Molecular Biology Commons^™

Spatial Crowding And Confinement Effects On Bursty Gene Expression, Charles Wei-Shing Chin

Doctoral Dissertations

Synthetic biology and genetic engineering are valuable tools in the development of new, sustainable energy generation technologies. The characterization of stochastic gene expression is vital to the efficient application of genetic engineering techniques. Transcriptional bursting, in which periods of high expression are punctuated by periods of no expression, is extensively observed in gene expression. While various molecular mechanisms have been hypothesized to be responsible for transcriptional bursting, spatial considerations have largely been neglected. This work uses computational modeling to examine in detail the influence of spatial factors such as macromolecular crowding and confinement on gene expression.

In the first part …

Electron Transport To Photosystem I By Soluble Carriers: Evolution Of The Interacting Pair, Khoa Dang Nguyen

Doctoral Dissertations

Oxygenic photosynthesis is driven via sequential action of Photosystem II (PSII) and (PSI) reaction centers via the Z-­‐scheme. Both of these pigment– membrane protein complexes are found in cyanobacteria, algae, and plants. PSI, unlike PSII, is remarkably stable and does not undergo limiting photo-­‐damage. This stability, as well as other fundamental structural differences, makes PSI the most attractive reaction centers for applied photosynthetic applications. These applied applications exploit the efficient light harvesting and high quantum yield of PSI where the isolated PSI particles are redeployed providing electrons directly as a photocurrent or, via a coupled catalyst to yield H2. Here, …

Modification Of Carbohydrate Active Enzymes In Switchgrass (Panicum Virgatum L.) To Improve Saccharification And Biomass Yields For Biofuels, Jonathan Duran Willis

Doctoral Dissertations

The natural recalcitrance of plant cell walls is a major commercial hurdle for plant biomass to be converted into a viable energy source as alternative to fossil fuels. To circumvent this hurdle manipulation of carbohydrate enzymes active in the cellulose and hemicellulose portions of the plant cell wall can be utilized to improve feedstocks. Production of cellulolytic enzymes by plants have been evaluated for reducing the cost associated with lignocellulosic biofuels. Plants have successfully served as bioreactors producing bacterial and fungal glycosyl hydrolases, which have altered plant growth to improve saccharification. A bioprospecting opportunity lies with the utilization of insect …

Characterization Of An Ethylene Receptor In Synechocystis Sp. Pcc 6803, Randy Francis Lacey

Doctoral Dissertations

In plants, ethylene functions as a hormone regulating many growth and developmental processes. Ethylene receptors in plants resemble bacterial two-component signaling systems. Because of this it, ethylene receptors are thought to have been acquired by gene transfer from the cyanobacterial endosymbiont that lead to the development of the chloroplast. However, prior to this work, functional ethylene receptors were thought to only be found in green plants. Here, we show that the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis) contains a functional ethylene receptor, SynEtr1. SynEtr1 contains a predicted ethylene binding domain, a photosensory cyanobacteriochrome (CBCR) domain, and a histidine …

Nanocomposite Adhesive Of English Ivy (Hedera Helix): Bioproduction, Nanoparticle Isolation, And Molecular Analysis, Jason Neil Burris

Doctoral Dissertations

English ivy naturally produces organic nanoparticles from its adventitious root hairs, and possesses characteristics that may allow them to replace metal-based nanoparticles in common applications, such as sunscreen. At the onset of the research, it was hypothesized that a physical mechanism of attachment, similar to the gecko footpad, was used to generate the adhesive force for attachment; however, through the results obtained from recent work, it is clear that a biochemical mechanism is involved in the generation of the strength of adhesion. Therefore, the goal of this research was to provide a better understanding of the genetic basis of nanoparticle …

Control Of Proteolysis During The Caulobacter Cell Cycle, Joanne Lau

Doctoral Dissertations

Intracellular protein destruction is a carefully coordinated and timed regulatory mechanism that cells utilize to modulate growth, adaptation to environmental cues, and survival. In Caulobacter crescentus, a bacterium known for studies of bacterial cell division cycle, the response regulator CpdR couples phosphorylation events with the AAA+ protease ClpXP to provide punctuated degradation of crucial substrates involved in cell cycle regulation. CpdR functions like an adaptor to alter substrate choice by ClpXP, however it remains unclear how CpdR influences its multiple targets. In this thesis, we show that, unlike canonical ClpXP adaptors, CpdR alone does not strongly bind its substrate. …

Novel Advancements For Improving Sprout Safety, Kyle S. Landry

Doctoral Dissertations

All varieties of bean sprouts (mung bean, alfalfa, broccoli, and radish) are classified as a “super-food” and are common staples for health conscious consumers. Along with the proposed health benefits, there is also an inherent risk of foodborne illness. When sprouts are cooked, there is little risk of illness. The purpose of this dissertation was to explore novel techniques to minimize or prevent the incidence of foodborne illness associated with the consumption of sprouts. Three areas were investigated: 1) the use of a biocontrol organism, 2) the use of a novel spontaneous carvacrol nanoemulsion, and 3) the influence of the …

Photolysis Of Triazenylbenzoic Acids For Click Chemistry, Adam Gann

Doctoral Dissertations

Copper catalyzed cycloaddition of terminal alkynes and azides has revolutionized the field of bioconjugate chemistry. Unfortunately, typical copper catalysts are known to disrupt relevant biological systems, so it has become necessary to develop new, copper-free methods that are less cytotoxic. particular interest are "click" probes which can be activated with an outside light source, giving the user spatial and temporal control over the system being investigated. We have developed a method in which an aryl diazonium salt is rapidly generated using photolysis of the triazene functional group, and subsequently coupled with an electron rich aromatic nucleophile to yield an azobenzene. …

Insulators: A “Safety Guard” For Genome Stability In Drosophila Melanogaster, Ran An

Doctoral Dissertations

Chromatin insulators are DNA-protein complexes that assist in the formation of chromatin loop structures by mediating long-range contacts between distant sites, which regulate proper organization of the chromatin fiber within the tridimensional space of the nucleus. It is considered that this function of insulators is required for the regulation of gene expression during development and in differentiated cells. This thesis focuses specifically in the Suppressor of Hairy wing [Su(Hw)] insulator of Drosophila and its associated proteins, and explores the possibility that chromatin insulators are not only significant for regulation of gene expression, but are also essential for DNA replication and …

In Silico Driven Metabolic Engineering Towards Enhancing Biofuel And Biochemical Production, Richard Adam Thompson

Doctoral Dissertations

The development of a secure and sustainable energy economy is likely to require the production of fuels and commodity chemicals in a renewable manner. There has been renewed interest in biological commodity chemical production recently, in particular focusing on non-edible feedstocks. The fields of metabolic engineering and synthetic biology have arisen in the past 20 years to address the challenge of chemical production from biological feedstocks. Metabolic modeling is a powerful tool for studying the metabolism of an organism and predicting the effects of metabolic engineering strategies. Various techniques have been developed for modeling cellular metabolism, with the underlying principle …

Exploring The Impact Of The E. Coli Proteostasis Network On The Folding Fate Of Proteins With Different Intrinsic Biophysical Properties, Kristine Faye R. Pobre

Doctoral Dissertations

The three-dimensional (3D) native structure of most proteins is crucial for their functions. Despite the complex cellular environment and the variety of challenges that proteins experience as they fold, proteins can still fold to their native states with high fidelity. The reason for this is the presence of the cellular proteostasis network (PN), consisting of molecular chaperones and degradation enzymes, that collaborates to maintain proteostasis, in which the necessary levels of functional proteins are optimized. Although extensive research has been carried out on the mechanisms of individual components of the proteostasis network, little is known about how these components contribute …