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Playl, Lauren A. "Sry Transcript Expression in Five Adult Male Rat Tissues and Correlation with Acsl3 Transcript Expression." University of Akron / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=akron1290632541.
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Holst, Andy. "Automatic Transcript Generator for Podcast Files." Thesis, Linnaeus University, School of Computer Science, Physics and Mathematics, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-6936.
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<p>In the modern world, Internet has become a popular place, people with speech hearing disabilities and search engines can't take part of speech content in podcast les. In order to solve the problem partially, the Sphinx decoders such as Sphinx-3, Sphinx-4 can be used to implement a Auto Transcript Generator application, by coupling already existing large acoustic model, language model and a existing dictionary, or by training your own large acoustic model, language model and creating your own dictionary to support continuous speaker independent speech recognition system.</p>
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Tripodis, Nicholas. "Physical and transcript map 6p21.2-p21.3." Thesis, King's College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286740.
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Bechard, Jarrod. "Armet transcript knockdown in Tribolium castaneum." Thesis, Kansas State University, 2014. http://hdl.handle.net/2097/35220.
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Master of Science<br>Biochemistry and Molecular Biophysics Interdepartmental Program<br>Gerald R. Reeck<br>Armet has been found in mammalian systems to be a bi-functional protein that is secreted extracellularly and is also found in the endoplasmic reticulum. It has been shown to be a neurotrophic factor and also a member of the unfolded protein response. Transcript knockdown of Armet via RNA interference in late instar larvae of Tribolium castaneum produces a fatal phenotype during eclosion from pupa to adult. Initial observations of pupae cuticle indicate disorganization of cuticles in insects with the Armet transcript knocked down. Here I expand studies on the effects of dsArmet RNA injection; both in a wild type strain and a fluorescent strain of Tribolium, and discuss possible mechanisms for the fatal phenotype.
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Korostowski, Lisa. "Transcript Regulation within the Kcnq1 Domain." Diss., Temple University Libraries, 2012. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/235191.
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Molecular Biology and Genetics<br>Ph.D.<br>Epigenetics was a term first coined to understand how cells with the same genetic make up can differentiate into various cell types. Elegant research over the past 30 years has shown that these mechanisms include heritable marks such as DNA methylation and histone modifications along with stable expression of non- coding RNAs. Within the realm of epigenetics is a phenomenon known as genomic imprinting. Imprints are marks that distinguish the maternal from the paternal chromosomes in the form of methylation. Methylation marks can influence transcript expression, resulting in only one allele being expressed. One imprinted domain is the Kcnq1 domain located on chromosome 11p15.5 in humans and chromosome 7 in the mouse. This domain is thought to be under the control of a paternally expressed long noncoding RNA (ncRNA) Kcnq1ot1. The Kcnq1ot1 ncRNA is expressed on the paternal chromosome due to a differentially methylation region located within its promoter. The promoter is methylated on the maternal allele thus inhibiting ncRNA expression, whereas the promoter is unmethylated on the paternal allele. In the placenta, a most of the genes located within a one mega-basepair region are exclusively expressed from the maternal chromosome, whereas the transcripts on the paternal chromosome are silenced by the ncRNA. The placenta seems to follow the classic idea of an imprinted domain. However, in the embryo and more specifically, in the embryonic heart, this is not the case. In the embryonic heart, only a 400kb region is restricted to maternal expression. In addition, one the genes, Kcnq1, starts out expressed exclusively from the maternal allele in early development but switches to biallelic expression during mid-gestation. The purpose of my research is to determine the underlying complexities that are involved in the regulation of transcripts within the Kcnq1 domain. This involves the Kcnq1 gene itself, which has been shown to transition from mono- to biallelic expression during mid-gestation and the Kcnq1ot1 ncRNA per se. I hypothesize that regulation by the Kcnq1ot1 ncRNA is not occurring in a uniform manner in the embryo; rather, the amount of regulation by the ncRNA is dependent on the developmental stage and specific tissue. In addition, this regulation involves complex interactions between enhancers, insulators and other regulatory elements to control the amount of silencing by the Kcnq1ot1 ncRNA. First, through a series of experiments looking at the Kcnq1 promoter, the mechanism of Kcnq1 paternal expression was determined. It was confirmed that Kcnq1 becomes biallelic during mid-gestation in the heart. Bisulfite mutagenesis and methylation sensitive chromatin immunoprecipitation were used to test the hypothesis that the Kcnq1 promoter was methylated in early development and then lost its methylation mark. However, a lack of methylation disproved this mechanism of paternal Kcnq1 activation. Rather, chromosome conformation capture (3C) determined that the Kcnq1 promoter interacts in a tissue-specific manner with regions within the domain that have enhancer activity. The role of the ncRNA within our system was also investigated. Interestingly, when Kcnq1ot1 allelic expression was profiled throughout development in heart, it transitioned to biallelic expression during heart development but remained monoallelic in the liver and brain. Several possibilities could account for this phenomenon, including loss of promoter methylation and/or an alternative transcript start site. Both of these options were explored using bisulfite mutagenesis and 5' RACE. However, the Kcnq1ot1 promoter region retained its methylation mark even after the maternal transcript was turned on, disproving this idea. Rather, a maternal specific transcript was found in the heart to start downstream of the CpG islands. Lastly, to gain a better understand of the Kcnq1ot1 ncRNA, experiments were carried out on a mutant mouse in which a truncated form of the ncRNA was transmitted paternally; this is dubbed the "Kterm" mouse. Unexpectedly, Kcnq1 still followed the same mono- to biallelic transition as seen in the wild-type, whereas the head and body counterparts from the same stage embryos were biallelic for Kcnq1. Also, the immediate upstream genes, Cdk1nc and Slc22a18, lost their mono-allelic expression in neonatal heart, liver and brain when the Kterm mutation was transmitted. This suggested that Kcnq1ot1 did not function as a silencer for Kcnq1 paternal expression in the heart, but rather had an alternative and previously unknown function. From qRT-PCR, 3C and ChIP assays, it was determined that the Kcnq1ot1 ncRNA plays a role in regulating Kcnq1 gene expression in the heart by limiting its interaction to specific cis-acting enhancers. When the ncRNA was absent, the Kcnq1 promoter interacted with non-native sites along the domain, possibly causing the increase in transcript expression. This phenomenon was specific to the heart and was not seen in other tissues. These findings showed that Kcnq1 paternal expression is the result of strong developmental and tissue specific enhancers. Chromatin interactions in cis put a strong enhancer in contact with the Kcnq1 promoter to increase its expression in later development. In addition, a truncation mutation model identified a key role for the Kcnq1ot1 ncRNA in regulating Kcnq1 expression. Instead of regulating the imprinting status of Kcnq1, the ncRNA regulates the amount of Kcnq1 transcript being produced in the heart by regulating chromatin interactions. Finally, these studies identified a maternally expressed Kcnq1ot1 transcript whose role in heart development is still not fully understood. Taken together, these findings support a model where an inhibitory factor(s) silence the paternal Kcnq1 transcript and maternal Kcnq1ot1 transcript and in later development, this factor is released allowing for expression and chromatin interactions to occur.<br>Temple University--Theses
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Traulsen, Kathryn E. A. "Towards a transcript map of 4q32--q34." Thesis, University of Ottawa (Canada), 2003. http://hdl.handle.net/10393/26406.
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With the completion of the sequencing of the human genome near, the next phase will be to identify and annotate all transcriptional units. We have utilized a procedure that directly selects cDNA from genomic DNA in order to isolate putative transcriptional units for identification of novel genes at the 4q34 locus. In this procedure, cDNA fragments were isolated following the hybridization of cDNA pools to 7 BAC clones spanning the 4q34 region. The 4q34 region is approximately 2.0 Mb and contains 7 known genes and 8 predicted genes. In addition, EST evidence annotated in the public databases supports the notion that there are additional transcriptional units in this region. The primary cDNA pool used in this procedure was generated with a universal primer for amplification and cloning. Approximately 350 clones were analyzed by automated fluorescence sequencing and 26 clones were shown to originate from DNA at the 4q34 locus. The other clones included rRNA, mitochondrial DNA, repetitive sequences and low-copy repeat elements, similar to the results obtained in comparable cDNA selection attempts. The tentative transcriptional units have been arranged on the current map of the 4q34 region. This map will provide insight into the organization and function of this chromosome, and provide the preliminary framework for a detailed transcription map of the region. Furthermore, novel gene identification at this locus will provide candidates for Parkinson's disease, which has been mapped to this region by our laboratory.
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Ferrasi, Adriana Camargo [UNESP]. "Transcript finishing initiative: contribuição do laboratório IL2." Universidade Estadual Paulista (UNESP), 2003. http://hdl.handle.net/11449/87745.
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ferrasi_ac_me_rcla.pdf: 2629180 bytes, checksum: c178eeb179f2c77ab45bfcddeb648f51 (MD5)<br>O principal objetivo na análise de um genoma é a identificação gênica. Várias ferramentas computacionais estão disponíveis para este propósito e são baseadas em similaridade (BLAST e BLAT) ou em predição de genes (Genscan e Fgenes). Entretanto, estes programas estão se mostrando ineficientes para detectar e caracterizar todos os genes presentes no genoma humano. A importância das informações de cDNAs tem sido reconhecida desde o início do Projeto Genoma Humano, entretanto, o seqüenciamento em larga escala de cDNAs completos ainda requer técnicas avançadas tais como a produção de bibliotecas de cDNAs enriquecidas por transcritos grandes e raros. O seqüenciamento parcial de etiquetas de seqüências expressas (ESTs) foi desenvolvido como uma técnica alternativa para gerar, em larga escala, vários tipos de cDNAs. Atualmente, a maioria das informações de cDNAs no GenBank são representadas por ESTs convencionais 3þ e 5þ e ORESTES (provenientes das porções centrais dos transcritos). Baseados nos bancos de dados gerados pelo alinhamento de todas essas seqüências com as seqüências genômicas humanas disponíveis foi proposta a estratégia transcript finishing para a caracterização e validação de novos genes humanos, como parte do consórcio entre FAPESP e Instituto Ludwig de Pesquisa sobre o Câncer. O projeto Transcript Finishing Initiative está sendo realizado por uma rede de 31 diferentes grupos de pesquisa do Estado de São Paulo. Foram selecionados pela coordenação do projeto, 602 transcritos e destes 300 (50%) foram validados. Destes transcritos, 20 foram atribuídos ao laboratório validador IL2, e destes, 11 (55%) foram validados. Utilizando ferramentas de bioinformática, o laboratório IL2 realizou uma anotação preliminar dos consensos de seus transcritos validados (disponibilizados pela coordenação do projeto)... .<br>A fundamental task in analyzing genome is gene identification. This is relatively straightforward for compact genome but much more challenging for complex genomes. Some computational tools are available for this purpose, but they are bases on similarity (BLAST) or prediction analysis (Genscan and Fgenes). However, these programs are inefficient to detect and characterize all genes present in the genome. The importance of cDNA information has been recognized since the beginning of the Human Genome Project, however cost-effective and hightroughput sequencing of full-length cDNA still requires technical advances such as the production of cDNA libraries enriched for large and rare transcripts. Partial sequencing of expressed sequences (EST) has been developed as an alternative approach for the generation, in large-scale, of several kinds of cDNAs. Currently, the vast majority of cDNA data in the GenBank is represented both by conventional 5þand 3þexpressed sequence tags (ESTs) and by ORESTES (open reading frame ESTs), which is derived from central portions of the transcripts. Based on a database generated through alignment of all of these sequences to the available human genomic sequences, have been proposed the transcript finishing strategy for characterization and validation of new human genes, as part of the FAPESP-LICR Transcript Finishing Initiative. The strategy utilizes the ORESTES scaffold EST sequence to build primers for reverse transcription (RT) - PCR reactions in order to bridge gaps, thereby confirming the membership of ESTs to a common transcript and providing information on the intervening sequence (validation strategy). The FAPESP-LICR Transcript Finishing Initiative is being pursed by a network of 31 different research groups from the State of São Paulo (The Transcript Finishing Consortium) coordinated by 2 different laboratories... (Complete abstract click electronic address below).
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Akter, Parvis. "Transcript mapping in human cytomegalovirus strain AD169." Thesis, University of Glasgow, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394827.
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Ferrasi, Adriana Camargo. ""Transcript finishing initiative" : contribuição do laboratório IL2 /." Rio Claro : [s.n.], 2003. http://hdl.handle.net/11449/87745.
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Orientador: Maria Inês de Moura Campos Pardini<br>Banca: Maurício Bacci Junior<br>Banca: Magaly Machado Sales<br>Resumo: O principal objetivo na análise de um genoma é a identificação gênica. Várias ferramentas computacionais estão disponíveis para este propósito e são baseadas em similaridade (BLAST e BLAT) ou em predição de genes (Genscan e Fgenes). Entretanto, estes programas estão se mostrando ineficientes para detectar e caracterizar todos os genes presentes no genoma humano. A importância das informações de cDNAs tem sido reconhecida desde o início do Projeto Genoma Humano, entretanto, o seqüenciamento em larga escala de cDNAs completos ainda requer técnicas avançadas tais como a produção de bibliotecas de cDNAs enriquecidas por transcritos grandes e raros. O seqüenciamento parcial de etiquetas de seqüências expressas (ESTs) foi desenvolvido como uma técnica alternativa para gerar, em larga escala, vários tipos de cDNAs. Atualmente, a maioria das informações de cDNAs no GenBank são representadas por ESTs convencionais 3þ e 5þ e ORESTES (provenientes das porções centrais dos transcritos). Baseados nos bancos de dados gerados pelo alinhamento de todas essas seqüências com as seqüências genômicas humanas disponíveis foi proposta a estratégia "transcript finishing" para a caracterização e validação de novos genes humanos, como parte do consórcio entre FAPESP e Instituto Ludwig de Pesquisa sobre o Câncer. O projeto "Transcript Finishing Initiative" está sendo realizado por uma rede de 31 diferentes grupos de pesquisa do Estado de São Paulo. Foram selecionados pela coordenação do projeto, 602 transcritos e destes 300 (50%) foram validados. Destes transcritos, 20 foram atribuídos ao laboratório validador IL2, e destes, 11 (55%) foram validados. Utilizando ferramentas de bioinformática, o laboratório IL2 realizou uma anotação preliminar dos consensos de seus transcritos validados (disponibilizados pela coordenação do projeto)... (Resumo completo, clicar acesso eletrônico abaixo).<br>Abstract: A fundamental task in analyzing genome is gene identification. This is relatively straightforward for compact genome but much more challenging for complex genomes. Some computational tools are available for this purpose, but they are bases on similarity (BLAST) or prediction analysis (Genscan and Fgenes). However, these programs are inefficient to detect and characterize all genes present in the genome. The importance of cDNA information has been recognized since the beginning of the Human Genome Project, however cost-effective and hightroughput sequencing of full-length cDNA still requires technical advances such as the production of cDNA libraries enriched for large and rare transcripts. Partial sequencing of expressed sequences (EST) has been developed as an alternative approach for the generation, in large-scale, of several kinds of cDNAs. Currently, the vast majority of cDNA data in the GenBank is represented both by conventional 5þand 3þexpressed sequence tags (ESTs) and by ORESTES (open reading frame ESTs), which is derived from central portions of the transcripts. Based on a database generated through alignment of all of these sequences to the available human genomic sequences, have been proposed the transcript finishing strategy for characterization and validation of new human genes, as part of the FAPESP-LICR Transcript Finishing Initiative. The strategy utilizes the ORESTES scaffold EST sequence to build primers for reverse transcription (RT) - PCR reactions in order to bridge gaps, thereby confirming the membership of ESTs to a common transcript and providing information on the intervening sequence (validation strategy). The FAPESP-LICR Transcript Finishing Initiative is being pursed by a network of 31 different research groups from the State of São Paulo (The Transcript Finishing Consortium) coordinated by 2 different laboratories... (Complete abstract click electronic address below).<br>Mestre
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Wollmann, Heike. "MiRNA targeting mechanisms - translation inhibition versus transcript cleavage /." Tübingen, 2009. http://opac.nebis.ch/cgi-bin/showAbstract.pl?sys=000251923.
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Day, Robert Charles, and n/a. "Transcript analysis of proliferative endosperm from Arabidopsis thaliana." University of Otago. Department of Biochemistry, 2008. http://adt.otago.ac.nz./public/adt-NZDU20080703.113233.
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Arabidopsis has emerged as an important model system for molecular plant biology. The extensive resources available for Arabidopsis make it an attractive system to study the molecular mechanisms involved in early seed development. During the early stages of seed development Arabidopsis endosperm is syncytial and proliferates rapidly through repeated rounds of mitosis without cytokinesis. This stage of endosperm development is both important in determining final seed size and is a model for studying various aspects of cellular and molecular biology, such as the cell cycle and genomic imprinting. However, the small size of Arabidopsis seed, the syncytial nature of the proliferative endosperm, and the surrounding maternal tissues make high throughput molecular analysis of the early endosperm technically difficult.
To get around this we used laser capture microdissection to enable transcript analysis of the early proliferative endosperm of Arabidopsis at 4 days after pollination (DAP). Microarray results identified several thousand genes with endosperm expression, including many that were endosperm preferred. A number of genes were validated by relative quantification PCR and were consistent with the findings of the microarray. Meta analysis of the endosperm transcriptome revealed a developmental program dominated by mitosis and under the influence of several phytohormones, predominated by cytokinin signaling.
The list of endosperm-preferred genes included all characterised imprinted genes in Arabidopsis. Imprinting is an epigenetic phenomenon by which genes are expressed predominantly from either their paternal or their maternal allele and very few imprinted genes have been identified in plants. The mono-allelic expression of the characterised imprinted genes appears to be limited to the endosperm where they provide important regulatory controls for seed development via direct effects on endosperm development. Genes from the endosperm-preferred list were screened for mono-allelic expression using sequence polymorphisms between the Colombia and Landsberg erecta ecotypes. We generated PCR products that spanned the polymorphisms of 67 genes from template obtained by laser capture of endosperm tissue from hybrid seed. Sequence analysis revealed three genes which gave strong allelic bias toward the maternal allele (At2g32460, At1g55550 and At2g21420) and one biased for the paternal allele (At1g47840).
In summary, laser capture microdissection has enabled high-resolution transcript analysis of the proliferative stage of Arabidopsis endosperm development. The data generated provides a useful resource providing novel insight into early seed development, facilitating both identification of endosperm expressed and novel imprinted genes.
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Adamo, Alessio. "Characterisation of unusual transcript classes in Arabidopsis thaliana." Thesis, University of Leeds, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.505089.
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Eades, T. L. "An analysis of transcript variation in human Xp11.23." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598721.
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This thesis describes an analysis of the genome features and gene content in human Xp11.22-p11.3. Human Xp11.23 has the highest density of genes in the human X chromosome, and this analysis identified 77 known and 11 novel genes. The pseudogene content of this region was also high – it contained 59 processed and 7 non-processed pseudogenes. More detailed investigation of these revealed that the number and diversity of gene products generated from genes within Xp11-23 greatly exceeded the number of coding regions that it contained. In order to further study the impact of alternative splicing in Xp11-23 detailed analysis was completed on 18 genes using bioinformatics and comparative analysis together with a targeted RT-PCR sequencing strategy. This analysis identified more than 120 transcripts variants. Preliminary tissue profiling of these transcripts was completed using RT-PCR. The functional consequences of alternative splicing were then investigated for one gene, polyglutamine binding protein 1, <i>PQBP1. </i>This ubiquitously expressed gene has been associated with various disease phenotypes including X-linked mental retardation. Renpenning syndrome and other neurodegenerative disorders. In concert with expression and evolutionary analysis, a cloned open reading frame collection was generated, for 16 transcript variants. The relative abundance of minor transcript variants was determined in a panel of 20 human tissues where it was found that together the minor variants accounted for less than 10% of the all <i>PQBP1 </i>transcripts. Following <i>in silico</i> analysis of the predicted protein sequences, it was found that transcript variation was associated with variable inclusion of a nuclear localisation signal.
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Gardner, M. J. "Circadian rhythms in transcript abundance in Arabidopsis thaliana." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.599310.
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To characterise the circadian transcriptome, the expression profiles of transcripts in whole leaves of mature, soil grown <i>A. thaliana </i>plants were analysed. Circadian-regulated transcripts constituted approximately 9.5% of the transcripts detected, and were found to encode proteins involved both a well-described circadian processes and in pathways that have not been previously identified as having circadian regulation. Transcripts encoding proteins involved in core metabolic processes and stress response pathways were particularly highly representative in the dataset, which suggested a potential basis for the fitness benefits associated with the possession of a functional biological clock. To determine the correlation between rhythms in transcript abundance in whole leaves and in a single cell type, the stomatal guard cell was selected as a model system. However, assessment of two published methods of guard cell isolation, epidermal fragmentation and guard cell protoplasting, revealed that neither method was suitable for analysis of circadian rhythms in transcript abundance. Consequently, single cell analysis was not pursued. Nevertheless, bio-informatic analysis of the whole leaf circadian transcriptome and published microarray data was employed in order to characterise components of the intra-cellular circadian signalling pathway. This analysis revealed a relationship between the circadian oscillator and the regulator of [Ca<sup>2+</sup>]<sub>cyt</sub> release, cyclic adenosine disphosphate ribose (cADPR). Evidence is presented suggesting that circadian [Ca<sup>2+</sup>]<sub>cyt</sub> oscillations form a component of the oscillator that maintains the periodicity of circadian rhythms in transcript abundance. Collectively the data presented provide an overview of the biological clock in <i>A. thaliana</i>, and form a resource for further analysis of the structure of the clock and its role in integrating diverse cellular and physiological processes into a coherent biological programme.
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Lu, Lu. "Statistical methods in a high school transcript survey." [Ames, Iowa : Iowa State University], 2009.
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Simpson, Yvonne A. "Investigation of a novel Ercc1 transcript predominant in skin." Thesis, University of Edinburgh, 2004. http://hdl.handle.net/1842/27399.
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In this project the skin-specific pattern of expression was studied by transfecting <i>Ercc1 </i>null cells with the minigenes. The <i>Ercc1 </i>null cells used were murine embryonic fibroblasts, PF24<sup>+</sup>#12D-4; Chinese hamster ovary cells, CHO43.3B (TG1); and murine keratinocytes; Ker. (-/-). IN survival studies were performed on transfected cells and RT-PCR was used to study the pattern of <i>Ercc1 </i>expression. Transfection with the <i>Ercc1 </i>minigenes corrected the IN sensitivity of the null cell lines. The <i>Ercc1 </i>expression pattern was usually, but not always; appropriate for the cell type transfected. Comparisons between the <i>Ercc1 </i>transcription of <i>in vitro </i>cultures and <i>in vivo </i>tissues taken from various stages of murine development were made by means of northern blotting. Irradiation of transfected cells and primary cultures with UV-B. UV-C and visible light was performed in an attempt to identify possible sources of transcript induction. Small changes in <i>Ercc1 </i>transcription following irradiation of primary cultures were observed, but these changes did not conclusively prove that visible light or UV could induce <i>Ercc1 </i>transcription. Serum starvation experiments were performed upon primary cultures to further study differences in <i>Ercc1 </i>transcription <i>in vitro. </i>Release from serum starvation resulted in increased skin-specific transcript production and total <i>Ercc1 </i>expression. The size of the skin-specific <i>Ercc1 </i>transcript in keratinocytes was found to be larger than that of fibroblasts. Sequencing demonstrated that the size difference was in the (CT)<sup>n</sup> repeat region of the gene. This region was deleted from one of the <i>Ercc1 </i>minigenes mentioned and results indicated that it may be required for correct expression of the novel transcript.
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Sievertzon, Maria. "Transcript profiling of small tissue samples using microarray technology." Doctoral thesis, Stockholm Department of Biotechnology, Royal Institute of Technology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-158.
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Buskist, Connie. "Transcript analysis and teacher study group improving comprehension instruction /." Auburn, Ala., 2005. http://repo.lib.auburn.edu/2005%20Fall/Dissertation/BUSKIST_CONNIE_7.pdf.
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Matsubara, Shigeki, Tomohiro Ohno, and Masaki Murata. "Automatic Linefeed Insertion for Improving Readability of Lecture Transcript." Springer, 2009. http://hdl.handle.net/2237/15115.
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Benovoy, David. "Characterization of transcript isoform variations in human and chimpanzee." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=66918.
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Transcript expression and pre-mRNA processing are emerging as important mechanisms that increase the complexity of eukaryotic transcriptomes. These processes allow a genomic locus to produce a number of mRNAs and proteins with distinct properties that affect function, stability, and sub-cellular localization by controlling the rate of transcript expression, by varying the initiation or termination of transcription and by modulating the inclusion of exons (alternative splicing) in mature mRNAs. Thus, it is crucial to determine the extent of these types of variations to better understand their importance in creating organism diversity. The studies described in this thesis provide the first genome-wide estimations of how single nucleotide polymorphisms (SNPs) affect the regulation of transcript expression and pre-mRNA processing in a human population as well as between humans and chimpanzees using a microarray-based approach. We first demonstrated that transcript expression changes at the isoform level are common between two unrelated individuals and that these changes are heritable and therefore have an underlying genetic component. We then investigated what proportion was under genetic control in a normal human population by conducting a genome-wide association analysis between single nucleotide polymorphisms and transcript isoform variants. We found that 50-55% of transcript expression variation is isoform based. We also extended our comparison of human transcript isoform variation to chimpanzee. We showed that genetic substitutions in regulatory sequences are responsible for some of the isoform variations observed between these two closely related species. We ascertained that in our study these isoform variations are responsible for certain phenotypic differences mostly related to immune responses. These results constitute an important change in the way genetic variations are viewed in humans and chimpa<br>Le niveau d'expression d'un transcrit et les processus de maturation de celui-ci en ARN messager (ARNm) se révèlent être des mécanismes augmentant la complexité du transcriptome des eucaryotes. Ces processus permettent au même locus génomique de produire plusieurs ARNm et protéines ayant des propriétés distinctes qui affectent leurs fonctions, leur stabilité et leurs localisations intra cellulaire en contrôlant la vitesse de transcription, en variant le site d'initiation ou de terminaison de la transcription et en modulant l'inclusion d'exons (épissage) dans les ARNm matures. Il est donc primordial de déterminer l'ampleur de ces types de variations afin de mieux comprendre leur impact sur la diversite des oraganismes. Les études décrites dans cette thèse fournissent les premières estimations de la façon dont les variations de polymorphism nucléotidique simple (SNP) peuvent affecter la régulation de l'expression d'un transcrit et ses processus de maturation à l'échelle du génome entier. Ces processus sont examinés dans une population humaine et entre humain et chimpanzé en utilisant une méthode basée sur les puces à ADN. Nous démontrons d'abord l'existence d'un nombre important de variations d'isoformes d'ARNm entre deux individus non apparentés et nous démontrons que ces variations sont héritées ce qui leur révèle une composante génétique. Par la suite, nous avons déterminé quelle proportion et quel type de variation au niveau de l'isoform était sous contrôle génétique dans une population humaine. En réalisant une analyse d'association entre l'expression des transcrits du génome entier et les SNPs présents dans cette population, nous avons observé que 50-55% de la variation était à l'échelle de l'isoforme du transcrit. Nous avons aussi étendu cette comparaison au chimpanzé en utilisant les profils d'expression mesurés lors de l'analyse précédente. N
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Arribere, Joshua A. (Joshua Alexander). "Transcript leaders : annotation and insight into functions in translation." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/83763.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2013.<br>CD-ROM contains PDF of title page and .txt of tables.<br>Cataloged from PDF version of thesis. Vita.<br>Includes bibliographical references.<br>For a eukaryotic mRNA to be properly expressed, it undergoes a series of several steps, including transcription, modification, splicing, packaging, export, localization, translation, and decay. Of these steps transcription is the most extensively studied, though the remaining steps are also indispensible for proper protein production. While we understand many of these steps in biochemical detail in vitro, we have a much poorer knowledge of how they occur and are regulated for a given gene in vivo. Posttranscriptional regulation is carried out primarily through the noncoding portions of the mRNA: the Transcript Leader (TL or 5'UTR) upstream of the Open Reading Frame (ORF), and the 3'Untranslated Region (3'UTR) downstream. To understand how these regions affect post-transcriptional gene expression, it is critical to have precise annotations of the mRNA(s) produced from a gene. In Chapter 2 I describe the development of Transcript Leader Sequencing (TL-seq), a technique to annotate TLs, and demonstrate its utility in yeast. TL-seq annotations reveal interesting TL-dependent regulation, including transcription within ORFs and short TLs that are associated with translation initiation at the second AUG of the ORE. To further study the roles of TLs in translation, I develop Translation-Associated Transcript Leader Sequencing (TATL-seq). TATL-seq works by applying TL-seq across fractions of a polysome gradient, generating TL-specific translational measurements. This approach demonstrates a widespread inhibitory function for upstream AUGs (uAUGs), and that ~6% of yeast genes express multiple TL species with distinct translational activities. This demonstrates that alternative TLs are prevalent and functional even in a relatively simple eukaryote like yeast. My interest in alternative TLs prompted me to explore TL variation in mammals, where many thousands of genes are known to have alternative TLs. In Chapter 3 I enumerate the contributions of alternative mRNA processing events to alternative TLs in mice. I observe alternative TLs produced by alternative Transcription Start Sites (TSSs), and also demonstrate that alternative splicing events, such as skipped exons and alternative splice sites, contribute substantially to functional TL diversity. To facilitate the future study of alternative TLs in mammals, in Appendix I I modify TL-seq to sequence longer TL fragments and optimize TL-seq's enzymatic steps to reduce input RNA requirements. This thesis is concerned with understanding post-transcriptional mRNA expression both globally and gene-specifically. In particular, I seek to understand the role the Transcript Leader has in affecting translation and degradation of its transcript. The findings detailed here define and analyze discernable features of TLs that relate to translational properties of the downstream message. Furthermore, the techniques developed enable analyses of TLs and translation that could not be carried out with previous technologies.<br>by Joshua A. Arribere.<br>Ph.D.
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Tarr, Sarah Jayne. "Drug-induced changes in transcript profiles in Plasmodium falciparum." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609333.
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De, Witt Riaan Neethling. "Correlating metabolite and transcript profiles in transgenic sugarcane lines." Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/80286.
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Thesis (MSc)--Stellenbosch University, 2013.<br>ENGLISH ABSTRACT: See item for full abstract<br>AFRIKAANS OPSOMMING: Sien item vir volteks<br>IPB, National Research Foundation (NRF) and SASRI for funding
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Domaszewska, Teresa. "Unraveling transcript-based variability of host responses to Tuberculosis." Doctoral thesis, Humboldt-Universität zu Berlin, 2019. http://dx.doi.org/10.18452/19829.
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Jedes Jahr treten weltweit über zehn Millionen Fälle von Tuberkulose (TB) auf. Die Weltgesundheitsorganisation (WHO) schätzt, dass ein Drittel der Weltbevölkerung mit dem Erreger Mycobacterium tuberculosis (Mtb) infiziert ist. Bei fünf bis zehn Prozent aller latent Infizierten bricht Tuberkulose im Laufe des Lebens aus. Dennoch sind bereits 100 Jahre seit der Entdeckung von Mtb vergangen, ohne dass die entscheidenden Faktoren für den unterschiedlichen Infektionsverlauf bekannt wären. In dieser Arbeit untersuche ich die unterschiedlichen Reaktionen auf eine Tuberkuloseinfektion in verschiedenen Wirten. In meinem ersten Ansatz habe ich öffentlich zugängliche Transkriptom-Datensätze von Tuberkulosepatienten und gesunden Probanden ausgewertet. Mit Hilfe der Gensatzanreicherungs-Analyse (eng. Gene Set Enrichment Analysis, GSEA) habe ich die Transkriptionsprofile von Tuberkulosepatienten betrachtet. Das besondere Augenmerk lag hierbei auf der Interferon (IFN)-Signalkaskade, die für den Krankheitsverlauf von besonderer Bedeutung ist. In dieser Arbeit zeige ich zunächst, dass Patienten ohne eine IFN-Signatur in der untersuchten Kohorte vorkommen und widme mich im Anschluss der Frage, ob diese Patienten einen anderen Phänotypus haben als jene mit einer starken IFN-Antwort. Indem ich nur Patienten ohne IFN-Antwort betrachte, werden Mechanismen deutlich, die allen Patientengruppen gemein sind, aber vorher von der starken IFN-Signatur überlagert wurden. Ich belege in dieser Arbeit, dass eine starke IFN-Regulation auch mit einer ausgeprägten Lungenpathologie in Tuberkulosepatienten einhergeht. Passend hierzu weisen auch gesunde Probanden nach Verabreichung des Impfstoffs FLUAD® einen erhöhten Blutwert IFN-induzierter Zytokine auf. Mit Hilfe maschinellen Lernens konnte ich Transkriptomsignaturen der Patienten mit bzw. ohne IFN-Antwort identifizieren und vergleichen. Im zweiten Ansatz widme ich mich den unterschiedlichen Transkriptionsantworten auf Mtb-Infektionen in humanen Kohorten und zwei verschiedenen Mausmodellen. Der humanen und der murinen Immunantwort auf Infektionen unterliegen gravierende Unterschiede. Trotzdem sind einige Elemente des Immunsystems in beiden Arten konserviert. In dieser Arbeit präsentiere ich einen neuen Ansatz der Datenintegration, der die Identifizierung von übereinstimmenden und nicht übereinstimmenden Regulationselementen der Genexpression in heterogenen Datensätzen ermöglicht. Die Analyse basiert auf öffentlich zugänglichen sowie de-novo-generierten Datensätzen, zu denen ich durch wissenschaftliche Kollaborationen meiner Kollegen in der Abteilung Immunologie sowie der zentralen Einheit Microarray des Max-Planck-Instituts für Infektionsbiologie, Zugang erhalten habe. Des Weiteren liegt ein Schwerpunkt auf der vergleichenden Analyse humaner und muriner Transkriptionsantworten auf Tuberkulose in Vollblut und Makrophagen. Die erhaltenen Ergebnisse weisen auf einen signifikanten Unterschied in der Regulierung der angeborenen sowie der erworbenen Immunität in Mensch und Maus als Reaktion auf eine Mtb-Infektion hin. In dieser Arbeit charakterisiere ich die unterschiedliche Regulierung von T-Zell bezogenen Genen, die mit unterschiedlich ausgeprägten Phänotypen bei stark oder schwach TB-anfälligen Mausstämmen korrespondiert. Darüber hinaus habe ich den 21. Tag nach einer Tuberkuloseinfektion in Mäusen als Zeitpunkt ermittelt, der die Transkriptionsantworten in den untersuchten humanen Kohorten am besten widerspiegelt. Die angewandten Ansätze erleichtern die Auswahl des am besten geeigneten Tiermodells für die Erforschung der humanen Immunantwort auf eine ausgewählte Krankheit und liefern die Basis für ein besseres Verständnis der unterschiedlichen Krankheitsverläufe in Mtb-infizierten Patienten.<br>Over 10 million tuberculosis (TB) cases are being reported annually and the World Health Organization (WHO) estimates that up to the 1/3 of the world population is infected with Mycobacterium tuberculosis (Mtb). Between 5 and 10% of the latently infected individuals develop TB during their lifetime. Yet, despite over 100 years of research since Mtb has been identified, we are not able to define all the factors which are responsible for the different infection outcomes in the hosts. In this thesis I investigate the variability in the response to TB presented by different hosts. In one approach, I collect publicly available transcriptomic datasets from TB patients and healthy donors. Using Gene Set Enrichment Analysis (GSEA) I examine transcriptional profiles of individuals with TB. In particular, focus is brought to interferon (IFN) signaling which has been previously described as crucial for the disease outcome. I show that patients lacking IFN signature are present in the studied cohorts and investigate whether these patients present different phenotype than patients with strong regulation of IFN responses. Moreover, by focusing on patients lacking IFN response I try to unearth mechanisms present in all patient groups but dominated by the signal of IFN response. I show that strong regulation of IFN genes is related to severe pathology in the lungs of TB patients and that it is reflected by the levels of IFN-inducible cytokines in blood of healthy volunteers after vaccination with FLUAD® vaccine. Using Machine Learning (ML) methods, I identify and compare transcriptomic signatures of the patients presenting and lacking the IFN response.
In the second approach I study the differences in the transcriptional responses to Mtb infection in human cohorts and two different mouse models. The immunity in infection, inflammation and malignancy differs markedly in man and mouse. Nevertheless, there are elements of immune system which have been conserved between the species. I propose a novel data integration approach which identifies concordant and discordant elements of gene expression regulation in heterologous datasets. The analysis is based on publicly available as well as novel experimental data acquired thanks to collaboration with my colleagues from the Department of Immunology and Microarray Core Facility of Max Planck Institute for Infection Biology (MPIIB). Additionally, I focus on the comparison of human and murine transcriptional responses to TB in whole blood (WB) and in macrophages. The results indicate profound differences between regulation of innate and adaptive immunity in man and mouse upon Mtb infection. I characterize differential regulation of T-cell related genes corresponding to the differences in phenotype between TB high and low susceptible mouse strains and identify the time point of 21 days p.i. of mice as best reflection of transcriptional responses in the studied human cohorts. The implemented approaches facilitate the choice of an appropriate animal model for studies of the human immune response to a particular disease and provide the basis for better understanding of differences in the outcomes of Mtb infection in individual hosts.
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Rosani, Umberto. "Transcriptional responses and AMP transcript diversity in M. galloprovincialis." Doctoral thesis, Università degli studi di Padova, 2012. http://hdl.handle.net/11577/3422157.
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The present dissertation contains the work done during my PhD in Biotechnology (2009-2011) and, through three published articles, shows how the research group which I worked in has contributed to the development of functional genomics in the mollusc bivalve Mytilus galloprovincialis.
Using different approaches, we aimed to better understand the peculiarities of a transcriptome only partially investigated, focusing our attention on molecules possibly explaining the mussel innate immunity, defense system that allows the survival of this organism in potentially lethal habitats.
Starting from a publicly available collection of expressed sequence tags (ESTs) generated from various tissues of native mussels or from mussels subjected to various stress conditions, we have analyzed and described relevant transcript groups and singletons involved in the mussel immune responses. A selection of these sequences has been used to design a new DNA-microarray platform (Immunochip 1.0), a new tool for the experimental validation of the many gene transcripts possibly playing a role in the sensing, signaling and effector functions of the mussel innate immunity (Venier et al., 2011).
DNA microarray platforms are widely used to investigate the expression of thousands of transcripts and, in general, they provide reliable and dynamic measures of transcriptional trends. As far as the genus Mytilus, species-specific platforms and also platforms including probes of evolutionary close species are available (Domeneghetti et al., 2011).
Using an advanced sequencing approach, we have finally explored and mapped the transcriptional diversity of nine typical antimicrobial peptides expressed in mussels (defensins, mytilins, myticins and mytimycin): although different one from the other, a high frequency of single nucleotide changes was globally evident (Rosani et al., 2011). These results pave the way to study genetic and epigenetic mechanisms able to explain the observed transcript diversity, yet undetermined in mussel, and to characterize, from a functional point of view, sequence variants expressed in response to different antigenic stimuli<br>La presente tesi raccoglie il lavoro svolto durante il mio dottorato in biotecnologie (2009-2011) e, tramite tre articoli pubblicati, mostra come il gruppo di ricerca entro il quale mi sono inserito ha contribuito ad ampliare le conoscenze nel campo della genomica funzionale del mollusco bivalve Mytilus galloprovincialis. Utilizzando differenti approcci abbiamo cercato di comprendere aspetti di un trascrittoma solo parzialmente conosciuto, soffermandoci sulle molecole dell'immunità innata, sistema difensivo grazie al quale questo organismo invertebrato sopravvive in ambienti ricchi di patogeni.
Avendo a disposizione una collezione di sequenze espresse (EST) rappresentativa di vari tessuti di mitili nativi e di mitili sottoposti a varie condizioni di stress, abbiamo analizzato e descritto alcuni importanti singole sequenze e gruppi di trascritti coinvolti nelle risposte immuni del comune mitilo mediterraneo. Una selezione di questi è stata utilizzata per disegnare una piattaforma DNA-microarray (Immunochip 1.0) utile a validare sperimentalmente la grande varietà di trascritti genici potenzialmente implicati nel sensing, nel signalling e in funzioni effettrici dell’immunità innata di M. galloprovincialis (Venier et al., 2011).
Le piattaforme DNA microarray sono ormai largamente utilizzate per lo studio in parallello dell'espressione di migliaia di trascritti e, in generale, forniscono misure affidabili e dinamiche degli andamenti trascrizionali. Riguardo al genere Mytilus, sono state sviluppate piattaforme specie-specifiche e piattaforme ibride che includono sonde nucleotidiche di specie evolutivamente affini (Domeneghetti et al., 2011).
Utilizzando un approccio di sequenziamento avanzato, abbiamo infine esplorato e mappato la diversità trascrizionale di nove tipici peptidi antimicrobici espressi in mitilo (varie defensine, mitiline, miticine e mitimicina) scoprendo così, pur con differenze da caso a caso, una elevata frequenza di cambiamenti a singolo nucleotide (Rosani et al., 2011). Sulla base di questi risultati sarà interessante studiare meccanismi genetici ed epigenetici che possano spiegare tale variabilità di sequenza, ancora indeterminati in mitilo, e caratterizzare da un punto di vista funzionale le varianti espresse in risposta a diversi stimoli antigenici
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Furbush, Mary M. "Analyzing and reporting high school transcript and academic achievement data." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 6.87 Mb., 124 p, 2006. http://proquest.umi.com/pqdlink?did=1176542701&Fmt=7&clientId=79356&RQT=309&VName=PQD.
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Ruan, Wenjie. "Evolution of two modes of intrinsic RNA polymerase transcript cleavage." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-136940.
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Kucuk, Muhammet Erdi. "Kollector : transcript-informed targeted de novo assembly of gene loci." Thesis, University of British Columbia, 2017. http://hdl.handle.net/2429/61362.
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The information stored in nucleotide sequences is of critical importance for modern biological and medical research. However, in spite of considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time-consuming task that requires a significant amount of computational resources and expertise, and remains beyond the reach of many researchers. One solution to this problem is restricting the assembly to a portion of the genome, which is typically a small region of interest. Genes are the most obvious choice for this kind of targeted assembly approach, as they contain the most relevant biological information, which can be acted upon downstream. Here we present Kollector, a targeted assembly pipeline that assembles genic regions using the information from the transcript sequences. Kollector not just enables researchers to take advantage of the rapidly expanding transcriptome data, but is also scalable to large eukaryotic genomes. These features make Kollector a valuable addition to the current crop of targeted assembly tools, a fact we demonstrate by comparing Kollector to the state-of-the-art. Furthermore, we show that by localizing the assembly problem, Kollector can recover sequences that cannot be reconstructed by a whole genome de novo assembly approach. Finally, we also demonstrate several use cases for Kollector, ranging from comparative genomics to viral strain detection.<br>Science, Faculty of<br>Graduate
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Passador-Gurgel, Gisele Candia. "Quantitative Trait Transcript Mapping for Drug Response in Drosophila melanogaster." NCSU, 2005. http://www.lib.ncsu.edu/theses/available/etd-11132005-160424/.
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Here I used microarrays to identify genes that are activated or repressed by nicotine and caffeine in Drosophila melanogaster. I compared genotypes with differential resistance to each drug in order to select genes that may be involved in resistance to the drugs. Comparison of the genes differentially expressed by both drugs leads me to propose that there are common mechanisms of metabolic resistance to caffeine and nicotine, in particular cytochrome P-450-mediated mechanisms. Caffeine seems to have a more dramatic influence on gene expression than nicotine, in particular on expression of genes involved in energy metabolism. Next, I extended the studies on nicotine resistance to ask whether there are differences in response between two populations of Drosophila. The gene expression patterns of both populations were evaluated separately and in a combined analysis. Most of the differentially expressed genes were up-regulated by nicotine in both populations and in the combined analysis. The induced transcripts were mainly related to protein, nucleic acid, amino acid and energy metabolism, and response to stimulus and stress. Those findings suggest that amino acid and energy metabolism may be important biological processes affected by nicotine and be interesting targets for further investigation related to the nicotine response in Drosophila. The two populations displayed considerable differences in gene expression profiling that may be the result of the observed phenotypic variation for nicotine response between the two populations. Most of the differential expression induced by nicotine seems to be specific to the more resistant population. Finally, I focused on genes whose expression showed significant correlation with survival time on nicotine food. Using a regression approach, it was possible to map quantitative trait transcripts associated to nicotine response. Control expression of alkaline phosphatase and ornithine aminotransferase displayed significant correlation to survival time in drug food. They seem to be linked to regulation of GABA/glutamate neurotransmission and detoxification mechanisms, which ultimately counteracts the stimulatory effects of nicotine.
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Huang, Hao 1967. "Transcript profiling of a MAP kinase pathway in C. albicans." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=98726.
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In C. albicans, a MAP kinase pathway has been implicated in aspects of controlling hyphal development. We have examined the transcription profile of cells deleted for the transcription factor Cph1 as well as Cst20, Hst7 and Cek1, three upstream kinases potentially involved in Cph1 regulation. Deletion of these four elements does not block filament induction by serum and does not dramatically affect the transcription profile of yeast-hyphal transition, but deletion of CPH1 delays filamentation. Over-expression of Cph1 by ADH1pt-CPH1 significantly enhances filamentation, suggesting that Cph1 is helpful but not essential for filament induction. Interestingly, the transcription profile of ADH1pt-CPH1 expressing cells under yeast conditions is similar to that of wild type strains undergoing the yeast-hyphal transition. Finally, it appears that Cek1 and its regulators Hst7 and Cst20 may control the repression of genes such as CHT2 through a process independent of the Cph1p transcription factor.
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Darch, Sarah Jane. "The physiology and pathology of cocaine and amphetamine regulated transcript." Thesis, Imperial College London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.425335.
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Boudonck, Kurt. "Dynamic organization of transcription and transcript processing components in plants." Thesis, University of East Anglia, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302341.
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Hobson, D. J. "RNA polymerase II collision & its role in transcript elongation." Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1365987/.
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Antisense non-coding transcripts, genes-within-genes, and convergent gene pairs are prevalent among eukaryotes. The existence of such transcription units raises the question of what happens when RNA polymerase II (RNAPII) molecules collide head-to-head. In this study a combination of biochemical and genetic approaches in yeast are used to show that polymerases transcribing opposite DNA strands cannot bypass each other. RNAPII stops, but does not dissociate upon head-to-head collision in vitro, suggesting that opposing polymerases represent insurmountable obstacles for each other. Head-to-head collision in vivo also results in RNAPII stopping, and removal of collided RNAPII from the DNA template can be achieved via ubiquitylation-directed proteolysis. Indeed, in cells lacking efficient RNAPII poly-ubiquitylation, the half-life of collided polymerases increases, so that they can be detected between convergent genes. These results provide new insight into fundamental mechanisms of gene traffic control, and point to an unexplored effect of antisense transcription on gene regulation via polymerase collision.
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Llibre, Alba. "Expression, regulation and function of lectin-like transcript 1 (LLT1)." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:bc16a4f5-103b-4322-9647-eda802ed7157.
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Receptor-ligand pairs of C-type lectin-like proteins have been shown to orchestrate and modulate immune responses within particular immune cell subsets or in distinct body locations. The function of CD161 and Lectin-Like Transcript 1 (LLT1) has not been extensively studied, partially due to the lack of validated anti-LLT1 antibodies. Here, I characterised two novel anti-LLT1 monoclonal antibodies (2H7 and 7G7). Using them for flow cytometric and immunohistological staining, I characterised the expression of LLT1 in different healthy human tissues and found that LLT1 levels were particularly high in immune-privileged sites. Germinal centres (GC) are microanatomical structures that are critical for the development of high-affinity antibodies and B cell memory. They are organised into two zones, light and dark, with coordinated roles controlled by local signalling. LLT1 protein is known to be expressed on B cells, but its functional role in the GC reaction has not been explored. I found high expression of LLT1 on GC-associated B cells, early plasmablasts and GC- derived lymphomas. LLT1 expression was readily induced via BCR, CD40 and CpG stimulation on B cells. Ubiquitous expression of CD161 on Follicular Dendritic Cells (FDCs) was revealed, as well as on a subset of T follicular cells. Triggering of LLT1 supported B cell activation, CD83 upregulation and Chemokine (C-X-C Motif) Receptor 4 (CXCR4) downregulation, which is consistent with a role in drivingtransition from a dark to a light zone phenotype. Overall, these data suggest that LLT1-CD161 interactions play a novel and important role in B cell maturation within the GC in humans. A deep understanding of the GC reaction and the process of B cell selection could provide invaluable knowledge into effective vaccine design, generation of auto-antibodies and malignant transformation.
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Shi, Xu. "Bayesian Modeling for Isoform Identification and Phenotype-specific Transcript Assembly." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/79772.
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The rapid development of biotechnology has enabled researchers to collect high-throughput data for studying various biological processes at the genomic level, transcriptomic level, and proteomic level. Due to the large noise in the data and the high complexity of diseases (such as cancer), it is a challenging task for researchers to extract biologically meaningful information that can help reveal the underlying molecular mechanisms. The challenges call for more efforts in developing efficient and effective computational methods to analyze the data at different levels so as to understand the biological systems in different aspects. In this dissertation research, we have developed novel Bayesian approaches to infer alternative splicing mechanisms in biological systems using RNA sequencing data.
Specifically, we focus on two research topics in this dissertation: isoform identification and phenotype-specific transcript assembly. For isoform identification, we develop a computational approach, SparseIso, to jointly model the existence and abundance of isoforms in a Bayesian framework. A spike-and-slab prior is incorporated into the model to enforce the sparsity of expressed isoforms. A Gibbs sampler is developed to sample the existence and abundance of isoforms iteratively. For transcript assembly, we develop a Bayesian approach, IntAPT, to assemble phenotype-specific transcripts from multiple RNA sequencing profiles. A two-layer Bayesian framework is used to model the existence of phenotype-specific transcripts and the transcript abundance in individual samples. Based on the hierarchical Bayesian model, a Gibbs sampling algorithm is developed to estimate the joint posterior distribution for phenotype-specific transcript assembly. The performances of our proposed methods are
evaluated with simulation data, compared with existing methods and benchmarked with real cell line data. We then apply our methods on breast cancer data to identify biologically meaningful splicing mechanisms associated with breast cancer. For the further work, we will extend our methods for de novo transcript assembly to identify novel isoforms in biological systems; we will incorporate isoform-specific networks into our methods to better understand splicing mechanisms in biological systems.<br>Ph. D.
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Sherwood, Tracy. "Characterization of Cannabinoid Receptor 2 Transcript Expression in B Cells." Scholar Commons, 2010. https://scholarcommons.usf.edu/etd/1767.
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Cannabinoids and cannabinoid receptors have been shown to play important roles in immune regulation particularly as modulators of anti-inflammatory cytokines and antibody production. The predominant cannabinoid receptor involved in this immune regulation is cannabinoid receptor 2 (CB2), which is robustly expressed in B cells. Utilizing a combination of bioinformatics, 5' RACE, real time RT-qPCR, and reporter assays, we showed that human B cells from peripheral blood mononuclear cells (PBMC) expressed one CB2 transcript while mouse B cells from spleen express three CB2 transcripts. Alignment of the sequenced B cell RACE products to either the mouse or human genome, along with the GenBank mRNA sequences, revealed that the transcripts isolated in this study contained previously unidentified transcriptional start sites (TSSs). In addition, expression construct testing of the genomic region containing the TSSs of the mouse CB2 exon 1 and 2 transcripts showed a significant increase of promoter activity. Bioinformatics analysis for cis-sequences in the promoter regions identified DNA binding sites for NF-kB, STAT6, and Elk1 transcription factors activated by LPS, IL-4 and anti-CD40. Regarding variations in CB2 transcript expression among the immune cell subtypes, RACE analysis showed that the exon 1b transcript is seen in B cells but not in T cells, dendritic cells or macrophages. Furthermore, RT-qPCR showed variations in transcript expression during B cell development as well as in resting versus LPS or IL-4/anti-CD40 stimulated B cells. The exon 1a transcript was predominant in pre-, immature and resting B cells whereas the exon 1b and 2 transcripts were enhanced in mature and activated B cells. These data showed for the first time that human B cells use one TSS for CB2 expression while mouse B cells use multiple TSSs for the expression of three CB2 transcripts, in which the expression of the individual transcript is related to immune cell type and/or cell activation state. Additionally, this is the first report in mouse B cells defining TSSs that are in genomic areas with promoter activity thus suggesting the location of two promoter regions. Defining the CB2 transcript expression during various stages of B cell activation provide clues to therapeutic methods.
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TRIA, VALERIA. "CHARACTERIZATION OF EIF3E TRANSCRIPT: ROLE IN MAMMARY DEVELOPMENT AND CARCINOGENESIS." Doctoral thesis, Università degli Studi di Milano, 2013. http://hdl.handle.net/2434/217466.
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Il gene EIF3E (eukaryotic translation initiation factor 3 subunit e) è stato identificato inizialmente in topo come sito di integrazione del virus MMTV (mouse mammary tumor virus). Nel genoma umano EIF3E è un gene di 45 Kb localizzato nella porzione 22-23 del braccio lungo del cromosoma 8 e codifica per un RNA messaggero di 1516 nucleotidi e una proteina di 445 amminoacidi (52 KDa). L’integrazione del virus MMTV negli introni (5, 9, 12) del gene EIF3E causa la trascrizione di RNA tronchi. L’espressione di tali trascritti tronchi è in grado di indurre un fenotipo tumorale sia in vitro che in vivo. Sebbene sia stata individuata l’esistenza di una correlazione tra il tumore mammario ed EIF3E, non è ancora noto l’esatto ruolo che il gene svolge nell’insorgenza e nella progressione del carcinoma mammario. Sono numerose le funzioni associate ad EIF3E nelle cellule eucariotiche. EIF3E è coinvolto nella regolazione dell’espressione proteica sia come subunità del complesso EIF3 (Eukaryotic translation Initiation Factor 3), sia controllando la qualità di specifici RNA messaggeri attraverso il nonsense-mediated decay (NMD) sia regolando il turnover di specifiche proteine. EIF3E è inoltre coinvolto nella regolazione dell’integrità e stabilità genomica in quanto coinvolto nel meccanismo del “DNA damage response”, nella replicazione del DNA e nella mitosi.
Questo progetto di dottorato è focalizzato sullo studio del gene EIF3E ed del suo coinvolgimento nella formazione e nella progressione del tumore mammario. Abbiamo analizzato attraverso RT-qPCR l’espressione di EIF3E in diversi tessuti umani non tumorali. EIF3E ha un livello di espressione più alto nella ghiandola mammaria rispetto ad altri tessuti, questo risultato suggerisce come EIF3E possa avere una peculiare funzione nella ghiandola mammaria e sue variazioni possano essere correlate al tumore al seno. Valutando l’espressione di EIF3E in tessuti normali e tumorali della ghiandola mammaria provenienti da diversi pazienti abbiamo osservato come l’espressione di EIF3E diminuisce nel tessuto tumorale rispetto al tessuto normale.
Attraverso esperimenti in vitro abbiamo dimostrato come la down-regolazione di EIF3E sia in grado di indurre un fenotipo tumorale in cellule primarie normali della ghiandola mammaria e aumentare la tumorigenicità nelle MCF7. Analizzando quale possa essere la funzione di EIF3E nella formazione e progressione tumorale abbiamo osservato come modificando l’espressione di EIF3E si causano cambiamenti nei livelli di alcuni mRNA, coinvolti in aspetti chiave della progressione tumorale .<br>The eukaryotic translation initiation factor 3 e-subunit (EIF3E) gene was originally identified in mouse as an integration site of the Mouse Mammary Tumour Virus (MMTV). EIF3E is a 45Kb gene localized to region q22-23 of the human chromosome 8, encodes a mRNA of 1516 nt that is translated into a 52KDa protein of 445 amino acids. Integration of MMTV into EIF3E introns (5, 9 or 12) causes the expression of truncated transcripts. These shortened EIF3E transcripts induce malignant transformation demonstrated both in vitro and in vivo. The exact nature of EIF3E involvement in tumorigenesis is not fully understood. The EIF3E protein controls various types of cellular processes in eukaryotic cells. Studies showed that EIF3E regulates protein expression through its role as a subunit of the eukaryotic translation initiation 3 complex, by controlling the quality of specific mRNAs by nonsense-mediate decay (NMD) and the process of the protein turnover. EIF3E is also involved in maintenance of genome integrity and stability by its role in DNA damage response, mitosis and replication.
This Ph.D. work focused on studying the involvement of EIF3E in the human breast cancer. We evaluated the EIF3E expression in different normal human tissues by RT-qPCR. We observed that EIF3E has higher expression levels in the human mammary gland compared to other tissues analyzed. We hypothesize that EIF3E deregulation has a role in breast cancer. Analyzing the EIF3E expression in normal and cancer breast tissues, we determined that the EIF3E expression level is lower in tumor samples compared to their healthy counterparts.
Down regulation of EIF3E was found to induce a malignant phenotype in normal primary cells and increase malignancy in MCF7 cells, respectively. We investigated the role of EIF3E in breast cancer initiation and progression. EIF3E modulation resulted in loss of control of the expression of specific mRNAs involved in key aspects in the cancer process.
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Bahari, Azlina. "Approaches to understanding diversity in rubber and carotenoid synthesis in Hevea brasiliensis latex." Thesis, University of Dundee, 2019. https://discovery.dundee.ac.uk/en/studentTheses/73b6fffb-faf0-4fb9-94f1-aa9bbb330154.
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<i>Hevea brasiliensis </i>latex contains a large quantity of high molecular weight rubber and is thus the primary commercial source of natural rubber. Rubber and other non-rubber isoprenoids in <i>Hevea </i>latex are synthesised from isopentenyl diphosphate (IPP) generated from the cytoplasmic mevalonate (MVA) pathway and the plastidic methyl erythritol phosphate pathway (MEP). This study utilised two rubber tree clones (RRIM600 and PB235) that show visibly contrasting levels of yellow carotenoids for the measurement of latex isoprenoids (carotenoids, rubber and isoprenoid intermediates) and transcript levels of the genes involved in isoprenoid biosynthesis. Metabolite extraction and analysis showed that four major carotenoids namely lutein, zeaxanthin, α-carotene and β-carotene were consistently present in both RRIM600 and PB235 latex. β-carotene was found to be the major carotenoid, at 1.2 μg/g in PB235 and 0.8 μg/g in RRIM600 fresh latex samples. However, the analytical method developed to measure isoprenoid intermediates needed to be further optimised to increase extraction efficiency. To enable accurate measurement of transcript levels of key genes involved in the isoprenoid biosynthetic pathway, a set of reference transcripts was constructed by merging short-reads (RNA-seq) and long-reads (Iso-seq and full-length cDNA sequences) data from <i>Hevea brasiliensis</i>. This produced a comprehensive set of 193,997 transcript sequences with good level of coverage of predicted transcripts and highly conserved core plant genes. Not only did the reference transcriptome update the annotation of rubber gene models, additional transcript variants were also discovered. Manual curation of gene models for key steps associated with rubber and carotenoids resulted in a repertoire of 115 genes, with 151 corresponding transcript variants. Subsequently, differential expression analysis on the basis of mapping RRIM600 and PB235 RNA-seq reads to the reference transcriptome revealed isoform-specific expression of genes for biosynthesis of carotenoids (PSY isoform 2), IPP (AACT2 and HMGR1) and rubber (REFSRPP gene members). In addition, the levels of these genes correlated positively with the carotenoid and rubber content measurements from the same latex of PB235 and RRIM600 used for metabolite extraction. Finally, the utility of the reference transcript catalogue was demonstrated by the characterisation of the REFSRPP gene family, which is involved in rubber elongation steps. REFSRPP gene family showed a local expansion which appear to be unique to <i>Hevea</i>. A pilot study has demonstrated there is considerable diversity of the genomic region containing the duplicated REFSRPP genes.
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Yang, Suk-Hwan. "Transcript profiling of differentiating xylem of loblolly pine (Pinus taeda L.)." Texas A&M University, 2004. http://hdl.handle.net/1969.1/1380.
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Wood formation (xylogenesis) is a critical developmental process for all woody land plants. As an initial step to understand the molecular basis for temporal and spatial regulation of xylogenesis and the effect of the expression of individual genes on physical and chemical properties of wood, microarray and realtime RTPCR analyses were performed to monitor gene expression during xylogenesis under various developmental and environmental conditions. The specific objectives established for this study were: Objective 1. Microarray analysis of genes preferentially expressed in differentiating xylem compared to other tissues of loblolly pine (see Chapter II); Objective 2. Microarray analysis of seasonal variation in gene expression for loblolly pines (Pinus taeda L.) from different geographical sources (see Chapter III); Objective 3. Realtime RTPCR analysis of loblolly pine AGP and AGPlike genes (see Chapter IV). Based on the results from this study, candidate genes may be further studied for association with significant traits, used for genetic modification of wood properties, or included in future studies to further examine the molecular mechanisms of wood
formation.
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Pesch, Robert [Verfasser], and Ralf [Akademischer Betreuer] Zimmer. "Cross-species network and transcript transfer / Robert Pesch. Betreuer: Ralf Zimmer." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2016. http://d-nb.info/1084582902/34.
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Dorrell, Richard G. "Coevolution of plastid genomes and transcript processing pathways in photosynthetic alveolates." Thesis, University of Cambridge, 2014. https://www.repository.cam.ac.uk/handle/1810/246266.
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Following their endosymbiotic uptake, plastids undergo profound changes to genome content and to their associated biochemistry. I have investigated how evolutionary transitions in plastid genomes may impact on biochemical pathways associated with plastid gene expression, focusing on the highly unusual plastids found in one group of eukaryotes, the alveolates. The principal photosynthetic alveolate lineage is the dinoflagellate algae. Most dinoflagellate species harbour unusual plastids derived from red algae. The genome of this plastid has been fragmented into small, plasmid-like elements termed “minicircles”. Transcripts of this genome receive a 3’ poly(U) tail and, in some species, undergo extensive sequence editing. Some dinoflagellates have replaced their original plastids with others, in a process termed “serial endosymbiosis”. The major non-photosynthetic alveolates are the apicomplexans, which include the malaria parasite Plasmodium. Apicomplexans are descended from free-living algae and possess a vestigial plastid, which originated through the same endosymbiosis as the ancestral red dinoflagellate plastid. This plastid has lost all genes involved in photosynthesis and does not possess a poly(U) tail addition pathway. I have investigated the consequences of the fragmentation of the red algal dinoflagellate plastid genome on plastid transcription. I have characterised non-coding transcripts in plastids of the dinoflagellate Amphidinium carterae, including the first evidence for antisense transcripts in an algal plastid. Antisense transcripts in dinoflagellate plastids do not receive poly(U) tails, suggesting that poly(U) tail addition may play a role in strand discrimination during transcript processing. I have additionally characterised transcript processing in dinoflagellate plastids that were acquired through serial endosymbiosis. I have shown that poly(U) tail addition and editing occur in the haptophyte-derived serial endosymbionts of the fucoxanthin-containing dinoflagellates Karenia mikimotoi and Karlodinium veneficum. This is the first evidence that plastids acquired through serial endosymbiosis may be supported by pathways retained from previous symbioses. Transcript editing constrains the phenotypic consequences of divergent mutations in fucoxanthin plastid genomes, whereas poly(U) tail addition plays a central role in recognising and processing translationally functional fucoxanthin plastid mRNAs. I have additionally shown that certain genes within fucoxanthin plastids are located on minicircles. This demonstrates convergent evolution in the organisation of the fucoxanthin and red algal dinoflagellate plastid genomes since their endosymbiotic acquisition. Finally, I have investigated transcript processing in the algae Chromera velia and Vitrella brassicaformis. These species are closely related to apicomplexans but are still photosynthetic and apply poly(U) tails to plastid transcripts, as with dinoflagellates. I have shown that poly(U) tails in these species are preferentially associated with translationally functional mRNAs of photosynthesis genes. This is the first plastid transcript processing pathway documented to target a specific functional gene category. Poly(U) tail addition may direct transcript cleavage and allow photosynthesis gene transcripts to accumulate to high levels. The loss of this pathway from ancestors of apicomplexans may have contributed to their transition from photosynthesis to parasitism.
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Matsubara, Shigeki, Tomohiro Ohno, and Masaki Murata. "Construction of linefeed insertion rules for lecture transcript and their evaluation." Inderscience, 2010. http://hdl.handle.net/2237/15206.
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Murphy, Kevin. "The biochemical and physiological role of cocaine-and amphetamine- regulated transcript." Thesis, Imperial College London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.396349.
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Borthwick, Jane Martha. "Determination of the transcript profiles of normal human endometrium and endometriosis." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596785.
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The human endometrium is a complex tissue that undergoes an idealised 28-day cycle, strictly controlled by the ovarian steroid hormones. Endometriosis is a common disease affecting 10% of all women of reproductive age. It is characterised by severe abdominal pain, and can result in infertility. Current treatment strategies for this disease are insufficient. In this study, I determine the transcript profiles of normal human endometrium and endometriosis, in the hope that they may lead to improved treatments for this debilitating disease. I use microarray technology to determine the levels of tens of thousands of transcripts in a range of endometrial samples. Through the application of a range of sophisticated statistical techniques, specifically designed for the analysis of extensive microarray data sets, I identify transcripts that are present at significantly different levels in eutopic endometrium, from women with and without endometriosis, and in peritoneal ectopic endometriotic lesions. I discover a number of transcripts that have not previously been identified in either the endometrium or endometriosis, and report three new factors that may be important in the correct cycling of the endometrium or in the pathology of endometriosis. I propose that glutathione peroxidase 3 is required in the endometrium during the secretory phase of the menstrual cycle to protect implanting blastocysts from free radical damage. I suggest that intestinal trefoil protein TFF3 may be required for the correct remodelling of the endometrium following menstruation, and I implicate the transcription factor four and a half LIM domains 1 in the establishment of endometriotic lesions at ectopic sites. These findings offer novel insights into the regulation of the endometrium and its potential pathologies. The identification of these new transcripts in the endometrial system are a step towards the development of improved treatments for endometriosis.
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Behr, Jonas [Verfasser], and Gunnar [Akademischer Betreuer] Rätsch. "Transcript identification from deep sequencing data / Jonas Behr ; Betreuer: Gunnar Rätsch." Tübingen : Universitätsbibliothek Tübingen, 2014. http://d-nb.info/1196801436/34.
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Mohr, Carmen [Verfasser], and Britta [Akademischer Betreuer] Hartmann. "Sex-specific transcript complexity in the neural system of Drosophila melanogaster." Freiburg : Universität, 2016. http://d-nb.info/1139639382/34.
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Abdulrazzak, Hassan. "Characterisation of the cerebellar Purkinje-cell type dystrophin transcript and promoter." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394323.
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Mikaeili, Hajar. "Investigating the role of FXN antisense transcript 1 in Friedreich ataxia." Thesis, Brunel University, 2017. http://bura.brunel.ac.uk/handle/2438/16496.
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Friedreich ataxia (FRDA) is a neurodegenerative disorder that is inherited in an autosomal recessive pattern. The most common FRDA mutation is hyperexpansion of a GAA triplet repeat sequence in the first intron of the affected gene, frataxin (FXN), resulting in decreased frataxin protein expression. The hyperexpanded GAA repeats can adopt unusual DNA structures and induce aberrant epigenetic changes leading to heterochromatin mediated gene silencing. Several epigenetic changes, including increased levels of DNA methylation, histone modifications, repressive chromatin formation and elevated levels of non-coding RNA have been reported in FRDA. It has been reported that a novel FXN antisense transcript (FAST-1), is present at higher levels in FRDA patient-derived fibroblasts and its overexpression is associated with the depletion of CTCF, a chromatin insulator protein, and heterochromatin formation involving the critical +1 nucleosome. Previously, characteristics of FAST-1 were investigated in our lab and a full-length FAST-1 transcript containing a poly (A) tail was identified. To investigate any possible effects of FAST-1 on FXN expression, I first overexpressed this FAST-1 transcript in three different non-FRDA cell lines and a consistent decrease of FXN expression was observed in each cell type compared to control cells. I also identified that FAST-1 copy number is positively correlated with increased FAST-1 expression, which in turn is negatively correlated with FXN expression in FAST-1 overexpressing cells. Additionally, we found that FAST-1 overexpression is associated with increased levels of DNA methylation at CpG sites U6 and U11 of the FXN upstream GAA repeat region, together with CTCF depletion and heterochromatin formation at the 5'UTR of the FXN gene. To further investigate the role of FAST-1 in FXN gene silencing, I used a small hairpin RNA (shRNA) strategy to knock down FAST-1 expression in FRDA fibroblast cells. I found that knocking down FAST-1 increases FXN expression, but not to the level of control cells. Lastly, I investigated the pattern of FAST-1 expression and histone modifications at the FXN transgene in our new FRDA mouse model, designated YG8LR. The YG8LR mice showed decreased levels of FXN expression and H3K9ac and increased levels of FAST-1 expression and H3K9me3. Our data suggest that since FAST-1 is associated with FXN gene silencing, inhibition of FAST-1 may be an approach for FRDA therapy.
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Gu, Muxin. "Functions of histone H2A.Z in regulating transcript levels in budding yeast." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/functions-of-histone-h2az-in-regulating-transcript-levels-in-budding-yeast(06037caf-3b7c-4442-a1f4-b6755fdec250).html.
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The histone variant H2A.Z is an important regulator of transcription. One unsolved mystery is that why H2A.Z can have both activating and repressive effects on gene expression. By examining both coding and non-coding RNA transcripts in S.cerevisiae, we established that H2A.Z is present at both coding and non-coding promoters and have positive effects on the level of transcripts. The repressive effect of H2A.Z can be partially explained by the sense transcripts of gene being antagonised by H2A.Z-activated antisense transcripts. We also established that H2A.Z-associated non-coding transcripts are predominantly located at bidirectional promoters. The sense and antisense pairs produced from bidirectional promoters show high degrees of coregulation (especially co-activation) during stress response. Surprisingly, we found that the non-coding RNA co-activated with stress-response genes tend to spread the activation signal to the neighbouring gene further upstream, indicating their potential functions in gene regulation. In addition, we also observed that accumulation of H2A.Z at gene promoters is associated with slower recovery from gene induction, which could be related to the Ino80 pathway. In general, our results confirmed the interleaved nature of regulatory system in eukaryotes and highlighted the importance of taking both coding and non-coding transcripts into account while studying the transcriptional regulation.
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Scruggs, Phouangmala C. "Cocaine- and amphetamine-regulated transcript peptide attenuates baroreflex in the rat." [Johnson City, Tenn. : East Tennessee State University], 2002. http://etd-submit.etsu.edu/etd/theses/available/etd-1220102-150637/restricted/ScruggsP013103a.pdf.
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