subject:(Ribonucleic acid sequence RNA seq )

1. Hekman, Jessica Perry. Transcriptome analysis of the hypothalamic-pituitary-adrenal axis in the experimentally domesticated fox.

Degree: PhD, Animal Sciences, 2017, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/98347

► Variation in activity of the hormonal stress response, or hypothalamic-pituitary-adrenal (HPA) axis, has been associated with different personality traits and coping styles in humans and… (more)

▼ Variation in activity of the hormonal stress response, or hypothalamic-pituitary-adrenal (HPA) axis, has been associated with different personality traits and coping styles in humans and animals, while its dysregulation has been implicated in psychological disorders. The molecular basis of HPA axis regulation, however, is not yet well understood. Here, foxes selectively bred for tameness or aggression are used as a model to investigate differences in regulation of the HPA axis. Activity of this axis is markedly reduced in tame compared to aggressive foxes, with reduced levels of HPA axis hormones such as adrenocorticotrophic hormone (ACTH) and cortisol both basally and in response to a stressor. Gene expression differences were analyzed using RNA sequencing in the anterior pituitary and adrenal glands of foxes from the tame and aggressive lines, and variant analysis was performed on RNA reads from hypothalamus, anterior pituitary, and adrenal tissues from the same foxes. Pituitary analysis revealed expression differences in genes related to exocytosis and cellular signaling; adrenals analysis identified differences in similar pathways, in addition to genes related to fatty acid and cholesterol synthesis. Variant analysis also implicated cell signaling and exocytosis, as well as ion transport and DNA damage repair. These findings suggest the importance of regulation of hormone release in the control of ACTH and cortisol levels. They also suggest that metabolism of precursors to cortisol, such as fatty acids and cholesterol, may be of greater importance in HPA axis regulation than synthesis of cortisol itself. Finally, in conjunction with previous genomic findings, they suggest an association between DNA repair mechanisms and selection for tameness. These findings provide possible new lines of investigation into biological underpinnings of the phenotypic differences between the tame and aggressive lines of foxes. More broadly, as the tame foxes are considered experimentally domesticated, the findings from this project may prove applicable to HPA axis regulation differences associated with domestication in other species. Additionally, a deeper understanding of HPA axis regulation and dysregulation may be applicable both to variation in the normal population, particularly as related to behavioral traits such as coping styles, and to a number of psychiatric disorders in humans, as well as to behavioral disorders in other species, such as dogs. Advisors/Committee Members: Kukekova, Anna V (advisor), Kukekova, Anna V (Committee Chair), Beever, Jonathan (committee member), Bell, Allison (committee member), Raetzman, Lori (committee member), Stubbs, Lisa (committee member).

Subjects/Keywords: Ribonucleic acid sequence (RNA-seq); Stress; Pituitary; Adrenals; Hypothalamic-pituitary-adrenal (HPA)

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APA (6^th Edition):

Hekman, J. P. (2017). Transcriptome analysis of the hypothalamic-pituitary-adrenal axis in the experimentally domesticated fox. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/98347

Chicago Manual of Style (16^th Edition):

Hekman, Jessica Perry. “Transcriptome analysis of the hypothalamic-pituitary-adrenal axis in the experimentally domesticated fox.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/98347.

MLA Handbook (7^th Edition):

Hekman, Jessica Perry. “Transcriptome analysis of the hypothalamic-pituitary-adrenal axis in the experimentally domesticated fox.” 2017. Web. 23 Apr 2021.

Vancouver:

Hekman JP. Transcriptome analysis of the hypothalamic-pituitary-adrenal axis in the experimentally domesticated fox. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/98347.

Council of Science Editors:

Hekman JP. Transcriptome analysis of the hypothalamic-pituitary-adrenal axis in the experimentally domesticated fox. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/98347

University of Illinois – Urbana-Champaign

2. Barling, Adam R. RNA-SEQ driven analysis of seasonal gene expression variation in miscanthus �� giganteus.

Degree: PhD, 0030, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/46926

► Miscanthus × giganteus is a C4 grass that has generated a large amount of interest as a potential biofuel crop due to its high level… (more)

Subjects/Keywords: Ribonucleic Acid Sequencing (RNA-Seq); Miscanthus; Biofuel

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APA (6^th Edition):

Barling, A. R. (2014). RNA-SEQ driven analysis of seasonal gene expression variation in miscanthus �� giganteus. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/46926

Chicago Manual of Style (16^th Edition):

Barling, Adam R. “RNA-SEQ driven analysis of seasonal gene expression variation in miscanthus �� giganteus.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/46926.

MLA Handbook (7^th Edition):

Barling, Adam R. “RNA-SEQ driven analysis of seasonal gene expression variation in miscanthus �� giganteus.” 2014. Web. 23 Apr 2021.

Vancouver:

Barling AR. RNA-SEQ driven analysis of seasonal gene expression variation in miscanthus �� giganteus. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/46926.

Council of Science Editors:

Barling AR. RNA-SEQ driven analysis of seasonal gene expression variation in miscanthus �� giganteus. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/46926

University of Illinois – Urbana-Champaign

3. Wei, Wei. Transcriptomic characterization of soybean – sclerotinia sclerotiorum interaction at early infection stages.

Degree: MS, Crop Sciences, 2017, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/98145

► Sclerotinia stem rot, also referred to as white mold, poses a threat to soybean production world-wide. The causal agent, Sclerotinia sclerotiorum (Lib.) de Bary, can… (more)

▼ Sclerotinia stem rot, also referred to as white mold, poses a threat to soybean production world-wide. The causal agent, Sclerotinia sclerotiorum (Lib.) de Bary, can survive in harsh environments and has an extremely broad host range. No naturally complete resistance has been reported to exist in soybean, which makes it a compelling problem. Studying the molecular interactions between soybean and S. sclerotiorum is a promising approach to identify the soybeans genes that are controlling the quantitative resistance and, on the other hand, to discover pathogenicity and virulence factors in S. sclerotiorum which could be considered as targets to disable and weaken the aggressiveness of the pathogen. This study utilized RNA-sequencing to characterize the transcriptomes of the leaves of a susceptible soybean line (AC) and an AC transgenic line (OxO) which contains an enzyme that degrades the oxalic acid (OA) produced by S. sclerotiorum thereby conferring resistance. The leaves were infected with S. sclerotiorum and samples were collected at 4 and 8 hours post inoculation (hpi) to characterize this interaction and to examine the key determinants of resistance and infection at these early infection stages. More than 600 soybean genes were detected with a fairly stringent cutoff as being significantly differentially expressed in response to S. sclerotiorum inoculation. Functional annotations and categorizations revealed that a large percentage of differentially expressed genes (DEGs) were annotated as kinases and transcription factors, depicting a complex network of signal transduction and gene regulation during the initiation of defense responses. Gene Ontology (GO) enrichment analysis demonstrated that host oxidative burst, jasmonic acid and ethylene signaling pathways, and biosynthetic pathways of several soybean anti-microbial secondary metabolites, were all quickly induced in this defense response. Our data also suggested that abscisic acid signaling was highly responsive to S. sclerotiorum infection, and that salicylic acid signaling might be largely inhibited. Interestingly, a potential interplay of a hypersensitive response-like programmed cell death (PCD) and autophagy was detected as a common reaction in both genotypes. It is speculated that, because S. sclerotiorum is a necrotrophic fungus that feeds on dead host cells, inhibiting host cell death could slow down its infection. Our expression data also identified six membrane trafficking-related genes that were proposed to contribute to negative regulation of PCD via suppressing the salicylic acid signaling pathway. Although no statistically significant differences between the two genotypes were due to fungal infection, the quantitative differences between them were discussed. Although apparently minor at these early time points, these quantitative differences could be reflective of defense-related processes that were more intense in OxO. This transcriptomic study also compared the gene expression of the pathogen, S. sclerotiorum, in infected leaves from AC and… Advisors/Committee Members: Clough, Steven (advisor), Hartman, Glen L (committee member), Zhao, Youfu (committee member).

Subjects/Keywords: Ribonucleic acid sequencing (RNA-Seq); Sclerotinia sclerotiorum

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

APA (6^th Edition):

Wei, W. (2017). Transcriptomic characterization of soybean – sclerotinia sclerotiorum interaction at early infection stages. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/98145

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):

Wei, Wei. “Transcriptomic characterization of soybean – sclerotinia sclerotiorum interaction at early infection stages.” 2017. Thesis, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/98145.

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

MLA Handbook (7^th Edition):

Wei, Wei. “Transcriptomic characterization of soybean – sclerotinia sclerotiorum interaction at early infection stages.” 2017. Web. 23 Apr 2021.

Vancouver:

Wei W. Transcriptomic characterization of soybean – sclerotinia sclerotiorum interaction at early infection stages. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/98145.

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

Council of Science Editors:

Wei W. Transcriptomic characterization of soybean – sclerotinia sclerotiorum interaction at early infection stages. [Thesis]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/98145

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

University of Illinois – Urbana-Champaign

4. Win, Hlaing. Analysis of soybean small RNA populations.

Degree: MS, 4026, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/29556

► Background: Small RNAs play an important role in the regulation of gene expression. Recent genome-wide profiling studies of small RNAs in Arabidopsis thaliana have revealed… (more)

▼ Background: Small RNAs play an important role in the regulation of gene expression. Recent genome-wide profiling studies of small RNAs in Arabidopsis thaliana have revealed the complexity of small RNA in plant genomes. Since soybean small RNA populations in Soybean [Glycine max] may regulate important processes in this crop plant, we used illumina sequencing-by-synthesis technology to sequence approximately 30 million small RNAs from seed coat and cotyledon tissues to identify small regulatory RNAs that are differentially expressed between these tissues. Results: Glycine max genome locations, genomic features, and small RNA sequence abundance information from the seed coat and cotyledon libraries were used to characterize the small RNA population and its expression. By analyzing small RNAs as clusters based on their closeness of the genomic matching location, we identified 177,314 small RNA generating loci from 20 chromosomes. 89% of small RNA generating loci mapped to the annotated repeat regions. More than 1% of small RNA generating loci mapped to genomic region where no functional information is available. 3017 small RNA generating loci also showed significant expression differences between libraries in our comparison. In addition, we identified 6 potential secondary siRNA triggers, 94 potential trans-acting siRNA (ta-siRNA) generation loci, at least 5 natural cis-antisense siRNA (cis-nat-siRNAs) generating loci. Conclusions: Identification of distinct candidate small RNA populations such as ta-siRNA, cis-nat-siRNAs, secondary siRNA triggers, and genomic regions where small RNAs are potentially involved in the regulation of gene expression in soybean seed coat and cotyledon gives a better understanding of small RNA populations in the Glycine max genome. In particular, the potential new ta-siRNA loci identified show that the ta-siRNA system in soybean is significantly more complex than the system previously characterized in the model system Arabidopsis. Advisors/Committee Members: Hudson, Matthew E. (advisor).

Subjects/Keywords: small RNA; Ribonucleic acid (RNA)

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APA (6^th Edition):

Win, H. (2012). Analysis of soybean small RNA populations. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/29556

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):

Win, Hlaing. “Analysis of soybean small RNA populations.” 2012. Thesis, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/29556.

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

MLA Handbook (7^th Edition):

Win, Hlaing. “Analysis of soybean small RNA populations.” 2012. Web. 23 Apr 2021.

Vancouver:

Win H. Analysis of soybean small RNA populations. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/29556.

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

Council of Science Editors:

Win H. Analysis of soybean small RNA populations. [Thesis]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/29556

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

University of Illinois – Urbana-Champaign

5. Han, Jennifer. Sex chromosome evolution of papaya: Dynamic structural and expression changes and identification of associated traits.

Degree: PhD, 0320, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/49690

► Sex chromosomes are found throughout many diverse lineages across the animal and plant kingdom. Most of the sex chromosomes that have been studied are well… (more)

▼ Sex chromosomes are found throughout many diverse lineages across the animal and plant kingdom. Most of the sex chromosomes that have been studied are well established and have already experienced many evolutionary forces, making it difficult to reconstruct the dynamic changes involved in the evolution of sex chromosomes. Sex chromosomes are evolved from a pair of autosomes with closely linked sex determining genes that have stopped recombining. Papaya has many qualities that make it attractive for studying sex chromosome genetics. It is trioecious (male, female, and hermaphrodite) with sex determined by a pair of nascent sex chromosomes approximately 7 million years old. The genome is relatively small (442.5 Mb) and the sex determining region of the sex chromosomes is small and well characterized; the hermaphrodite and male specific region of the Yh and Y chromosome respectively is 8.1 Mb and the corresponding X is 3.5 Mb. These sex specific regions of the X and Y chromosomes not only contain the genes that control sex type, but they also have genes associated with the different sexes. While the vegetative forms of the three sexes are phenotypically identical, the reproductive structures are unique. In stark contrast to female and hermaphrodite flowers on male plants are borne on long pendulous peduncles (60-90 cm) at the leaf axis. Female and hermaphrodite flowers are borne on short peduncles (0-4 cm). Gynodioecious varieties SunUp, SunUp Diminutive mutant and dioecious AU9 were used to test the response of papaya to gibberellic acid (GA3). Gibberellic acid is a hormone known to cause elongation of stems throughout the plant kingdom. It is also known as a masculinizing hormone. Exogenous applications of GA3 on female and hermaphrodite papaya did not yield any sex reversals but there was a significant increase in peduncle length and inflorescence branch number in all treated plants. There was an increase in plant height for all treated plants except SunUp Diminutive mutant, suggesting that the mechanism causing the dwarf phenotype is independent of gibberellins. Gibberellin metabolism genes were identified in the papaya genome, none of which mapped to the sex-determining region of either the male- or hermaphrodite-specific region of papaya Y or Yh chromosome. We hypothesize that a trans-acting regulatory element that enhances gibberellin biosynthesis plays a role in the extreme length of the male papaya peduncle Sex chromosomes experience several evolutionary forces. To further study the structure of the sex chromosomes, a mapping population was created to generate a high density genetic map. A female AU9 was crossed with a hermaphrodite SunUp, the resulting offspring was backcrossed to the hermaphrodite SunUp. Fifty-one individuals derived from this cross were used to create restriction-site associated DNA sequencing (RAD-seq) libraries. A total of 228 RAD-seq markers were mapped to 9 major and 2 minor linkage groups. Previous studies have shown that the Y chromosome experiences severe recombination suppression… Advisors/Committee Members: Ming, Ray R. (advisor), Ming, Ray R. (Committee Chair), Jacobs, Thomas W. (committee member), Vodkin, Lila O. (committee member), Hanzawa, Yoshie (committee member).

Subjects/Keywords: Papaya; sex chromosome; dosage compensation; restriction-site associated DNA sequencing (RAD-seq); Ribonucleic acid sequencing (RNA-seq); gibberellin; genetic map

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

APA (6^th Edition):

Han, J. (2014). Sex chromosome evolution of papaya: Dynamic structural and expression changes and identification of associated traits. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/49690

Chicago Manual of Style (16^th Edition):

Han, Jennifer. “Sex chromosome evolution of papaya: Dynamic structural and expression changes and identification of associated traits.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/49690.

MLA Handbook (7^th Edition):

Han, Jennifer. “Sex chromosome evolution of papaya: Dynamic structural and expression changes and identification of associated traits.” 2014. Web. 23 Apr 2021.

Vancouver:

Han J. Sex chromosome evolution of papaya: Dynamic structural and expression changes and identification of associated traits. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/49690.

Council of Science Editors:

Han J. Sex chromosome evolution of papaya: Dynamic structural and expression changes and identification of associated traits. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/49690

Texas Tech University

6. Schiflett, Samuel G. Naive rat performance affected by intra-peritoneal injections of RNA extracted from the brains of operant conditioned rats.

Degree: Psychology, 1968, Texas Tech University

URL: http://hdl.handle.net/2346/10412

Subjects/Keywords: Ribonucleic acid (RNA); Conditioned response

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APA (6^th Edition):

Schiflett, S. G. (1968). Naive rat performance affected by intra-peritoneal injections of RNA extracted from the brains of operant conditioned rats. (Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/10412

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):

Schiflett, Samuel G. “Naive rat performance affected by intra-peritoneal injections of RNA extracted from the brains of operant conditioned rats.” 1968. Thesis, Texas Tech University. Accessed April 23, 2021. http://hdl.handle.net/2346/10412.

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

MLA Handbook (7^th Edition):

Schiflett, Samuel G. “Naive rat performance affected by intra-peritoneal injections of RNA extracted from the brains of operant conditioned rats.” 1968. Web. 23 Apr 2021.

Vancouver:

Schiflett SG. Naive rat performance affected by intra-peritoneal injections of RNA extracted from the brains of operant conditioned rats. [Internet] [Thesis]. Texas Tech University; 1968. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2346/10412.

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

Council of Science Editors:

Schiflett SG. Naive rat performance affected by intra-peritoneal injections of RNA extracted from the brains of operant conditioned rats. [Thesis]. Texas Tech University; 1968. Available from: http://hdl.handle.net/2346/10412

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

University of Illinois – Urbana-Champaign

7. Srinivasan, Divya. Single molecule pull-down of viral RNA-protein complexes.

Degree: MS, 0318, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/31924

► Protein and RNA molecules interact with multiple protein partners to perform essential cellular processes such as post-transcriptional regulation of mRNA. Recently, a single molecule pull-down… (more)

Subjects/Keywords: single molecule; viral RNA; total internal reflection fluorescence microscopy; Ribonucleic acid (RNA)

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APA (6^th Edition):

Srinivasan, D. (2012). Single molecule pull-down of viral RNA-protein complexes. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/31924

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):

Srinivasan, Divya. “Single molecule pull-down of viral RNA-protein complexes.” 2012. Thesis, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/31924.

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

MLA Handbook (7^th Edition):

Srinivasan, Divya. “Single molecule pull-down of viral RNA-protein complexes.” 2012. Web. 23 Apr 2021.

Vancouver:

Srinivasan D. Single molecule pull-down of viral RNA-protein complexes. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/31924.

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

Council of Science Editors:

Srinivasan D. Single molecule pull-down of viral RNA-protein complexes. [Thesis]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/31924

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

University of New Orleans

8. Coco, Joseph. PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences.

Degree: MS, Computer Science, 2011, University of New Orleans

URL: https://scholarworks.uno.edu/td/1297

► RNA-Sequencing (RNA-Seq) has become one of the most widely used techniques to interrogate the transcriptome of an organism since the advent of next generation sequencing… (more)

Subjects/Keywords: exogenous agents; RNA-Seq; contamination; sequence alignment; cancer etiology; sequence assembly; taxonomical classification; cancer treatment

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APA (6^th Edition):

Coco, J. (2011). PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences. (Thesis). University of New Orleans. Retrieved from https://scholarworks.uno.edu/td/1297

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):

Coco, Joseph. “PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences.” 2011. Thesis, University of New Orleans. Accessed April 23, 2021. https://scholarworks.uno.edu/td/1297.

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

MLA Handbook (7^th Edition):

Coco, Joseph. “PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences.” 2011. Web. 23 Apr 2021.

Vancouver:

Coco J. PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences. [Internet] [Thesis]. University of New Orleans; 2011. [cited 2021 Apr 23]. Available from: https://scholarworks.uno.edu/td/1297.

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

Council of Science Editors:

Coco J. PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences. [Thesis]. University of New Orleans; 2011. Available from: https://scholarworks.uno.edu/td/1297

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

University of Illinois – Urbana-Champaign

9. Ge, Yejing. Regulation of skeletal myogenesis by the mTOR signaling network.

Degree: PhD, 4094, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/32047

► Skeletal muscle is composed of post-mitotic multinucleated myofibers. During embryonic skeletal myogenesis, cells in somites commit to myogenic lineage and differentiate into myoblasts, which then… (more)

▼ Skeletal muscle is composed of post-mitotic multinucleated myofibers. During embryonic skeletal myogenesis, cells in somites commit to myogenic lineage and differentiate into myoblasts, which then fuse to form multinucleated myofibers. Post-natal growth, repair, and maintenance of skeletal muscle are dependent on muscle satellite cells, which in response to stimuli differentiate and fuse to form new myofibers. Developmental or post-natal failure of skeletal myogenesis results in diverse muscular dystrophies and atrophies, largely impairing life quality and sometimes directly causing death. The myogenic process is guided by various environmental cues and regulated by distinct signaling pathways, resulting in the activation of specific transcription factors and subsequent reprogramming of gene expression. The mammalian target of rapamycin (mTOR) is a Ser/Thr kinase that controls a wide spectrum of cellular and developmental processes including regulation of skeletal myogenesis. In my dissertation work, I investigate the mechanisms of myogenic regulation, with a focus on the signaling network assembled by mTOR. Various processes of skeletal muscle differentiation and remodeling were known to be inhibited by the mTOR-specific inhibitor, rapamycin. In cultured myoblasts, the target of rapamycin – mTOR – had been reported to regulate differentiation at different stages through distinct mechanisms, including one that is independent of mTOR kinase activity. However, there had been no in vivo evidence to validate those mTOR myogenic mechanisms in vitro. In Chapter II, I show that rapamycin impairs injury-induced muscle regeneration. To validate the role of mTOR with genetic evidence and to probe the mechanism of mTOR function, I have generated and characterized transgenic mice expressing two mutants of mTOR under the control of human skeletal actin (HSA) promoter – rapamycin-resistant (RR) and RR/kinase-inactive (RR/KI) mTOR. My results show that muscle regeneration in rapamycin-administered mice is restored by RR-mTOR expression. In the RR/KI-mTOR mice, nascent myofiber formation during the early phase of regeneration proceeds in the presence of rapamycin, but growth of the regenerating myofibers is blocked by rapamycin. Igf2 mRNA levels increase drastically during early regeneration, which is sensitive to rapamycin in WT muscles but partially resistant to rapamycin in both RR- and RR/KI-mTOR muscles, consistent with mTOR regulation of Igf2 expression in a kinase-independent manner. Furthermore, systemic ablation of S6K1, a target of mTOR kinase, results in impaired muscle growth but normal nascent myofiber formation during regeneration. Therefore, mTOR regulates muscle regeneration through kinase-independent and kinaseiii dependent mechanisms at the stages of nascent myofiber formation and myofiber growth, respectively. MicroRNAs have emerged as key regulators of skeletal myogenesis, but our knowledge of the identity of the myogenic miRNAs and their targets remains limited. In Chapter III, I describe the identification and… Advisors/Committee Members: Chen, Jie (advisor), Belmont, Andrew S. (Committee Chair), Chen, Jie (committee member), Katzenellenbogen, Benita S. (committee member), Prasanth, Kannanganattu V. (committee member), Wang, Fei (committee member).

Subjects/Keywords: mTOR; myogenesis; myoblast differentiation; microRNA; miRNA; mammalian target of rapamycin (mTOR); Ribonucleic acid (RNA)

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

APA (6^th Edition):

Ge, Y. (2012). Regulation of skeletal myogenesis by the mTOR signaling network. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/32047

Chicago Manual of Style (16^th Edition):

Ge, Yejing. “Regulation of skeletal myogenesis by the mTOR signaling network.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/32047.

MLA Handbook (7^th Edition):

Ge, Yejing. “Regulation of skeletal myogenesis by the mTOR signaling network.” 2012. Web. 23 Apr 2021.

Vancouver:

Ge Y. Regulation of skeletal myogenesis by the mTOR signaling network. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/32047.

Council of Science Editors:

Ge Y. Regulation of skeletal myogenesis by the mTOR signaling network. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/32047

University of Illinois – Urbana-Champaign

10. Skariah, Geena. RNA helicase MOV10 is essential for gastrulation and normal CNS development.

Degree: PhD, Neuroscience, 2017, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/98256

► Neural circuitry, at its most basic level, is composed of multiple synaptic connections formed between the neurons within a circuit. These synaptic contacts are also… (more)

▼ Neural circuitry, at its most basic level, is composed of multiple synaptic connections formed between the neurons within a circuit. These synaptic contacts are also the sites of local protein synthesis, which is required for long-term synaptic plasticity underlying learning and memory. The Fragile X Mental Retardation Protein (FMRP) functions as a translational repressor and is critical for fine-tuning local protein synthesis at synapses. Recently, we demonstrated that FMRP associates with the RNA helicase Moloney Leukemia Virus 10 (Mov10) in brain and modulates its translational activity through the microRNA (miRNA) pathway. FMRP is critical for normal cognition and our findings hypothesize a role for Mov10 in brain function. Additionally, Mov10 has a well- documented role of protecting genomic integrity by suppressing actively transposing retroviral elements called LINE-1 (L1) in cell culture systems. This becomes relevant when we consider the studies that propose an increase in endogenous retrotransposition in fetal brain as well as in the hippocampus and other regions of the adult brain during neuronal differentiation. Furthermore, L1 retrotransposition is more common in brain compared to other tissues in the body. Despite the many findings that show a role for Mov10 in suppressing retrotransposition, there are currently no studies describing its role in the developing or adult brain. In order to address theses gaps, we generated a knockout mouse model for Mov10 and found that the deletion of Mov10 causes early embryonic lethality. We were able to show that lethality occurs prior to embryonic day 9.5 establishing a crucial role for Mov10 during mouse embryogenesis. We then used the externally developing Xenopus laevis embryos to establish the exact stage and cause of the Mov10 embryonic lethality. Our findings show that the blocking of translation of the Mov10 maternal mRNAs in one-cell stage embryos results in a gastrulation defect at Stage 10 of Xenopus embryonic development. RNA sequencing of embryos from Stage 10.5 of the Mov10 knockout shows an increase in mRNAs levels consistent with a miRNA-mediated role of Mov10 possibly at the Maternal to Zygotic Transition (MZT). In addition, we see that knockdown of zygotic Mov10 transcripts results in eye and ventricular neuronal differentiation defects in Stage 36 tadpoles. This suggests an important role for Mov10 in postnatal brain development. In agreement with this, we see that WT mice showed a significant increase in Mov10 protein levels in their brains from Postnatal Day 0 (P0) to P14 suggesting an important function for Mov10 during this critical period of synapse formation and neuronal differentiation. Mov10 expression was seen throughout the P1 brain including cortex, hippocampus and cerebellum and became localized mostly to the hippocampus in the adult brain. Interestingly, the subcellular localization of Mov10 was nucleo-cytoplasmic in P1 brains and predominantly cytoplasmic in the adult brain. The same age-dependent change in cellular localization was… Advisors/Committee Members: Ceman, Stephanie (advisor), Ceman, Stephanie (Committee Chair), Chung, Hee Jung (committee member), Stubbs, Lisa J (committee member), Galvez, Roberto (committee member).

Subjects/Keywords: Moloney Leukemia Virus 10 (Mov10); Ribonucleic acid (RNA) helicase; Gastrulation; Brain; Development

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APA (6^th Edition):

Skariah, G. (2017). RNA helicase MOV10 is essential for gastrulation and normal CNS development. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/98256

Chicago Manual of Style (16^th Edition):

Skariah, Geena. “RNA helicase MOV10 is essential for gastrulation and normal CNS development.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/98256.

MLA Handbook (7^th Edition):

Skariah, Geena. “RNA helicase MOV10 is essential for gastrulation and normal CNS development.” 2017. Web. 23 Apr 2021.

Vancouver:

Skariah G. RNA helicase MOV10 is essential for gastrulation and normal CNS development. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/98256.

Council of Science Editors:

Skariah G. RNA helicase MOV10 is essential for gastrulation and normal CNS development. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/98256

University of Illinois – Urbana-Champaign

11. Bhate, Amruta. Identification of a conserved alternative mRNA splicing program that supports hepatic growth and maturation during development and regeneration.

Degree: PhD, Biochemistry, 2017, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/99467

► Analysis of metazoan genomes has led to the extraordinary observation that mammals contain only ~25000 protein-coding genes. Therefore, post-transcriptional gene regulatory mechanisms (PTGRMs) are thought… (more)

▼ Analysis of metazoan genomes has led to the extraordinary observation that mammals contain only ~25000 protein-coding genes. Therefore, post-transcriptional gene regulatory mechanisms (PTGRMs) are thought to be crucial for generating the diverse proteome required to support their high cellular complexity. Alternative splicing (AS), the most common PTGRM, is a process by which the exons of a pre-mRNA are spliced into different arrangements to produce structurally and functionally distinct mature mRNAs thereby contributing to the transcriptome complexity. Regulated AS events are known to play a determinative role in the brain, heart and skeletal muscle development; however, regulation of splicing or its function in hepatic growth and maturation is not well understood. The mammalian liver is a major metabolic organ responsible for a variety of functions and has an exceptional capacity for regeneration. Liver undergoes dramatic transitions with regards to structure and function during postnatal development and during regeneration implying that intricate regulatory mechanisms must control these processes. Signaling and transcriptional networks that regulate postnatal liver development are extensively studied, but the role of post-transcriptional mechanisms is poorly explored. My goal thus was to identify conserved AS networks in postnatal liver development and establish relationships between these splicing changes and their putative regulators, RNA Binding proteins, in normal liver maturation and regeneration. In the second chapter of the thesis, I studied the changes occurring in the liver transcriptome during postnatal periods of development. To characterize the conserved AS program during mammalian liver maturation, high throughput RNA-seq of mouse livers at E18 (embryonic day 18), P14 (postnatal day 14), P28 and P90 was performed. We observed ~5000 genes change in mRNA abundance, ~530 genes change in AS and ~200 genes change in alternative polyadenylation with minimal overlap among these categories. This indicates that postnatal liver maturation is accomplished by three separate modes of regulatory mechanisms. Analysis of AS at intervening timepoints (E16, E18, P0, P2, P7, P14, P28 and P90) showed that postnatal shift in AS is temporally coordinated and subsets of AS events follow distinct patterns of splicing change grouped as early (E16-P2), late (P14-P90) or biphasic (E18-P7 and P7-P90). As the liver is actively going through the process of maturation, we wanted to understand whether the changes occurring in the transcriptome are a result of the maturing parenchyma or due to a cell population change occurring in the liver. Comparison of AS in purified hepatocytes (Hep), major cell type of the liver, and the other cell types, non-parenchymal cells (NPCs) showed that a majority of AS are cell-type specific with most being Hep-specific. These AS transitions are evolutionarily conserved in mice and humans. RNA binding proteins (RBPs) play pivotal roles in regulating splicing transitions by binding near the… Advisors/Committee Members: Kalsotra, Auinash (advisor), Kalsotra, Auinash (Committee Chair), Martinis, Susan (committee member), Ceman, Stephanie S. (committee member), Zhang, Kai (committee member).

Subjects/Keywords: Alternative splicing; Ribonucleic acid (RNA); Epithelial Splicing Regulatory Protein 2 (ESRP2); Liver development; Liver maturation

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APA (6^th Edition):

Bhate, A. (2017). Identification of a conserved alternative mRNA splicing program that supports hepatic growth and maturation during development and regeneration. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/99467

Chicago Manual of Style (16^th Edition):

Bhate, Amruta. “Identification of a conserved alternative mRNA splicing program that supports hepatic growth and maturation during development and regeneration.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/99467.

MLA Handbook (7^th Edition):

Bhate, Amruta. “Identification of a conserved alternative mRNA splicing program that supports hepatic growth and maturation during development and regeneration.” 2017. Web. 23 Apr 2021.

Vancouver:

Bhate A. Identification of a conserved alternative mRNA splicing program that supports hepatic growth and maturation during development and regeneration. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/99467.

Council of Science Editors:

Bhate A. Identification of a conserved alternative mRNA splicing program that supports hepatic growth and maturation during development and regeneration. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/99467

Lehigh University

12. Bicher, Devan L. A Volumetric Survey of Focusing and Electrostatic Contributions to Protein RNA Interactions.

Degree: MS, Computer Science, 2015, Lehigh University

URL: https://preserve.lehigh.edu/etd/2516

► Electrostatic focusing has been shown to be a major component in DNA to protein interfaces. Since ribonucleic acid molecules are notoriously less consistent and uniform… (more)

Subjects/Keywords: Electrostatic; Focusing; Protein; ribonucleic acid; RNA; Computer Sciences; Physical Sciences and Mathematics

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APA (6^th Edition):

Bicher, D. L. (2015). A Volumetric Survey of Focusing and Electrostatic Contributions to Protein RNA Interactions. (Thesis). Lehigh University. Retrieved from https://preserve.lehigh.edu/etd/2516

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):

Bicher, Devan L. “A Volumetric Survey of Focusing and Electrostatic Contributions to Protein RNA Interactions.” 2015. Thesis, Lehigh University. Accessed April 23, 2021. https://preserve.lehigh.edu/etd/2516.

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

MLA Handbook (7^th Edition):

Bicher, Devan L. “A Volumetric Survey of Focusing and Electrostatic Contributions to Protein RNA Interactions.” 2015. Web. 23 Apr 2021.

Vancouver:

Bicher DL. A Volumetric Survey of Focusing and Electrostatic Contributions to Protein RNA Interactions. [Internet] [Thesis]. Lehigh University; 2015. [cited 2021 Apr 23]. Available from: https://preserve.lehigh.edu/etd/2516.

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

Council of Science Editors:

Bicher DL. A Volumetric Survey of Focusing and Electrostatic Contributions to Protein RNA Interactions. [Thesis]. Lehigh University; 2015. Available from: https://preserve.lehigh.edu/etd/2516

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

Indian Institute of Science

13. Senthil Kuma, DK. Structural and Conformational Feature of RNA Duplexes.

Degree: PhD, Faculty of Science, 2017, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/2770

► In recent years, several interesting biological roles played by RNA have come to light. Apart from their known role in translation of genetic information from… (more)

Subjects/Keywords: RNA Duplexes; Ribonucleic Acids (RNA); Molecular Dynamics Simulation; RNA-Protein Interactions; RNA Double-Helical Structures; RNA Crystal Structures; Ribonucleic Acid (RNA) Structure; Backbone Torsion Angle Conformers; RNA Duplex; NUCGEN-Plus; Molecular Biology

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APA (6^th Edition):

Senthil Kuma, D. (2017). Structural and Conformational Feature of RNA Duplexes. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/2770

Chicago Manual of Style (16^th Edition):

Senthil Kuma, DK. “Structural and Conformational Feature of RNA Duplexes.” 2017. Doctoral Dissertation, Indian Institute of Science. Accessed April 23, 2021. http://etd.iisc.ac.in/handle/2005/2770.

MLA Handbook (7^th Edition):

Senthil Kuma, DK. “Structural and Conformational Feature of RNA Duplexes.” 2017. Web. 23 Apr 2021.

Vancouver:

Senthil Kuma D. Structural and Conformational Feature of RNA Duplexes. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2017. [cited 2021 Apr 23]. Available from: http://etd.iisc.ac.in/handle/2005/2770.

Council of Science Editors:

Senthil Kuma D. Structural and Conformational Feature of RNA Duplexes. [Doctoral Dissertation]. Indian Institute of Science; 2017. Available from: http://etd.iisc.ac.in/handle/2005/2770

Boston College

14. 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 (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 April 23, 2021. 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. 23 Apr 2021.

Vancouver:

Busby MA. Measuring Gene Expression With Next Generation Sequencing Technology. [Internet] [Doctoral dissertation]. Boston College; 2012. [cited 2021 Apr 23]. 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 New South Wales

15. Naznin, Farhana. Evolutionary Algorithms for Multiple Sequence Alignments.

Degree: Engineering & Information Technology, 2011, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/51535 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:10222/SOURCE01?view=true

► Multiple sequence alignment (MSA) is a valuable technique for studying molecular evolution, analysing sequence structure, and drug design. To date, in the literature, many algorithms… (more)

▼ Multiple sequence alignment (MSA) is a valuable technique for studying molecular evolution, analysing sequence structure, and drug design. To date, in the literature, many algorithms for solving the MSA problems, based on progressive, iterative and stochastic approaches, have been proposed. As their performances vary depending on the characteristics of the test problems, there is a need for an effective algorithm that consistently performs better over a range of problems. Therefore, the objective of this thesis was to develop a new algorithm for solving MSA problems more effectively. However, our systematic analyses of the existing approaches encouraged us to propose not only a new algorithm but also the sequential development of increasingly effective algorithms. Firstly, this thesis presents a new iterative method, namely MSA-IT, which has two new mechanisms: the first generates guide trees with randomly selected sequences; and the second shuffles the sequences inside these trees, within an iterative process, to generate new and better guide trees. This method is simple and fast. Its performance was tested on standard benchmark problems and, compared with well-known algorithms, was convincing. However, as its solutions made clear that there was room for further improvement, we developed another algorithm based on a genetic algorithm with a progressive alignment approach, namely GAPAM. In GAPAM, the initial population is generated using the two mechanisms used in MSA-IT, and two new genetic search operators are implemented. To test its performance on benchmark datasets, the results from GAPAM were compared withthose from MSA-IT as well as the well-known algorithms. The comparisons showed that GAPAM not only provides better solutions than MSA-IT and the other algorithms for most of the test problems, but also achieves an overall better performance. However, analyses of the results uncovered the fact that, for sequences of longer length, GAPAM was trapped in local optima. To overcome this local optima problem, the vertical decomposition technique was used with GAPAM. In vertical decomposition, sequences are vertically divided into a number of shorter length MSA problems which are solved individually using a guide tree approach and then joined them together to form a complete MSA. This technique was applied to the solutions of both initial and child generations inside a GA and its algorithm called the Vertical Decomposition with Genetic Algorithm (VDGA). The performance of this method was compared with those of GAPAM, MSA-IT and the well-known algorithms which confirmed that VDGA outperformed all of them. The results also showed that, for shorter sequences, GAPAM and VDGA were not significantly different, and it was established that VDGA with three vertical divisions was the most successful variant compared with the other divisions considered. In this thesis, the Weigthed Sum of Pairs method is taken as the fitness measure and the benchmark datasets from the BAliBase 2.0 database are used for experimentation. For… Advisors/Committee Members: Sarker, Ruhul, Engineering & Information Technology, Australian Defence Force Academy, UNSW, Essam, Daryl, Engineering & Information Technology, Australian Defence Force Academy, UNSW.

Subjects/Keywords: Amino Acid Sequences; Deoxyribonucleic Acid; Ribonucleic Acid; Dynamic Algorithm / Programming; Pairwise Sequence Alignment; Guide Tree / Progressive Alignment Approach; Multiple Sequence Alignment; Iterative Approach; Genetic Algorithm

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APA (6^th Edition):

Naznin, F. (2011). Evolutionary Algorithms for Multiple Sequence Alignments. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/51535 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:10222/SOURCE01?view=true

Chicago Manual of Style (16^th Edition):

Naznin, Farhana. “Evolutionary Algorithms for Multiple Sequence Alignments.” 2011. Doctoral Dissertation, University of New South Wales. Accessed April 23, 2021. http://handle.unsw.edu.au/1959.4/51535 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:10222/SOURCE01?view=true.

MLA Handbook (7^th Edition):

Naznin, Farhana. “Evolutionary Algorithms for Multiple Sequence Alignments.” 2011. Web. 23 Apr 2021.

Vancouver:

Naznin F. Evolutionary Algorithms for Multiple Sequence Alignments. [Internet] [Doctoral dissertation]. University of New South Wales; 2011. [cited 2021 Apr 23]. Available from: http://handle.unsw.edu.au/1959.4/51535 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:10222/SOURCE01?view=true.

Council of Science Editors:

Naznin F. Evolutionary Algorithms for Multiple Sequence Alignments. [Doctoral Dissertation]. University of New South Wales; 2011. Available from: http://handle.unsw.edu.au/1959.4/51535 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:10222/SOURCE01?view=true

University of Illinois – Urbana-Champaign

16. Postin, Cody. Effect of nitrogen form and genetic variations of the Asparagine-cycling pathway on maize ear growth.

Degree: MS, 0030, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/49781

► The positive growth response of maize ears to nitrate supplementation declines during late vegetative development, whereas ammonia addition continues to promote ear growth through the… (more)

Subjects/Keywords: RNA-Seq; ammonium; nitrate; asparagine synthetase; asparaginase; amino acid; corn

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APA (6^th Edition):

Postin, C. (2014). Effect of nitrogen form and genetic variations of the Asparagine-cycling pathway on maize ear growth. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/49781

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):

Postin, Cody. “Effect of nitrogen form and genetic variations of the Asparagine-cycling pathway on maize ear growth.” 2014. Thesis, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/49781.

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

MLA Handbook (7^th Edition):

Postin, Cody. “Effect of nitrogen form and genetic variations of the Asparagine-cycling pathway on maize ear growth.” 2014. Web. 23 Apr 2021.

Vancouver:

Postin C. Effect of nitrogen form and genetic variations of the Asparagine-cycling pathway on maize ear growth. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/49781.

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

Council of Science Editors:

Postin C. Effect of nitrogen form and genetic variations of the Asparagine-cycling pathway on maize ear growth. [Thesis]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/49781

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

Texas Tech University

17. Kim, Kyu Mee. Inhibition of metallo-beta-lactamase by RNA.

Degree: 2004, Texas Tech University

URL: http://hdl.handle.net/2346/16806

► This work describes the discovery and characterization of various RNA oligomers that act as metallo-â-lactamase inhibitors. Screening of Bacillus cereus metallo-â-lactamase using RNA generated by… (more)

Subjects/Keywords: Ribonucleic acid (RNA); Oligomers; Beta lactamases – Inhibitors

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APA (6^th Edition):

Kim, K. M. (2004). Inhibition of metallo-beta-lactamase by RNA. (Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/16806

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):

Kim, Kyu Mee. “Inhibition of metallo-beta-lactamase by RNA.” 2004. Thesis, Texas Tech University. Accessed April 23, 2021. http://hdl.handle.net/2346/16806.

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

MLA Handbook (7^th Edition):

Kim, Kyu Mee. “Inhibition of metallo-beta-lactamase by RNA.” 2004. Web. 23 Apr 2021.

Vancouver:

Kim KM. Inhibition of metallo-beta-lactamase by RNA. [Internet] [Thesis]. Texas Tech University; 2004. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2346/16806.

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

Council of Science Editors:

Kim KM. Inhibition of metallo-beta-lactamase by RNA. [Thesis]. Texas Tech University; 2004. Available from: http://hdl.handle.net/2346/16806

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

University of Illinois – Urbana-Champaign

18. Williams, Jennifer Nicole. Effects of 2ʹ-fucosyllactose on brain and cognitive development of intrauterine growth restricted piglets.

Degree: MS, Nutritional Sciences, 2017, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/99130

► Intrauterine growth restriction (IUGR) leads to small for gestational age (SGA) neonates, increasing risk of brain and cognitive impairments that persist into adulthood. Human milk… (more)

▼ Intrauterine growth restriction (IUGR) leads to small for gestational age (SGA) neonates, increasing risk of brain and cognitive impairments that persist into adulthood. Human milk oligosaccharides (HMO) have been postulated to exert positive effects on brain development. HMOs are the third most abundant solid component of breast milk with 2′-fucosyllactose (2′FL) being the most abundant HMO. We aimed to determine whether orally administered 2′FL enhances brain and cognitive development in small for gestational aged neonates. Sex-matched, littermate pairs of SGA (0.5-0.9kg) and appropriate for gestational age (AGA, 1.3-1.8kg) piglets were acquired on postnatal day (PD) 2, placed in individual cages, and divided into two diet groups. One group was provided a sow milk replacer diet (300ml/kg/d) while the other received the same diet supplemented with 2′FL (1.17g/L). On PD 14, spatial learning was assessed using a T-maze task, and on PD 28, brain macrostructure, microstructure, and hippocampal metabolites were assessed by magnetic resonance imaging. A sub-set of pigs was euthanized at PD14 and hippocampal tissue was dissected and used for RNA-sequencing. Body weight was different between SGA and AGA throughout the course of the study (p<0.05), with 2′FL having no effect. At PD 28, the brain-to-body-weight ratio of SGA piglets was greater than that of AGA piglets (p<0.0001), suggesting a “brain-sparing” effect during IUGR. The brain-to-body-weight ratio was not affected by 2′FL. Performance of all piglets during acquisition and reversal phases of the spatial T-maze task improved over time (p<0.0001), but SGA piglets reached criterion faster than AGA piglets (p<0.05), with no effect of diet. MRI revealed 12 brain regions (p<0.01) that were larger in AGA than SGA piglets. Furthermore, SGA piglets had less grey matter than AGA (p<0.001) in 4 subcortical regions and reduced whole brain fractional anisotropy (p<0.01) suggesting lower white matter integrity. No effects of 2′FL on brain structure were found. RNA-sequencing revealed 529 differentially expressed genes (DEGs) in hippocampal tissue (p<0.006). A total of 115 DEGs were identified in response to size, of which 62 were up-regulated and 53 were down-regulated in SGA piglets compared to AGA piglets. Up-regulated genes in SGA piglets were associated with chromatin silencing, DNA binding, nuclear chromatin, and the nucleosome; and down-regulated genes in SGA piglets were associated with KEGG pathways for measles, influenza A, hepatitis C, and herpes simplex infection. A main effect of diet revealed 252 DEGs, of which 144 up-regulated and 108 down-regulated genes in 2′FL piglets compared to CON. Genes that were up-regulated in response to 2′FL were connected to integral components of membranes and transmembrane helix, while down-regulated genes were clustered based on ion channel and transport, zinc ion binding, zinc-finger, and metal-binding. Finally, in the size by diet interaction, there were no clusters discovered as a result of up-regulated gene expression, however,… Advisors/Committee Members: Johnson, Rodney W (advisor), Johnson, Rodney W (committee member), Holscher, Hannah D (committee member).

Subjects/Keywords: Intrauterine growth restriction (IUGR); Small for gestational age (SGA); Piglet; Brain; Magnetic resonance imaging (MRI); Cognition; Ribonucleic acid (RNA)-sequencing

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APA (6^th Edition):

Williams, J. N. (2017). Effects of 2ʹ-fucosyllactose on brain and cognitive development of intrauterine growth restricted piglets. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/99130

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):

Williams, Jennifer Nicole. “Effects of 2ʹ-fucosyllactose on brain and cognitive development of intrauterine growth restricted piglets.” 2017. Thesis, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/99130.

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

MLA Handbook (7^th Edition):

Williams, Jennifer Nicole. “Effects of 2ʹ-fucosyllactose on brain and cognitive development of intrauterine growth restricted piglets.” 2017. Web. 23 Apr 2021.

Vancouver:

Williams JN. Effects of 2ʹ-fucosyllactose on brain and cognitive development of intrauterine growth restricted piglets. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/99130.

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

Council of Science Editors:

Williams JN. Effects of 2ʹ-fucosyllactose on brain and cognitive development of intrauterine growth restricted piglets. [Thesis]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/99130

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

Columbia University

19. Fleisher, Rachel Chaya. Examining the Effects of D-Amino Acids on Translation.

Degree: 2016, Columbia University

URL: https://doi.org/10.7916/D8X92BH4

► The ribosome is responsible for mRNA-templated protein translation in all living cells. The translational machinery (TM) has evolved to use 20 amino acids each esterified… (more)

▼ The ribosome is responsible for mRNA-templated protein translation in all living cells. The translational machinery (TM) has evolved to use 20 amino acids each esterified onto one of several tRNA bodies. While the active site of the ribosome, known as the peptidyl transferase center (PTC), is able to handle a remarkable amount of substrate diversity, many classes of unnatural amino acids are not compatible with the TM. For example, in the field of unnatural amino acid mutagenesis, the site-specific incorporation of biologically useful amino acids into proteins, such as fluorophores, has often proven to be unfeasible. This runs counter to the accepted notion that the ribosome is blind to the structure of the amino acid and is capable of accepting any amino acid as long as the mRNA codon: tRNA anticodon pairing is correct. Two studies by our group set out to test the hypothesis that the ribosome can indeed discriminate the structure of the amino acid. Using a fully purified E. coli translation system, the first study showed that natural amino acids misacylated onto fully modified but non-native tRNAs show small but reproducible effects on the steps of aminoacyl-tRNA (aa-tRNA) selection. The second study, in which I participated, utilized D-aa-tRNAs in the same E. coli translation system to study how amino acids of the inverted stereochemistry to those found in ribosomally-synthesized proteins affect translation elongation. We showed that these unnatural substrates serve as peptidyl acceptors but once translocated into the P-site of the ribosome, fail as peptidyl donors and stall translation elongation by inactivating the PTC. The motivation of my work has been to further characterize the effects of D-aa-tRNAs on translation elongation. To this end, I examined how the PTC is affected structurally and functionally by the presence of ribosomal substrates containing D-amino acids. Chapter one contains an introduction to this work. Chapter two describes chemical probing experiments that demonstrate that the presence of peptidyl-D-aminoacyl-tRNAs in the P-site of the ribosome allosterically modulates the secondary structure of ribosomal exit tunnel nucleotides A2058 and A2059. Chapter three describes how the reactivity of peptidyl-D-aminoacyl-tRNAs to form tripeptides is highly dependent on the identity of the amino acid it is reacting with; protein yields can be close to what is obtained with natural amino acids or almost completely abolished. Chapter four contains the methods used to do this research. From the observations presented here as well as from the work of other laboratories, a picture of the PTC emerges in which the pairing of the A- and P- site substrates is integral in either promoting or suppressing catalysis by the PTC. This work has implications for the field of unnatural amino acid mutagenesis, particularly for strategies to improve the incorporation of interesting unnatural amino acid by the ribosome. In addition, this work adds an important aspect to the growing body of knowledge of ribosome…

Subjects/Keywords: Messenger RNA; Amino acids; Amino acid sequence; Ribosomes; Biochemistry; Chemistry

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

APA (6^th Edition):

Fleisher, R. C. (2016). Examining the Effects of D-Amino Acids on Translation. (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/D8X92BH4

Chicago Manual of Style (16^th Edition):

Fleisher, Rachel Chaya. “Examining the Effects of D-Amino Acids on Translation.” 2016. Doctoral Dissertation, Columbia University. Accessed April 23, 2021. https://doi.org/10.7916/D8X92BH4.

MLA Handbook (7^th Edition):

Fleisher, Rachel Chaya. “Examining the Effects of D-Amino Acids on Translation.” 2016. Web. 23 Apr 2021.

Vancouver:

Fleisher RC. Examining the Effects of D-Amino Acids on Translation. [Internet] [Doctoral dissertation]. Columbia University; 2016. [cited 2021 Apr 23]. Available from: https://doi.org/10.7916/D8X92BH4.

Council of Science Editors:

Fleisher RC. Examining the Effects of D-Amino Acids on Translation. [Doctoral Dissertation]. Columbia University; 2016. Available from: https://doi.org/10.7916/D8X92BH4

University of Manchester

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

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 April 23, 2021. 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. 23 Apr 2021.

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 2021 Apr 23]. 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

UCLA

21. Jin, Zhenning. The Role of CPT2 in Head and Neck Squamous Cell Carcinoma.

Degree: Oral Biology, 2019, UCLA

URL: http://www.escholarship.org/uc/item/4838r41f

► Background: The initiation and development of head and neck squamous carcinoma (HNSCC) is a complicated and multistep process with unclear mechanisms, involving both genetic alternations… (more)

▼ Background: The initiation and development of head and neck squamous carcinoma (HNSCC) is a complicated and multistep process with unclear mechanisms, involving both genetic alternations and epigenetic modifications. CPT2 was found to function as a potential tumor suppressor in hepatocellular carcinoma and its high expression was correlated with better prognosis in colorectal cancer. However, the role of CPT2 in the development of HNSCC remains unclear. Methods: Data from the Gene Expression Omnibu (GEO) and The Cancer Genome Atlas (TCGA) databases were utilized to analyze the CPT2 gene expression in HNSCC. TCGA-HNSC RNASeq V2 datasets of cancer patients were obtained to investigate the association between CPT2 expression and HNSCC overall survival rate. MTT, migration, Matrigel invasion, and colony-forming assays were performed to evaluate the effect of CPT2 downregulation or upregulation in SCC1 and SCC23 head and neck cancer cells. RNA-sequencing was also performed to analyze the gene expression alterations following CPT2 downregulation. Meanwhile, we also used c-Myc inhibitor to test c-Myc function on CPT2 expression.Results: Based on the data from the GEO and TCGA databases, the expression level of CPT2 was significantly downregulated in HNSCC tumor tissues, in comparison with the normal controls. After analyzing the datasets of TCGA-HNSC, we found that the patients with high CPT2 expression had better overall survival rate than those with low CPT2 expression. On one hand, knockdown of CPT2 significantly promoted the proliferation, migration, and invasion capability of SCC1 and SCC23 cells. On the other hand, overexpression of CPT2 in HNSCC cells significantly impaired the cell proliferation, migration, and invasion ability in HNSCC cells. RNA-Seq analysis following CPT2 knockdown in SCC23 cells revealed that lysosome, focal adhesion, ECM-receptor interaction, MAPK, ErbB, RIG-I-like receptor, and Toll-like receptor signaling pathways were upregulated after CPT2 suppression. Meanwhile, oxidative phosphorylation, citrate cycle (TCA cycle), RNA degradation, and propanoate metabolism were downregulated following CPT2 downregulation in HNSCC cells. Meanwhile, c-Myc suppressed CPT2 expression on HNSCC cells.Conclusion: Our study revealed that CPT2 expression was lowered in HNSCC tumor tissues versus normal tissues. Moreover, knockdown of CPT2 enhanced the tumor cell proliferation, migration, and invasion ability, and vice versa. Our findings indicate that CPT2 may function as a tumor suppressor in HNSCC. Moreover, c-Myc suppressed CPT2 expression in SCC1 and SCC23 cells, which could be a potential upstream target. Further studies are warranted to investigate the molecular mechanisms of CPT2 in HNSCC.

Subjects/Keywords: Dentistry; CPT2; fatty acid oxidation; head and neck squamous cell carcinoma; RNA-Seq

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

APA (6^th Edition):

Jin, Z. (2019). The Role of CPT2 in Head and Neck Squamous Cell Carcinoma. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/4838r41f

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):

Jin, Zhenning. “The Role of CPT2 in Head and Neck Squamous Cell Carcinoma.” 2019. Thesis, UCLA. Accessed April 23, 2021. http://www.escholarship.org/uc/item/4838r41f.

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

MLA Handbook (7^th Edition):

Jin, Zhenning. “The Role of CPT2 in Head and Neck Squamous Cell Carcinoma.” 2019. Web. 23 Apr 2021.

Vancouver:

Jin Z. The Role of CPT2 in Head and Neck Squamous Cell Carcinoma. [Internet] [Thesis]. UCLA; 2019. [cited 2021 Apr 23]. Available from: http://www.escholarship.org/uc/item/4838r41f.

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

Council of Science Editors:

Jin Z. The Role of CPT2 in Head and Neck Squamous Cell Carcinoma. [Thesis]. UCLA; 2019. Available from: http://www.escholarship.org/uc/item/4838r41f

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

University of Western Ontario

22. Woolfson, Kathlyn Natalie. Suberin Biosynthesis and Deposition in the Wound-Healing Potato (Solanum tuberosum L.) Tuber Model.

Degree: 2018, University of Western Ontario

URL: https://ir.lib.uwo.ca/etd/5935

► Suberin is a heteropolymer comprising a cell wall-bound poly(phenolic) domain (SPPD) covalently linked to a poly(aliphatic) domain (SPAD) that is deposited between the cell wall… (more)

▼ Suberin is a heteropolymer comprising a cell wall-bound poly(phenolic) domain (SPPD) covalently linked to a poly(aliphatic) domain (SPAD) that is deposited between the cell wall and plasma membrane. Potato tuber skin contains suberin to protect against water loss and microbial infection. Wounding triggers suberin biosynthesis in usually non-suberized tuber parenchyma, providing a model system to study suberin production. Spatial and temporal coordination of SPPD and SPAD-related metabolism are required for suberization, as the former is produced soon after wounding, and the latter is synthesized later into wound-healing. Many steps involved in suberin biosynthesis remain uncharacterized, and the mechanism(s) that regulate and coordinate SPPD and SPAD production and assembly are not understood. To explore the role of abscisic acid (ABA) in the differential regulation of SPPD and SPAD biosynthesis, I subjected wounded tubers to exogenous treatments including additional ABA, or the ABA biosynthesis inhibitor fluridone. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) expression analysis of SPPD and SPAD biosynthetic genes, coupled with metabolite analyses, revealed that ABA positively influenced SPAD-, but not SPPD-associated, transcript and metabolite accumulation, indicating a role for ABA in the differential induction of wound-induced phenolic and aliphatic metabolism. I took an RNA-seq approach to study broader transcriptional changes that occur during wound-healing. The wound-healing transcriptome time-course illustrated that wounding leads to a substantial reconfiguration of transcription, followed by fine-tuning of responses dominated by suberization. Transcriptome analysis revealed that primary metabolic pathways demonstrate similar temporal expression patterns during wound-healing, but suberin-specific steps display distinct patterns at entire pathway and sub-branch levels. The observed transcriptional changes support a model in which wounding initially alters primary metabolism required to fuel SPPD, and subsequent SPAD, production. This investigation also provided support for uncharacterized biosynthetic steps, and highlighted putative transcription factors and suberin polymer assembly genes (Casparian strip membrane domain proteins and GDSL lipase/esterases) that may play key roles in the regulation and coordination of SPPD and SPAD monomer biosynthesis, polymer assembly and deposition. Overall, my findings offer further insight into the coordination and timing of metabolic and regulatory events involved in wound-healing and associated suberization.

Subjects/Keywords: suberin; potato; wound response; abscisic acid; gene expression; RNA-seq; Plant Biology

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APA (6^th Edition):

Woolfson, K. N. (2018). Suberin Biosynthesis and Deposition in the Wound-Healing Potato (Solanum tuberosum L.) Tuber Model. (Thesis). University of Western Ontario. Retrieved from https://ir.lib.uwo.ca/etd/5935

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):

Woolfson, Kathlyn Natalie. “Suberin Biosynthesis and Deposition in the Wound-Healing Potato (Solanum tuberosum L.) Tuber Model.” 2018. Thesis, University of Western Ontario. Accessed April 23, 2021. https://ir.lib.uwo.ca/etd/5935.

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

MLA Handbook (7^th Edition):

Woolfson, Kathlyn Natalie. “Suberin Biosynthesis and Deposition in the Wound-Healing Potato (Solanum tuberosum L.) Tuber Model.” 2018. Web. 23 Apr 2021.

Vancouver:

Woolfson KN. Suberin Biosynthesis and Deposition in the Wound-Healing Potato (Solanum tuberosum L.) Tuber Model. [Internet] [Thesis]. University of Western Ontario; 2018. [cited 2021 Apr 23]. Available from: https://ir.lib.uwo.ca/etd/5935.

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

Council of Science Editors:

Woolfson KN. Suberin Biosynthesis and Deposition in the Wound-Healing Potato (Solanum tuberosum L.) Tuber Model. [Thesis]. University of Western Ontario; 2018. Available from: https://ir.lib.uwo.ca/etd/5935

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

Punjabi University

23. Singh, Shailendra. Design and development of a model for sequences and structure of biomolecules.

Degree: 2012, Punjabi University

URL: http://shodhganga.inflibnet.ac.in/handle/10603/3588

►

In the recent past it was observed that a growing interest of computer professionals in the field of molecular biology has resulted into development of… (more)

Subjects/Keywords: Bioinformatics; Biomolecules; siRNA; Deoxyribonucleic acid; Ribonucleic acid

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APA (6^th Edition):

Singh, S. (2012). Design and development of a model for sequences and structure of biomolecules. (Thesis). Punjabi University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/3588

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):

Singh, Shailendra. “Design and development of a model for sequences and structure of biomolecules.” 2012. Thesis, Punjabi University. Accessed April 23, 2021. http://shodhganga.inflibnet.ac.in/handle/10603/3588.

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

MLA Handbook (7^th Edition):

Singh, Shailendra. “Design and development of a model for sequences and structure of biomolecules.” 2012. Web. 23 Apr 2021.

Vancouver:

Singh S. Design and development of a model for sequences and structure of biomolecules. [Internet] [Thesis]. Punjabi University; 2012. [cited 2021 Apr 23]. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/3588.

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

Council of Science Editors:

Singh S. Design and development of a model for sequences and structure of biomolecules. [Thesis]. Punjabi University; 2012. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/3588

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

24. Sridhar, Bharat. RNA in the nucleus: insight into location and biological function.

Degree: PhD, Molecular & Integrative Physi, 2017, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/98111

► RNA is an important constituent of the nucleus with functions including regulation of RNA biogenesis, regulation of gene expression, and dosage compensation. Currently used technologies… (more)

▼ RNA is an important constituent of the nucleus with functions including regulation of RNA biogenesis, regulation of gene expression, and dosage compensation. Currently used technologies to study RNA chromatin interactions pull down individual RNAs and sequence the associated DNA. However, it remains challenging to identify chromatin associated RNAs and their genomic target sites. In this thesis, I will describe MARGI-seq, a method to identify chromatin associated RNAs and their genomic target sites in one unbiased experiment. This method thus challenges the one-RNA-at-a-time paradigm of currently available technologies. The technique involves ligating RNA and DNA together via a novel linker and sequencing these chimeric molecules via paired end next generation sequencing. We have developed two variations to this protocol called proximity MARGI (pxMARGI) and direct MARGI (diMARGI). pxMARGI identifies all RNA and DNA in close proximity, while diMARGI prioritizes protein mediated direct interactions. We have applied this technique to study RNA-chromatin interactions in three cell types, mouse E14 embryonic stem cell line, human H9 embryonic stem cells and human HEK 293T cells. Among the top caRNAs identified by MARGI were several nuclear body associated RNAs including SNHG1, MALAT1, NEAT1 and XIST. 80 – 95% of the DNA targets of caRNA were observed to be connected to the loci of RNA transcription, 1-2% were observed to be on the same chromosome but distal to the loci of RNA transcription and about 5 – 10 % of the DNA targets were observed to be inter-chromosomal connections. RNA attachment levels were observed to be positively correlated to H3K4me3 and H3K27Ac levels and negatively correlated to H3K9me3 levels. We also developed a new plasmid called pCRISPTET as an easily clonable system to tether RNA of interest to specific genomic loci based on the CRISPR-display technique. Gibson assembly can be used to introduce RNA of interest, while golden gate cloning can be used to clone in the PAM sequence to provide information regarding the genomic loci of interest. We used pCRISTET to study the effect of tethering lncRNA EVX1as to the EVX1/ EVX1as promoter region. Advisors/Committee Members: Zhong, Sheng (advisor), Bagchi, Milan K (Committee Chair), Prasanth, Kannanganattu V (committee member), Kemper, Jongsook K (committee member).

Subjects/Keywords: Chromatin associated Ribonucleic acids (RNAs); Mapping ribonucleic acid (RNA)-genome interactions (MARGI); Ribonucleic acid (RNA) chromatin interactions

…antisense purification – seq (RAP-seq)4 Chromatin Isolation by RNA purification coupled… …with sequencing (ChIRP-seq)8 and Capture hybridization analysis of RNA targets… …RNA and then sequence the chromatin that is associated with this RNA. However, these… …sequence. This portion is then transcribed into a pre – CRISPR RNA (pre crRNA) that… …easier. In this convenient plasmid system RNA of interest and target genomic sequence can…

10 more images…

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

APA (6^th Edition):

Sridhar, B. (2017). RNA in the nucleus: insight into location and biological function. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/98111

Chicago Manual of Style (16^th Edition):

Sridhar, Bharat. “RNA in the nucleus: insight into location and biological function.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/98111.

MLA Handbook (7^th Edition):

Sridhar, Bharat. “RNA in the nucleus: insight into location and biological function.” 2017. Web. 23 Apr 2021.

Vancouver:

Sridhar B. RNA in the nucleus: insight into location and biological function. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/98111.

Council of Science Editors:

Sridhar B. RNA in the nucleus: insight into location and biological function. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/98111

Texas A&M University

25. Watts, Tylan Aubrey. Mechanism of MDA5 Recognition of Short RNA Ligands and Crystal Structure of PepQ.

Degree: MS, Biochemistry, 2013, Texas A&M University

URL: http://hdl.handle.net/1969.1/150979

► The innate immune pathways that stimulate the expression of cytokines and proapoptotic factors in response to infection are triggered by the activation of the cytosolic… (more)

▼ The innate immune pathways that stimulate the expression of cytokines and proapoptotic factors in response to infection are triggered by the activation of the cytosolic receptors retinoic acid-inducible gene I (RIG-I) and melanoma differentiationassociated gene 5 (MDA5). Activation of both receptors occurs as a result of binding to RNA. MDA5 only recognizes double stranded forms of RNA, whereas RIG-I is capable of recognizing both single and double stranded RNA. In vivo, MDA5 is known to be stimulated by long (>1 kb) strands of RNA, forming filaments along the phosphate backbone. However, the manner in which MDA5 can recognize the terminal end of its RNA ligand is uncertain. I have examined the mechanism of binding of the MDA5 protein by comparing MDA5 binding to short (<18 bp) blunt RNA, 5’ triphosphate RNA, and RNA with a 3’ or 5’ overhang. It is shown that while the MDA5 protein regulatory domain (RD) is essential for RNA recognition, the MDA5 RD only weakly recognizes short double stranded RNA ligands with overhangs or a 5’ triphosphate group. The Cys951 residue was shown to disrupt stability of the MDA5 RD-RNA complex. Binding analyses were performed using a combination of SDS-PAGE, gel filtration analysis, and nondenaturing gel electrophoresis. In addition, structural data was gathered by crystallization of the MDA5 RD-RNA complex using X-ray crystallography. These results help to establish the manner in which MDA5 is regulated predominantly to the binding of long RNA ligands. Also included in this document is structural data on the dimer form of the PepQ protein from E. coli. PepQ is a highly conserved proline peptidase that has a secondary activity of hydrolyzing organophosphorus triesters, toxic compounds found in many pesticides. The PepQ protein was crystallized and analyzed by X-ray diffraction. The dimer interface was clearly defined within the structure and provides insight into how the active dimer forms from the PepQ monomer. Advisors/Committee Members: Li, Pingwei (advisor), Glasner, Margaret E (committee member), Igumenova, Tatyana (committee member), Park, William (committee member).

Subjects/Keywords: melanoma differentiation-associated gene 5; MDA5; RIG-I-like receptor; RLR; proline peptidase; PepQ; ribonucleic acid; RNA; X-ray crystallography; protein binding; RNA binding; crystal structure

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APA (6^th Edition):

Watts, T. A. (2013). Mechanism of MDA5 Recognition of Short RNA Ligands and Crystal Structure of PepQ. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/150979

Chicago Manual of Style (16^th Edition):

Watts, Tylan Aubrey. “Mechanism of MDA5 Recognition of Short RNA Ligands and Crystal Structure of PepQ.” 2013. Masters Thesis, Texas A&M University. Accessed April 23, 2021. http://hdl.handle.net/1969.1/150979.

MLA Handbook (7^th Edition):

Watts, Tylan Aubrey. “Mechanism of MDA5 Recognition of Short RNA Ligands and Crystal Structure of PepQ.” 2013. Web. 23 Apr 2021.

Vancouver:

Watts TA. Mechanism of MDA5 Recognition of Short RNA Ligands and Crystal Structure of PepQ. [Internet] [Masters thesis]. Texas A&M University; 2013. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/1969.1/150979.

Council of Science Editors:

Watts TA. Mechanism of MDA5 Recognition of Short RNA Ligands and Crystal Structure of PepQ. [Masters Thesis]. Texas A&M University; 2013. Available from: http://hdl.handle.net/1969.1/150979

26. Λεουτσάκου, Θεώνη. Ανάπτυξη υπερευαίσθητης ποσοτικής μεθόδου προσδιορισμού του mRNA του νέου γονιδίου SPA1 και κλινική αξιολόγηση του στον καρκίνο του μαστού και της ωοθήκης.

Degree: 2007, University of Patras

URL: http://nemertes.lis.upatras.gr/jspui/handle/10889/3595

- Advisors/Committee Members: Σκορίλας, Ανδρέας, Leoutsakou, Theoni, Χριστόπουλος, Θεόδωρος, Σκορίλας, Ανδρέας, Σωτηροπούλου, Γεωργία, Τσεγενίδης, Θεόδωρος, Καραμάνος, Νικόλαος, Βύνιος, Δημήτριος, Θεοχάρης, Αχιλλέας.

Subjects/Keywords: Αγγελιοφόρο RNA; Ριβονουκλεϊνικό οξύ; Καρκίνος; 572.88; Messenger RNA; Ribonucleic acid; Cancer

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APA (6^th Edition):

Λεουτσάκου, �. (2007). Ανάπτυξη υπερευαίσθητης ποσοτικής μεθόδου προσδιορισμού του mRNA του νέου γονιδίου SPA1 και κλινική αξιολόγηση του στον καρκίνο του μαστού και της ωοθήκης. (Doctoral Dissertation). University of Patras. Retrieved from http://nemertes.lis.upatras.gr/jspui/handle/10889/3595

Chicago Manual of Style (16^th Edition):

Λεουτσάκου, Θεώνη. “Ανάπτυξη υπερευαίσθητης ποσοτικής μεθόδου προσδιορισμού του mRNA του νέου γονιδίου SPA1 και κλινική αξιολόγηση του στον καρκίνο του μαστού και της ωοθήκης.” 2007. Doctoral Dissertation, University of Patras. Accessed April 23, 2021. http://nemertes.lis.upatras.gr/jspui/handle/10889/3595.

MLA Handbook (7^th Edition):

Λεουτσάκου, Θεώνη. “Ανάπτυξη υπερευαίσθητης ποσοτικής μεθόδου προσδιορισμού του mRNA του νέου γονιδίου SPA1 και κλινική αξιολόγηση του στον καρκίνο του μαστού και της ωοθήκης.” 2007. Web. 23 Apr 2021.

Vancouver:

Λεουτσάκου �. Ανάπτυξη υπερευαίσθητης ποσοτικής μεθόδου προσδιορισμού του mRNA του νέου γονιδίου SPA1 και κλινική αξιολόγηση του στον καρκίνο του μαστού και της ωοθήκης. [Internet] [Doctoral dissertation]. University of Patras; 2007. [cited 2021 Apr 23]. Available from: http://nemertes.lis.upatras.gr/jspui/handle/10889/3595.

Council of Science Editors:

Λεουτσάκου �. Ανάπτυξη υπερευαίσθητης ποσοτικής μεθόδου προσδιορισμού του mRNA του νέου γονιδίου SPA1 και κλινική αξιολόγηση του στον καρκίνο του μαστού και της ωοθήκης. [Doctoral Dissertation]. University of Patras; 2007. Available from: http://nemertes.lis.upatras.gr/jspui/handle/10889/3595

University of Illinois – Urbana-Champaign

27. Knowlton, Aaron. Enhancement of Dicer as a personalized anticancer strategy.

Degree: MS, 0318, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/34568

► Normal miRNA production is essential for regulating protein expression and cellular fate. Misregulation of miRNA production is emerging as a key factor in the development… (more)

Subjects/Keywords: Dicer; transactivating response RNA-binding protein (TRBP); Dicer1; transactivating response RNA-binding protein 2 (tarbp2); micro ribonucleic acid (miRNA); cancer; Hereditary nonpolyposis colorectal cancer (HNPCC); aptamer; Malachite green

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

APA (6^th Edition):

Knowlton, A. (2012). Enhancement of Dicer as a personalized anticancer strategy. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/34568

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):

Knowlton, Aaron. “Enhancement of Dicer as a personalized anticancer strategy.” 2012. Thesis, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/34568.

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

MLA Handbook (7^th Edition):

Knowlton, Aaron. “Enhancement of Dicer as a personalized anticancer strategy.” 2012. Web. 23 Apr 2021.

Vancouver:

Knowlton A. Enhancement of Dicer as a personalized anticancer strategy. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/34568.

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

Council of Science Editors:

Knowlton A. Enhancement of Dicer as a personalized anticancer strategy. [Thesis]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/34568

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

28. Price, William. Understanding the mechanisms of the photoperiod flowering pathway in soybean.

Degree: MS, 0030, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/34233

► UNDERSTANDING THE MECHANISMS OF THE PHOTOPERIOD FLOWERING PATHWAY IN SOYBEAN BY WILLIAM BRIAN PRICE THESIS Submitted in partial fulfillment of the requirements for the degree… (more)

▼ UNDERSTANDING THE MECHANISMS OF THE PHOTOPERIOD FLOWERING PATHWAY IN SOYBEAN BY WILLIAM BRIAN PRICE THESIS Submitted in partial fulfillment of the requirements for the degree of Master of Science in Crop Sciences in the Graduate College of the University of Illinois at Urbana-Champaign, 2012 Urbana, Illinois Master’s Committee: Assistant Professor Yoshie Hanzawa Professor Lila Vodkin Professor Randall Nelson Associate Professor Matthew Hudson ABSTRACT Flower transition is the shift from the vegetative phase to the reproductive phase of a plant. Flowering transition determines a plant’s survivability and reproductive success. Flowering transition is triggered by environmental and endogenous cues. The general purpose of this thesis was to gain insight into the genetics of flower transition in the major crop specie, soybean (Glycine max). Chapter One introduces the long day dicot model species Arabidopsis thaliana that serves as the paradigm of understanding the genetic basis of flower transition. The six flowering pathways of A. thaliana are described in detail to introduce the reader to the complex molecular networks that act to initiate flowering. Next, the focus narrows to advance the understanding of the photoperiodic flowering pathway. The mechanisms of photoperiod flowering in short day monocot model species Oryza sativa are introduced and described to illustrate conservation and divergence between the photoperiod flowering pathway components in the two model species. Finally, the known components of soybean photoperiod flowering are introduced, and the question is raised whether CONSTANS a known flowering promoter in Arabidopsis and rice is conserved in soybean. Chapter Two discusses the research to characterize CO homolog expression in soybean across two day length treatments by qRT-PCR through a candidate gene approach. The candidate gene approach applies bioinformatics techniques along with the recently published G. max genome to infer evolutionary history of the CO gene to identify homologs in the soybean genome for further study. Once identified, the genes can then be characterized via expression analysis to determine possible function analogous to CO. Chapter Three discusses the research to characterize CO homolog expression in soybean across two day length treatments by RNA sequencing to support the qRT-PCR results and to characterize differences in expression between seven soybean genotypes. Although the results do not provide definitive results for differences across genotypes, they do provide two putative candidates for CO-like genes that function in photoperiodic flowering pathway to induce floral initiation. Advisors/Committee Members: Hanzawa, Yoshie (advisor).

Subjects/Keywords: flowering; photoperiod; soybean; glycine soja; arabidopsis; co; constans; Pathways; oryza sativa; glycine max; arabidopsis thaliana; quantitative reverse transcriptase polymerase chain reaction (qrt-pcr); Ribonucleic acid sequencing (RNA-Seq)

10 more images…

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

APA (6^th Edition):

Price, W. (2012). Understanding the mechanisms of the photoperiod flowering pathway in soybean. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/34233

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):

Price, William. “Understanding the mechanisms of the photoperiod flowering pathway in soybean.” 2012. Thesis, University of Illinois – Urbana-Champaign. Accessed April 23, 2021. http://hdl.handle.net/2142/34233.

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

MLA Handbook (7^th Edition):

Price, William. “Understanding the mechanisms of the photoperiod flowering pathway in soybean.” 2012. Web. 23 Apr 2021.

Vancouver:

Price W. Understanding the mechanisms of the photoperiod flowering pathway in soybean. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2142/34233.

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

Council of Science Editors:

Price W. Understanding the mechanisms of the photoperiod flowering pathway in soybean. [Thesis]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/34233

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

Texas Tech University

29. Reeves, James Patton. The immune response of CF-1 mice to single stranded DNA.

Degree: 1974, Texas Tech University

URL: http://hdl.handle.net/2346/21020

Subjects/Keywords: Deoxyribonucleic acid (DNA); Anti-antibodies; Mice as laboratory animals; Ribonucleic acid (RNA)

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

APA (6^th Edition):

Reeves, J. P. (1974). The immune response of CF-1 mice to single stranded DNA. (Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/21020

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):

Reeves, James Patton. “The immune response of CF-1 mice to single stranded DNA.” 1974. Thesis, Texas Tech University. Accessed April 23, 2021. http://hdl.handle.net/2346/21020.

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

MLA Handbook (7^th Edition):

Reeves, James Patton. “The immune response of CF-1 mice to single stranded DNA.” 1974. Web. 23 Apr 2021.

Vancouver:

Reeves JP. The immune response of CF-1 mice to single stranded DNA. [Internet] [Thesis]. Texas Tech University; 1974. [cited 2021 Apr 23]. Available from: http://hdl.handle.net/2346/21020.

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

Council of Science Editors:

Reeves JP. The immune response of CF-1 mice to single stranded DNA. [Thesis]. Texas Tech University; 1974. Available from: http://hdl.handle.net/2346/21020

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

Brigham Young University

30. Sharp, Aaron Robert. Improving Cotton Agronomics with Diverse Genomic Technologies.

Degree: MS, 2016, Brigham Young University

URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=6844&context=etd

► Agronomic outcomes are the product of a plant's genotype and its environment. Genomic technologies allow farmers and researchers new avenues to explore the genetic… (more)

Subjects/Keywords: cotton; agriculture; conservation tillage; RNA-Seq; subgenome expression bias; BioNano physical mapping; genome sequence assembly; Animal Sciences; Plant Sciences

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

APA (6^th Edition):

Sharp, A. R. (2016). Improving Cotton Agronomics with Diverse Genomic Technologies. (Masters Thesis). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=6844&context=etd

Chicago Manual of Style (16^th Edition):

Sharp, Aaron Robert. “Improving Cotton Agronomics with Diverse Genomic Technologies.” 2016. Masters Thesis, Brigham Young University. Accessed April 23, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=6844&context=etd.

MLA Handbook (7^th Edition):

Sharp, Aaron Robert. “Improving Cotton Agronomics with Diverse Genomic Technologies.” 2016. Web. 23 Apr 2021.

Vancouver:

Sharp AR. Improving Cotton Agronomics with Diverse Genomic Technologies. [Internet] [Masters thesis]. Brigham Young University; 2016. [cited 2021 Apr 23]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=6844&context=etd.

Council of Science Editors:

Sharp AR. Improving Cotton Agronomics with Diverse Genomic Technologies. [Masters Thesis]. Brigham Young University; 2016. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=6844&context=etd

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Open Access Theses and Dissertations