published_or_final_version / Zoology / Master / Master of Philosophy

No description available.

No description available.

The transcriptional promoter sequences for the Rhizobium meliloti nitrogen fixation genes nifA and nifB were cloned to a β-galactosidase gene fusion plasmid vector and transferred by homologous recombination to a specialized transducing phage. The promoter fusions were then transduced to a recombination deficient strain of Escherichia coli as single-copy lysogens and analysed under defined aerobic and anaerobic conditions. The lysogenic strains contained plasmids encoding either of two transcriptional activator proteins, NifA or FixJ, produced from a constitutive plasmid promoter. The expression of the nifA and the nifB promoters was found to be sensitively regulated by the carbon source used for anaerobic fermentation or anaerobic respiration, the redox potential of the terminal electron acceptor used for anaerobic respiration, and the growth phase of anaerobic cultures. The repression of nit promoter expression by oxygen respiration was specifically compared to anaerobic respiration of alternative electron acceptors. Both nifA and nifB promoter expression decreased exponentially as the reduction potential of the terminal respiration reaction increased. The repressive effect of oxygen appears to be due soley to the exponential relationship between nit promoter expression and the redox potential of oxygen respiration. In addition to separate fusions of the nifA and nifB promoters to β-galactosidase, a single-copy fusion of the entire nifA-nifB region was constructed. In this construct, plasmid-encoded FixJ protein stimulated the expression of a chromosomal nifA gene to produce the NifA protein, which then stimulated the expression of the nitB promoter. This strain produced 20-fold lower activity than a strain in which nifB promoter expression was stimulated by plasmid-encoded NifA protein. Finally, the nifA locus was found to contain a transcriptionally active element, oriented opposite to the nifA promoter. / Graduation date: 1992

Ageing is difficult to study because of the complexity and multi-factorial nature of traits that result from a combination of environmental, genetic, epigenetic and stochastic factors, each contributing to the overall phenotype. In light of this challenge, transcriptomic studies of aging organisms are of particular interest, since transcription is an intermediate step that links genotype and phenotype. In recent years microarrays have been widely used for elucidation of changes that occur with age in the transcriptome in Caenorhabditis elegans. However, different microarray studies of C. elegans report sets of differentially expressed genes of varying consistence, with different functional annotations. Failures to find a consistent set of transcriptomic alterations may reflect the absence of a specific genetic program that would guide age-related changes but may also, to some extent, be a consequence of a small sample sizes and a lack of study power in transcriptomic researches. To tackle this issue we analyzed RNA sequences of samples from a time-series experiment of normal aging of C. elegans, performing the first, to our knowledge, NGS-based study of such kind. As a result, evidences were collected that promote a union of two competing theories: the theory of DNA damage accumulation and the theory of programmed aging. Next, we applied two alternative methods, namely the Short Time-series Expression Mining and the Network Smoothing algorithm, in order to obtain and analyze sets of genes that represent distinct modules of age-related changes in the transcriptome. Besides characterization of age-related changes, we were also interested in assessment and validation of the Network Smoothing algorithm. Generally, results of clustering of smoothed scores are consistent with results of short time-series clustering, allowing robust elucidation of functions that are perturbed during aging. At the last phase of the project we questioned if observed changes in the transcriptome can be controlled by specific transcription factors. Thus we used Chip-seq data to predict plausible transcription factor regulators of gene sets obtained using time series clustering and Network smoothing. On the one hand, all predicted transcription factors had documented relevance to aging. On the other hand, we did not achieve gene set specific prediction of transcription factors. In fact, genes with the opposite dynamics were predicted to respond to the same transcription factors.  To summarize, we characterized in details age-related changes in the transcriptome of C. elegans, validated the performance of the Network Smoothing algorithm and showed that integration of gene expression with Chip-seq data allows to predict transcription factors that are capable to modulate the lifespan of C. elegans.

published_or_final_version / Biochemistry / Doctoral / Doctor of Philosophy

published_or_final_version / Zoology / Doctoral / Doctor of Philosophy

published_or_final_version / Surgery / Master / Master of Philosophy

All cellular processes depend on the coordinate expression of genes and their interactions. Regulatory sequences encoded in the genome stipulate the necessary instructions interpreted by sequence-specific transcription factors (TFs) to control the spatial-temporal output of gene expression. Detection of cis-regulatory signals is challenging, owing to the lack of distinguishing features such as open reading frames and an overwhelming excess of spurious to functional TF binding site matching sequences embedded within the vast non-coding regions of vertebrate genomes. From an evolutionary standpoint, functional alterations in cis-regulatory architecture are thought to be important in diversifying morphology and physiology in the evolution of vertebrates, which share a similar body plan and complement of genes. Correspondingly, recent studies have highlighted the plasticity of cis-regulatory architecture organization over evolutionary time, finding associations with examples of both diverged and conserved patterns of gene expression. These observations underscore the gap in our collective knowledge with respect to the rules by which TFs recognize and bind their targets in vivo, as well as how this process evolves in vertebrates, and serve as a motivating basis for this thesis work. To begin, I probed the extent of conservation and divergence of sequence and expression profiles across tissues of diverse vertebrate species, identifying thousands of candidate genes with conserved expression by microarray analysis. However, corresponding conservation of non-exonic and potentially regulatory sequence was lacking, suggestive of binding site turnover over evolutionary time. Next, I analyzed the sequence specificity of a wide array of mouse and yeast TFs, finding great diversity and complexity in their binding preferences, with many factors recognizing multiple distinct motifs. Furthermore, comparative analysis of orthologous TFs suggest well conserved binding specificities. I also demonstrate the likely biological relevance of sequences highly preferred by these TFs by revealing distinctive signatures in their distribution and organization within putative regulatory regions in each genome. Lastly, I have begun to explore the organization of cis-regulatory sequences active in vertebrate tissues by high-throughput sequencing of open chromatin. Together, these data help illuminate the organization and evolution of vertebrate regulatory architectures, providing a useful toolkit for the testing of new models and hypotheses.

The most critical biochemistry in an organism supports the central dogma of molecular biology: transcription of DNA to RNA and translation of RNA to peptide sequence. Proteins are then responsible for catalyzing, regulating and ensuring the fidelity of transcription and translation. At the heart of these processes lie selective biomolecular interactions and specific dynamics that are necessary for complex formation and catalytic activity. Through advanced biophysical and computational methods, it has become possible to probe these macromolecular dynamics and interactions at the molecular and atomic levels to tease out their underlying physical bases. To the end of a more thorough understanding of these physical bases, we have performed studies to probe the motions and interactions intrinsic to the function of biomolecular complexes: modeling the dual-base flipping strategy of alkylpurine glycosylase D, dynamically tracing evolution and epistasis in the 3-ketosteroid family of nuclear receptors, discovering the allosteric and conformational aspects of transcription regulation in liver receptor homologue 1, leveraging specific contacts in tyrosyl-DNA phosphodiesterase 2 for the development of novel inhibitor scaffolds, and detailing the experimentally observed connection between solvation and sequence-specific binding affinity in PU.1-DNA complexes at the atomic level. While each study seeks to solve system-specific problems, the collection outlines a general and broadly applicable description of the biophysical motivations of biochemical processes.