Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 75 for “"sRNA"”.
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Mitigating the effects of ribosome limitations on synthetic circuits via high-gain sRNA-mediated negative feedback
… to one of the circuits. The loop includes an sRNA construct. We explore different implementations of this circuit and model them mechanistically. Furthermore, we begin physically implementing one of the circuit designs by testing intermediate constructs. Finally, we also explore the hypothesis …
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New Methods of DNA Assembly, Gene Regulation with a Synthetic sRNA, and Cyanobacterium Phenotype Monitoring with Raman Spectroscopy
… techniques. Then, novel synthetic small RNA (sRNA) regulators were designed in a cell-free-system (in vitro) in order to modulate protein expression in biosynthetic pathways. The ability of the sRNAs to regulate mRNA expression with statistical significance was demonstrated. Up to 70% decrease …
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Small RNAs within the developing seed of Arabidopsis thaliana
… relatively little is known about the small RNA (sRNA) populations found within the tissues composing the seed. We set out to profile the sRNA complement found within whole seeds and the embryo and endosperm tissues within the seed. In whole seeds, variation in sRNA activity at TEs near genes is …
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Understanding small RNA-mediated post-transcriptional regulation of Salmonella pathogenicity island 1 activator HilA in Salmonella typhimurium
… and we have identified a number of small RNAs (sRNAs) that control the SPI1 regulatory circuit. The transcriptional regulator HilA activates the expression of the genes encoding the SPI1 T3SS structural and primary effector proteins. The hilA mRNA 5' untranslated region (UTR) is ~350 nucleotides …
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An E. coli small RNA inhibits translation initiation from a distance
In bacterial systems, small RNA (sRNA)-dependent translational repression is commonly carried out via sRNA-mRNA base pairing interactions near the Shine-Dalgarno (SD) region. In this so-called “canonical” mechanism, the sRNA is the direct regulator; it competes with the initiating ribosomes while …
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Quality checking and expression analysis of high-throughput small RNA sequencing data
… identi�cation of small non-coding RNAs (sRNAs) and to assess their regulation using di�erential expression analysis by comparing two or more di�erent conditions. During an analysis of a typical set of sRNA sequencing (sRNA-seq) libraries, a large variety of tools and methods are used on …
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Discovery and Characterization of a Novel Regulatory Small RNA, VcrS, Required for Virulence in Brucella abortus
… through the use of small regulatory RNAs (sRNAs). sRNAs bind to messenger RNA (mRNA) targets via complementary base pairing. sRNAs are a class of regulatory molecules in bacteria that elicit rapid post-transcriptional regulation. sRNA-mRNA binding can positively or negatively influence gene …
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Epigenetics and sex expression in trioecious papaya
… this gap, we analyzed the small non-coding RNAs (sRNA) and DNA methylation in different papaya sex types. Endogenous small RNA molecules of ~18-30 nucleotides play an important role in regulating gene expression and genome defense. Using large scale sequencing reads, we analyzed sRNA biogenesis …
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Computational analysis of small RNAs and the RNA degradome with application to plant water stress
… regulatory mechanisms involves small RNAs (sRNAs), which can regulate gene expression by targeting messenger RNAs (mRNAs) and directing endonucleolytic cleavage resulting in mRNA degradation. A snapshot of an mRNA degradation profile (degradome) can be captured through a new high-throughput …
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Small RNA and genome interactions in Chlamydomonas reinhardtii recombinants
… relying on 20Q24nt single stranded small RNAs (sRNAs). Small RNAs, due to their ability to set up persistent epigenetic marks at a locus, have the potential to create heritable transgressive gene expression. For example, when genetic variation from one parental genome presents novel targets to …
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Epigenetic Responses of Arabidopsis to Abiotic Stress
… modification (methylation) and small RNA (sRNA). For all of the treatments except shade, the stress was limited in duration, and the plants were allowed to recover until flowering, to identify changes that persist to reproduction. At flowering, DNA for methylation bisulfite sequencing, RNA, …
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Investigating Hfq-dependent Small Regulatory RNA, Bsr34, and Its Roles in Brucella abortus Physiology and Pathogenicity
… within host cells. Small regulatory RNAs (sRNAs), often chaperoned by Hfq, are key post-transcriptional regulators of bacterial virulence and stress adaptation, yet remain largely uncharacterized in Brucella. Following the identification of Hfq-associated sRNA candidates in B. suis, this …
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A combinatorial approach for improved target prediction, validation, and characterization of small RNAs in Escherichia coli
Bacterial small RNAs (sRNAs) are involved in regulating targets involved in various processes in the cell, including stress responses and metabolic processes. As RNA regulators that are degraded rapidly, they are ideal for fine-tuning gene expression in response to rapid environmental changes. Even …
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Molecular analysis of small RNA and small protein regulation of Escherichia coli stress responses
Small RNA (sRNA) regulators control gene expression throughout all domains of life. In bacteria, they typically affect virulence, metabolism, and stress response genes posttranscriptionally through imperfect antisense pairing with their mRNAs. While most sRNAs are non-coding, a small number act as …
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Modes and mechanisms of hfq mediated stress regulation in bacteria
… to its ever-changing environmental conditions. sRNAs have been implicated in a variety of stress-response pathways that help bacterial systems modulate gene expression. The RNA binding protein Hfq facilities this process by, helping sRNA to base pair with its target mRNAs to initiate gene …
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Transcription analysis of virulent strains of Mycobacterium tuberculosis
… expression and target profiles for the known sRNA, and identified a large number of novel sRNA. Transcriptomic data from 4 di↵erent growth conditions was integrated with this sRNA data as well as variant data using the Cell pipeline. From this data we identified multiple sets of genes linked …
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Bacteroides fragilis outer membrane vesicles are used for secretion of a discrete subset of bacterial RNAs that stimulate an immune response in colonic epithelial cells.
… established, while the contribution of bacterial sRNA to host physiology remain unclear. We hypothesize that pathogenic and commensal microbes use OMV-associated small RNA species to differentially affect host inflammatory responses. First, we profiled the small RNA contents of purified OMVs from …
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Fantastic ribonucleoprotein complexes and how to study them. Architectural principles of regulatory assemblies in bacteria.
… proteins (RBPs) and small regulatory RNAs (sRNAs). Together these form an information-rich regulatory network that exercises post-transcriptional control of gene expression. A key RBP in bacteria is Hfq, which is best studied as a facilitator for sRNA-mRNA pairing. In Pseudomonas aeruginosa, …
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Roles of Small Rnas and Paralogous Proteins In Bacillus Anthracis Virulence Gene Regulation
… through the function of small regulatory RNAs (sRNAs). Small regulatory RNAs (sRNAs) are short transcripts that base-pair to mRNA targets or interact with regulatory proteins. sRNA function has been studied extensively in Gram-negative bacteria; comparatively less is known about sRNAs in …
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Systems Biology Approaches to Probe Gene Regulation In Bacteria
… method to infer the small non-coding RNA (sRNA) regulatory network in <em>Mtb</em>. The method identifies sRNA-mRNA interactions by integrating <em>a priori</em> knowledge of possible binding sites with structure-driven identification of binding sites. The reconstructed network was useful …
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