subject:(RNA Seq)

Boston College

1. Busby, Michele Anne. Measuring Gene Expression With Next Generation Sequencing Technology.

Degree: PhD, Biology, 2012, Boston College

URL: http://dlib.bc.edu/islandora/object/bc-ir:101179

► While 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… (more)

▼ While 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… Advisors/Committee Members: Gabor Marth (Thesis advisor).

Subjects/Keywords: RNA-Seq

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Busby, M. A. (2012). Measuring Gene Expression With Next Generation Sequencing Technology. (Doctoral Dissertation). Boston College. Retrieved from http://dlib.bc.edu/islandora/object/bc-ir:101179

Chicago Manual of Style (16^th Edition):

Busby, Michele Anne. “Measuring Gene Expression With Next Generation Sequencing Technology.” 2012. Doctoral Dissertation, Boston College. Accessed September 21, 2019. http://dlib.bc.edu/islandora/object/bc-ir:101179.

MLA Handbook (7^th Edition):

Busby, Michele Anne. “Measuring Gene Expression With Next Generation Sequencing Technology.” 2012. Web. 21 Sep 2019.

Vancouver:

Busby MA. Measuring Gene Expression With Next Generation Sequencing Technology. [Internet] [Doctoral dissertation]. Boston College; 2012. [cited 2019 Sep 21]. Available from: http://dlib.bc.edu/islandora/object/bc-ir:101179.

Council of Science Editors:

Busby MA. Measuring Gene Expression With Next Generation Sequencing Technology. [Doctoral Dissertation]. Boston College; 2012. Available from: http://dlib.bc.edu/islandora/object/bc-ir:101179

University of Manchester

2. Lia, Andrei-Stefan. An RNA-Seq approach to investigate light-controlled gene expression in Neurospora crassa with emphasis on red light-mediated responses.

Degree: 2015, University of Manchester

URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259316

► ABSTRACTThe University of ManchesterAndrei-Stefan LiaMaster of PhilosophyAn RNA-Seq approach to investigate light-controlled gene expression in Neurospora crassa with emphasis on red light-mediated responses14th of October… (more)

Subjects/Keywords: RNA-Seq; phytochrome

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APA (6^th Edition):

Lia, A. (2015). An RNA-Seq approach to investigate light-controlled gene expression in Neurospora crassa with emphasis on red light-mediated responses. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259316

Chicago Manual of Style (16^th Edition):

Lia, Andrei-Stefan. “An RNA-Seq approach to investigate light-controlled gene expression in Neurospora crassa with emphasis on red light-mediated responses.” 2015. Doctoral Dissertation, University of Manchester. Accessed September 21, 2019. http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259316.

MLA Handbook (7^th Edition):

Lia, Andrei-Stefan. “An RNA-Seq approach to investigate light-controlled gene expression in Neurospora crassa with emphasis on red light-mediated responses.” 2015. Web. 21 Sep 2019.

Vancouver:

Lia A. An RNA-Seq approach to investigate light-controlled gene expression in Neurospora crassa with emphasis on red light-mediated responses. [Internet] [Doctoral dissertation]. University of Manchester; 2015. [cited 2019 Sep 21]. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259316.

Council of Science Editors:

Lia A. An RNA-Seq approach to investigate light-controlled gene expression in Neurospora crassa with emphasis on red light-mediated responses. [Doctoral Dissertation]. University of Manchester; 2015. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259316

3. Frazee, Alyssa Christine. High-resolution gene expression analysis.

Degree: 2015, Johns Hopkins University

URL: http://jhir.library.jhu.edu/handle/1774.2/37934

► RNA sequencing (RNA-seq) measures gene expression in cell populations at an unprecedented resolution. The advent of this new technology around 2008 spurred the need for… (more)

Subjects/Keywords: RNA-seq; differential expression

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APA (6^th Edition):

Frazee, A. C. (2015). High-resolution gene expression analysis. (Thesis). Johns Hopkins University. Retrieved from http://jhir.library.jhu.edu/handle/1774.2/37934

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Frazee, Alyssa Christine. “High-resolution gene expression analysis.” 2015. Thesis, Johns Hopkins University. Accessed September 21, 2019. http://jhir.library.jhu.edu/handle/1774.2/37934.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Frazee, Alyssa Christine. “High-resolution gene expression analysis.” 2015. Web. 21 Sep 2019.

Vancouver:

Frazee AC. High-resolution gene expression analysis. [Internet] [Thesis]. Johns Hopkins University; 2015. [cited 2019 Sep 21]. Available from: http://jhir.library.jhu.edu/handle/1774.2/37934.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Frazee AC. High-resolution gene expression analysis. [Thesis]. Johns Hopkins University; 2015. Available from: http://jhir.library.jhu.edu/handle/1774.2/37934

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universidade Estadual de Campinas

4. Calzado, Felipe, 1991-. Análise comparativa do mecanismo de secreção de proteínas heterólogas em Aspergillus nidulans = Comparative analysis of the heterologous protein secretion in Aspergillus nidulans .

Degree: 2017, Universidade Estadual de Campinas

URL: http://repositorio.unicamp.br/jspui/handle/REPOSIP/325418

► Resumo: Como forma de diminuir o uso de energias de origem fóssil e aumentar a utilização de energias renováveis, há um grande incentivo mundial recente… (more)

▼ Resumo: Como forma de diminuir o uso de energias de origem fóssil e aumentar a utilização de energias renováveis, há um grande incentivo mundial recente no desenvolvimento de biorrefinarias, o que envolve processos de conversão integrada de biomassa vegetal e equipamentos para produção de energia, combustíveis e produtos químicos renováveis. Nesta perspectiva o etanol de segunda geração obtido a partir da conversão de biomassa vegetal lignocelulósica em açúcares fermentáveis tem sido foco de muitas pesquisas atualmente a fim de viabilizar seu uso. No entanto, devido à natureza recalcitrante da biomassa lignocelulósica, o custo de processamento corrente na produção de biocombustíveis se torna um importante gargalo a ser superado. Uma das formas de superar este problema é melhorar a produção de enzimas necessárias na etapa de hidrólise enzimática da biomassa vegetal, um processo ainda hoje considerado muito caro. Os fungos filamentosos se destacam na produção e secreção de enzimas lignocelulolíticas de forma homóloga e heteróloga, entretanto pouco se sabe sobre a regulação dos mecanismos de secreção de proteínas nestes microrganismos. Pensando nisso, a utilização do fungo filamentoso modelo Aspergillus nidulans se torna um importante recurso de estudos por ser geneticamente bem caracterizado. Nosso objetivo neste trabalho foi realizar a análise comparativa dos mecanismos de secreção de diferentes proteínas heterólogas em A. nidulans a partir de dados de transcriptoma gerados pela técnica de RNA-seq (Next Generation RNA sequencing). Para monitorar o processo de secreção, adotamos 3 genes alvo: alfa-arabinofuranosidase GH51 (AbfA) e beta-glucosidase GH3 (BglC) de A. fumigatus, e mananase GH5 termofílica (1542) de Thermotoga petrophila. Estes genes foram transformados em A. nidulans, sendo que para AbfA atingiu-se altos níveis de secreção, diferente de BglC e 1542, onde os níveis de secreção foram mínimos. Com isso foram definidos perfis transcriptômicos dos genes relacionados a secreção de proteínas em A. nidulans, representando a resposta da super expressão de três genes heterólogos em diferentes tempos de indução. Em geral houveram processos biológicos super-regulados relacionados principalmente ao metabolismo, proteínas com função ligante, transporte e defesa celulares. Além disso, foram identificados 17 genes diferencialmente expressos envolvidos diretamente com a via de secreção de A. nidulans, representando importantes alvos para manipulação genética deste organismo. Este foi o primeiro estudo que descreve a resposta transcriptômica da secreção de proteínas heterólogas em A. nidulans, gerando uma nova perspectiva ao comparar três diferentes proteínas heterólogas com níveis crescentes de secreção; Abstract: As a way to reduce the use of fossil fuels and increase the use of renewable energies, there is a major recent worldwide incentive in the development of biorefineries, which involves integrated conversion processes of plant biomass and equipment for the production of energy, fuels and renewable chemicals. In this… Advisors/Committee Members: Damásio, André Ricardo de Lima, 1983- (advisor), Persinoti, Gabriela Felix (advisor), Silva, Roberto do Nascimento (committee member), Winck, Flavia Fisch (committee member).

Subjects/Keywords: Aspergillus; RNA-seq; Expressão heteróloga

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Calzado, Felipe, 1. (2017). Análise comparativa do mecanismo de secreção de proteínas heterólogas em Aspergillus nidulans = Comparative analysis of the heterologous protein secretion in Aspergillus nidulans . (Thesis). Universidade Estadual de Campinas. Retrieved from http://repositorio.unicamp.br/jspui/handle/REPOSIP/325418

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Calzado, Felipe, 1991-. “Análise comparativa do mecanismo de secreção de proteínas heterólogas em Aspergillus nidulans = Comparative analysis of the heterologous protein secretion in Aspergillus nidulans .” 2017. Thesis, Universidade Estadual de Campinas. Accessed September 21, 2019. http://repositorio.unicamp.br/jspui/handle/REPOSIP/325418.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Calzado, Felipe, 1991-. “Análise comparativa do mecanismo de secreção de proteínas heterólogas em Aspergillus nidulans = Comparative analysis of the heterologous protein secretion in Aspergillus nidulans .” 2017. Web. 21 Sep 2019.

Vancouver:

Calzado, Felipe 1. Análise comparativa do mecanismo de secreção de proteínas heterólogas em Aspergillus nidulans = Comparative analysis of the heterologous protein secretion in Aspergillus nidulans . [Internet] [Thesis]. Universidade Estadual de Campinas; 2017. [cited 2019 Sep 21]. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/325418.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Calzado, Felipe 1. Análise comparativa do mecanismo de secreção de proteínas heterólogas em Aspergillus nidulans = Comparative analysis of the heterologous protein secretion in Aspergillus nidulans . [Thesis]. Universidade Estadual de Campinas; 2017. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/325418

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Louisiana State University

5. Bedre, Renesh. Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline.

Degree: PhD, 2016, Louisiana State University

URL: etd-07112016-114436 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2251

► Aflatoxins are toxic and potent carcinogenic metabolites produced by Aspergillus flavus and A. parasiticus. Aflatoxins can contaminate cottonseed under conducive environmental conditions. Much success has… (more)

▼ Aflatoxins are toxic and potent carcinogenic metabolites produced by Aspergillus flavus and A. parasiticus. Aflatoxins can contaminate cottonseed under conducive environmental conditions. Much success has been achieved by the application of atoxigenic strains of A. flavus for controlling aflatoxin contamination in cotton, peanut and maize. Development of aflatoxin-resistant cultivars overexpressing resistance-associated genes and/or knocking down aflatoxin biosynthesis of A. flavus could be an effective strategy for controlling aflatoxin contamination in cotton. In this study, differentially expressed genes (DEGs) were identified in response to infection with both toxigenic and atoxigenic strains of A. flavus pericarp and seed of cotton through genome-wide transcriptome profiling. The genes involved in antifungal response, oxidative burst, transcription factors, defense signaling pathways and stress response were highly differentially expressed in pericarp and seed tissues in response to A. flavus infection. The cell-wall modifying genes and genes involved in the production of antimicrobial substances were more active in pericarp than seed. Genes involved in defense response in cotton were highly induced in pericarp. The DEGs will serve as the source for identifying biomarkers for breeding, potential candidate genes for transgenic manipulation, and will help in understanding complex plant-fungal interaction for future downstream research. The increasing volume of sequence data generated by the rapidly decreasing cost of RNA sequencing (RNA-Seq) necessitates the development of software pipeline(s) that can analyze the massive amounts of RNA-Seq data in an efficient manner. Through the present study, a comprehensive and flexible Standalone RNA-Seq Analysis Pipeline (SRAP) implemented with the parallel programming approach was developed, which can analyze transcriptome for any genome. SRAP consists of high-level modules, including sequence reads filtering, mapping to reference genome (or transcriptome), sequence assembly, gene expression analysis and variant discovery along with low-level modules for other common NGS utilities. The high-level modules, unlike low-level modules, require intense computation in terms of memory and processor. SRAP is developed with in-house developed scripts (Python), parallel computing and open source bioinformatics tools. It can be executed as a batch and/or individual mode for single or multiple sample files. SRAP generates RNA-Seq data analysis output files with statistical summary and graphic visualization.

Subjects/Keywords: NGS; SRAP; Aflatoxins; RNA-Seq

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Bedre, R. (2016). Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-07112016-114436 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2251

Chicago Manual of Style (16^th Edition):

Bedre, Renesh. “Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline.” 2016. Doctoral Dissertation, Louisiana State University. Accessed September 21, 2019. etd-07112016-114436 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2251.

MLA Handbook (7^th Edition):

Bedre, Renesh. “Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline.” 2016. Web. 21 Sep 2019.

Vancouver:

Bedre R. Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline. [Internet] [Doctoral dissertation]. Louisiana State University; 2016. [cited 2019 Sep 21]. Available from: etd-07112016-114436 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2251.

Council of Science Editors:

Bedre R. Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline. [Doctoral Dissertation]. Louisiana State University; 2016. Available from: etd-07112016-114436 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2251

McMaster University

6. Gu, Chu-Shu. A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA.

Degree: PhD, 2016, McMaster University

URL: http://hdl.handle.net/11375/20257

►

In recent years, the RNA-sequencing (RNA-seq) method, which measures the transcriptome by counting short sequencing reads obtained by high-throughput sequencing, is replacing the microarray technology… (more)

▼

In recent years, the RNA-sequencing (RNA-seq) method, which measures the transcriptome by counting short sequencing reads obtained by high-throughput sequencing, is replacing the microarray technology as the major platform in gene expression studies. The large amount of discrete data in RNA-seq experiments calls for effective analysis methods. In this dissertation, a new method to detect differentially expressed genes based on quasi-likelihood theory is developed in experiments with a completely randomized design with two experimental conditions. The proposed method estimates the variance function empirically and consequently it has similar sensitivities and FDRs across distributions with different variance functions. In a simulation study, the method is shown to have similar sensitivities and FDRs across the data with three different types of variance functions compared with some other popular methods. This method is applied to a real dataset with two experimental conditions along with some competing methods. The new method is then extended to more complex designs such as an experiment with multiple experimental conditions, an experiment with block design and an experiment with factorial design. The same advantages for the new method have been found in simulation studies. This method and some competing methods are applied to three real datasets with complex designs. The new method is also applied to analyze reads per kilobase per million mapped reads (RPKM) data. In the simulation, the method is compared with the Linear Models for Microarray Data (LIMMA) originally developed for microarray analysis (Smyth, 2004) and the question of normalization is also examined. It is shown that the new method and the LIMMA method have similar performance. Further normalization is required for the proper analysis of the RPKM data and the best such normalization is the scaling method. Analyzing raw count data properly has better performance than analyzing the RPKM data. Different normalization and statistical methods are applied to a real dataset with varied gene length across samples.

Thesis

Doctor of Philosophy (PhD)

Advisors/Committee Members: Canty, Angelo, Clinical Epidemiology/Clinical Epidemiology & Biostatistics.

Subjects/Keywords: RNA-seq; Quasi-likelihood; RPKM

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gu, C. (2016). A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/20257

Chicago Manual of Style (16^th Edition):

Gu, Chu-Shu. “A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA.” 2016. Doctoral Dissertation, McMaster University. Accessed September 21, 2019. http://hdl.handle.net/11375/20257.

MLA Handbook (7^th Edition):

Gu, Chu-Shu. “A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA.” 2016. Web. 21 Sep 2019.

Vancouver:

Gu C. A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA. [Internet] [Doctoral dissertation]. McMaster University; 2016. [cited 2019 Sep 21]. Available from: http://hdl.handle.net/11375/20257.

Council of Science Editors:

Gu C. A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA. [Doctoral Dissertation]. McMaster University; 2016. Available from: http://hdl.handle.net/11375/20257

McMaster University

7. Srinivasan, Krishna. CADMIUM EXPOSURE ALTERS GENE EXPRESSION OF LENS, RETINA, AND EYE-RELATED GENES IN ZEBRAFISH AND HUMAN LENS EPITHELIAL CELLS.

Degree: MSc, 2018, McMaster University

URL: http://hdl.handle.net/11375/24128

►

Vision is a crucial aspect of life for humans and animals. Impaired vision can lead to reduced quality of life along with other complications. Cataracts… (more)

▼

Vision is a crucial aspect of life for humans and animals. Impaired vision can lead to reduced quality of life along with other complications. Cataracts are a leading cause of impaired vision and blindness worldwide. Cataracts develop as a process of aging, although several environmental and lifestyle factors increase the risk of this disease. The toxic metal cadmium (Cd) has been associated with cataract formation and other ocular diseases such as macular degeneration. Cadmium exposure experiments were conducted to investigate potential pathways or mechanisms by which Cd may contribute to cataract formation and ocular disease. Zebra fish larvae (72, 96, and 120 hours post fertilization), adult zebra sh (6-month male, 10-month male, and 10-month female) and the B3 human lens epithelial (HLE) cell line were acutely exposed to varying concentrations of Cd. Transcriptomic changes relative to control (0 μM Cd) were determined using microarray analysis for zebra sh larvae and RNA sequencing (RNA-Seq) for adult zebra sh and HLE cells. Gene Ontology (GO) enrichment analysis for the zebra sh larvae exposure (50 μM Cd for 4 or 8 hours) enriched the "retina development in camera-type eye" term, and genes involved in enrichment (dnmt1, ccna2, fen1, mcm3 and slbp) were down-regulated. Gene set enrichment analysis (GSEA) for the 10-month male zebra sh exposure (50 μM Cd for 4 hours) enriched the "embryonic eye morphogenesis" gene set and signi ficant genes involved in enrichment (tcf7l1a, pitx2, fzd8a, sfrp5, lmx1bb, mfap2, six3b, lum, phactr4b, and foxc1a) were down-regulated. GSEA for the 10-month female zebra sh (50 μM Cd for 4 hours) enriched the "photoreceptor cell differentiation" gene set and signi cant genes involved in enrichment (odc1, thrb, and ush2a) were up-regulated. GO enrichment analysis for up-regulated genes in the HLE cell exposure (10 μM Cd for 4 hours) enriched the terms "eye development" (22 genes) and "lens development in camera-type eye" (CITED2, SKIL, CRYAB, SLC7A11, TGFB2, EPHA2, BCAR3, WNT5B, and BMP4). These results show cadmium is capable of altering transcription of eye-related genes in both zebra sh and human models, which may contribute to the formation of ocular disease. Many of these genes are involved in lens and retina development, yet they are also associated with diseases in these eye structures. Future studies could assess the consequences of altered transcription of these genes which could help elucidate the mechanisms of these changes and the overall effect of cadmium exposure on ocular disease. Ultimately, our study characterized the regulation of eye-related genes in response to Cd exposure and provided valuable knowledge laying the foundation for identi fication of the molecular mechanisms contributing to ocular diseases.

Thesis

Master of Science (MSc)

The eye is a sphere-like organ which is important for visualizing your surroundings. It is composed of many different structures such as the cornea, lens and retina. Many eye diseases have been…

Advisors/Committee Members: McArthur, Andrew, Biochemistry and Biomedical Sciences.

Subjects/Keywords: Environmental Toxicology; RNA-Seq; Cadmium

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Srinivasan, K. (2018). CADMIUM EXPOSURE ALTERS GENE EXPRESSION OF LENS, RETINA, AND EYE-RELATED GENES IN ZEBRAFISH AND HUMAN LENS EPITHELIAL CELLS. (Masters Thesis). McMaster University. Retrieved from http://hdl.handle.net/11375/24128

Chicago Manual of Style (16^th Edition):

Srinivasan, Krishna. “CADMIUM EXPOSURE ALTERS GENE EXPRESSION OF LENS, RETINA, AND EYE-RELATED GENES IN ZEBRAFISH AND HUMAN LENS EPITHELIAL CELLS.” 2018. Masters Thesis, McMaster University. Accessed September 21, 2019. http://hdl.handle.net/11375/24128.

MLA Handbook (7^th Edition):

Srinivasan, Krishna. “CADMIUM EXPOSURE ALTERS GENE EXPRESSION OF LENS, RETINA, AND EYE-RELATED GENES IN ZEBRAFISH AND HUMAN LENS EPITHELIAL CELLS.” 2018. Web. 21 Sep 2019.

Vancouver:

Srinivasan K. CADMIUM EXPOSURE ALTERS GENE EXPRESSION OF LENS, RETINA, AND EYE-RELATED GENES IN ZEBRAFISH AND HUMAN LENS EPITHELIAL CELLS. [Internet] [Masters thesis]. McMaster University; 2018. [cited 2019 Sep 21]. Available from: http://hdl.handle.net/11375/24128.

Council of Science Editors:

Srinivasan K. CADMIUM EXPOSURE ALTERS GENE EXPRESSION OF LENS, RETINA, AND EYE-RELATED GENES IN ZEBRAFISH AND HUMAN LENS EPITHELIAL CELLS. [Masters Thesis]. McMaster University; 2018. Available from: http://hdl.handle.net/11375/24128

Cornell University

8. Villarino Pizarro, Gonzalo. Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress .

Degree: 2014, Cornell University

URL: http://hdl.handle.net/1813/38983

► Abiotic stresses, such as salinity and drought, are among the most limiting factors to crop yield. In sodic saline soils, sodium chloride (NaCl) disrupts normal… (more)

▼ Abiotic stresses, such as salinity and drought, are among the most limiting factors to crop yield. In sodic saline soils, sodium chloride (NaCl) disrupts normal plant growth and development. Many studies have used both forward and reverse genetic techniques to understand the complex interactions of plant systems with abiotic stress. These approaches have been invaluable in deciphering some mechanisms of plant salt stress tolerance. Salt tolerance research has also been an important part of basic plant biology, increasing the understanding in areas encompassing gene regulation, mineral nutrition, signaling components, ion transport and osmoregulation. To better understand the detrimental effects of NaCl, as well the fundamental questions associated with salt tolerance, transcript regulation in response to NaCl stress was undertaken using ultra-high-throughput RNA sequencing technology (RNA-seq). RNA-seq has quickly become the method of choice to perform transcriptomic analysis owing to many advantages over existing platforms. The transcriptomic research presented here was carried out in Petunia hybrida, a salt resistant Solanaceous plant that has also been an excellent model species in molecular genetic research regarding flower development and senescence, synthesis and regulation of volatiles, and so on. In chapter one, to bypass the absence of an available Petunia genome, a de-novo assembled Petunia transcriptome was reconstructed by assembling over one- hundred million Illumina cDNA reads with Trinity software. The de-novo assembled contigs represents the most in-depth transcriptome ever reported for a Petunia species, which can be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome. The transcriptome has been made publically available on the SOL Genomics Network (SGN) http://solgenomics.net. Using this newly assembled reference transcriptome, more than 7,000 differentially expressed genes were identified within 24 h of acute NaCl stress. Genes related to regulation of reactive oxygen species, transport, and signal transduction as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. Gene ontology analyses revealed that plants by 24 h after acute NaCl undertook many changes occurring at the molecular level including genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. RNA-seq, despite the many advantages it offers, it is a relatively new methodology with developments and improvements to be made. At the end of chapter one a modification to the library preparation protocol is presented whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. This methodological improvement could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments. In chapter two, root and leaf transcriptomic response to salt stress was investigated, utilizing the Petunia… Advisors/Committee Members: Hanson, Maureen R (committeeMember), Scanlon, Michael J. (committeeMember), Nero, Debra (committeeMember), Hanson, Maureen R (committeeMember), Scanlon, Michael J. (committeeMember), Nero, Debra (committeeMember).

Subjects/Keywords: transcriptomics; RNA-seq; Salt stress

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APA (6^th Edition):

Villarino Pizarro, G. (2014). Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress . (Thesis). Cornell University. Retrieved from http://hdl.handle.net/1813/38983

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Villarino Pizarro, Gonzalo. “Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress .” 2014. Thesis, Cornell University. Accessed September 21, 2019. http://hdl.handle.net/1813/38983.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Villarino Pizarro, Gonzalo. “Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress .” 2014. Web. 21 Sep 2019.

Vancouver:

Villarino Pizarro G. Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress . [Internet] [Thesis]. Cornell University; 2014. [cited 2019 Sep 21]. Available from: http://hdl.handle.net/1813/38983.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Villarino Pizarro G. Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress . [Thesis]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/38983

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

9. 野口, 淳. mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オモチイタ Papaver somniferum ノイデンシハツゲンカイセキ.

Degree: Nara Institute of Science and Technology / 奈良先端科学技術大学院大学

URL: http://hdl.handle.net/10061/12488

Subjects/Keywords: RNA-seq

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APA (6^th Edition):

野口, �. (n.d.). mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オモチイタ Papaver somniferum ノイデンシハツゲンカイセキ. (Thesis). Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10061/12488

Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

野口, 淳. “mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オモチイタ Papaver somniferum ノイデンシハツゲンカイセキ.” Thesis, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Accessed September 21, 2019. http://hdl.handle.net/10061/12488.

Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

野口, 淳. “mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オモチイタ Papaver somniferum ノイデンシハツゲンカイセキ.” Web. 21 Sep 2019.

Note: this citation may be lacking information needed for this citation format:
No year of publication.

Vancouver:

野口 �. mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オモチイタ Papaver somniferum ノイデンシハツゲンカイセキ. [Internet] [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; [cited 2019 Sep 21]. Available from: http://hdl.handle.net/10061/12488.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

Council of Science Editors:

野口 �. mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オモチイタ Papaver somniferum ノイデンシハツゲンカイセキ. [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; Available from: http://hdl.handle.net/10061/12488

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

Princeton University

10. Watson, Colin. Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing .

Degree: PhD, 2016, Princeton University

URL: http://arks.princeton.edu/ark:/88435/dsp01tb09j815t

► Characterizing Early Zygotic Dosage Compensation in Drosophila melanogaster using RNA-Seq Sexual reproduction in flies, mammals, and worms results in males and females receiving different numbers… (more)

▼ Characterizing Early Zygotic Dosage Compensation in Drosophila melanogaster using RNA-Seq Sexual reproduction in flies, mammals, and worms results in males and females receiving different numbers of X chromosomes. A chromosome wide regulatory process termed dosage compensation counteracts the differences in X-linked gene expression between sexes by balancing X-chromosome transcript levels. In Drosophila melanogaster, the Dosage Compensation Complex (DCC) forms in the presence of Msl-2 and activates a two-fold increase in gene expression. However multiple questions still remain regarding the function of the DCC as recent studies indicate the presence of an alternative dosage compensation mechanism. Sex lethal (Sxl), an RNA binding protein involved in sex determination is believed to play a role in this alternative model by regulating X-linked female transcripts. In this study we will examine the mechanism behind early zygotic dosage compensation using a novel high-throughput approach to sort male and female embryos during early embryogenesis. We use RNA-Seq to measure zygotic expression levels in male and female embryos. We then characterize Sxl and Msl-1 loss-of-function mutants to determine the mechanism behind early dosage compensation. Our study intends to further our understanding of sex specific transcription on a global scale during early Drosophila development. Determining Spiroplasma MSRO’s role in Drosophila melanogaster male lethality Spiroplasma MSRO are maternally transmitted bacteria that infect Drosophila melanogaster and induce apoptosis in male embryos during early embryogenesis. Previous reports have implicated the male dosage compensation complex (DCC) as a factor in male lethality as the loss of any DCC gene suppresses Spiroplasma induced apoptosis. In this study we characterize Spiroplasma’s impact on the male embryo’s molecular and morphogenetic development. We use RNA-Seq to measure transcript levels in infected male and female embryos during early embryogenesis. To determine if the loss of the dosage compensation system rescues transcript mis-regulation we quantify gene expression in homozygous Msl-1 embryos. We show that mis-regulation is sex specific and that Drosophila autosomal and X-linked genes are affected. We demonstrate that the loss of DCC functionality rescues transcript mis-regulation in infected male embryos. Our study intends to further our understanding of sex specific host-symbiont interactions. Advisors/Committee Members: Wieschaus, Eric (advisor).

Subjects/Keywords: Dosage Compensation; RNA-Seq; Spiroplasma

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APA (6^th Edition):

Watson, C. (2016). Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing . (Doctoral Dissertation). Princeton University. Retrieved from http://arks.princeton.edu/ark:/88435/dsp01tb09j815t

Chicago Manual of Style (16^th Edition):

Watson, Colin. “Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing .” 2016. Doctoral Dissertation, Princeton University. Accessed September 21, 2019. http://arks.princeton.edu/ark:/88435/dsp01tb09j815t.

MLA Handbook (7^th Edition):

Watson, Colin. “Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing .” 2016. Web. 21 Sep 2019.

Vancouver:

Watson C. Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing . [Internet] [Doctoral dissertation]. Princeton University; 2016. [cited 2019 Sep 21]. Available from: http://arks.princeton.edu/ark:/88435/dsp01tb09j815t.

Council of Science Editors:

Watson C. Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing . [Doctoral Dissertation]. Princeton University; 2016. Available from: http://arks.princeton.edu/ark:/88435/dsp01tb09j815t

University of Minnesota

11. Gao, Liangliang. Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage.

Degree: PhD, Plant pathology, 2013, University of Minnesota

URL: http://purl.umn.edu/146706

► Wild potato Solanum bulbocastanum is a rich source of genetic resistance against a variety of pathogens. This project developed molecular tools and expanded biological knowledge… (more)

▼ Wild potato Solanum bulbocastanum is a rich source of genetic resistance against a variety of pathogens. This project developed molecular tools and expanded biological knowledge useful for the improvement of cultivated potato (S. tuberosum) using genetic resistance from S. bulbocastanum. First, the genome structure of S. bulbocastanum relative to those of its relatives, cultivated potato and tomato (S. lycopersicon) was determined. Second, to facilitate efforts to improve cultivated potato through the introgression and deployment disease resistance derived from S. bulbocastanum, the phenotypic function and molecular mechanisms of one S. bulbocastanum disease resistance gene were explored in cultivated potato foliage and tubers. For determination of genome structure for S. bulbocastanum, Diversity Arrays Technology (DArT) was employed to generate genome wide linkage maps for the species. Employing a pseudo-testcross mapping strategy, 631 DArT markers were integrated into a composite map comprising 12 linkage groups. Our results represent an over ten-fold increase of total marker density compared to previously available genetic maps for the species. Sequencing and alignment of corresponding DArT clones to reference physical maps from tomato and cultivated potato allowed a direct comparison of marker orders between species. Overall, the S. bulbocastanum genetic maps show higher collinearity with reference potato maps than tomato maps, with seven genome regions supporting a closer phylogenetic relationship between potato and S. bulbocastanum than between tomato and S. bulbocastanum. One dominant US cultivar ‘Russet Burbank’(WT; late blight susceptible in foliage and tuber) and its RB (a late blight resistance gene derived from S. bulbocastanum) transgenic line SP2211 (+RB; late blight resistant in foliage and tuber) were compared in both tubers and foliage in their responses to late blight pathogen attack using an RNA-seq approach. In the tubers, a total of 483 million paired end Illumina RNA-seq reads were generated, representing the transcription of 29,319 potato genes. Differentially expressed genes, gene groups and ontology bins that exhibited differences between the WT and +RB lines were identified. P. infestans transcripts, including those of known effectors, were also identified. Faster and stronger activation of defense related genes, gene groups and ontology bins correlated with successful tuber resistance against P. infestans. Our results suggest that the hypersensitive response is likely a general form of resistance against the hemibiotrophic P. infestans—even in potato tubers, organs that develop below ground. In the foliage, a total of 515 million paired end RNA-seq reads were generated, representing the transcription of 29,970 genes. We compared the differences and similarities of responses to P. infestans in potato foliage and tubers. Differentially expressed genes, gene groups and ontology bins were identified to show similarities and differences in foliage and tuber…

Subjects/Keywords: Late blight; Potato; RNA-seq

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gao, L. (2013). Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage. (Doctoral Dissertation). University of Minnesota. Retrieved from http://purl.umn.edu/146706

Chicago Manual of Style (16^th Edition):

Gao, Liangliang. “Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage.” 2013. Doctoral Dissertation, University of Minnesota. Accessed September 21, 2019. http://purl.umn.edu/146706.

MLA Handbook (7^th Edition):

Gao, Liangliang. “Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage.” 2013. Web. 21 Sep 2019.

Vancouver:

Gao L. Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage. [Internet] [Doctoral dissertation]. University of Minnesota; 2013. [cited 2019 Sep 21]. Available from: http://purl.umn.edu/146706.

Council of Science Editors:

Gao L. Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage. [Doctoral Dissertation]. University of Minnesota; 2013. Available from: http://purl.umn.edu/146706

University of Notre Dame

12. Sheri A. Sanders. Conservation Transcriptomics of Ambystomatid Salamanders and Their Polyploid Hybrids</h1>.

Degree: PhD, Biological Sciences, 2016, University of Notre Dame

URL: https://curate.nd.edu/show/x633dz03m7r

► Amphibians are declining worldwide, in part due to Batrachochytridium dendrobatidis (Bd), a pandemic chytrid fungal disease. This disease affects salamanders more than initially thought,… (more)

▼ Amphibians are declining worldwide, in part due to Batrachochytridium dendrobatidis (Bd), a pandemic chytrid fungal disease. This disease affects salamanders more than initially thought, but several gaps in knowledge hinder response to this and other disease threats. Current demographic information for salamanders is lacking. Without an efficient means of surveying salamander populations, it is difficult to monitor or respond to these declines. Additionally, little is known about how salamanders respond to chytrid fungus, a major contributor to amphibian decline. This is particularly worrisome in the Great Lakes Region, as it is home to a cryptic polyploid complex that makes up the majority of many salamander communities. These polyploids may be particularly susceptible to disease, but little is known about vertebrate response to polyploidy. In this doctoral dissertation, I address these gaps in salamander conservation. First I developed eDNA markers that allows for quick, non-invasive identification of laboratory and field samples without the need for technical or taxonomic expertise. I used this method to identify cryptic polyploid and diploid salamanders of the genus Ambystoma. These salamanders were used in a transcriptomic study on the functional response of salamanders to Bd. I was able to sequence, assemble, annotate, and analyze three salamander transcriptomes using this data. I characterized the immune response of one of these salamanders to Bd, finding links to wound healing pathways characteristic of salamanders and generally much quicker response time to chytrid challenge than is observed in frogs. Additionally, I investigated the expression patterns of polyploid salamanders in comparison to the parental taxa in normal and disease conditions. I found that different genomic copies within the polyploids maintain their own regulation patterns under normal conditions, but are disrupted in disease conditions. This may indicate an increase susceptibility to chytrid in the highly common salamander polyploids and other vertebrate polyploids. What follows are an introductory chapter, three data chapters, and a conclusion where I offer my concluding remarks on the utility of these chapters and the future importance of such analyses in conservation genomics, particularly in light of recently discovery of a more pathogenic chyrid fungus, Batrachochytridium salamandervorans. Advisors/Committee Members: Michael Pfrender, Research Director.

Subjects/Keywords: RNA-seq; chytrid; salamander; Ambystoma

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APA (6^th Edition):

Sanders, S. A. (2016). Conservation Transcriptomics of Ambystomatid Salamanders and Their Polyploid Hybrids</h1>. (Doctoral Dissertation). University of Notre Dame. Retrieved from https://curate.nd.edu/show/x633dz03m7r

Chicago Manual of Style (16^th Edition):

Sanders, Sheri A.. “Conservation Transcriptomics of Ambystomatid Salamanders and Their Polyploid Hybrids</h1>.” 2016. Doctoral Dissertation, University of Notre Dame. Accessed September 21, 2019. https://curate.nd.edu/show/x633dz03m7r.

MLA Handbook (7^th Edition):

Sanders, Sheri A.. “Conservation Transcriptomics of Ambystomatid Salamanders and Their Polyploid Hybrids</h1>.” 2016. Web. 21 Sep 2019.

Vancouver:

Sanders SA. Conservation Transcriptomics of Ambystomatid Salamanders and Their Polyploid Hybrids</h1>. [Internet] [Doctoral dissertation]. University of Notre Dame; 2016. [cited 2019 Sep 21]. Available from: https://curate.nd.edu/show/x633dz03m7r.

Council of Science Editors:

Sanders SA. Conservation Transcriptomics of Ambystomatid Salamanders and Their Polyploid Hybrids</h1>. [Doctoral Dissertation]. University of Notre Dame; 2016. Available from: https://curate.nd.edu/show/x633dz03m7r

University of New South Wales

13. Muskovic, Walter. Investigating the Endogenous Role of MicroRNAs in Glioblastoma.

Degree: Women's & Children's Health, 2018, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/60456

► Glioblastoma (GBM) is a tumour characterised by its extreme inter- and intra-tumoural heterogeneity. Subpopulations of cells display distinct genetic alterations leading to variability in responses… (more)

▼ Glioblastoma (GBM) is a tumour characterised by its extreme inter- and intra-tumoural heterogeneity. Subpopulations of cells display distinct genetic alterations leading to variability in responses and resistance to current treatments. MicroRNAs, through their unique post-transcriptional mechanism of regulation, have been demonstrated to target multiple effectors of critical pathways concurrently, generating interest as a means to circumvent treatment resistance in GBM. A rational microRNA-based therapeutic strategy requires precise elucidation of the role of individual microRNAs to identify which, if any, may prove useful. Analysis of matched microRNA and mRNA expression profiles from primary GBM tumours provided by The Cancer Genome Atlas indicated co-expression of microRNAs and target genes. Although simultaneous activation and repression appears counterintuitive, in silico modelling suggested a potential functional role for this targeting; to facilitate in tuning the timing and magnitude of target gene expression. To determine whether co-expressed microRNA and mRNA interact, matched totalRNA-seq and smallRNA-seq datasets were created by harvesting synchronised populations of GBM cells responding to environmental perturbation. Taking advantage of the intracellular separation of transcription and microRNA targeting, expression estimates of nascent and mature mRNA transcripts were incorporated into a suitable mathematical model to allow inference of transcript-specific dynamic degradation rates. Following optimisation, the granularity of measurement was reduced to ten-minute intervals to provide 41 time points. Clusters of genes were identified, for which transient increases in degradation were required to explain observed transcription dynamics. Clusters were enriched for seed sequences of microRNAs with expression profiles corresponding closely to inferred degradation rates. These results are interpreted to support the hypothesis that while all microRNAs operate through a repressive mechanism, their function within the context of a dynamic gene regulatory network need not be simply repressive. Rather their function may depend on the unique context in which individual microRNA-target interactions occur. These results suggest a more nuanced role for microRNAs in GBM and highlight the power of high-temporal-resolution measurements to illuminate the complex dynamic interactions of regulatory elements within gene regulatory networks. Advisors/Committee Members: Kavallaris, Maria, Children's Cancer Institute Australia for Medical Research, Faculty of Medicine, UNSW, McDonald, Kerrie, Prince of Wales Clinical School, Faculty of Medicine, UNSW.

Subjects/Keywords: RNA-seq; microRNA; Glioblastoma

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APA (6^th Edition):

Muskovic, W. (2018). Investigating the Endogenous Role of MicroRNAs in Glioblastoma. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/60456

Chicago Manual of Style (16^th Edition):

Muskovic, Walter. “Investigating the Endogenous Role of MicroRNAs in Glioblastoma.” 2018. Doctoral Dissertation, University of New South Wales. Accessed September 21, 2019. http://handle.unsw.edu.au/1959.4/60456.

MLA Handbook (7^th Edition):

Muskovic, Walter. “Investigating the Endogenous Role of MicroRNAs in Glioblastoma.” 2018. Web. 21 Sep 2019.

Vancouver:

Muskovic W. Investigating the Endogenous Role of MicroRNAs in Glioblastoma. [Internet] [Doctoral dissertation]. University of New South Wales; 2018. [cited 2019 Sep 21]. Available from: http://handle.unsw.edu.au/1959.4/60456.

Council of Science Editors:

Muskovic W. Investigating the Endogenous Role of MicroRNAs in Glioblastoma. [Doctoral Dissertation]. University of New South Wales; 2018. Available from: http://handle.unsw.edu.au/1959.4/60456

University of New South Wales

14. Mills, James. Human brain transcriptomic: towards understanding multiple system atrophy.

Degree: Biotechnology & Biomolecular Sciences, 2015, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true

► The human brain is a remarkably complex organ. It is a heterogeneous collection of billions of neurons and glial cells that are interconnected to form… (more)

▼ The human brain is a remarkably complex organ. It is a heterogeneous collection of billions of neurons and glial cells that are interconnected to form a finely tuned network capable of higher cognition. It is thought that the transcriptome may hold the key to understanding the complexity seen in the human brain. Next-generation sequencing allows the brain’s transcriptome to be probed at an unmatched resolution. This has uncovered a myriad of RNA elements, including RNA that does not code for protein, known as non-coding RNA (ncRNA). Originally, thought to be transcriptional noise, it is now appreciated that ncRNAs have numerous functional properties, with the ability to interact with DNA, other RNA molecules and proteins in different cellular compartments. It is thought that an increase in the number of ncRNAs being expressed throughout the brain, is a major driver of the increased intellectual capacity seen in humans and primates. The increase in the complexity of the human brain, also makes it prone to a number of different neurodegenerative and psychiatric diseases. These diseases are set to have dramatic economic and social impacts by the middle of the 21st century. To avert this looming epidemic an adequate understanding of the human brain is needed, so diagnostic tools and treatment targets can be developed. One such disorder is multiple system atrophy(MSA). MSA is a sporadic, rapidly progressing neurodegenerative disease. Currently no treatment exists and very little is known about the molecular basis of MSA. Before an understanding of the diseased brain can be reached an understanding of the healthy brain is necessary.Here, the transcriptome of grey matter (GM) and white matter (WM) from the superior frontal gyrus (SFG) of the healthy prefrontal cortex (PFC) was analysed. This revealed pervasive transcription and highlighted the differences in the transcriptome profiles of distinct cortical structures throughout the brain. A number of protein-coding genes were expressed exclusively in GM or WM, including gamma-aminobutyric acid A receptor, beta 2 (GABRB2) and P21 Protein (Cdc42/Rac)-Activated Kinase 2 (PAK2), respectively. Further, an interesting phenomenon known as isoform switching was detected in genes such as the G protein-coupled receptor 123 (GPR123). It was also revealed that in the healthy frontal cortex long intervening non-coding RNAs (lincRNAs), a subclass of long non-coding RNAs (lncRNAs), appear to be important drivers of tissue differentiation.To further establish the role of lincRNAs in the healthy human brain a comprehensive analysis of the oligodendrocyte maturation-associated lincRNA (OLMALINC) was carried out. It was found that OLMALINC is a recently evolved lincRNA with its highest expression levels in the human brain. OLMALINC was knocked down in human neurons and oligodendrocytes. Depletion of OLMALINC transcription revealed that it plays a role oligodendrocyte maturation. This study was one of the first functional characterisations of a lincRNA expressed in the human brain, and thus… Advisors/Committee Members: Janitz, Michael, Faculty of Science, UNSW.

Subjects/Keywords: Neurodegeneration; RNA-Seq; Long non-coding RNA

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APA (6^th Edition):

Mills, J. (2015). Human brain transcriptomic: towards understanding multiple system atrophy. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true

Chicago Manual of Style (16^th Edition):

Mills, James. “Human brain transcriptomic: towards understanding multiple system atrophy.” 2015. Doctoral Dissertation, University of New South Wales. Accessed September 21, 2019. http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true.

MLA Handbook (7^th Edition):

Mills, James. “Human brain transcriptomic: towards understanding multiple system atrophy.” 2015. Web. 21 Sep 2019.

Vancouver:

Mills J. Human brain transcriptomic: towards understanding multiple system atrophy. [Internet] [Doctoral dissertation]. University of New South Wales; 2015. [cited 2019 Sep 21]. Available from: http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true.

Council of Science Editors:

Mills J. Human brain transcriptomic: towards understanding multiple system atrophy. [Doctoral Dissertation]. University of New South Wales; 2015. Available from: http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true

University of Minnesota

15. Nair, Asha. A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.

Degree: PhD, Biomedical Informatics and Computational Biology, 2018, University of Minnesota

URL: http://hdl.handle.net/11299/199034

► High-throughput Next Generation RNA sequencing (RNA-Seq) technology is affluent with information about the transcriptome, which includes both protein-coding and multiple non-coding regions. In a diseased… (more)

▼ High-throughput Next Generation RNA sequencing (RNA-Seq) technology is affluent with information about the transcriptome, which includes both protein-coding and multiple non-coding regions. In a diseased state, complex interactions between these regions can go awry. Identification of such interactions is critical to translate the underlying biology of the transcriptome, especially for lethal diseases such as cancer. The field of bioinformatics is currently deficient in workflows that can analyze both coding and non-coding regions together efficiently, to identify disease-specific interactions. In this dissertation, I developed three coherent bioinformatics solutions that aim to address these shortcomings in RNA-Seq. First, a comprehensive workflow called MAPR-Seq was developed to analyze and report various features of protein-coding messenger RNAs. Second, a workflow for non-coding circular RNAs, called Circ-Seq, was developed to identify, quantify and annotate expressed circular RNAs. Third, an integration workflow called ReMIx was developed to identify microRNA response elements (MREs) and integrate them with the different types of RNAs (messenger RNAs, circular RNAs, and microRNAs). Collectively, the three workflows were applied to the largest cohort of breast cancer samples (n=885) from The Cancer Genome Atlas (TCGA). Based on the results obtained from these workflows, I present several key findings that are pertinent to breast cancer. I show that circular RNAs may be a marker for tumor proliferation in estrogen response positive (ER+) breast cancer subtype. I also show how triple negative (TN) breast cancer subtype-specific MRE signatures of messenger RNA – microRNA interactions can be obtained using RNA-Seq data, which has not been explored to date and thus, is a novel undertaking. In the end, my results highlight candidate messenger RNAs, circular RNAs and microRNAs that are found to be associated with MAPK and PI3K/AKT signaling cascades in TN breast cancer subtype. In general, the developed bioinformatics solutions can also be applied to RNA-Seq data of other cancer subtypes and diseases to identify unique messenger RNA – microRNA – circular RNA candidates that could be promising diagnostic targets towards improving treatment options for complex diseases.

Subjects/Keywords: circular RNA; integration; messenger RNA; micro RNA; MRE; RNA-Seq

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nair, A. (2018). A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/199034

Chicago Manual of Style (16^th Edition):

Nair, Asha. “A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.” 2018. Doctoral Dissertation, University of Minnesota. Accessed September 21, 2019. http://hdl.handle.net/11299/199034.

MLA Handbook (7^th Edition):

Nair, Asha. “A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.” 2018. Web. 21 Sep 2019.

Vancouver:

Nair A. A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. [Internet] [Doctoral dissertation]. University of Minnesota; 2018. [cited 2019 Sep 21]. Available from: http://hdl.handle.net/11299/199034.

Council of Science Editors:

Nair A. A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. [Doctoral Dissertation]. University of Minnesota; 2018. Available from: http://hdl.handle.net/11299/199034

Louisiana State University

16. Korde, Asawari. Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes.

Degree: PhD, 2014, Louisiana State University

URL: etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274

► Transcription by RNA polymerase III (Pol III) requires sequential assembly of Pol III-specific transcription factors. At the tRNA gene, the TFIIIC complex recognizes and specifically… (more)

▼ Transcription by RNA polymerase III (Pol III) requires sequential assembly of Pol III-specific transcription factors. At the tRNA gene, the TFIIIC complex recognizes and specifically binds at intragenic promoter elements A-box and B-box and aids the assembly of TFIIIB to upstream of the transcriptional start site. Upon binding, Pol III is recruited near start sites and transcription of tRNA genes is initiated. Apart from transcription of a gene, these bound Pol III complexes influence transcription, chromatin state and genome organization of neighboring RNA polymerase II (Pol II)-transcribed genes. Such effects are known as extra-transcriptional effects of Pol III complex. Our study provides evidence of a unique “extra-transcriptional” activity of assembled Pol III transcription complexes at the tRNA gene that blocks progression of intergenic RNA polymerase II transcription. We demonstrated that the Pol III transcription complex bound to the tRNA gene upstream of the Saccharomyces cerevisiae ATG31 gene protects the ATG31 promoter against readthrough transcriptional interference from the upstream non-coding intergenic SUT467. The protection is predominately mediated by binding of the TFIIIB complex. Failure to block this readthrough resulted in compromised ATG31 translation. Given the recent discovery of widespread pervasive transcription in yeast, protection of neighboring genes from intergenic transcriptional interference may be a key extra-transcriptional function of assembled RNA polymerase III complexes. Our data from RNA-seq analysis demonstrated genome-wide effects of DNA bound Pol III complexes on neighboring chromosomal loci, by comparing expression profiles from tfc6 under-expressing mutants and wild-type S. cerevisiae strains. Reduced TFIIIC occupancy in mutant strains altered Pol II derived transcripts and displayed 5’ or 3’ extension of protein-coding genes, readthrough from non-coding transcripts and increase in the transcription of genes near the potential TFIIIC binding sites, including tRNA genes and putative ETC sites. Interestingly, not all genes in the vicinity of TFIIIC binding sites were transcriptionally mis-regulated, suggesting variable strength of influence on Pol II transcripts by TFIIIC bound sites. Finally, as observed in SUT467-ATG31 readthrough, we anticipated translation defects in 5’ or 3’ extended transcripts in mutants. Overall these genome-wide results suggest much complex regulatory role of Pol III transcription factors bound sites than previously anticipated.

Subjects/Keywords: RNA-seq; tRNA gene; barriers; non-coding RNA; insulators; RNA polymerases

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Korde, A. (2014). Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274

Chicago Manual of Style (16^th Edition):

Korde, Asawari. “Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes.” 2014. Doctoral Dissertation, Louisiana State University. Accessed September 21, 2019. etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274.

MLA Handbook (7^th Edition):

Korde, Asawari. “Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes.” 2014. Web. 21 Sep 2019.

Vancouver:

Korde A. Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes. [Internet] [Doctoral dissertation]. Louisiana State University; 2014. [cited 2019 Sep 21]. Available from: etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274.

Council of Science Editors:

Korde A. Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes. [Doctoral Dissertation]. Louisiana State University; 2014. Available from: etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274

University of California – Santa Cruz

17. Smith, Andrew Martin. Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores.

Degree: Chemistry, 2017, University of California – Santa Cruz

URL: http://www.escholarship.org/uc/item/24b97646

► This work describes advances in nanopore sequencing technology as they apply to RNA. RNAs in the cellular environment have a wide range of functions and… (more)

▼ This work describes advances in nanopore sequencing technology as they apply to RNA. RNAs in the cellular environment have a wide range of functions and structures, by nature being much more dynamic in their activities than their chemical counterpart, DNA. The diversity of activities and functions that RNAs assume in the cell is reflected in the diverse research interests of those who study RNA. Any effort to develop nanopore-based direct RNA sequencing applications requires accounting for this diversity.Given the spectrum of interests in RNA biology, much of this dissertation attempts to address a fundamental challenge in directly analyzing RNAs by nanopore - how to deliver and read diverse classes of RNA at single-nucleotide resolution using a nanopore sequencer? The introductory first chapter describes background on nanopores as sequencing sensors and samples of some biology surrounding this diverse class of molecules. The state of the art and challenges in RNA sequencing in general are discussed. The second chapter of this work demonstrates a method specifically preparing tRNA for nanopore sequencing. The primary challenge in this effort is to be able to consistently load a single tRNA end and process the tRNA strand through the pore in a linear order. A molecular adapter composed of double-stranded DNA ligated to the tRNA termini facilitates this process. The adapter specifically targets tRNA by hybridizing to the universally conserved CCA tail of tRNA. It also provides a binding site for ϕ29 DNA polymerase, which acts a molecular brake on RNA under non-catalytic conditions. These two features allow for discrimination between two tRNA species from E. coli. This work demonstrates that it is possible to use a nanopore to analyze individual tRNAs as linear strands, which is a necessary prerequisite for nanopore-based tRNA sequencing.The third chapter of this work describes applying the Oxford Nanopore MinION sequencer to directly sequence 16S ribosomal RNA (16S rRNA). Demonstration of direct RNA sequencing of poly-adenylated RNA by Oxford Nanopore in August of 2016 was a critical development towards direct sequencing of RNA in general. The work described in Chapter 3 again involves designing an adapter, but this time specific for prokaryotic 16S rRNA. This adapter can be used with the existing Oxford Nanopore direct RNA sequencing kit. Sequencing of 16S rRNA from E. coli and other three other microbial species is demonstrated. The data and confirmatory experiments show that it is possible to directly detect modified ribonucleotides in nanopore-based sequencing data, which has long been a promised benefit of direct RNA sequencing methods. The 16S rRNA adapter is designed to hybridize to conserved 3′-end sequence of E. coli 16S rRNA. It could be generalized to all prokaryotic 16S rRNA, which would be desirable for rapid identification of prokaryotic microbes in a clinical or environmental setting.The appendices cover unpublished work on helicase proteins to control RNA strand movement through a nanopore. The…

Subjects/Keywords: Biochemistry; Biophysics; Nanotechnology; epigenetics; nanopore; RNA; RNA-seq; RNA sequencing; tRNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Smith, A. M. (2017). Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores. (Thesis). University of California – Santa Cruz. Retrieved from http://www.escholarship.org/uc/item/24b97646

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Smith, Andrew Martin. “Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores.” 2017. Thesis, University of California – Santa Cruz. Accessed September 21, 2019. http://www.escholarship.org/uc/item/24b97646.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Smith, Andrew Martin. “Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores.” 2017. Web. 21 Sep 2019.

Vancouver:

Smith AM. Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores. [Internet] [Thesis]. University of California – Santa Cruz; 2017. [cited 2019 Sep 21]. Available from: http://www.escholarship.org/uc/item/24b97646.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Smith AM. Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores. [Thesis]. University of California – Santa Cruz; 2017. Available from: http://www.escholarship.org/uc/item/24b97646

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of California – Santa Cruz

18. Uzilov, Andrew V. Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs.

Degree: Biomolecular Engineering and Bioinformatics, 2013, University of California – Santa Cruz

URL: http://www.escholarship.org/uc/item/5284w609

► High-throughput RNA sequencing (RNA-Seq), although still novel, has primarily been applied as a method for assessing differential RNA abundance or mapping of primary structure of… (more)

Subjects/Keywords: Bioinformatics; archaea; circular RNA; FragSeq; ncRNA; RNA-Seq; RNA structure

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Uzilov, A. V. (2013). Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs. (Thesis). University of California – Santa Cruz. Retrieved from http://www.escholarship.org/uc/item/5284w609

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Uzilov, Andrew V. “Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs.” 2013. Thesis, University of California – Santa Cruz. Accessed September 21, 2019. http://www.escholarship.org/uc/item/5284w609.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Uzilov, Andrew V. “Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs.” 2013. Web. 21 Sep 2019.

Vancouver:

Uzilov AV. Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs. [Internet] [Thesis]. University of California – Santa Cruz; 2013. [cited 2019 Sep 21]. Available from: http://www.escholarship.org/uc/item/5284w609.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Uzilov AV. Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs. [Thesis]. University of California – Santa Cruz; 2013. Available from: http://www.escholarship.org/uc/item/5284w609

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas – Austin

19. Qin, Yidan. Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.

Degree: PhD, Microbiology, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/41602

► Thermostable group II intron reverse transcriptases (TGIRTs) from thermophilic bacteria are advantageous for biotechnological applications that require cDNA synthesis, such as RT-qPCR and RNA-seq. TGIRTs… (more)

▼ Thermostable group II intron reverse transcriptases (TGIRTs) from thermophilic bacteria are advantageous for biotechnological applications that require cDNA synthesis, such as RT-qPCR and RNA-seq. TGIRTs have higher thermostability, processivity and fidelity than conventional retroviral RTs, along with a novel end-to-end template-switching activity that attaches RNA-seq adapters to target RNAs without RNA ligation. First, I optimized the TGIRT template-switching method for RNA-seq analysis of small non-coding RNAs (ncRNAs). I showed that TGIRT-seq gives full-length reads of tRNAs, which are refractory to retroviral RTs, and enables identification of a variety of base modifications in tRNAs by distinctive patterns of misincorporated nucleotides. With collaborators, I developed an efficient and quantitative high-throughput tRNA sequencing method, identified RNAs bound by the human interferon-induced protein IFIT5, yielding new insights into its functions in tRNA quality control and innate immunity, and uncovered a novel mRNA-independent mechanism for elongation of nascent peptides. Second, I developed a new, streamlined TGIRT-seq method for comprehensive analysis of all RNA size classes in a single RNA-seq. This method enables RNA-seq library construction from <1 ng of fragmented RNAs in <5 h. By using the method, I showed that human plasma contains large numbers of protein-coding and long ncRNAs together with diverse classes of small ncRNAs, which are mostly present as full-length transcripts. With collaborators, I showed that TGIRT-seq analysis of circulating RNAs identified potential biomarkers at different stages of multiple myeloma and may provide a sensitive, non-invasive diagnostic tool for a variety of human diseases. Finally, I adapted TGIRTs for use in mapping of RNA structures and RNA-protein interaction sites, and identification of RNA targets of cellular RNA-binding proteins. My research led to a series of new biological insights, which would have been difficult or impossible to obtain by current methods, and established TGIRTs as a tool for a broad range of applications in RNA research and diagnostics. Advisors/Committee Members: Lambowitz, Alan (advisor), Iyer, Vishwanath R (committee member), Krug, Robert M (committee member), Russell, Rick (committee member), Stevens, Scott W (committee member), Sullivan, Christopher S (committee member).

Subjects/Keywords: RNA-seq; Diagnostics; Precision medicine; Non-coding RNA; Circulating RNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Qin, Y. (2016). Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/41602

Chicago Manual of Style (16^th Edition):

Qin, Yidan. “Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed September 21, 2019. http://hdl.handle.net/2152/41602.

MLA Handbook (7^th Edition):

Qin, Yidan. “Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.” 2016. Web. 21 Sep 2019.

Vancouver:

Qin Y. Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2019 Sep 21]. Available from: http://hdl.handle.net/2152/41602.

Council of Science Editors:

Qin Y. Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/41602

University of California – Irvine

20. Le, Rebekah Charney. The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network.

Degree: Biological Sciences, 2016, University of California – Irvine

URL: http://www.escholarship.org/uc/item/22r462c6

► Germ layer specification is one of the earliest developmental events in metazoan organisms, and relies upon the combinatorial interactions of signaling pathways and transcription factors… (more)

▼ Germ layer specification is one of the earliest developmental events in metazoan organisms, and relies upon the combinatorial interactions of signaling pathways and transcription factors (TFs), and the epigenetic landscape. A complete understanding of the gene regulatory program that contribute to the specification of the mesoderm and endoderm (‘mesendoderm’) in vivo is a crucial unanswered question. The Nodal signaling pathway, which is zygotically activated in the vegetal hemisphere of the early Xenopus embryo, is transcriptionally mediated by the TF Foxh1 and plays a key role in mesendoderm development. It has been suggested that Foxh1 plays dual regulatory roles in transcriptional mediation, and also functions independently of Nodal signaling. However, little is known about the contribution of Foxh1 to the activation of the mesendoderm program via TF binding to cis-regulatory modules (CRMs).Here, I have investigated the early functions of Xenopus Foxh1. I have utilized chromatin immunoprecipitation (ChIP) coupled with deep sequencing to investigate the genome-wide in vivo binding patterns of Foxh1 over the time course of early mesendoderm development, and compared Foxh1 occupancy to the recruitment of RNA polymerase II, epigenetic marks, and zygotic factors. I have found that Foxh1 binding is dynamic and bookmarks the early embryonic genome before zygotic genome activation. Furthermore, this early binding recruits the co-repressor Groucho/Tle. I identified a population of Foxh1 persistent peaks that are occupied throughout early mesendoderm development. These persistent peaks are marked as active enhancers, and recruit Smad2/3 and the zygotic pioneer factor Foxa. Therefore, they are likely critical mesendoderm CRMs, likely pioneered by Foxh1.Further, through mRNA-seq coupled with loss-of-function, I’ve expanded the list of bona-fide direct Foxh1 and Nodal signaling targets throughout mesendoderm development. Foxh1 direct targets appear dynamically regulated across the time course, and I confirm that Foxh1 functions dually as an activator and repressor. Temporal analysis of the expression of Foxh1 repressed targets suggests that Foxh1 plays a role in the regulation of maternal genes.My findings indicate a complex role for maternal Foxh1 at the top of a temporal hierarchy in the regulation of the early mesendoderm gene regulatory program. I propose a model whereby Foxh1 interacts with transcriptional co-repressors and activators in a context-specific fashion to regulate enhancer activation through both time and space. As the roles of Nodal signaling and Foxh1 in mesoderm and endoderm development are conserved among vertebrates, the findings presented here will have broad impacts in the fields of developmental, evolutionary, and stem cell biology.

Subjects/Keywords: Developmental biology; ChIP-seq; endoderm; Foxh1; Groucho/Tle; RNA-seq; Xenopus

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Le, R. C. (2016). The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network. (Thesis). University of California – Irvine. Retrieved from http://www.escholarship.org/uc/item/22r462c6

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Le, Rebekah Charney. “The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network.” 2016. Thesis, University of California – Irvine. Accessed September 21, 2019. http://www.escholarship.org/uc/item/22r462c6.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Le, Rebekah Charney. “The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network.” 2016. Web. 21 Sep 2019.

Vancouver:

Le RC. The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network. [Internet] [Thesis]. University of California – Irvine; 2016. [cited 2019 Sep 21]. Available from: http://www.escholarship.org/uc/item/22r462c6.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Le RC. The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network. [Thesis]. University of California – Irvine; 2016. Available from: http://www.escholarship.org/uc/item/22r462c6

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of California – Berkeley

21. Roberts, Adam. Ambiguous fragment assignment for high-throughput sequencing experiments.

Degree: Computer Science, 2013, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/7zx1s4hr

► As the cost of short-read, high-throughput DNA sequencing continues to fall rapidly, new uses for the technology have been developed aside from its original purpose… (more)

▼ As the cost of short-read, high-throughput DNA sequencing continues to fall rapidly, new uses for the technology have been developed aside from its original purpose in determining the genome of various species. Many of these new experiments use the sequencer as a digital counter for measuring biological activities such as gene expression (RNA-Seq) or protein binding (ChIP-Seq).A common problem faced in the analysis of these data is that of sequenced fragments that are "ambiguous", meaning they resemble multiple loci in a reference genome or other sequence. In early analyses, such ambiguous fragments were ignored or were assigned to loci using simple heuristics. However, statistical approaches using maximum likelihood estimation have been shown to greatly improve the accuracy of downstream analyses and have become widely adopted Optimization based on the expectation-maximization (EM) algorithm are often employed by these methods to find the optimal sets of alignments, with frequent enhancements to the model. Nevertheless, these improvements increase complexity, which, along with an exponential growth in the size of sequencing datasets, has led to new computational challenges.Herein, we present our model for ambiguous fragment assignment for RNA-Seq, which includes the most comprehensive set of parameters of any model introduced to date, as well as various methods we have explored for scaling our optimization procedure. These methods include the use of an online EM algorithm and a distributed EM solution implemented on the Spark cluster computing system. Our advances have resulted in the first efficient solution to the problem of fragment assignment in sequencing.Furthermore, we are the first to create a fully generalized model for ambiguous fragment assignment and present details on how our method can provide solutions for additional high-throughput sequencing assays including ChIP-Seq, Allele-Specific Expression (ASE), and the detection of RNA-DNA Differences (RDDs) in RNA-Seq.

Subjects/Keywords: Computer science; Bioinformatics; chip-seq; expectation-maximization; rna-seq; sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Roberts, A. (2013). Ambiguous fragment assignment for high-throughput sequencing experiments. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/7zx1s4hr

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Roberts, Adam. “Ambiguous fragment assignment for high-throughput sequencing experiments.” 2013. Thesis, University of California – Berkeley. Accessed September 21, 2019. http://www.escholarship.org/uc/item/7zx1s4hr.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Roberts, Adam. “Ambiguous fragment assignment for high-throughput sequencing experiments.” 2013. Web. 21 Sep 2019.

Vancouver:

Roberts A. Ambiguous fragment assignment for high-throughput sequencing experiments. [Internet] [Thesis]. University of California – Berkeley; 2013. [cited 2019 Sep 21]. Available from: http://www.escholarship.org/uc/item/7zx1s4hr.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Roberts A. Ambiguous fragment assignment for high-throughput sequencing experiments. [Thesis]. University of California – Berkeley; 2013. Available from: http://www.escholarship.org/uc/item/7zx1s4hr

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Rochester Institute of Technology

22. Freewoman, Julia. Identification of Differential Expression of p53 associated RNAs at 3 Different Treatment Timepoints, and Association with ChIP-seq Identified p53 Genes.

Degree: MS, Thomas H. Gosnell School of Life Sciences (COS), 2017, Rochester Institute of Technology

URL: https://scholarworks.rit.edu/theses/9489

► Called “the guardian of the genome,” p53 is one of the most studied proteins associated with cancer. After activation, p53 induces its target genes… (more)

Subjects/Keywords: 5-fluorouracil; ChIP-seq; p53; RNA-seq; Time course

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Freewoman, J. (2017). Identification of Differential Expression of p53 associated RNAs at 3 Different Treatment Timepoints, and Association with ChIP-seq Identified p53 Genes. (Masters Thesis). Rochester Institute of Technology. Retrieved from https://scholarworks.rit.edu/theses/9489

Chicago Manual of Style (16^th Edition):

Freewoman, Julia. “Identification of Differential Expression of p53 associated RNAs at 3 Different Treatment Timepoints, and Association with ChIP-seq Identified p53 Genes.” 2017. Masters Thesis, Rochester Institute of Technology. Accessed September 21, 2019. https://scholarworks.rit.edu/theses/9489.

MLA Handbook (7^th Edition):

Freewoman, Julia. “Identification of Differential Expression of p53 associated RNAs at 3 Different Treatment Timepoints, and Association with ChIP-seq Identified p53 Genes.” 2017. Web. 21 Sep 2019.

Vancouver:

Freewoman J. Identification of Differential Expression of p53 associated RNAs at 3 Different Treatment Timepoints, and Association with ChIP-seq Identified p53 Genes. [Internet] [Masters thesis]. Rochester Institute of Technology; 2017. [cited 2019 Sep 21]. Available from: https://scholarworks.rit.edu/theses/9489.

Council of Science Editors:

Freewoman J. Identification of Differential Expression of p53 associated RNAs at 3 Different Treatment Timepoints, and Association with ChIP-seq Identified p53 Genes. [Masters Thesis]. Rochester Institute of Technology; 2017. Available from: https://scholarworks.rit.edu/theses/9489

University of Southern California

23. Dai, Chao. Integrating high-throughput sequencing data to study gene regulation.

Degree: PhD, Computational Biology and Bioinformatics, 2015, University of Southern California

URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/340117/rec/3533

► High-throughput sequencing is a powerful technique for gene regulation study, which can provide information about isoform expression as well as transcription factors / epigenetic factors… (more)

▼ High-throughput sequencing is a powerful technique for gene regulation study, which can provide information about isoform expression as well as transcription factors / epigenetic factors binding signal measurements. Chromosome conformation capture followed by high-throughput sequencing were recently applied to study spatial genome organization and shed light on functional associations between genome organization and gene regulation. By integrating genome wide high-throughput sequencing data, this dissertation investigates gene regulation in three different layers: co-splicing; coupling between transcription and splicing; and functional implications of spatial genome organization. ❧ In the exon co-splicing project, we designed a tensor-based approach to identify co-spliced exon clusters that frequently appear in multiple RNA-seq datasets. We found that co-splicing clusters can reveal novel functional groups which cannot be identified by co-expression clusters, and they can grant new insights of functions associated with post-transcriptional regulation. Our results also demonstrated that the same exons can dynamically participate in different pathways depending on different conditions and different other exons that are co-spliced. ❧ In the transcription and splicing coupling project, by using tensor-based approach to identify frequent coupled clusters on two layered co-expression networks and co-splicing networks, we demonstrated that protein-protein interactions between transcription factors and splicing factors could potentially serve as important mediators for transcription-splicing coupling. ❧ In spatial genome organization and genome function association project, we applied our tensor-based integrative network pattern mining method on a population of genome structures modeled from chromosome conformation capture data, and integrated public epigenetic marks and transcription factors ChIP-seq and RNA-seq data, to systematically investigate functional implications of spatial genome organization. Our results strongly demonstrated that transcriptional regulation and epigenetic regulation are functionally coupled with spatial genome organization, and centromeric influence plays an important role to shape spatial genome organization. Advisors/Committee Members: Zhou, Xianghong Jasmine (Committee Chair), Waterman, Michael S. (Committee Member), Alber, Frank (Committee Member), Liu, Yan (Committee Member).

Subjects/Keywords: gene regulation; RNA-seq; ChIP-seq; spatial genome organization

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dai, C. (2015). Integrating high-throughput sequencing data to study gene regulation. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/340117/rec/3533

Chicago Manual of Style (16^th Edition):

Dai, Chao. “Integrating high-throughput sequencing data to study gene regulation.” 2015. Doctoral Dissertation, University of Southern California. Accessed September 21, 2019. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/340117/rec/3533.

MLA Handbook (7^th Edition):

Dai, Chao. “Integrating high-throughput sequencing data to study gene regulation.” 2015. Web. 21 Sep 2019.

Vancouver:

Dai C. Integrating high-throughput sequencing data to study gene regulation. [Internet] [Doctoral dissertation]. University of Southern California; 2015. [cited 2019 Sep 21]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/340117/rec/3533.

Council of Science Editors:

Dai C. Integrating high-throughput sequencing data to study gene regulation. [Doctoral Dissertation]. University of Southern California; 2015. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/340117/rec/3533

Universidade Estadual de Campinas

24. Carvalho, Lucas Miguel de, 1991-. Avaliação de montadores de novo de RNA-Seq para análise de expressão diferencial de transcritos .

Degree: 2015, Universidade Estadual de Campinas

URL: http://repositorio.unicamp.br/jspui/handle/REPOSIP/321442

► Resumo: RNA-Seq é uma tecnologia desenvolvida a partir de dados de sequenciamento de nova geração (NGS) para estudos de transcriptomas. Um pesquisador pode reconstruir isoformas… (more)

▼ Resumo: RNA-Seq é uma tecnologia desenvolvida a partir de dados de sequenciamento de nova geração (NGS) para estudos de transcriptomas. Um pesquisador pode reconstruir isoformas a partir de dados de RNA-Seq sem utilizar um genoma de referência (montagem de novo). Uma das diversas análises possíveis utilizando dados de RNA-Seq é encontrar genes ou transcritos diferencialmente expressos. O objetivo deste trabalho é avaliar metodologias de análises em larga escala aplicadas na área da transcriptômica para encontrar transcritos diferencialmente expressos, propondo um critério de classificação que maximize a chance da escolha de algum transcrito montado por um montador de novo ser diferencialmente expresso. Esse critério pode auxiliar a eliminar transcritos falsos positivos a serem analisados posteriormente em bancada por metodologias, como PCR Real Time (Polimerase Chain Reaction Real Time). Dados reais foram testados para validar as montagens de novo na procura de transcritos diferencialmente expressos e resultados mostram que na alteração do volume de dados, a quantidade de verdadeiros positivos (transcritos realmente diferencialmente expressos) se altera. Concluímos que o melhor montador de novo foi o Trinity; Abstract: RNA-Seq is a next-generation sequencing data (NGS) technology developed for transcriptome studies. For an organism, a researcher can perform isoform reconstructions from RNA-Seq data without the reference genome (de novo assembly). One of the several possible analyses using RNA-Seq data is finding differentially expressed genes or transcripts. This study evaluates analytic methods used in large-scale transcriptome studies for finding differentially expressed transcripts, proposing a data classification criterium that maximizes the chance of choosing a differentially expressed transcript in a de novo assembly. This criterium helps eliminate false positives that hinder posterior methods, such as Real-Time PCR (Polymerase Chain Reaction Real Time). Real data were tested to evaluate de novo assemblies, searching for differentially expressed transcripts, and the results show that the amount of true positives (truly differentially expressed transcripts) varies with the data volume, favoring libraries with more data. We concluded that the best de novo assembler is Trinity Advisors/Committee Members: Silva, Felipe Rodrigues da (advisor), Dias, Zanoni, 1975- (advisor), Lobo, Francisco Pereira (committee member), Carvalho, Benilton de Sa (committee member).

Subjects/Keywords: RNA-seq; Bioinformática; Transcriptoma; Genetica - Expressão

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Carvalho, Lucas Miguel de, 1. (2015). Avaliação de montadores de novo de RNA-Seq para análise de expressão diferencial de transcritos . (Thesis). Universidade Estadual de Campinas. Retrieved from http://repositorio.unicamp.br/jspui/handle/REPOSIP/321442

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Carvalho, Lucas Miguel de, 1991-. “Avaliação de montadores de novo de RNA-Seq para análise de expressão diferencial de transcritos .” 2015. Thesis, Universidade Estadual de Campinas. Accessed September 21, 2019. http://repositorio.unicamp.br/jspui/handle/REPOSIP/321442.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Carvalho, Lucas Miguel de, 1991-. “Avaliação de montadores de novo de RNA-Seq para análise de expressão diferencial de transcritos .” 2015. Web. 21 Sep 2019.

Vancouver:

Carvalho, Lucas Miguel de 1. Avaliação de montadores de novo de RNA-Seq para análise de expressão diferencial de transcritos . [Internet] [Thesis]. Universidade Estadual de Campinas; 2015. [cited 2019 Sep 21]. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/321442.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Carvalho, Lucas Miguel de 1. Avaliação de montadores de novo de RNA-Seq para análise de expressão diferencial de transcritos . [Thesis]. Universidade Estadual de Campinas; 2015. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/321442

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universidade Estadual de Campinas

25. Sanchez, Camila Cristina, 1983-. Estudos genômicos da expressão gênica global de "Aspergillus niger" crescido em bagaço e colmo de cana-de-açúcar = Global gene expression of "Aspergillus niger" grown on bagasse and culm of sugarcane .

Degree: 2016, Universidade Estadual de Campinas

URL: http://repositorio.unicamp.br/jspui/handle/REPOSIP/321164

► Resumo: O aumento pela demanda de utilização de energia e o consenso crescente sobre a necessidade de se reduzir significativamente as emissões de gases do… (more)

▼ Resumo: O aumento pela demanda de utilização de energia e o consenso crescente sobre a necessidade de se reduzir significativamente as emissões de gases do efeito estufa e a dependência de combustíveis fósseis vem impulsionando o desenvolvimento e melhoramento da produção de biocombustíveis. O etanol é o biocombustível atualmente mais utilizado, sendo obtido a partir da fermentação dos açúcares extraídos principalmente da cana-de-açúcar (Brasil) e do milho (EUA), e estes dois países são responsáveis por aproximadamente 83% da produção mundial. A safra brasileira de cana-de-açúcar de 2015/2016 foi estimada em 655 milhões de toneladas, e deste total, aproximadamente 366 milhões foram destinados a produção de etanol (cerca de 28 bilhões de litros). Apesar desta grande produção, para atender a demanda mundial por biocombustível, grandes esforços vêm sendo feitos para aumentar estes números, e uma das opções seria a produção do denominado etanol de segunda geração (2G). Este etanol é produzido através da fermentação de açúcares liberados de polissacarídeos complexos encontrados na biomassa vegetal. Neste sentido, como subproduto do setor sucro-energético, estima-se que anualmente sejam gerados cerca de 178 milhões de toneladas de bagaço, o resíduo agroindustrial produzido em maior abundância no Brasil. E estudos sugerem que se 8% do bagaço for destinado à produção de etanol, o Brasil poderia aumentar cerca de 40% a produção deste biocombustível. Mas para a utilização deste bagaço e consequente produção do etanol 2G é necessário que diversos desafios biotecnológicos sejam superados, principalmente para diminuir o custo da hidrólise deste material. Deste modo, inúmeros estudos visam entender o metabolismo de micro-organismos que naturalmente evoluíram para utilizar os açúcares presentes na parede vegetal e as enzimas responsáveis pela quebra e modificação desses polissacarídeos (denominadas CAZymes) que são produzidas por eles. O fungo "Aspergillus niger" destaca-se como um ótimo produtor e secretor destas enzimas, e embora vários estudos já tenham sido realizados, pouco ainda é conhecido sobre seu metabolismo. Assim, o presente trabalho realizou estudos de transcriptômica (utilizando a abordagem de RNA-seq) e secretômica (através de espectrometria de massa) de "A. niger" crescido em colmo e bagaço por 6, 12 e 24 horas. Os resultados mostraram que a hidrólise dos substratos já se inicia logo após as 6 horas de inóculo, verificado através da presença de monômeros (principalmente xilose e glicose) nos sobrenadantes. Adicionalmente, foram observados 237 genes que codificam à CAZymes hiper-expressos, o que representa mais de 50% das CAZymes codificadas pelo genoma de A. niger, sendo cerca da metade encontrada no sobrenadante. As principais celulases, hemicelulases foram transcritas e secretadas, e de modo geral, os valores de expressão foram altos já nas primeiras seis horas de crescimento. A grande maioria dos genes que codificam às CAZymes foram hiper-expressos em colmo e bagaço, mas algumas diferenças quali e quantitativas… Advisors/Committee Members: Squina, Fabio Marcio (advisor), Ruller, Roberto (committee member), Goldbeck, Rosana (committee member).

Subjects/Keywords: Aspergillus niger; RNA-seq; Celulose; Hemicelulose

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sanchez, Camila Cristina, 1. (2016). Estudos genômicos da expressão gênica global de "Aspergillus niger" crescido em bagaço e colmo de cana-de-açúcar = Global gene expression of "Aspergillus niger" grown on bagasse and culm of sugarcane . (Thesis). Universidade Estadual de Campinas. Retrieved from http://repositorio.unicamp.br/jspui/handle/REPOSIP/321164

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sanchez, Camila Cristina, 1983-. “Estudos genômicos da expressão gênica global de "Aspergillus niger" crescido em bagaço e colmo de cana-de-açúcar = Global gene expression of "Aspergillus niger" grown on bagasse and culm of sugarcane .” 2016. Thesis, Universidade Estadual de Campinas. Accessed September 21, 2019. http://repositorio.unicamp.br/jspui/handle/REPOSIP/321164.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sanchez, Camila Cristina, 1983-. “Estudos genômicos da expressão gênica global de "Aspergillus niger" crescido em bagaço e colmo de cana-de-açúcar = Global gene expression of "Aspergillus niger" grown on bagasse and culm of sugarcane .” 2016. Web. 21 Sep 2019.

Vancouver:

Sanchez, Camila Cristina 1. Estudos genômicos da expressão gênica global de "Aspergillus niger" crescido em bagaço e colmo de cana-de-açúcar = Global gene expression of "Aspergillus niger" grown on bagasse and culm of sugarcane . [Internet] [Thesis]. Universidade Estadual de Campinas; 2016. [cited 2019 Sep 21]. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/321164.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sanchez, Camila Cristina 1. Estudos genômicos da expressão gênica global de "Aspergillus niger" crescido em bagaço e colmo de cana-de-açúcar = Global gene expression of "Aspergillus niger" grown on bagasse and culm of sugarcane . [Thesis]. Universidade Estadual de Campinas; 2016. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/321164

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Otago

26. Baker, Estelle Swainson. Characterisation of the NS1-2 and NS4 proteins of murine norovirus .

Degree: 2012, University of Otago

URL: http://hdl.handle.net/10523/2320

► Human noroviruses are highly infectious viruses that cause the majority of acute, non-bacterial epidemic gastroenteritis cases worldwide. Noroviruses belong to the family Caliciviridae and have… (more)

▼ Human noroviruses are highly infectious viruses that cause the majority of acute, non-bacterial epidemic gastroenteritis cases worldwide. Noroviruses belong to the family Caliciviridae and have a positive-sense RNA genome of around 7.5 kb. Murine norovirus is a useful model for the uncultivable human strains, and has a 7.4 kb genome with four open reading frames (ORFs). Two of these, ORF2 and ORF3, encode structural proteins and ORF4 encodes a virulence factor. The first open reading frame (ORF1) encodes a polyprotein that is cleaved by the viral protease into six nonstructural proteins. There is limited functional and biophysical information available for two of these nonstructural proteins, NS1-2 and NS4. The aims of this research were to characterise these two proteins. The NS1-2 protein lacks any significant sequence similarity to other viral or cellular proteins. Bioinformatic analyses identified an inherently disordered region (residues 1 – 142) in the highly divergent N-terminal region of the NS1-2 protein. Expression and purification of the NS1-2 protein of murine norovirus confirmed these predictions by identifying features typical of an inherently disordered protein. These were a biased amino acid composition with enrichment in the disorder promoting residues serine and proline, a lack of predicted secondary structure, a hydrophilic nature, an aberrant electrophoretic migration, an increased Stokes radius similar to that predicted for a protein from the pre-molten globule family, a high sensitivity to thermolysin proteolysis and a circular dichroism spectrum typical of an inherently disordered protein. The purification of the NS1-2 protein identified the presence of an NS1-2 dimer when expressed in Escherichia coli, which was also identified in transfected HEK293T cells and MNV-infected RAW264.7 cells. The NS4 protein is often referred to as the 3A-like protein due to a similar position in the genome as the 3A protein of poliovirus. However, NS4 shares only limited sequence similarity to polio 3A. The NS4 protein of murine norovirus was expressed in Escherichia coli and purified for the generation of a polyclonal antibody. Whole transcriptome RNA-Seq analysis was conducted on transfected RAW264.7 cells to provide important leads on functional roles, effects and host cell responses to in vitro transcripts encoding the complete MNV genome, the ORF1 nonstructural polyprotein, the full-length NS1-2 protein and the disordered region of NS1-2. Each transfected cell sample showed an upregulation in anti-apoptotic genes and a downregulation of pro-apoptotic genes, suggesting that MNV, and in particular the disordered region of NS1-2, manipulates the induction of apoptosis. A downregulation of sterol lipid synthesis genes and an upregulation of Th1-type chemokines were observed in MNV- and ORF1-transfected cells. NS1-2-transfected cells showed an increased expression for genes encoding intercellular junctions and regulatory proteins, indicating that NS1-2 is likely to have a multi-functional role affecting… Advisors/Committee Members: Ward, Vernon (advisor).

Subjects/Keywords: Norovirus; RNA-Seq; Disorder; NS1-2; NS4

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Baker, E. S. (2012). Characterisation of the NS1-2 and NS4 proteins of murine norovirus . (Doctoral Dissertation). University of Otago. Retrieved from http://hdl.handle.net/10523/2320

Chicago Manual of Style (16^th Edition):

Baker, Estelle Swainson. “Characterisation of the NS1-2 and NS4 proteins of murine norovirus .” 2012. Doctoral Dissertation, University of Otago. Accessed September 21, 2019. http://hdl.handle.net/10523/2320.

MLA Handbook (7^th Edition):

Baker, Estelle Swainson. “Characterisation of the NS1-2 and NS4 proteins of murine norovirus .” 2012. Web. 21 Sep 2019.

Vancouver:

Baker ES. Characterisation of the NS1-2 and NS4 proteins of murine norovirus . [Internet] [Doctoral dissertation]. University of Otago; 2012. [cited 2019 Sep 21]. Available from: http://hdl.handle.net/10523/2320.

Council of Science Editors:

Baker ES. Characterisation of the NS1-2 and NS4 proteins of murine norovirus . [Doctoral Dissertation]. University of Otago; 2012. Available from: http://hdl.handle.net/10523/2320

Oregon State University

27. Zhuo, Bin. Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes.

Degree: PhD, Statistics, 2016, Oregon State University

URL: http://hdl.handle.net/1957/59543

► Differential expression (DE) analysis is a key task in gene expression study, because it uncovers the association between expression levels of a gene and the… (more)

▼ Differential expression (DE) analysis is a key task in gene expression study, because it uncovers the association between expression levels of a gene and the covariates of interest. This dissertation pertains to two particular aspects of DE analysis—identifying stably expressed genes for count normalization and accounting for correlation between DE test statistics in gene-set test. RNA-Sequencing (RNA-Seq) has become the tool of choice for measuring gene expression over the past few years, and data generated from RNA-Seq experiments are the focus of this thesis. Identifying stably expressed genes is useful for count normalization and DE analysis. We examined RNA-Seq data on 211 biological samples from 24 different experiments conducted by different labs, and identified genes that are stably expressed across samples, treatment conditions, and experiments. We fit a Poisson log-linear mixed-effect model to the count data, and decomposed the total variance into between-sample, between-treatment and between-experiment variance components. The variance component analysis that we explore here is a first step towards understanding the sources and nature of the RNA-Seq count variation. The stability ranking of genes, when quantified by a numerical stability measure, is dependent on several factors: the background sample set and the reference gene set used for count normalization, the technology used to measure gene expression, and the specific stability measure. Since DE is measured by relative frequencies, we argue that DE is a relative concept. We advocate using an explicit reference gene set for count normalization to improve interpretability of DE results, and recommend using a common reference gene set when analyzing multiple RNA-Seq experiments to avoid potential inconsistent conclusions. We investigate the relationship between correlation among test statistics and the correlation of underlying observed data. For false discovery control (FDR) procedures and gene-set tests, pooling DE test statistics together is a frequently used idea and the correlation among test statistics needs to be taken into account. The sample correlation of observed data is often used to approximate the test statistics correlation. We show, however, that such an approximation is only valid under limited settings. In particular, we derive a formula for correlation between test statistics when they take a specific form, and as a special case, we present the exact expression of test-statistic correlation for equal-variance two-sample t-test statistic under bivariate normal assumption. We conclude that test-statistic correlation is weaker than the correlation of underlying observed data (normally distributed) in the context of equal-variance two-sample t-test. Competitive gene-set test is a widely used tool for interpreting high-throughput biological data, such as gene expression and proteomics data. It aims at testing categories of genes for enriched association signals in a list of genes inferred from genome-wide data. Most conventional… Advisors/Committee Members: Di, Yanming (advisor), Emerson, Sarah (committee member).

Subjects/Keywords: RNA-Seq; Gene expression – Statistical methods

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhuo, B. (2016). Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/59543

Chicago Manual of Style (16^th Edition):

Zhuo, Bin. “Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes.” 2016. Doctoral Dissertation, Oregon State University. Accessed September 21, 2019. http://hdl.handle.net/1957/59543.

MLA Handbook (7^th Edition):

Zhuo, Bin. “Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes.” 2016. Web. 21 Sep 2019.

Vancouver:

Zhuo B. Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes. [Internet] [Doctoral dissertation]. Oregon State University; 2016. [cited 2019 Sep 21]. Available from: http://hdl.handle.net/1957/59543.

Council of Science Editors:

Zhuo B. Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes. [Doctoral Dissertation]. Oregon State University; 2016. Available from: http://hdl.handle.net/1957/59543

Universidade Estadual de Campinas

28. Reis Junior, Osvaldo, 1986-. Identificação e padrões de expressão de transcritos derivados de RNA-Seq : caracterização molecular do fungo Moniliophthora perniciosa, causador da vassoura-de-bruxa do cacaueiro .

Degree: 2014, Universidade Estadual de Campinas

URL: http://repositorio.unicamp.br/jspui/handle/REPOSIP/316759

► Resumo: As tecnologias de sequenciamento de segunda geração geram um grande número de sequências em um curto espaço de tempo e com baixo custo. O… (more)

▼ Resumo: As tecnologias de sequenciamento de segunda geração geram um grande número de sequências em um curto espaço de tempo e com baixo custo. O sequenciamento em larga escala de cDNA, conhecido como RNA-seq, tem permitido análises precisas de transcriptomas inteiros sem a necessidade de conhecimento prévio sobre sequências genômicas, conforme exigido pela tecnologia de microarranjos. No entanto, existem muitas discussões sobre os métodos utilizados para o alinhamento de reads, identificação de genes diferencialmente expressos e montagem de transcriptomas. Desde 2000, o Laboratório de Genômica e Expressão (LGE), tem estudado a doença da vassoura-de-bruxa do cacaueiro (Theobroma cacao), que é causada pelo fungo basidiomiceto Moniliophthora perniciosa. Recentemente, 54 bibliotecas RNA-seq da interação planta-patógeno foram sequenciadas pelo nosso grupo, a fim de ajudar na elucidação da complexa biologia da doença. Desta forma, este trabalho tem como objetivo gerar informações sobre o perfil de transcrição do M. perniciosa e do T. cacao durante a doença vassoura-de-bruxa. Os resultados estão divididos em três seções principais, sendo que na primeira apresentamos uma análise de alinhamento e expressão gênica nas condições e tecidos amostrados. Na segunda, analisamos o estágio inicial da doença, conhecido como vassoura-verde, onde através da análise de expressão diferencial identificamos genes relacionados aos mecanismos de interação entre o cacaueiro e o fungo M. perniciosa. Na ultima seção, desenvolvemos uma estratégia para identificar sequências de possíveis RNAs não codificantes longos (lncRNA) e aplicamos esta estratégia no fungo M. perniciosa. De uma maneira geral estes dados apresentam um importante avanço no estudo desta doença e poderão ser utilizados em trabalhos futuro; Abstract: Next-generation sequencing technologies generate large numbers of sequences in a short time and at low cost. The high-throughput sequencing of cDNA, known as RNA-seq, has allowed precise analyses of entire transcriptomes without the need of previous knowledge on genomic sequences, as required by microarrays. However, there are many discussions about the methods used for read alignment, identification of differentially expressed genes and assembly of transcriptomes. Since 2000, the Genomics and Expression Laboratory (LGE), has been studying the Witches' Broom Disease (WBD) of cacao (Theobroma cacao), which is caused by the basidiomycete fungus Moniliophthora perniciosa. Recently, 54 RNA-seq libraries of this plant-pathogen interaction were sequenced by our group in order to help in the elucidation of the complex biology of the disease. Thus, this work aims to generate information about the transcription profile of M. perniciosa and T. cacao during the Witches' Broom Disease (WBD). The results are divided into three main sections, the first is an analysis of alignment and gene expression under the conditions and sampled tissues. In the second section, we analyze the initial stage of the disease, known as green broom, where through… Advisors/Committee Members: Pereira, Gonçalo Amarante Guimarães, 1964- (advisor), Yamagishi, Michel Eduardo Beleza (committee member), Brandão, Marcelo Mendes (committee member).

Subjects/Keywords: RNA-seq; Transcriptoma; Vassoura-de-bruxa (Fitopatologia)

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Reis Junior, Osvaldo, 1. (2014). Identificação e padrões de expressão de transcritos derivados de RNA-Seq : caracterização molecular do fungo Moniliophthora perniciosa, causador da vassoura-de-bruxa do cacaueiro . (Thesis). Universidade Estadual de Campinas. Retrieved from http://repositorio.unicamp.br/jspui/handle/REPOSIP/316759

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Reis Junior, Osvaldo, 1986-. “Identificação e padrões de expressão de transcritos derivados de RNA-Seq : caracterização molecular do fungo Moniliophthora perniciosa, causador da vassoura-de-bruxa do cacaueiro .” 2014. Thesis, Universidade Estadual de Campinas. Accessed September 21, 2019. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316759.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Reis Junior, Osvaldo, 1986-. “Identificação e padrões de expressão de transcritos derivados de RNA-Seq : caracterização molecular do fungo Moniliophthora perniciosa, causador da vassoura-de-bruxa do cacaueiro .” 2014. Web. 21 Sep 2019.

Vancouver:

Reis Junior, Osvaldo 1. Identificação e padrões de expressão de transcritos derivados de RNA-Seq : caracterização molecular do fungo Moniliophthora perniciosa, causador da vassoura-de-bruxa do cacaueiro . [Internet] [Thesis]. Universidade Estadual de Campinas; 2014. [cited 2019 Sep 21]. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/316759.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Reis Junior, Osvaldo 1. Identificação e padrões de expressão de transcritos derivados de RNA-Seq : caracterização molecular do fungo Moniliophthora perniciosa, causador da vassoura-de-bruxa do cacaueiro . [Thesis]. Universidade Estadual de Campinas; 2014. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/316759

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

29. Wang, Fengchao. Targets Identification and Characterization of Tramp Comples in Mouse.

Degree: 2015, Marquette University

URL: https://epublications.marquette.edu/theses_open/305

► RNA surveillance and degradation play an important role in the development and growth of organisms by eliminating RNA that contains errors, or that is no… (more)

Subjects/Keywords: RNA-Seq; Target; TRAMP; Cell Biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wang, F. (2015). Targets Identification and Characterization of Tramp Comples in Mouse. (Thesis). Marquette University. Retrieved from https://epublications.marquette.edu/theses_open/305

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Wang, Fengchao. “Targets Identification and Characterization of Tramp Comples in Mouse.” 2015. Thesis, Marquette University. Accessed September 21, 2019. https://epublications.marquette.edu/theses_open/305.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Wang, Fengchao. “Targets Identification and Characterization of Tramp Comples in Mouse.” 2015. Web. 21 Sep 2019.

Vancouver:

Wang F. Targets Identification and Characterization of Tramp Comples in Mouse. [Internet] [Thesis]. Marquette University; 2015. [cited 2019 Sep 21]. Available from: https://epublications.marquette.edu/theses_open/305.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Wang F. Targets Identification and Characterization of Tramp Comples in Mouse. [Thesis]. Marquette University; 2015. Available from: https://epublications.marquette.edu/theses_open/305

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Louisiana State University

30. Chen, Ruoxi. Integrated functional anlaysis of quorum-sensing in the rice pathogenic bacterium Burkholderia glumae.

Degree: PhD, Plant Sciences, 2013, Louisiana State University

URL: etd-11132013-230025 ; https://digitalcommons.lsu.edu/gradschool_dissertations/1287

► Quorum sensing (QS) is a cell-to-cell communication mechanism that allows bacterial cells to collectively behave like a multicellular organism. It regulates the expression of toxoflavin,… (more)

Subjects/Keywords: RNA-seq; mutation; quorum sensing; Burkholderia glumae

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Chen, R. (2013). Integrated functional anlaysis of quorum-sensing in the rice pathogenic bacterium Burkholderia glumae. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-11132013-230025 ; https://digitalcommons.lsu.edu/gradschool_dissertations/1287

Chicago Manual of Style (16^th Edition):

Chen, Ruoxi. “Integrated functional anlaysis of quorum-sensing in the rice pathogenic bacterium Burkholderia glumae.” 2013. Doctoral Dissertation, Louisiana State University. Accessed September 21, 2019. etd-11132013-230025 ; https://digitalcommons.lsu.edu/gradschool_dissertations/1287.

MLA Handbook (7^th Edition):

Chen, Ruoxi. “Integrated functional anlaysis of quorum-sensing in the rice pathogenic bacterium Burkholderia glumae.” 2013. Web. 21 Sep 2019.

Vancouver:

Chen R. Integrated functional anlaysis of quorum-sensing in the rice pathogenic bacterium Burkholderia glumae. [Internet] [Doctoral dissertation]. Louisiana State University; 2013. [cited 2019 Sep 21]. Available from: etd-11132013-230025 ; https://digitalcommons.lsu.edu/gradschool_dissertations/1287.

Council of Science Editors:

Chen R. Integrated functional anlaysis of quorum-sensing in the rice pathogenic bacterium Burkholderia glumae. [Doctoral Dissertation]. Louisiana State University; 2013. Available from: etd-11132013-230025 ; https://digitalcommons.lsu.edu/gradschool_dissertations/1287

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