Rozprawy doktorskie na temat „Gene technology”
Kliknij ten link, aby zobaczyć inne rodzaje publikacji na ten temat: Gene technology.
Utwórz poprawne odniesienie w stylach APA, MLA, Chicago, Harvard i wielu innych
Sprawdź 50 najlepszych rozpraw doktorskich naukowych na temat „Gene technology”.
Przycisk „Dodaj do bibliografii” jest dostępny obok każdej pracy w bibliografii. Użyj go – a my automatycznie utworzymy odniesienie bibliograficzne do wybranej pracy w stylu cytowania, którego potrzebujesz: APA, MLA, Harvard, Chicago, Vancouver itp.
Możesz również pobrać pełny tekst publikacji naukowej w formacie „.pdf” i przeczytać adnotację do pracy online, jeśli odpowiednie parametry są dostępne w metadanych.
Przeglądaj rozprawy doktorskie z różnych dziedzin i twórz odpowiednie bibliografie.
1
Busby, Michele Anne. "Measuring Gene Expression With Next Generation Sequencing Technology". Thesis, Boston College, 2012. http://hdl.handle.net/2345/3145.
Pełny tekst źródłaStreszczenie:
Thesis advisor: Gabor MarthWhile a PhD student in Dr. Gabor Marth's laboratory, I have had primary responsibility for two projects focused on using RNA-Seq to measure differential gene expression. In the first project we used RNA-Seq to identify differentially expressed genes in four yeast species and I analyzed the findings in terms of the evolution of gene expression. In this experiment, gene expression was measured using two biological replicates of each species of yeast. While we had several interesting biological findings, during the analysis we dealt with several statistical issues that were caused by the experiment's low number of replicates. The cost of sequencing has decreased rapidly since this experiment's design and many of these statistical issues can now practically be avoided by sequencing a greater number of samples. However, there is little guidance in the literature as to how to intelligently design an RNA-Seq experiment in terms of the number of replicates that are required and how deeply each replicate must be sequenced. My second project, therefore, was to develop Scotty, a web-based program that allows users to perform power analysis for RNA-Seq experiments. The yeast project resulted in a highly accessed first author publication in BMC Genomics in 2011. I have structured my dissertation as follows: The first chapter, entitled General Issues in RNA-Seq, is intended to synthesize the themes and issues of RNA-Seq statistical analysis that were common to both papers. In this section, I have discussed the main findings from the two papers as they relate to analyzing RNA-Seq data. Like the Scotty application, this section is designed to be "used" by wet-lab biologists who have a limited background in statistics. While some background in statistics would be required to fully understand the following chapters, the essence of this background can be gained by reading this first chapter. The second and third chapters contain the two papers that resulted from the two RNA-Seq projects. Each chapter contains both the original manuscript and original supplementary methods and data section. Finally, I include brief summaries of my contributions to the two papers on which I was a middle author. The first was a functional analysis of the genomic regions affected by mobile element insertions as a part of Chip Stewart's paper with the 1000 Genome Consortium. This paper was published in Plos Genetics. The second was a cluster analysis of microarray gene expression in Toxoplasma gondii, which was included as part of Alexander Lorestani et al.'s paper, Targeted proteomic dissection of Toxoplasma cytoskeleton sub-compartments using MORN1. This paper is currently under review. The yeast project was a collaborative effort between Jesse Gray, Michael Springer, and Allen Costa at Harvard Medical School, Jeffery Chuang here at Boston College, and members of the Marth lab. Jesse Gray conceived of the project. While I wrote the draft for the manuscript, many people, particularly Gabor Marth, provided substantial guidance on the actual text. I conceived of and implemented Scotty and wrote its manuscript with only editorial assistance from my co-authors. I produced all figures for the two manuscripts. Chip Stewart provided extensive guidance and mentorship to me on all aspects of my statistical analyses for both projects
Thesis (PhD) — Boston College, 2012
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
2
Heywood, Jacqualine, i n/a. "'Talking' and 'doing' gene technology politics: a policy analysis". Griffith University. Australian School of Environmental Studies, 2004. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20041029.100010.
Pełny tekst źródłaStreszczenie:
This thesis explores the environmental politics surrounding agricultural biotechnology innovations and diffusion. Recent developments in agricultural biotechnology are accompanied by growing social concerns that such innovations pose risks to the environment and to human health. Biosafety is a term used to discuss the possibility of such risks. Currently, the regulation of agricultural gene-technology and biosafety are contentious environmental issues for national and international policy communities. However, detailed studies of the conflicts and complexities generated by biotechnology for environmental governance are scarce. In particular, little is understood of the ways in which biotechnology issues emerge on regulatory agendas, and research gaps remain on how differing perspectives of biotechnological risks impact on policy outcomes. This thesis makes a significant contribution to these outstanding research issues. My contribution is a new analytical framework that unearths the discursive role biotechnology plays in constructing international environmental policy regimes. I develop this framework on the understanding that the use of language resources like storylines, metaphors and other rhetorical devices are critical in shaping environmental policy in general and biotechnology governance in particular. This analytical framework couples a language analysis to an investigation of the practices of institutional power. The result is a discourse analysis that provides important and useful insights into the theory and practice of biosafety policy. In other words, my thesis explores both the talking and the doing of policymaking and thereby provides new insights into the contested and uncertain environmental policy area of international gene-technology regulation. Specifically, I undertake a discourse analysis of international biosafety politics within the Convention on Biological Diversity. I apply my discourse analysis to a case study: the Cartagena Protocol on Biosafety to the Convention on Biological Diversity, 2000. My research provides a different reading of international gene-technology politics, one that questions the constructed nature of biotechnology as a policy problem and reveals the power relations involved in producing particular policy options and outcomes on biosafety. There are a number of key research findings that emerged from the application of my discursive analytical framework to the Cartagena Protocol on Biosafety. I find that biosafety is a highly fluid concept. It can enlarge or contract depending on the way in which language resources are mobilised by policy actors and interest groups to secure definitions and generate consensus around their preferred understandings of biosafety. Moreover, my research indicates that the more radical texts for biosafety can be recast by dominant interest groups into scripts for shallow reform agendas. Institutionalised policy practices also effect policy outcomes. My research finds that the use of Expert Panels, for example, is important in shaping international policy communities understanding of the policy problems posed by biotechnology risks. In the light of these findings, my thesis argues that the ability of interest groups and policy actors to win language games within institutional settings also enables them to secure their preferred policy outcomes. I import the concept of authorship as a new policy concept to discuss the ways in which such groups exercise social power to secure their understanding of biosafety, which thereby effect the writing of the dominant accounts of what constitutes an acceptable international biosafety standard within the Cartagena Protocol. In short, my thesis is a new account of biosafety politics that fills some of the current knowledge gaps about how biotechnology is emerging onto regulatory agendas. It also demonstrates the mechanisms of power and the language struggles that determine biosafety policy outcomes within multi-lateral environmental agreements such as the Convention on Biological Diversity.
3
Naujoks, Daniel. "Developing a gene targeting technology for Anopheles gambiae mosquitoes". Thesis, Imperial College London, 2012. http://hdl.handle.net/10044/1/9864.
Pełny tekst źródłaStreszczenie:
Studying gene function in the human malaria vector Anopheles gambiae is the key to understanding its biology and vector-parasite interactions. Existing tools to study gene function do not include gene targeting, which would allow insights into gene function by permitting a range of specific modifications to any gene of choice. Based on developments in Drosophila (RONG and GOLIC 2000) this PhD project proposes to establish a method for gene targeting in Anopheles by homologous recombination, using a linear targeting construct generated in vivo. To this end, a transgenic strain was generated that expresses FLP recombinase and I-SceI endonuclease under the control of the germline-specific vasa promoter. Together they were to excise and linearise a targeting molecule from a transgenic “donor” locus. Homology in the targeting construct would enable integration, via recombination in the germline, at a gene of interest, thereby permitting its targeted modification. Expression of vasa-driven I-SceI resulted in high cleavage activity in the germline. A systematic analysis using a variety of transgenic target loci revealed that homologous repair, rather than non-homologous end joining, was the predominant mechanism employed to repair the double stranded breaks generated by I-SceI. These findings offer encouraging prospects for population genetic engineering using homing endonuclease genes (BURT 2003). FLP activity was shown in Anopheles cell culture, yet in vivo excision via FLP at two independent loci in the germline was not observed, precluding the obtainment of a knock-out. After eliminating many possible sources of error, likely causes include antagonistic interference between I-SceI and FLP or unfavourable reaction kinetics of FLP. Examination of the ortholog of Drosophila yellow-g1 as a target gene suggests it is required somatically for female fertility, making it a good candidate for vector population control with a genetic drive system based on homing endonuclease genes. Furthermore, the above finding that recombination is promoted by endonuclease activity driven by the vasa promoter augurs well for its use in mediating efficient drive in such a system.
4
Heywood, Jacqualine. "'Talking' and 'doing' gene technology politics: a policy analysis". Thesis, Griffith University, 2004. http://hdl.handle.net/10072/365762.
Pełny tekst źródłaStreszczenie:
This thesis explores the environmental politics surrounding agricultural biotechnology innovations and diffusion. Recent developments in agricultural biotechnology are accompanied by growing social concerns that such innovations pose risks to the environment and to human health. Biosafety is a term used to discuss the possibility of such risks. Currently, the regulation of agricultural gene-technology and biosafety are contentious environmental issues for national and international policy communities. However, detailed studies of the conflicts and complexities generated by biotechnology for environmental governance are scarce. In particular, little is understood of the ways in which biotechnology issues emerge on regulatory agendas, and research gaps remain on how differing perspectives of biotechnological risks impact on policy outcomes. This thesis makes a significant contribution to these outstanding research issues. My contribution is a new analytical framework that unearths the discursive role biotechnology plays in constructing international environmental policy regimes. I develop this framework on the understanding that the use of language resources like storylines, metaphors and other rhetorical devices are critical in shaping environmental policy in general and biotechnology governance in particular. This analytical framework couples a language analysis to an investigation of the practices of institutional power. The result is a discourse analysis that provides important and useful insights into the theory and practice of biosafety policy. In other words, my thesis explores both the ‘talking’ and the ‘doing’ of policymaking and thereby provides new insights into the contested and uncertain environmental policy area of international gene-technology regulation. Specifically, I undertake a discourse analysis of international biosafety politics within the Convention on Biological Diversity. I apply my discourse analysis to a case study: the Cartagena Protocol on Biosafety to the Convention on Biological Diversity, 2000. My research provides a different reading of international gene-technology politics, one that questions the constructed nature of biotechnology as a policy problem and reveals the power relations involved in producing particular policy options and outcomes on biosafety. There are a number of key research findings that emerged from the application of my discursive analytical framework to the Cartagena Protocol on Biosafety. I find that biosafety is a highly fluid concept. It can enlarge or contract depending on the way in which language resources are mobilised by policy actors and interest groups to secure definitions and generate consensus around their preferred understandings of biosafety. Moreover, my research indicates that the more radical texts for biosafety can be recast by dominant interest groups into scripts for shallow reform agendas. Institutionalised policy practices also effect policy outcomes. My research finds that the use of Expert Panels, for example, is important in shaping international policy communities’ understanding of the policy problems posed by biotechnology risks. In the light of these findings, my thesis argues that the ability of interest groups and policy actors to win language games within institutional settings also enables them to secure their preferred policy outcomes. I import the concept of authorship as a new policy concept to discuss the ways in which such groups exercise social power to secure their understanding of biosafety, which thereby effect the ‘writing’ of the dominant accounts of what constitutes an acceptable international biosafety standard within the Cartagena Protocol. In short, my thesis is a new account of biosafety politics that fills some of the current knowledge gaps about how biotechnology is emerging onto regulatory agendas. It also demonstrates the mechanisms of power and the language struggles that determine biosafety policy outcomes within multi-lateral environmental agreements such as the Convention on Biological Diversity.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Australian School of Environmental Studies
Full Text
5
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/.
Pełny tekst źródła
6
He, Huiqi. "Miniaturized electroporation system for gene transfer using bio-MEMS technology /". View abstract or full-text, 2007. http://library.ust.hk/cgi/db/thesis.pl?BIEN%202007%20HE.
Pełny tekst źródła
7
White, Adam. "Microfluidic technology for high-throughput single cell gene expression analysis". Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/27838.
Pełny tekst źródłaStreszczenie:
Transcription measurements with single cell resolution are critical to understanding variable responses in immunity, measuring stochastic noise in gene expression, and assessing the disease and developmental state of heterogeneous populations. The latter is particularly important in stem cell science, developmental biology, and cancer, where minority cells may be most significant. To see these populations requires the quick and cost-effective measurement of hundreds to thousands of individual cells. Quantitative real-time polymerase chain reaction (RT-qPCR) is a sensitive method for quantitative analysis of transcript levels that provides excellent sensitivity and dynamic range in the detection of transcripts. However, the use of RT-qPCR is generally limited to ensemble measurements of bulk cells or plasma, and is blind to minority cell populations. This aggregation obscures the underlying biological response and variability. To address this limitation, we exploit recent advances in scalable microfluidics to develop robust lab-on-chip technology capable of highly parallel and cost-effective measurements of transcript levels from single cells. The microfluidic device integrates single-cell capture, lysis, reverse transcription of contained RNA, and precise measurement of cDNA using RT-qPCR. We demonstrate this system in the study of microRNA expression in a cell line representing chronic myelogenous leaukemia, pluripotency markers in differentiating human embryonic stem cells, and the detection of somatic mutations in a primary breast cancer sample. The ability to screen isolated cells by simultaneously measuring the fraction of cells expressing a specific gene and quantifying the abundance of expression, may provide a new modality for the early detection of disease such as cancer.
8
Kotnik, Katarina [Verfasser]. "Gene knockdown in transgenic rats by shRNA technology / Katarina Kotnik". Berlin : Freie Universität Berlin, 2008. http://d-nb.info/1023169665/34.
Pełny tekst źródła
9
Catteruccia, Flaminia. "Systematic attempts to develop gene transfer technology for anopheline mosquitoes". Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323867.
Pełny tekst źródła
10
Alete, Julia. "Safe, site-specific gene delivery using ultrasound and microbubble technology". Thesis, Imperial College London, 2008. http://hdl.handle.net/10044/1/4256.
Pełny tekst źródłaStreszczenie:
The following study investigates the use of diagnostic ultrasound in combination with microbubbles (ultrasound contrast agents) as a physical enhancer for non-viral gene delivery. The aim of this work was firstly, to demonstrate that ultrasound exposure using settings within the range of diagnostic ultrasound, in combination with microbubbles can improve gene delivery, and secondly, to show that it is a safe, site-specific technique which mitigates the risk of tissue damage often seen with other physical enhancers of gene delivery such as, electroporation. Initially, a feasibility study was carried out to test the efficiency and safety of microbubble ultrasound (MBUS) in a reporter gene setting. Experiments using intravenous injections of a luciferase reporter gene established that MBUS is a safe, site-specific technique which improved levels of the luciferase expression in the organ targeted by MBUS. Luciferase was successfully delivered to the liver and heart, showing significantly higher levels compared to injections without MBUS, and with no detectable expression in other non-target organs. A therapeutic application of MBUS was tested using the mdx mouse, an animal model for Duchenne Muscular Dystrophy (DMD), a genetic disorder caused by the lack of functional dystrophin in muscle fibres due to premature termination of translation. The most successful treatment approach in the mdx mouse thus far had been the injection of Phosphorodiamidate Morpholino Oligomers (PMOs), which by inducing exon skipping, re-introduced dystrophin expression in most muscles in the body, with the exception of the heart. Injections of PMOs with MBUS to the heart successfully re-introduced dystrophin expression in cardiomyocytes. Furthermore, treatment parameters were investigated in more detail in order to optimize PMO delivery to the heart. Finally, an investigation into different types of commercially available microbubbles compared the efficiencies (with respect to gene delivery) of the different bubbles, in order to understand why different microbubbles show different results when used for MBUS, potentially enabling the design of microbubbles specifically for gene delivery.
11
Rogowski, Wolf. "Key issues in the economic evaluation of gene technology in healthcare /". [S.l. : s.n.], 2007. http://www.gbv.de/dms/zbw/559909535.pdf.
Pełny tekst źródła
12
Vizcaino, Caston Isaac. "Monitoring bacterial physiology during recombinant protein production using reporter gene technology". Thesis, University of Birmingham, 2012. http://etheses.bham.ac.uk//id/eprint/3309/.
Pełny tekst źródłaStreszczenie:
This work presents an evaluation of the applicability of gene reporter technology to monitor Escherichia coli stress in industrial conditions with special interest in recombinant protein production. Different reporter plasmids containing promoter sequences of genes of the heatshock response were utilized to monitor chaperone expression upon different sources of stress such as exposure to chemicals, temperature and anaerobic growth. Activation of the heat shock response was monitored by \(\beta\)-galactosidase activity from the reporter plasmid pQF50groE. Cultures responded to heat-shock, anaerobiosis and \(\beta\)-mercaptoethanol by increasing the expression of \(\sigma\)\(^{32}\)-related genes. The performance of fluorescence reporters containing varieties of GFP was measured by fluorimetry and flow cytometry. Low copy number plasmids were demonstrated to be better suited than medium-high copy plasmids to report stress in industrial conditions. Reporter plasmids containing the promoters of the chaperones DnaK and GroES were utilized to measure E. coli stress in reducing environments and during recombinant protein production. It was demonstrated that the production strategy caused an impact in the host physiology which determined the outcome of the process. Flow cytometry showed excellent potential to obtain reliable measurements providing data of reporter activity cell death and cell morphology.
13
Yoshimura, Shigehiro. "Nano-biology of the Gene : Application of Nano-technology to the Structural and Functional Analysis of the Gene". Kyoto University, 2002. http://hdl.handle.net/2433/149880.
Pełny tekst źródłaStreszczenie:
Kyoto University (京都大学)0048
新制・課程博士
博士(人間・環境学)
甲第9673号
人博第157号
13||142(吉田南総合図書館)
新制||人||37(附属図書館)
UT51-2002-G431
京都大学大学院人間・環境学研究科人間・環境学専攻
(主査)教授 速水 正憲, 教授 津田 謹輔, 助教授 倉橋 和義, 教授 竹安 邦夫
学位規則第4条第1項該当
14
McTaggart, Sally. "Retroviral vector production for gene therapy applications". Thesis, University of Birmingham, 2001. http://etheses.bham.ac.uk//id/eprint/7571/.
Pełny tekst źródłaStreszczenie:
The production of retroviral vectors for gene therapy applications faces a number of challenges. Of primary concern is the low titre of vector stocks produced by packaging cells in culture and the inherent instability of retroviral vector activity. A systematic investigation of culture parameters that can effect vector titre was conducted. Physical and chemical factors including temperature, pH, medium composition, dissolved oxygen and serum concentration were all assessed. In addition, a number of studies were undertaken to assess the effects of packaging cell growth rate on vector production. The use of a packed bed, as a novel system for large-scale vector production, was also investigated. Prolonged production of retroviral vector stocks was demonstrated in the packed bed system with immobilised packaging cells. Determination of the critical culture parameters allowed optimisation of culture conditions, which can be continuously controlled in the packed bed system, thereby ensuring optimal vector production throughout the production period. Furthermore, vector decay rates can be reduced by the immediate collection of vectors into a recovery vessel. The studies within this thesis will aid the development of appropriate procedures for the large-scale production and handling of retroviral vector stocks for human gene therapy applications.
15
Calus, Szymon Tomasz. "Evaluation of nanopore-based sequencing technology for gene marker based analysis of complex microbial communities : method development for accurate 16S rRNA gene amplicon sequencing". Thesis, University of Glasgow, 2018. http://theses.gla.ac.uk/41086/.
Pełny tekst źródłaStreszczenie:
Nucleic acid sequencing can provide a detailed overview of microbial communities in comparison with standard plate-culture methods. Expansion of high-throughput sequencing (HTS) technologies and reduction in analysis costs has allowed for detailed exploration of various habitats with use of amplicon, metagenomics, and metatranscriptomics approaches. However, due to a capital cost of HTS platforms and requirements for batch analysis, genomics-based studies are still not being used as a standard method for the comprehensive examination of environmental or clinical samples for microbial characterization. This research project investigated the potential of a novel nanopore-based sequencing platform from Oxford Nanopore Technologies (ONT) for rapid and accurate analysis of various environmentally complex samples. ONT is an emerging company that developed the first-ever portable nanopore-based sequencing platform called MinIONTM. Portability and miniaturised size of the device gives an immense opportunity for de-centralised, in-field, and real-time analysis of environmental and clinical samples. Nonetheless, benchmarking of this new technology against the current gold-standard platform (i.e., Illumina sequencers) is necessary to evaluate nanopore data and understand its benefits and limitations. The focus of this study is on the evaluation of nanopore sequencing data: read quality, sequencing errors, alignment quality but also bacterial community structure. For this reason, mock bacterial community samples were generated, sequenced and analysed with use of multiple bioinformatics approaches. Furthermore, this study developed sophisticated library preparation and data analyses methods to enable high-accuracy analysis of amplicon libraries from complex microbial communities for sequencing on the nanopore platform. Besides, the best performing library preparation and data analyses methods were used for analysis of environmental samples and compared to high-quality Illumina metagenomics data. This work opens a new possibility for accurate, in-field amplicon analysis of complex samples with the use of MinIONTM and for the development of autonomous biosensing technology for culture-free detection of pathogenic and non-pathogenic microorganisms in water, soil, food, drinks or blood.
16
Thorsén, Jenny, Stina Wahlström, Anna Nilsson, Johanna Öberg i Sebastian Persson. "Immunoassay Applications in Gene and Cell Therapy : A Market Analysis of Companies Conducting Gene and Cell Therapy Product Development". Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-352164.
Pełny tekst źródła
17
Xie, Dan, i 謝丹. "Application of high-throughput tissue microarray technology in cancer research". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B30283619.
Pełny tekst źródła
18
Glare, Eric M. 1965. "The application of competitive PCR technology to asthma research". Monash University, Dept. of Medicine, 2001. http://arrow.monash.edu.au/hdl/1959.1/7975.
Pełny tekst źródła
19
Ruryk, Andriy. "Development of microsystem technology suitable for bacterial identification and gene expression monitoring". [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=974502286.
Pełny tekst źródła
20
Howell, Brandon George. "Gene expression profiling of UV-induced skin cancer using cDNA microarray technology". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/MQ63108.pdf.
Pełny tekst źródła
21
Jirajaroenrat, Kanya. "Development of ribozyme technology for gene down-regulation in farm animal species". Thesis, University of Nottingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.408887.
Pełny tekst źródła
22
Gibbings, J. George. "Transcript profiling in rice using Serial Analysis of Gene Expression (SAGE) technology". Thesis, University of Reading, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.401446.
Pełny tekst źródła
23
Allum, Nicholas Charles. "Risk, social trust and knowledge : public perceptions of gene technology in Britain". Thesis, London School of Economics and Political Science (University of London), 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.415888.
Pełny tekst źródła
24
Chono, Hideto. "Development of retroviral vector technology and application to HIV-1 gene therapy". Kyoto University, 2012. http://hdl.handle.net/2433/157729.
Pełny tekst źródła
25
Williams, Darren William. "Gene transfer and transient expression of transgenes in zebrafish Danio Refrio". Thesis, University of Southampton, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242103.
Pełny tekst źródła
26
Belshaw, N. J. "The nuclear matrix and gene expression in Trichoderma reesei". Thesis, University of East Anglia, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296346.
Pełny tekst źródła
27
Warnock, James Neill. "Optimisation of retroviral production systems for gene therapy applications". Thesis, University of Birmingham, 2003. http://etheses.bham.ac.uk//id/eprint/3592/.
Pełny tekst źródłaStreszczenie:
Retroviral vectors are a promising tool for gene therapy. However, there are two major problems to overcome if a viable commercial production process is to be established. These are the instability of virus particles and the low virus titres. The characteristics of the producer cells were determined in batch culture, semicontinuous culture and semi-continuous culture at 32°C. Additionally, cell attachment, growth and virus production on various macroporous microcarriers was assessed under static and stirred conditions. Alternative strategies for the cultivation of cells were also investigated. These included spinner basket, packed bed and spinner flask cultures with semi-continuous feeding and packed bed, fixed bed, fluidised bed and stirred tank cultures with continuous perfusion of culture medium. Of these the fixed bed bioreactor had the highest cell specific productivity and was capable of running for 28 days. The fluidised bed bioreactor had the highest reactor productivity, due to the higher cell number. Optimisation of culture medium was performed with regard to serum concentration. The greatest production was observed at an initial serum concentration of 2.5% (v/v). The findings in this thesis will assist the development of an efficient method for the production of clinical grade retro viral vectors for gene therapy applications.
28
Randel, Melissa. "New Technology Development for Next-Generation Sequencing". Thesis, University of Oregon, 2017. http://hdl.handle.net/1794/22704.
Pełny tekst źródłaStreszczenie:
Next-Generation Sequencing (NGS) technologies have been evolving at an unparalleled pace. The ability to generate millions of base pairs of data in a short time and at lower cost than previously has led to a dramatic expansion of technologies within the field. This dissertation discusses the development and validation of new methods for assessing genomic variation, dynamic changes in gene expression, high-accuracy sequencing, and analysis of recombination events.
By reducing the cost of analyzing many samples for genetic divergence by genotyping the same region of the genome in multiple samples, researchers can pursue investigations on a larger scale. Next-RAD (Nextera fragmentation with Restriction-Associated Digestion) allows analysis of a uniform subset of loci between organisms for comparison of populations by genetic differences with reduced burdens of cost and data analysis. This method was applied to the Anopheles darlingi mosquito to identify three distinct species that were thought to be a uniform population.
The lowering cost of large-scale sequencing investigations allows for massively parallel analysis of genomic function in a single assay. Regulation of gene expression in response to stress is a complex process which can only be understood by analyzing many pathways in tandem. A novel method is described which quantifies on a genome-wide scale the expression of millions of randomer tags driven by associated transcriptional enhancers. This method provides novel data in the form of high-resolution analysis of gene regulation.
Aside from generating novel data types, another force behind development of new technologies is to improve data quality. One limitation of NGS is the inherent error rate. PELE-Seq (Paired End Low Error Sequencing) was developed to address this problem, by employing completely overlapping paired-end reads as well as a dual barcoding strategy to eliminate incorrect sequences resulting from final library amplification. This new tool improves data quality dramatically.
Finally, the rapid expansion of tools necessitates the identification of new applications for these technologies. To this end, 10x Genomics Linked-Read sequencing was employed to identify recombination events in multiple species. The haplotype-resolved nature of the data generated from such assays has many promising applications.
29
Costello, Cait. "Horizontal gene transfer in bacterial co-cultures in micro-fabricated environments". Thesis, University of Birmingham, 2012. http://etheses.bham.ac.uk//id/eprint/3311/.
Pełny tekst źródłaStreszczenie:
In recent years, the majority of research on surface patterning, as a means of precisely controlling cell positioning and adhesion on surfaces, has focused on eukaryotic cells. Such research has led to new insights into cell biology, advances in tissue engineering, and cell motility. In contrast, considerably less work has been reported on tightly-controlled patterning of bacteria, despite its potential in a wide variety of applications, including fabrication of in vitro model systems for studies of bacterial processes such as quorum sensing and horizontal gene transfer. We report a rapid and convenient method to generate patterned bacterial co-cultures using surface chemistry to regulate bacterial adhesion and liftoff patterning for controlling cellular positioning at the surface. A mannoside-terminated SAM formed an adhesive surface for bacterial monolayer formation, allowing fabrication of patterned regions using a subtractive microcontact printing process with a hydrogel stamp. The patterned substrates were subsequently inoculated with a second strain of bacteria from solution which deposited onto the unpatterned regions, forming a robust micropatterned coculture, providing platforms for spatially controlled studies of conjugation between donor and recipient bacterial cells. Towards this aim, donor cells were transformed with a modified conjugative plasmid that would bind fluorescent molecules and become visible upon entering a recipient cell. We discovered during the course of the project that bacterial co-cultures on metal surfaces exhibit slower growth rates than on semi-solid agar, and as such the time scale required for efficient conjugation lead to photobleaching of fluorescent foci. However, we were able to demonstrate through cultivation techniques that conjugation could occur in these micropatterned co-cultures after three hours.
30
Thomas, Alistair Owen. "Detection of bacterial gene expression by a novel isothermic nucleic acid amplification technology". Thesis, University of Bath, 2004. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.410924.
Pełny tekst źródłaStreszczenie:
A novel probe-based technique called Signal-Mediated Amplification Reaction Technology (SMART) was optimised for detection of RNA targets in order to quantify gene expression. The SMART assay was used to quantify both 23 S rRNA in P. aeruginosa PAOl and gfpmuti mRNA in the plasmid-borne rpoSwgfpmvXi fusions P. aeruginosa SS429 and SS431. However, the assay was not sufficiently sensitive to detect gfpmvfo mRNA from the chromosomal rpoS::gfpmut3 fusion P. aeruginosa SS336. SDS-PAGE analysis of outer membrane proteins of P. aeruginosa PAOl revealed that cells grown in a reported iron-replete chemically defined medium CDMio were in fact limiting for iron. Modifications to the growth medium such as increased iron concentration, reduction in pH and the addition of citrate and ascorbate all failed to produce an iron-replete phenotype. This was achievable only when MOPSO buffer was replaced with phosphate buffer, indicating that by some unknown mechanism MOPSO can reduce iron availability in minimal media. The effects of nutrient limitation on rpoS expression in P. aeruginosa planktonic and biofilm culture were investigated using direct fluorescence measurement of rpoS::gfpmut3 chromosomal and plasmid fusions. In planktonic culture, nutrient-replete and magnesium-limited conditions resulted in an increase in rpoS expression whilst minimal levels of rpoS expression were seen in both iron-limited and glucose-limited conditions. Furthermore, minimal expression of rpoS was noted in P. aeruginosa biofilms in glucose, magnesium and iron-limited conditions.
31
Ziou, Arisa. "Gene expression of MYPT1 and ROCK1 in endometrial cancer". Thesis, Högskolan i Skövde, Institutionen för hälsovetenskaper, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19249.
Pełny tekst źródłaStreszczenie:
Endometrial adenocarcinoma is a cancer that develops from the endometrium, from cells thatform the glands in the endometrium. Animal models such as the BDII rat have thecharacteristic property that they are prone to cancers, characterized by rapid tumor growth,that resemble human cancers. Such rat models are therefore used to study gene expression andsignal pathways in cancer. Cancer cells have the ability to invade surrounding tissues throughlymphatic and/or vascular circulation to produce secondary tumors at new sites. TheRho/ROCK pathway orchestrates cell motility thereby contributing in significantly tometastasis. ROCK, through phosphorylation of myosin phosphatase target subunit 1(MYPT1), inhibits MYPT1 and induces actomyosin contraction which contributes to manycellular processes. In this study, we were interested in investigating the expression of MYPT1and ROCK1 genes in malignant and non-malignant endometrial cell lines in BDII rat model,in human endometrial cancer cells represented by the Ishikawa cells line, and in humanembryonic kidney 293 (HEK293) human non-malignant control cells. Although statisticalsignificance was not reached due to the small sample size, a difference in the gene expressionlevels in malignant and non-malignant cells was observed. The results from the present studyshowed a higher expression of MYPT1 and ROCK1 genes in cancer cells (rat and human)compared to non-cancer cells, and we can conclude that this implicates the significance of theMYPT1/ROCK pathway in endometrial cancer and its deregulation.
32
Chan, V. T. W. "Evaluation of the of the C-HA-RAS in human breast disease by nonisotopic hybridization technology". Thesis, University of Oxford, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.233535.
Pełny tekst źródła
33
Eklöf, Jenny. "Gene technology at stake : Swedish governmental commissions on the border of science and politics". Doctoral thesis, Umeå University, Historical Studies, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1424.
Pełny tekst źródłaStreszczenie:
This thesis examines the Swedish political response to the challenges posed by gene technology, seen through the prism of governmental commissions. It discerns and analyses continuities and changes in the Swedish political conception of gene technology, over the course of two decades, 1980–2000. This is done by thematically following ideas of “risks” and “ethics” as they are represented in the inner workings and reception of three governmental commissions. The Gene-Ethics Commission (1981–1984), the Gene Technology Commission (1990–1992) and the Biotechnology Commission (1997–2000) form the empirical focal points of this analysis. The first two provided preparatory policy proposals that preceded the implementation of the Swedish gene technology laws of 1991 and 1994. The last one aimed at presenting a comprehensive Swedish biotechnology policy for the new millennium.
The study takes into account the role of governmental commissions as arenas where science and politics intersect in Swedish political life, and illuminates how this type of “boundary organisation”, placed on the border of science and politics, impinges on the understanding of the gene technology issue. The commissions have looked into the limits, dangers, possibilities and future applications of gene technology. They have been appointed to deal with the problematic task of distinguishing between what is routine and untested practices, realistic prediction and “science fiction”, what are unique problems and what are problems substantially similar to older ones, what constitutes a responsible approach as opposed to misconduct and what it means to let things “get out of hand” in contrast to being “in control”. Throughout a period of twenty years, media reports have continued to frame the challenges posed by gene technology as a task of balancing risks and benefits, walking the fine line between “frankenfoods” and “miracle drugs”.
One salient problem for the commissions to solve was that science and industry seemed to promote a technology the public opposed and resisted, at least in parts. For both politics and science to gain, or regain, public trust it needed to demonstrate that risks – be it environmental, ethical or health related ones – were under control. Under the surface, it was much more complicated than “science helping politics” to make informed and rational decisions on how to formulate a regulatory policy. Could experts be trusted to participate in policy-making in a neutral way and was it not important, in accordance with democratic norms, to involve the public?
34
Tong, Lily. "Probing the function of RNase E family using biochemical techniques and gene array technology". Thesis, University of Leeds, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414514.
Pełny tekst źródła
35
Berger, Adeline. "Gene therapy for autosomal dominant retinitis pigmentosa : repair of rhodopsin mRNA by SMaRT technology". Thesis, Paris 6, 2014. http://www.theses.fr/2014PA066190/document.
Pełny tekst źródłaStreszczenie:
La rétinite pigmentaire est une maladie héréditaire rétinienne menant à la cécité, et pour laquelle il n’existe aucun traitement. La cause la plus fréquente des formes autosomiques dominantes de la maladie est une mutation ponctuelle dans le gène de la rhodopsine (RHO) induisant la mort des photorécepteurs (PR). Pour éviter la dégénérescence des PR, la stratégie thérapeutique doit supprimer l’expression de la protéine mutante tout en restaurant celle de la protéine normale et ce à un niveau physiologique. Mon projet était de réparer le pré-ARNm RHO par la technologie SMaRT (trans-épissage (TE) médié par le splicéosome). Ceci nécessite d’introduire par transfert de gène, dans la cellule cible, un ARN exogène, appelé PTM pour molécule pre-ARNm de TE, pouvant induire un épissage en trans.Nous avons créé 20 PTM différents et obtenu un taux maximal de TE in vitro de 40% après co-transfection transitoire des constructions RHO et PTM dans les cellules HEK293T. Nous avons générés des lignées cellulaires d’expression stable de RHO normale ou mutée par transduction lentivirale. Alors que la RHO normale se localise à la membrane plasmique, la mutation induit la rétention cytoplasmique de la protéine. La transfection du PTM dans la lignée cellulaire de RHO mutée a induit du TE, capable de restaurer partiellement la localisation de la RHO réparée à la membrane.Nous avons alors testé le TE in vivo dans un modèle murin humanisé de rétinite pigmentaire. L’injection sous-rétinienne d’un AAV2/8-bRho-PTM a permis le TE in vivo, mais n’a pas suffi à prévenir la dégénérescence des PR observée par SD-OCT (technologie que nous avons améliorée au cours de ce projet)Retinitis pigmentosa is an hereditary retinal dystrophy involving degeneration of photoreceptors leading to blindness and for which there is currently no treatment. The most frequent cause of autosomal dominant forms of the disease is a point mutation in the rhodopsin gene (RHO). Therapeutic strategy should both suppress mutant protein expression and restore that of the normal one to physiologic level to prevent photoreceptor degeneration. My PhD project was to repair RHO pre-mRNA by SMaRT (Spliceosome Mediated RNA Trans-splicing) technology. This implies to introduce by gene transfer into the target cell an exogenous RNA, called PTM for Pre-mRNA Trans-splicing Molecule. This one was able to promote a splice reaction in trans, leading to the replacement of the mutated exons. We designed 20 different PTM and obtained in vitro a maximum trans-splicing rate of 40% after transient co-transfection of PTM and RHO constructs in HEK293T cells. We then created WT or mutated RHO stable expression cell lines by lentiviral transduction. Mutation induced retention of the protein into the cytoplasm, while the WT RHO was localized to the plasma membrane. We observed that the PTM transfection in the mutated RHO cell line induced trans-splicing, which was able to partially restore localization to the plasma membrane of repaired RHO. We then tested trans-splicing in vivo in mRho+/- RHO P347S+ mice, a humanized heterozygous mouse model of retinitis pigmentosa. After subretinal injection of AAV2/8-bRho-PTM we observed that trans-splicing occurred in vivo. Unfortunately we did not observe by SD-OCT (a technology that we improve in this project) any rescue of the degenerative phenotype
36
Aoyama, Teruyoshi. "Improvement of technology for non-viral gene delivery system using DNA-cationized gelatin complex". Kyoto University, 2003. http://hdl.handle.net/2433/148731.
Pełny tekst źródła
37
Eklöf, Jenny. "Gene technology at stake : Swedish governmental commissions on the border of science and politics /". Umeå : Department of Historical Studies, Umeå University, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1424.
Pełny tekst źródła
38
Mori, Tomoaki. "Application of artificial zinc-finger protein technology: gene regulation and site-specific DNA cleavage". 京都大学 (Kyoto University), 2010. http://hdl.handle.net/2433/120946.
Pełny tekst źródła
39
Ragan, Paula Marie. "The effect of mechanical compression on chondrocyte gene expression". Thesis, Massachusetts Institute of Technology, 1999. http://hdl.handle.net/1721.1/85347.
Pełny tekst źródłaStreszczenie:
Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 1999.Includes bibliographical references (leaves 115-122).
by Paula M. Ragan.
Ph.D.
40
Holland, Chad D. (Chad Darrel). "Personalized medicine, population genetics and privacy : an empirical study of international gene banks". Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/33089.
Pełny tekst źródłaStreszczenie:
Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology; and, (S.M.M.O.T.)--Massachusetts Institute of Technology, Sloan School of Management, Management of Technology Program, 2005.Includes bibliographical references.
The promise of personalized medicine lies in its potential to fundamentally change healthcare. In the past, pharmaceuticals were prescribed on a "one size fits all" basis-patients with certain disease phenotypes were given what were thought to be appropriate drugs. There is growing evidence however that the effectiveness of these drugs may differ by individual and by sub-group; presumably due to fundamental genetic differences in disease and metabolic pathways. Drugs like Herceptin, Gleevec and Iressa are part of an emerging trend in the biopharmaceutical arena of drugs that are accompanied by genetic diagnostic tests and prescribed only for patients with genotypes in which the agents are most effective.
by Chad D. Holland.
S.M.M.O.T.
S.M.
41
Bhattacharya, Kanishka. "Gene x gene interactions in genome wide association studies". Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:6cb7ab29-90df-4d70-bc2f-531f874b79d0.
Pełny tekst źródłaStreszczenie:
Genome wide association studies (GWAS) have revolutionized our approach to mapping genetic determinants of complex human diseases. However, even with success from recent studies, we have typically been able to explain only a fraction of the trait heritability. GWAS are typically analysed by testing for the marginal effects of single variants. Consequently, it has been suggested that gene-gene interactions might contribute to the missing heritability of complex diseases. GWAS incorporating interaction effects have not been routinely applied because of statistical and computational challenges relating to the number of tests performed, genome-wide. To overcome this issue, I have developed novel methodology to allow rapid testing of pairwise interactions in GWAS of complex traits, implemented in the IntRapid software. Simulations demonstrated that the power of this approach was equivalent to computationally demanding exhaustive searches of the genome, but required only a fraction of the computing time. Application of IntRapid to GWAS of a range of complex human traits undertaken by the Wellcome Trust Case Control Consortium (WTCCC) identified several interaction effects at nominal significance, which warrant further investigation in independent studies. In an attempt to fine-map the identified interacting loci, I undertook imputation of the WTCCC genotype data up to the 1000 Genomes Project reference panel (Phase 1 integrated release, March 2012) in the neighbourhood of the lead SNPs. I modified the IntRapid software to take account of imputed genotypes, and identified stronger signals of interaction after imputation at the majority of loci, where the lead SNP often had moved by hundreds of kilobases. The X-chromosome is often overlooked in GWAS of complex human traits, primarily because of the difference in the distribution of genotypes in males and females. I have extended IntRapid to allow for interactions with the X chromosome by considering males and females separately, and combining effect estimates across the sexes in a fixed-effects meta-analysis. Application to genotype data from the WTCCC failed to identify any strong signals of association with the X-chromosome, despite known epidemiological differences between the sexes for the traits considered. The novel methods developed as part of this doctoral work enable a user friendly, computationally efficient and powerful way of implementing genome-wide gene-gene interaction studies. Further work would be required to allow for more complex interaction modelling and deal with the associated computational burden, particularly when using next-generation sequencing (NGS) data which includes a much larger set of SNPs. However, IntRapid is demonstrably efficient in exhaustively searching for pairwise interactions in GWAS of complex traits, potentially leading to novel insights into the genetic architecture and biology of human disease.
42
Gerber, Georg Kurt 1970. "Computational discovery of gene modules, regulatory networks and expression programs". Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42201.
Pełny tekst źródłaStreszczenie:
Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2007.Includes bibliographical references (p. 163-181).
High-throughput molecular data are revolutionizing biology by providing massive amounts of information about gene expression and regulation. Such information is applicable both to furthering our understanding of fundamental biology and to developing new diagnostic and treatment approaches for diseases. However, novel mathematical methods are needed for extracting biological knowledge from high-dimensional, complex and noisy data sources. In this thesis, I develop and apply three novel computational approaches for this task. The common theme of these approaches is that they seek to discover meaningful groups of genes, which confer robustness to noise and compress complex information into interpretable models. I first present the GRAM algorithm, which fuses information from genome-wide expression and in vivo transcription factor-DNA binding data to discover regulatory networks of gene modules. I use the GRAM algorithm to discover regulatory networks in Saccharomyces cerevisiae, including rich media, rapamycin, and cell-cycle module networks. I use functional annotation databases, independent biological experiments and DNA-motif information to validate the discovered networks, and to show that they yield new biological insights. Second, I present GeneProgram, a framework based on Hierarchical Dirichlet Processes, which uses large compendia of mammalian expression data to simultaneously organize genes into overlapping programs and tissues into groups to produce maps of expression programs. I demonstrate that GeneProgram outperforms several popular analysis methods, and using mouse and human expression data, show that it automatically constructs a comprehensive, body-wide map of inter-species expression programs.
(cont.) Finally, I present an extension of GeneProgram that models temporal dynamics. I apply the algorithm to a compendium of short time-series gene expression experiments in which human cells were exposed to various infectious agents. I show that discovered expression programs exhibit temporal pattern usage differences corresponding to classes of host cells and infectious agents, and describe several programs that implicate surprising signaling pathways and receptor types in human responses to infection.
by Georg Kurt Gerber.
Ph.D.
43
Pierce, Lain Xylia. "Analysis of Rhythmic Gene Transcription using the TimeR, a Novel Technology to Capture Zebrafish Embryos". Cleveland, Ohio : Case Western Reserve University, 2008. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=case1212770242.
Pełny tekst źródła
44
Glover, Hilary Rose. "The design and use of reporter gene technology in the understanding of oestrogen receptor function". Thesis, Queen Mary, University of London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.417216.
Pełny tekst źródła
45
Mitra, Robi David. "Polony sequencing : DNA sequencing technology and a computational analysis reveals chromosomal domains of gene expression". Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/8797.
Pełny tekst źródłaStreszczenie:
Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000.Includes bibliographical references.
The first part of this thesis describes the development of polony sequencing, a sequencing technology in which DNA is cloned, amplified and sequenced in a polymer matrix. A complex library of one to ten million linear DNA molecules is amplified by performing polymerase chain reaction (PCR) in a thin polyacrylamide film poured on a glass microscope slide. The polyacrylamide matrix retards the diffusion of the DNA molecules so that each amplification product remains localized near its parent molecule. At the end of the reaction, a number of polymerase colonies, or "polonies", have formed, each one grown from a single template molecule. As many as 5 million clones can be amplified in parallel on a single slide. By including an acrydite modification at the 5' end of one of the PCR primers, the amplified DNA will be covalently attached to the polyacrylamide matrix, allowing further enzymatic manipulations to be performed on all clones simultaneously. Also described in this thesis is my progress in development of a protocol to sequence the polonies by repeated cycles of extension with fluorescent deoxynucleotide. Because polony sequencing is inherently parallel, and sub-picoliter volumes are used for each reaction, the technology should be substantially faster and cheaper than existing methods. Applications for polony sequencing such as gene expression analysis, SNP discovery, and SNP screening will also be discussed. The second part of this thesis describes a computational analysis that tests the hypothesis that chromosomal position affects gene expression. It is shown that, throughout the genome, genes lying close together on the same chromosome often show significant coexpression. This coexpression is independent of the orientation of genes to each other, but is dependent on the distance between genes. In several cases where adjacent genes show highly correlated expression, the promoter of only one of the genes contains an upstream activating sequence (UAS) known to be associated with the expression pattern. These results suggest that in certain regions of the genome a single transcription factor binding site may regulate several genes. It is also shown that evolution may take advantage of this phenomenon by keeping genes with similar functions in adjacent positions along the chromosomes. The techniques that are presented provide a computational method to delineate the locations of chromosomal domains and identify the boundary elements that flank them.
Robi David Mitra.
Ph.D.
46
Leandersson, Viktor. "GENVO: GENE EVOLUTIONVISUALIZATION : A 3D reconciliation software for phylogenies". Thesis, KTH, Medieteknik och interaktionsdesign, MID, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-189179.
Pełny tekst źródłaStreszczenie:
Gene evolution is important in several areas, not least the understanding of thehuman body. Since the time of Darwin, researchers have visualized evolution withrooted binary trees. Hence, genes evolve constrained to how species have evolvedand that relationship is interesting to understand and explore. To solve this, onemethod is to infer the gene tree into the species tree, a so called reconciliation, butvisualizing reconciled trees with classical binary trees often results in clutteredvisualizations that quickly become difficult to understand. Therefore, in this thesisI present a new visualization method, Genvo, for reconciled phylogenies, and definea simple tree layout algorithm. I also present a problem characterization for thedomain-specific tasks, performed when working with gene evolution visualizations.A prototype of Genvo is then studied in a small pair analytics study, where fivepairs of master students tested the developed a prototype of Genvo. The results areanalyzed compared to a workshop with three participants, all with prior knowledgein the field of gene evolution. The analysis indicates a faster understanding of thegene data in Genvo, most likely through the pre-attentive features.Att förstå geners evolution är relevant för flertalet områden, inte minst för attutforska den mänskliga kroppen. Ända sedan Darwin har forskare visualiseratevolution med hjälp av rotade binära träd. Dock utvecklas gener begränsat till hurdess arter utvecklats, och denna relation är av intresse att förstå och utforska. Attgöra en sammanslagning av ett gen-träd med sitt art-träd (reconciliation) är ett sättatt visualisera relationen, men lösningen blir ofta väldigt rörig och svårförståelig.Därför presenterar jag i detta examensarbete Genvo, ett reconciliation programsom använder en simpel träd-layout-algoritm för att visualisera geners evolution irelation till arters evolution i 3D. Jag presenterar även en gedigen problemkarakteriseringför de uppgifter forskarna utför när de jobbar med dagensvisualiseringsverktyg. En prototyp av Genvo testades sedan i en pairanalytics studie, med en testgrupp bestående av fem par. Studien är sedan jämfördmed en workshop där tre testpersoner, med tidigare erfarenhet, jobbade medsamma uppgifter. Analysen av studiernas resultat tyder på en snabbare förståelseav datan när användarna använde sig av Genvo.
47
Burkhart, Tandace L. "The Search for Novel Sponge genes: Comparative Analysis of Gene Expression in Multiple Sponges". NSUWorks, 2012. http://nsuworks.nova.edu/occ_stuetd/194.
Pełny tekst źródłaStreszczenie:
This project focuses on the use of sponge genetic transcripts in the form of expressed sequence tags (ESTs) readily available in Genbank to search for novel genes using bioinformatics analysis tools. Marine sponge species are known to house a diversity of marine microbes and are known as the ‘living fossils’ of the animal kingdom because of the large number of ancient genes they house. Genomic mining can be a useful tool in discovering these orthologous genes. This study utilized the techniques of genomic mining of 11 previously described sponge species transcripts. The results of this study provide a better understanding of the genomic structure of the organisms studied by creating a more detailed genetic map and examining a specific environmental snapshot of the genes in each sponge. Novel methods for dissecting beneficial information from large scale data sets available in genomic libraries utilizing bioinformatics search tool MGRAST were examined. The results of this study indicate that sponges house numerous genes that are likely to be evolutionary predecessors of genes in higher eukaryotes. Support was also given to the notion that microbial communities play a role in metabolic pathways of sponges.
48
Caldarelli, Antonio. "A study on endocrine disrupters in the environment through the microarray technology". Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2007. http://nbn-resolving.de/urn:nbn:de:swb:14-1175076879253-16448.
Pełny tekst źródłaStreszczenie:
Due to the current rise of exposure to natural and synthetic compounds in our daily life, the debate concerning the safety of many substances is becoming increasingly relevant. The estrogenic activity of various compounds, described as xenoestrogens, is the major part of this debate. Humans beings are exposed to these substances from different environmental contaminations ranging from conscious intake of estrogenic substances, as in contraception or in hormone replace therapy (HRT), to unconscious exposure, from food, the use of synthetic material in daily life and air and water pollution. At this point the need for methods to investigate the activity and the safety of these substances is becoming increasingly important. Classical methods for the analysis of the estrogenic activity of substances, like batteries of in vivo test systems on the rat uterotrophic assay are not able to describe the different pathways of action of recently discovered estrogenic substances. This evidence was already shown by the Organization for Economic Cooperation and Development (OECD), introducing new test guidelines for the investigation of effects of endocrine disruptors (according to enhanced Test Guideline 407). As reviewed by Nilsson (Nilsson et al., 2001), after the interaction of the estrogens with the Estrogen Receptor (ER) in the cells, the mechanism of activation possible is not only via direct binding of the ER to the Estrogen Responsive Elements (EREs) present in the promoter region of the target gene, very well described for many target genes, but that also other mechanisms are used: the interaction of the ER with the AP 1, Sp 1 and NFkB modes, that are discovered but not yet comprehensively described. The aim of my work is to produce a microarray DNA chip for the investigation of the estrogenic activity of different compounds present in the environment. The chip will consist of a selection of 100 genes that are estrogen responsive and it will cover the spectrum of activities of estrogenic compounds in various organs of the body. In the gene selection, genes were chosen that are estrogen responsive in the classical target tissues of estrogens, linked to reproduction, like uterus and mammary gland, and also in tissues not related to reproduction like liver, bones and capillars. In addition, other genes are included to monitor different pathways that are related to disease states; control of cell proliferation, apoptosis or cancer related genes. Currently these kinds of investigations are already in process, but by other methods which are more time consuming and with a lower throughput e.g. the gene expression profiling using the real time RT-PCR. The use of microarray’s satisfies the need for a less time consuming, high throughput method, to obtain a fast characterization of the gene expression finger print of the candidate substances and their mechanism of action in the organism. In my work I investigated the estrogenic potency of different Xenoestrogens that commonly occur in our daily life, in rat cells and tissue using well known estrogen sensitive genes like C3, Clu, IGFBP1 and CaBP9k. I focused on their effect on cell proliferation, studying PCNA expression. For the first time sensitivity of the gene CA2 was proofed in liver and uterus. A new identified mRNA sequence, r52, was characterized for its sensitivity to estrogenic exposure. This sequence was investigated at the molecular level expanding the known nucleic sequence. I produce a microarray chip with 16 genes to investigate the estrogenic potency of different compounds. As proof of principle of the microarray method completely produced in house I compared the result of gene expression obtained by the chip to that obtained by real time RT PCR finding a similarity of results. This new established method is less sensitive than the real-time RT PCR but allows a high throughput of gene expression analysis producing at the end a more complete picture of the expression signature of a compound.
49
King, Kevin R. (Kevin Robert) 1976. "High-throughput microfluidic living cell arrays for spatiotemporal gene expression profiling". Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/43809.
Pełny tekst źródłaStreszczenie:
Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008.Page 146 blank.
Includes bibliographical references.
The cellular microenvironment is remarkably complex. In the small space near each cell, growth factors are liberated from extracellular matrix, cytokines are secreted from neighboring cells, and hormones arrive from distant organs. These spatially and temporally diverse cues are integrated by signal transduction cascades to modulate the activity of transcription factors, the principle regulators of gene expression. To date, experimental investigation of spatial and temporal transcription factor activation patterns has been limited by the use of destructive measurement techniques that require averaging responses over large cell populations. Similarly, control of complex microenvironments has been limited by the use of static tissue culture platforms. This thesis describes development of a high-throughput experimental platform called the microfluidic living cell array (mLCA) that combines fluidically-addressable cell arrays with a library of GFP reporter cells to enable nondestructive spatiotemporal gene expression profiling in living cells. The first section describes construction of the GFP reporter library and the development of methodologies for performing routine seeding and culture of cells in microfluidic channels. Microfluidic circuits are then designed to achieve parallel control of soluble stimulus concentration and timing for delivery to downstream cells. A novel "Flow-encoded Switching" (FES) design strategy is introduced to control simultaneous delivery of temporally distinct stimulus patterns using a single input. These circuits are demonstrated by profiling dynamic transcriptional responses to cytokine stimulation, and in each case, cell responses are found to depend quantitatively and qualitatively on the timing of the stimulus.
(cont.) The second section describes development of a two-dimensional valve-controlled mLCA for simultaneously profiling the entire transcriptional reporter library in response to a panel of stimuli. Integrated microvalve arrays control row-seeding and column-stimulation of 256 nanoliter-scale bioreactors, creating a high density matrix of stimulus-response experiments. The platform is demonstrated in the context of the hepatocyte stress response by collecting -5000 single-time-point measurements in each automated and unattended experiment. Results from these studies revealed a novel relationship between TNF-alpha and heat shock response activation, and more generally, illustrated that a single cytokine can activate multiple transcription factors with distinct dynamics. The third section transitions from temporal to spatial profiling and describes discovery and exploration of a spatially heterogeneous gene expression pattern in the innate immune system. Using a stable monoclonal ISRE-GFP reporter, double-stranded DNA (dsDNA) stimulation is found to result in 'colonylike' patterns of reporter activity in an otherwise confluent monolayer. Cell sorting and expression profiling reveal that activated reporter colonies are functionally distinct from their non-activated neighbors, and that colonies are responsible for the majority of cytokine and chemokine expression, including the potent antiviral interferon-beta. Using a novel transplant co-culture experiment, colonies are shown to form by contact-dependent intercellular communication and furthermore, this communication is found to depend on gap junctions. In summary, this thesis introduces promising new tools for conducting high-throughput investigations of spatiotemporal gene expression patterns in living cells, and it provides evidence for a novel dsDNA-induced intercellular communication mechanism that amplifies innate immune responses.
by Kevin R. King.
Ph.D.
50
Sakian, Sina. "Investigation of methylation and gene expression in placenta of pregnancies conceived by assisted reproductive technology (ART)". Thesis, University of British Columbia, 2011. http://hdl.handle.net/2429/31191.
Pełny tekst źródłaStreszczenie:
With the increasing use of assisted reproductive techniques (ART) every year, concerns have been raised regarding the possible effect these procedures have on the health of the children procured by them. Although patients born via ART are usually healthy, studies have associated these procedures with increased incidence of low birth weight (LBW), chromosomal abnormalities, birth defects and imprinting disorders. No study has proposed a single defined cause for any of these defects in ART infants, however it is believed that they may be due to both the invasiveness of ART and to genetic defects that are at the root of the infertility in the parents. In this study, changes in the methylation of the H19 and IGF2 imprinting control region 1 (ICR1) were investigated for both ART (n=92) and naturally conceived controls (n=19) using pyrosequencing. Expression of H19 and IGF2 was also investigated for both the ART population (n=31) and controls (n=14) using quantitative real-time PCR.
No significant changes in H19 or IGF2 methylation or gene expression were found between the ART groups and the natural conception group. Methylation levels at ICR1 for the IVF, ICSI and control cases were averaged at 49.3% ±3.4%, 49.6%±1.9% and 48.7%±1.7%, respectively. Compared to the controls IVF and ICSI patients both showed an increase in H19 gene expression (by a factor of 1.78±0.74 and 1.93±0.71, respectively) while showing a decrease (by a factor of 0.83±0.34 and 0.74±0.27, respectively) for the expression of IGF2; these differences were not proven significant using ANOVA (P > 0.05). The study did find, however, that the previously proposed H19 and IGF2 regulatory model is not a good indicator of how these two genes are controlled in human placenta. Comparing methylation analysis with expression analysis did not show the expected negative correlation implying that there may be other factors influencing the expression of H19 and IGF2 in human placental tissue. Although our results suggest that ART does not have a significant negative effect on H19 and IGF2 imprinting in the placenta, it merits further investigation looking at the regulation of these two genes in this tissue.