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 19 of 19 for “"Gene expression dynamics"”.
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New Tools for Measuring and Analyzing Bacterial Gene-Expression Dynamics
Messenger RNAs (mRNAs) are essential targets of gene regulation. The cell adapts and grows by changing its gene-expression profile, which it can achieve by manipulating the rates of mRNA initiation and decay and thus changing the relative abundances of transcripts. To understand the biological …
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How bacteria tune mixed positive/negative feedback loops to generate diverse gene expression dynamics
… of possible behaviours. These are often heterogeneous across isogenic populations, suggesting that sigma factor systems are highly noisy. In this thesis, we use stochastic modelling techniques to study what responses alterna- tive sigma factors can generate, and how these are generated. First, …
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Engineering Robust and Programmable Biological Systems
… biological systems using complex artificial gene networks has great potential to unlock important innovative solutions to many biotechnological challenges. While cells have been engineered to implement complex information processing algorithms and to produce food, materials, and …
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Integrative Analysis of the Myc and E2F pathway Reveal the Roles for microRNAs in Cell Fate Control
… roles for microRNAs(miRNA) in control of gene expression, we asked if we may better understand the underlying regulatory (transcription factor, microRNA) structure that contribute to Myc and E2F pathway activities. Through integrative analysis of mRNA and miRNA expression profile, we …
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A Computational Framework for Learning from Complex Data: Formulations, Algorithms, and Applications
… As a consequence, the observed complex data generated by these processes also evolve smoothly. For example, in computational biology, the expression data matrices are evolving, since gene expression controls are deployed sequentially during development in many biological processes. …
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Towards a complete human cell atlas: a single-nucleus RNA sequencing study of the paediatric and adult human brain
… for neuropsychiatric risk. While temporal gene expression dynamics over this period have been studied extensively, there are no studies exploring the paediatric brain at single cell resolution. To address this, we present the first paediatric brain cell atlas comprising of 6 single nucleus …
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Investigating the Capacity of Generative AI to Learn Genotype-by-Environment Interactions in Brachypodium distachyon
… plasticity: environment-induced changes in gene expression that vary among genotypes, representing one way that genotype-by-environment (GxE) interactions manifest at the molecular level. While transcriptomic data offers a unique and powerful view into these responses, traditional modeling …
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Dynamics of Cell Fate Decision Making Between Sporulation and Competence in Bacillus Subtilis
… question. To study cell-fate decision-making dynamics, I utilized the soil bacterium Bacillus subtilis which under stress can either become competent for DNA uptake or undergo sporulation. The master regulator of sporulation is the transcription factor Spo0A. Single cell measurements of Spo0A …
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Gene expression control and antimicrobial peptide production by haute couture bacteria
… synthetic systems have been built with novel gene expression dynamics. Additionally, cells have been engineered to efficiently produce high value compounds, including a number of recombinant protein molecules. Now, wonderful opportunities abound for improving the human condition with synthetic …
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Understanding the role of CD4+ T cells in common immune-mediated diseases
… studies (GWAS) have demonstrated that genetic susceptibility to these diseases is explained by thousands of loci spread throughout the genome, most of which lie within non-coding DNA. Moreover, these loci are enriched in CD4+ T cell regulatory elements, which suggests they might disrupt …
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Iron and the ecology of marine microbes
… iron availability impacts microbial community gene expression dynamics. Using a metatranscriptomic approach I showed that in that environment, the impact of iron was tightly connected to the supply of other limiting macronutrients, and seems to mostly affect photosynthetic organisms. This …
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Decoding Dynamic Gene Regulation in Hair Cell Development and Regeneration
<p>Identifying the causal interactions between genes and their proteins during the differentiation of specialized cells such as mechanosensory hair cells in vertebrates' inner ears and fishes' lateral lines requires an accurate description of the time-lagged relationships between transcription …
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Investigating the role of DPPA2 and DPPA4 in the Epigenetic Control of Lineage Programs in Human Embryonic Stem Cells
… To navigate the dynamic transcriptional and epigenetic changes associated with germ layer allocation, pluripotent cells maintain developmentally important genes and their regulatory regions in a poised but repressed chromatin state. The poised state has been proposed to allow for precise and …
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Comparative analysis of transcriptome of fracture healing under normal and hypophosphatemic conditions
… and molecular processes involved in bone regeneration. This transcriptomic analysis investigates the intricate relationship between environmental effects of phosphate deficiency on the time course of fracture healing within the C57BL/6J (B6) mouse strain. To manipulate the healing …
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Exploiting network-based approaches for understanding gene regulation and function
… 2, I address the questions, how and why are genes organized on a particular fashion on bacterial genomes and what are the constraints bacterial transcriptional regulatory networks impose on their genomic organization. I then extend this one step further to unravel the constraints imposed on …
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Investigating Transcription Factor Networks That Drive Biological Clocks and Oscillators
… part, by coordinated programs of</p><p>periodic gene expression. Up to 40% of all mouse genes are periodically expressed with</p><p>respect to the circadian cycle, and almost 20% of all yeast genes are periodic during the</p><p>cell cycle. Furthermore, more than half of the most frequently …
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Methods for Dissecting High Dimensional Single Cell RNA Sequencing Data
… for interrogating cellular identity in heterogeneous populations. Researchers routinely capture transcriptome-wide snapshots of thousands or even millions of individual cells. From these readouts the challenge is to accurately identify distinct patterns of mRNA expression that separate cells …
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Investigation of natural and synthetic coupling of the circadian clock in the cyanobacterium Synechococcus elongatus
… First, to enable multiplexed observation of gene expression dynamics, spectrally distinct fluorescent protein reporter pairings were identified. A shortlist of such proteins: mTFP1, mTQ2, EYFP and mNG, were then built as transcriptional reporters of the P*kaiBC* circadian promoter, into both …