on a screening of the entire coding region of FOXP1 for nucleotide changes in a panel of 883 probands with intellectual disability. Eight non-synonymous coding changes, three synonymous and nine non-coding variants were identified.
In addition to the de novo cases of ID, also patients suffering from an autosomal recessive form of ID were found in our cohort. We detected three partial heterozygous deletions of the COH1 gene at locus 8q22 which is mutated in Cohen syndrome. After sequencing the entire coding region and the exon/intron boundaries of COH1 we identified a stop mutation, a frameshift and two missense mutations in the remaining allele, respectively. Therefore, three compound heterozygous mutations were identified in the COH1 gene, thus providing a distinctive Cohen Syndrome diagnose to three unrelated patients of our ID cohort.
We studied the genetic basis of a rare human autosomal disorder such as diffuse Congenital Hyperinsulinsm (CHI) in a cohort of 40 patients with inconspicuous mutation screening of ABCC8 and KCNJ11 genes.
Chromosomal abnormalities detected by SNP oligonucleotide arrays accounted for 20% of the studied cases. The most interesting rearrangement was a 970kb deletion at the chromosomal band 1p31.1 which was found to encompass the PTGER3 and ZRANB2 genes and the last exon of the NEGR1 gene. We hypothesized that the haploinsufficiency of PTGER3 gene induces a 50% reduction of the stimulation by PGE2, thus diminishing the inhibition of glucose-stimulated insulin secretion (GSIS) and resulting in elevated insulin secretion. The screening for point mutations in the candidate gene PTGER3 did not reveal any pathogenic variant neither in the second allele of the patient in which a de novo deletion was detected nor in a cohort of 39 unrelated patients with unexplained CHI. Instead we identified a novel polymorphic variant which was also detected in 18 individuals of our control cohort.
CNV analysis in a family with both atypical Holt-Oram syndrome and additional mammary glands was performed allowing the detection of a contiguous heterozygous duplication at the chromosomal band 12q24.21. The maximal duplication size could be estimated as aproximately 345,6kb including the whole coding region of the TBX5 and TBX3 genes. Gene dosage assessment at specific genetic loci demonstrated the cosegregation of the duplication and the Holt-Oram syndrome/supernumerary mammary glands phenotype in this pedigree, this being a strong indicator of its pathogenecity. Up to date, this is the first report of a heterozygous duplication encompassing both TBX5 and TBX3 genes, and consequently the first report of a combined phenotype of Holt-Oram syndrome and supernumerary mammary glands.
35
Edwards, Jeremy, Jaroslav Janda, Megan Sweeney, Ambika Gaikwad, Bin Liu, Hei Leung e David Galbraith. "Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice". BioMed Central, 2008. http://hdl.handle.net/10150/610235.
Testo completoAbstract (sommario):
BACKGROUND:We report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model. In contrast to methods employing whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features.RESULTS:We have produced a genotyping microarray for rice, comprising 880 single feature polymorphism (SFP) elements derived from insertions/deletions identified by aligning genomic sequences of the japonica cultivar Nipponbare and the indica cultivar 93-11. The SFPs were experimentally verified by hybridization with labeled genomic DNA prepared from the two cultivars. Using the genotyping microarrays, we found high levels of polymorphism across diverse rice accessions, and were able to classify all five subpopulations of rice with high bootstrap support. The microarrays were used for mapping of a gene conferring resistance to Magnaporthe grisea, the causative organism of rice blast disease, by quantitative genotyping of samples from a recombinant inbred line population pooled by phenotype.CONCLUSION:We anticipate this microarray-based genotyping platform, based on its low cost-per-sample, to be particularly useful in applications requiring whole-genome molecular marker coverage across large numbers of individuals.
36
Shippy, Richard, Timothy Sendera, Randall Lockner, Chockalingam Palaniappan, Tamma Kaysser-Kranich, George Watts e John Alsobrook. "Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations". BioMed Central, 2004. http://hdl.handle.net/10150/610395.
Testo completoAbstract (sommario):
BACKGROUND:Despite the widespread use of microarrays, much ambiguity regarding data analysis, interpretation and correlation of the different technologies exists. There is a considerable amount of interest in correlating results obtained between different microarray platforms. To date, only a few cross-platform evaluations have been published and unfortunately, no guidelines have been established on the best methods of making such correlations. To address this issue we conducted a thorough evaluation of two commercial microarray platforms to determine an appropriate methodology for making cross-platform correlations.RESULTS:In this study, expression measurements for 10,763 genes uniquely represented on Affymetrix U133A/B GeneChips(R) and Amersham CodeLinkTM UniSet Human 20 K microarrays were compared. For each microarray platform, five technical replicates, derived from the same total RNA samples, were labeled, hybridized, and quantified according to each manufacturers' standard protocols. The correlation coefficient (r) of differential expression ratios for the entire set of 10,763 overlapping genes was 0.62 between platforms. However, the correlation improved significantly (r = 0.79) when genes within noise were excluded. In addition to levels of inter-platform correlation, we evaluated precision, statistical-significance profiles, power, and noise levels for each microarray platform. Accuracy of differential expression was measured against real-time PCR for 25 genes and both platforms correlated well with r values of 0.92 and 0.79 for CodeLink and GeneChip, respectively.CONCLUSIONS:As a result of this study, we recommend using only genes called 'present' in cross-platform correlations. However, as in this study, a large number of genes may be lost from the correlation due to differing levels of noise between platforms. This is an important consideration given the apparent difference in sensitivity of the two platforms. Data from microarray analysis need to be interpreted cautiously and therefore, we provide guidelines for making cross-platform correlations. In all, this study represents the most comprehensive and specifically designed comparison of short-oligonucleotide microarray platforms to date using the largest set of overlapping genes.
37
Wong, Chi-wai. "High resolution mapping of loss of heterozygosity and chromosomal aberrations using oligonucleotide single nucleotide polymorphism genotyping arrays in colorectal adenoma to carcinoma progression". Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B3871923X.
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Neves, Carlos Eduardo. "Experimentos de microarrays e teoria da resposta ao item". Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/45/45133/tde-24052010-140944/.
Testo completoAbstract (sommario):
Recentemente desenvolvida, a biotecnologia denominada por Microarrays permite o monitoramento simultâneo dos valores de expressão gênica de centenas de milhares de genes, fator este que traz uma nova interpretação aos resultados obtidos em pesquisas desenvolvidas nas mais diversas áreas do conhecimento incluindo, por exemplo, a Farmacologia e Medicina, uma vez que os resultados obtidos são interpretados ao nível molecular. Contudo, apesar de muita tecnologia ser empregada à técnica de Microarrays, sua aplicação ainda ocasiona algumas complicações decorrentes, por exemplo, das inúmeras fontes de variação existentes, da escala das respostas ou da natural dificuldade de se analisar uma grande quantidade de fragmentos genéticos avaliados sob poucas unidades experimentais. Frente a estas complicações, atualmente, muitas são as propostas metodológicas de análises estatísticas para atenuar ou eliminar os problemas inerentes à técnica de Microarrays e propiciar a extração de resultados mais confiáveis a partir dos valores de expressão gênica, porém muitos desafios ainda persistem. Sob esta colocação, o presente trabalho procurou explorar duas metodologias de análise estatística alternativas no que diz respeito a seus conceitos, embora ambas tenham sido contextualizadas ao problema de Microarrays e aplicadas para se atingir o mesmo objetivo: possibilitar a identificação dos genes diferencialmente expressos sob distintas condições experimentais. A primeira metodologia consistiu da aplicação de Modelos de Análise de Variância de efeitos fixos com a adoção de modificações nas estatísticas de teste, metodologias de correções para múltiplos testes e a construção de gráficos vulcão. Já, a segunda metodologia consistiu da contextualização e aplicação da Teoria da Resposta ao Item TRI aos experimentos de Microarrays, abordagem esta pouco explorada na análise deste tipo de dado, mas a qual possibilita a seleção de genes diferencialmente expressos a partir de uma medida latente estimada para cada gene e a construção de uma escala para as categorias de resposta de expressão gênica. A motivação para este trabalho originou de um experimento de Microarrays com ratos congênicos disponibilizado pelo Laboratório de Cardiologia e Genética Molecular do Instituto do Coração (InCor-USP) cujo objetivo é identificar genes associados à hipertensão.Recently developed, the biotechnology denominated Microarrays permits a simultaneous monitoring of the gene expression values of hundred thousands of genes; fact that introduces a new interpretation of the results obtained in researches developed in many distinct areas including, for example, Pharmacology and Medicine, once the obtained results are read according to the molecular level. However, despite the fact that much technology is used in the Microarrays technique, its application still causes some implications, for example, the countless sources of existing variance, the scale of answers or the natural difficulty in analyzing a large number of genetic fragments measured by few experimental units. Facing such complications, a lot of methodologies were suggested in order to reduce or eliminate the problems caused by the Microarrays technique and also foster the obtainment of more reliable results from the gene expression values, yet many challenges still persist. Under this perspective, the present work aimed at exploring two alternative methodologies regarding concepts, despite both were contextualized according to the Microarrays problem and applied with the same objective: enabling the identification of the genes differently expressed under different experimental conditions. The first methodology was composed by the application of Analysis of Variance Models of fixed effects with changes in the test statistics, correction methodologies for multiple tests and volcano plot. The second methodology consisted of the contextualization and application of the Item Response Theory IRT towards the Microarrays experiments, being this one not much explored in analysis that use this kind of data, but enabling the selection of genes differently expressed from an estimated latent trait for each gene and the construction of a scale for the categories of gene expression answers. The motivation for the present work came from an experiment of Microarrays with congenic mice made available by the Cardiology and Molecular Genetics Laboratory of the Heart Institute (InCor-USP) that aimed at identifying genes associated with hypertension.
39
Wong, Chi-wai, e 黃志偉. "High resolution mapping of loss of heterozygosity and chromosomal aberrations using oligonucleotide single nucleotide polymorphismgenotyping arrays in colorectal adenoma to carcinoma progression". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B3871923X.
Testo completo
40
Tort, Escribà Núria. "Desenvolupament d’una plataforma universal per a la multidetecció mitjançant la codificació espaial de cadenes d’ADN". Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/128670.
Testo completoAbstract (sommario):
Aquesta tesi ha estat focalitzada en demostrar la possibilitat de crear plataformes de diagnòstic,
multiplexades i universals, a través de la hibridació de cadenes d'oligonucleòtids complementàries (DNA-directed immobilization, DDI). La multiplexació és possible degut al gran nombre de cadenes d'oligonucleòtids diferents que es poden crear al combinar les 4 bases nitrogenades de l'ADN (A, T, C i G), permetent detectar simultàniament tants analits diferents com cadenes d’oligonucleòtids es disposi. La universalitat, be donada per la possibilitat de regenerar una superfície amb una simple etapa de deshibridació, i reutilitzar-la per a la detecció d’analits de diferent naturalesa. Concretament, s'ha demostrat la possibilitat de crear microarrays d'haptens, emprant microarrays d'ADN i aprofitant l'especificitat de la reacció d'hibridació entre les cadenes d’oligonucleòtids immobilitzades en la superfície i les cadenes d'oligonucleòtids unides covalentment als diferents haptens. Com a prova de concepte, s'ha desenvolupat un microarray d’haptens esteroïdals per a l'anàlisi quantitatiu i multiplexat d'hormones anabolitzants amb detecció fluorescent. També s'ha demostrat la possibilitat d'utilitzar aquesta estratègia d'immobilització pel desenvolupament d'immunosensors òptics multiplexats basats en la ressonància del plasmó superficial per imatge (SPRi), evitant així la necessitat d’emprar marcadors per tal d’obtenir el senyal. Per altra banda, s'ha demostrat la universalitat de l'estratègia DDI, al emprar un microarray d'ADN per a la creació de superfícies nanoestructurades, posteriorment emprades com a transductors en immunosensors basats en la ressonància del plasmó superficial localitzat (LSPR). Concretament, cadenes d'oligonucleòtids han estat unides a nanopartícules d'or de diferents mides, que després han estat immobilitzades de forma controlada i selectiva sobre la plataforma, a través de la hibridació entre les cadenes d’oligonucleòtids complementàries. I finalment, també s’ha demostrat l’aplicabilitat de l’estratègia DDI per a la immobilització de proteïnes, al crear microarrays d’anticossos, en format estàtic i en flux, que han estat emprats per a la diferenciació de cèl•lules segons les proteïnes expressades en la membrana cel•lular.
41
Green, Roland Daniel. "Oligonucleotide microarray synthesis with a micromirror array". 1999. http://catalog.hathitrust.org/api/volumes/oclc/45371129.html.
Testo completoAbstract (sommario):
Thesis (Ph. D.)--University of Wisconsin--Madison, 1999.Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 132-141).
42
Zhang, Mingquan. "Label-free Detection of Oligonucleotide Microarrays by the Scanning Kelvin Nanoprobe". Thesis, 2008. http://hdl.handle.net/1807/17252.
Testo completoAbstract (sommario):
The Kelvin measurement is a sensitive and label-free method based on work function measurements. Work function, the minimum energy required to extract an electron from a metallic material, can be shifted by ionic charges and dipoles present on the surface. The scanning Kelvin nanoprobe (SKN), a probe-based microscopic imaging device, was used in the detection of work function changes induced by surface-immobilized oligonucleotide / DNA microarrays.
The scanning Kelvin nanoprobe was able to study DNA microarrays smaller than 100 µm in size, produced with solution concentrations lower than 10 µmol/L. The limit of detection was estimated to be 15 ng DNA. Better than ± 10% relative variation was achieved for replicate spots. It was observed that higher surface densities of immobilized DNA molecules produced greater work function changes than lower surface densities. Surface saturation with increasing solution concentrations was observed as well. Also, longer strands of DNA produced greater work function changes than shorter strands. Statistical analysis of the results confirmed that non-complementary DNA strands could be differentiated from complementary strands by the Kelvin measurement. Single base mismatches on the complementary DNA strands were also detected by the Kelvin measurement.
Different substrate materials were tested in the search for reliable and inexpensive sample slides with satisfactory DNA immobilization efficiency. Materials such as silicon wafers, gold-coated glass slides, gold-coated stainless steel slides, and gold compact discs (CD) were tested. A surface property comparison of gold-coated glass slides and compact discs was made by atomic force microscopy (AFM), and revealed very different microscopic features. The effect of cleaning on gold-coated glass slides was examined by time-of-flight secondary ion mass spectrometry (TOF-SIMS). Technical improvements were made to the SKN equipment progressively. Several revisions to the tip holder design have been employed for better electromagnetic shielding, enhanced robustness and easier tip change. An older signal generator was replaced with a professional PC audio card to provide more stable signal and more convenient on-screen fine tuning, also at a reduced cost. The Labview-based controlling program has also been improved through multiple iterations.
43
Naiser, Thomas. "Characterization of oligonucleotide microarray hybridization microarray fabrication by light-directed in situ synthesis - development of an automated DNA microarray synthesizer, characterization of single base mismatch discrimination and the position-dependent influence of point defects on oligonucleotide duplex binding affinities /". 2008. http://opus.ub.uni-bayreuth.de/volltexte/2008/461/.
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Wu, Hsiao-Ping, e 吳小萍. "A Simulation Study on High Density Oligonucleotide Microarray Data With Discussion of Normalization Methods". Thesis, 2006. http://ndltd.ncl.edu.tw/handle/44101881971131726522.
Testo completoAbstract (sommario):
碩士國立政治大學
統計研究所
94
Microarray technology is now widely used in many areas of biomedical research. In this thesis, we are interested in the normalization for oligonucleotide Microarray data. We aimed to simulate more realistic oligonucleotide microarry data in order to compare different normalization methods. The data simulation was based on Li and Wong's model with a hierarchical setup for parameters. In order to compare normalization methods, 100 data sets were simulated data. The performance of ten normalization methods was assessed based on four comparison criteria. Simulation results suggest that our new proposed normalization method, LOESS to Average, is generally a better method than other normalization methods.
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Wei, Fnag-Hui, e 魏芳慧. "Transcription Analysis in Asthmatic Children With Han Zheng or Re Zheng by Oligonucleotide Microarray". Thesis, 2005. http://ndltd.ncl.edu.tw/handle/81337360375125127231.
Testo completoAbstract (sommario):
碩士中國醫藥大學
中國醫學研究所
93
Transcription Analysis in Asthmatic Children with Han Zheng or Re Zheng by Oligonucleotide Microarray Fang-Hui Wei Major professor: Shung-Te Kao Institute of Chinese Medical Science, China Medical University Background: Allergic asthma is a chronic inflammatory disease of lungs. It is also a common disease in pediatrics. Asthma results from a complex interplay between genetic and environmental factors. According to traditional Chinese medicine, allergic asthma can be differentiated between Han Zheng and Re Zheng. Objective: To Analyze the gene expression in Asthmatic children with Han Zheng or Re Zheng using oligonucleotide microarray. Methods: Firstly, we designed a pediatrician examination chart for allergic asthma of Han Zheng or Re Zheng. Based on the chart, we recruited typical patients with Han Zheng or Re Zheng asthma. Healthy children were considered as normal controls. Patients’ mRNAs in their peripheral blood were used for microarray analysis. More than 13,000 genes were compared. Pathway of the differentially expressed genes with the bioinformation software on line was investigated. Result: We found there were 170 differentially expressed genes between Han Zheng asthma group (n = 2) and control group (n = 2), including 5 genes with associated pathway (P < 0.05). There were 226 differentially expressed genes between Re Zheng asthma group (n = 4) and the controls (n = 4), including 17 genes with associated pathway (P < 0.05). There were 137 differentially expressed genes between Han Zheng asthma group (n = 4) and Re Zheng asthma group (n = 4), including 8 genes with associated pathway (P < 0.05). Conclusion: The gene expression of allergic asthma could be correlated with immune and Zheng points. We believe that some genes are associated with Han Zheng or Re Zheng. These differentially expressed genes could be potential molecular targets to treat asthma with traditional Chinese medicine. Key words: pediatrics, allergic asthma, Han Zheng, Re Zheng, microarray
46
Naiser, Thomas [Verfasser]. "Characterization of oligonucleotide microarray hybridization : microarray fabrication by light-directed in situ synthesis ; development of an automated DNA microarray synthesizer, characterization of single base mismatch discrimination and the position-dependent influence of point defects on oligonucleotide duplex binding affinities / von Thomas Naiser". 2008. http://d-nb.info/989870049/34.
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Chen, Hsi-Chia, e 陳希嘉. "Study on identification of lactic acid bacteria by denaturing gradient gel electrophoresis and oligonucleotide microarray". Thesis, 2009. http://ndltd.ncl.edu.tw/handle/69162826021385651302.
Testo completoAbstract (sommario):
博士國立臺灣大學
動物科學技術學研究所
97
Lactic acid bacteria (LAB) are widely employed as starter cultures in the dairy industry and supplemented in different commercial products. Detecting and identifying various species of lactic acid bacteria with rapid method is often important for quality control of dairy products and monitoring fermentation processes. However, identification of lactic acid bacteria in the complex bacterial communities is still difficult for both phenotypic methods and genotypic methods. The aim of this study focused on polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and oligonucleotide microarray method to develop a rapid, reproducible and easy to handle molecular tool for identification of lactic acid bacteria in dairy products. For PCR-DGGE, selection of primers is the key to analyze highly conserved genetic profiles among LAB. Four primer sets, targeted for 20 reference LAB strains, were evaluated and primer set GC338f/518r was selected due to its highly discriminating power at species level. After selection of primer sets, LAB in kefir grains and commercial probiotic products were assessed using PCR-DGGE by a culture-independent and a culture-dependent way, and were further confirmed by DNA sequencing techniques. Kefir grains results indicated that a combined method of cultivation with PCR-DGGE and subsequent DNA sequencing could successfully identify four LAB strains, Lactobacillus kefiranofaciens, Lb. kefiri, Leuconostoc mesenteroides and Lactococcus lactis from three kefir grains from Taiwan (named Hsinchu, Mongolia and Ilan). It was interesting to find that all three kefir grains contain similar LAB species. Furthermore, the DGGE as a culture-independent method indicated that Lb. kefiranofaciens was found in all three kefir grains, whereas Lb. kefiri was only observed in Hsinchu kefir grain and Lc. lactis was found in both Mongolia and Ilan samples. Two additional strains, Pseudomonas spp. and E. coli, were also detected in kefir grains. The DGGE profiles for commercial probiotic products demonstrated that the samples contained most lactic acid bacteria that specified on the product label except of the lyophilized mixed starter powder. This may be due to a concentration below the detection limit or due to the fact that none of these bacteria were present in the probiotic product. For microarray method, oligonucleotide probes targeting variable regions of the 16S rRNA gene were designed and tested for the identification of LAB. The strategy involved designing possible oligomer probes, using two software (ARB and PRIMROSE), for each target at species and genus level. All candidate 25-mer probes were poly(T)-tailed to reach an overall length of 60 oligonucleotides. Microarrays were manufactured by in situ synthesis (Agilent Technologies). Eight samples, including 5 pure LAB (Lb. acidophilus, Lc. lactis, Str. thermophilus, Leu. mesenteroides and Bif. animalis), 1 non-targeted stain (B. cereus) and 2 mixed strain, were then assessed. Results indicated that, of the 21438 individual hybridization reaction (3573 validated probes × 6 references strains), 20082 probes (93.67%) yielded the expected result by showing significantly differential signal. Further inspection of each species probe, over 50 % of species probes designed for Lb. acidophilus, Str. thermophilus and Bif. animalis had true-positive signals with target bacteria. Whereas, true-positive signals were lower than 10% for probes designed for Lc. lactis and Leu. mesenteroides. For mixed strain samples, most of significantly positive signals would not be decreased when the amount of target DNA was down to 0.1
48
"DNA microarray analysis in Chinese multiple myeloma". 2008. http://library.cuhk.edu.hk/record=b5893411.
Testo completoAbstract (sommario):
Wong, Ling Yee.Thesis submitted in: August 2007.
Thesis (M.Phil.)--Chinese University of Hong Kong, 2008.
Includes bibliographical references (leaves 110-127).
Abstracts in English and Chinese.
Thesis Abstract --- p.i
論文摘要 --- p.iv
Acknowledgements --- p.vi
Abbreviations --- p.vii
Thesis Content --- p.xii
List of Figures --- p.xv
List of Tables --- p.xvii
Chapter Chapter 1 --- Introduction --- p.1
Chapter Chapter 2 --- Literature Review --- p.3
Chapter 2.1. --- Multiple Myeloma (MM) --- p.3
Chapter 2.1.1 --- Epidemiology --- p.4
Chapter 2.1.2 --- Cause and Risk Factors --- p.5
Chapter 2.1.3 --- Pathophysiology --- p.5
Chapter 2.1.4 --- Diagnosis and Clinical Presentation --- p.6
Chapter 2.1.5 --- Classification of Plasma Cell Disorders --- p.6
Chapter 2.1.5.1 --- Monoclonal Gammopathy of Undetermined Significance (MGUS) --- p.6
Chapter 2.1.5.2 --- Asymptomatic (Smouldering) MM --- p.7
Chapter 2.1.5.3 --- Indolent MM --- p.7
Chapter 2.1.5.4 --- Symptomatic MM --- p.8
Chapter 2.1.6 --- Staging --- p.9
Chapter 2.1.7 --- Treatment --- p.11
Chapter 2.1.8 --- Molecular Abnormality --- p.12
Chapter 2.2 --- DNA Microarray Analysis in MM --- p.13
Chapter 2.2.1 --- MM Pathogenesis --- p.15
Chapter 2.2.2 --- Molecular Classification of MM --- p.18
Chapter 2.2.3 --- Anti-MM Drug Studies --- p.22
Chapter 2.3 --- Cancer Treatment Response Prediction --- p.24
Chapter 2.3.1 --- MP Treatment --- p.24
Chapter 2.3.1.1 --- Melphalan --- p.25
Chapter 2.3.1.2 --- Prednisone --- p.27
Chapter 2.3.1.3 --- MP Treatment Response Prediction in MM --- p.29
Chapter 2.3.2 --- Cancer Prognosis using DNA Microarray --- p.31
Chapter Chapter 3 --- Materials and Methods --- p.36
Chapter 3.1. --- Patient Specimens for Gene Expression Profiling and Quantitative Real-time PCR --- p.36
Chapter 3.2. --- Magnetic Cell Sorting of CD138-positive Plasma Cells --- p.37
Chapter 3.2.1 --- Density Gradient Centrifugation --- p.37
Chapter 3.2.2 --- Positive Selection of CD138-positive Cells --- p.37
Chapter 3.3 --- Generation of Gene Expression Profiles --- p.39
Chapter 3.3.1 --- RNA Extraction --- p.39
Chapter 3.3.2 --- RNA Assessment --- p.40
Chapter 3.3.3 --- Synthesis and Purification of Double-strand cDNA --- p.40
Chapter 3.3.4 --- In vitro Transcription (IVT) and Recovery of Biotin-labeled cRNA --- p.41
Chapter 3.3.5 --- cRNA Fragmentation and Hybridization Reaction Mixture Preparation --- p.41
Chapter 3.3.6 --- Hybridization --- p.42
Chapter 3.3.7 --- Post-hybridization Wash --- p.42
Chapter 3.3.8 --- Detection with Streptavidin-dye Conjugate --- p.43
Chapter 3.3.9 --- Bioarray Scanning and Spot Signal Quantitation --- p.43
Chapter 3.4 --- Microarray Data Analysis --- p.45
Chapter 3.4.1 --- Normalization and Filtering --- p.45
Chapter 3.4.2 --- Unsupervised Clustering Analysis --- p.45
Chapter 3.4.3 --- Supervised Class Comparison Analysis --- p.46
Chapter 3.5 --- Microarray Verification and Candidate Gene Validation --- p.47
Chapter 3.5.1 --- RNA Extraction --- p.47
Chapter 3.5.2 --- Reverse Transcription PCR --- p.47
Chapter 3.5.3 --- Quantitative Real-time PCR --- p.48
Chapter 3.6 --- Predictive Value Calculation --- p.49
Chapter 3.7 --- Experimental Flow --- p.49
Chapter Chapter 4 --- Results --- p.53
Chapter 4.1 --- Gene Expression Profiling of Chinese MM --- p.53
Chapter 4.1.1 --- Unsupervised Clustering Analysis --- p.53
Chapter 4.1.1.1 --- Hierarchical Clustering --- p.53
Chapter 4.1.1.2 --- Principal Component Analysis (PCA) --- p.54
Chapter 4.1.2 --- Identification of Statistically Differentially Expressed Genes --- p.58
Chapter 4.1.2.1 --- Two-Sample t-statistics --- p.58
Chapter 4.1.2.2 --- Significance Analysis of Microarrays (SAM) --- p.58
Chapter 4.1.2.3 --- Microarray Verification --- p.66
Chapter 4.2 --- Development of MP Treatment Response Biomarker in MM --- p.70
Chapter 4.2.1 --- Unsupervised Clustering Analysis --- p.70
Chapter 4.2.1.1 --- Hierarchical Clustering --- p.70
Chapter 4.2.1.2 --- PCA --- p.70
Chapter 4.2.2 --- Identification of Statistically Differentially Expressed Genes --- p.74
Chapter 4.2.2.1 --- Two sample t-statistics --- p.74
Chapter 4.2.2.2 --- SAM --- p.74
Chapter 4.2.3 --- Verification of Candidate Gene CYB5D1 --- p.76
Chapter Chapter 5 --- Discussion --- p.79
Chapter 5.1 --- Global Gene Expression Profiling: DNA Microarray --- p.79
Chapter 5.2 --- Microarray Data Normalization and Gene Filtering --- p.81
Chapter 5.3 --- Microarray Data Analysis --- p.83
Chapter 5.3.1 --- Unsupervised Clustering Analysis --- p.83
Chapter 5.3.1.1 --- Hierarchical Clustering --- p.83
Chapter 5.3.1.2 --- PCA --- p.85
Chapter 5.3.2 --- Identification of Statistically Differentially Expressed Genes --- p.86
Chapter 5.4 --- Verification of Candidate Genes by Quantitative Real-time PCR --- p.89
Chapter 5.5 --- Gene Expression Profiling of Chinese MM --- p.90
Chapter 5.5.1 --- Comparison of Gene Expression Patterns of MM and Normal Plasma Cells --- p.90
Chapter 5.5.2 --- Differentially Expressed Genes between MM and Normal Plasma Cells..… --- p.91
Chapter 5.5.2.1 --- Common Differentially Expressed Genes with Previous Studies --- p.94
Chapter 5.5.2.2 --- Potential Tumor Suppressor Genes in Differentially Expressed Genes..… --- p.96
Chapter 5.5.2.3 --- Verified Differentially Expressed Genes --- p.98
Chapter 5.5.3 --- Future Studies --- p.101
Chapter 5.6 --- Development of MP Treatment Response Biomarker in MM --- p.103
Chapter 5.6.1 --- Comparison of Gene Expression Patterns of MP Good Responders (GR) and Poor Responders (PR) --- p.103
Chapter 5.6.2 --- Differentially Expressed Gene between MP GR and PR: CYB5D1 --- p.104
Chapter 5.6.3 --- Possible Role of CYB5D1 in MP Resistance in MM Cells --- p.104
Chapter 5.6.4 --- Potential Clinical Application of CYB5D1 in MP Treatment Response Prediction in MM --- p.106
Chapter 5.6.5 --- Future Studies --- p.106
Chapter Chapter 6 --- Conclusion --- p.108
Chapter 6.1 --- Gene Expression Profiling of Chinese MM --- p.108
Chapter 6.2 --- Development of MP Treatment Response Biomarker in MM --- p.108
References --- p.110
Appendix --- p.128
49
"DNA microarray for authentication of medicinal dendrobium species". 2003. http://library.cuhk.edu.hk/record=b6073616.
Testo completoAbstract (sommario):
by Zhang Yanbo."December 2003."
Thesis (Ph.D.)--Chinese University of Hong Kong, 2003.
Includes bibliographical references (p. 163-185).
Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
Mode of access: World Wide Web.
Abstracts in English and Chinese.
50
Chi, Tin-Ling, e 紀廷霖. "Development and Evaluation of an Oligonucleotide Microarray-based Assay for the Detection of Fungal Pathogens in Lily". Thesis, 2007. http://ndltd.ncl.edu.tw/handle/48596720285495988406.
Testo completoAbstract (sommario):
碩士國立嘉義大學
生物科技研究所
95
Several fungal pathogens, including Fusarium oxysporum f. sp. lilii, Phytophthora parasitica, Sclerotium rolfsii, Rhizotonia solani, and Botrytis elliptica, could significently affect the yield and quality of lily production. The identification and detection of these fungal pathogens in lily become important for plant health inspection and quarantine control of lily. In the present study, an oligonucleotide microarry-based system was developed and evaluated for the detection of major fungal pathogens in lily. The intergenic spacer (IGS) regions of the rRNA were amplified, cloned, and sequenced. These sequences were submitted to NCBI Genebank database and acquired accession numbers (EF648219, EF661646, EF661647, EF661648, EF661649). In the blast results of these IGS sequence, we find many Fusarium spp. IGS in database. Compared with the 81.2-88.8% identity of different Fusarium species, the 94.6-99.8% identity of different Fusarium oxysporum forma pecialis is hight .In this study we could indentify different Fusarium species by 5 mer mismatch oligonucleotide probe. At present, There are four sequence of Botrytis IGS in NCBI Genebank database, including two Botrytis elliptica, B. tulipae,and B. cinerea. Compared to each other identity are between 74.6-99.5%. there are no blast result in Phytophthora cinnamomi, Rhizoctonia solani ,and Sclerotium rolfsii IGS in the database. Compared to each genus IGS identity are low between 30.5-42.6%. Based on the sequences of IGS region, 60 mer long oligonucleotides specific to those lily fungal pathogens were designed. A total of 15 oligonucleotide probes were synthesized to fabricate the oligonucleotide microarray, followed by testing in the viii specificities as hybridized to the dig-labeled rDNA fragments from tested pathogens and lily tissues infected by different fungal pathogens. The results in the present study showed the microarray-based assay could efficiently identify fungal pathogens in lily, and represented a rapid and reliable method for potential applications in quarantine investigation. Key words : lily fungal pathogens, intergenic spacer, microarray, detection, oligonucleotide probes