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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer Dec 2017

Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer

Doctoral Dissertations

The coupling of high performance multi-dimensional liquid chromatography and tandem mass spectrometry for characterization of microbial proteins from complex environmental samples has paved the way for a new era in scientific discovery. The field of metaproteomics, which is the study of protein suite of all the organisms in a biological system, has taken a tremendous leap with the introduction of high-throughput proteomics. However, with corresponding increase in sample complexity, novel challenges have been raised with respect to efficient peptide separation via chromatography and bioinformatic analysis of the resulting high throughput data. In this dissertation, various aspects of metaproteomic characterization, including ...


Pore Forming Protein Assembly And The Use In Nanopore Sensing: A Study On E. Coli Proteins Clya And Ompg, Monifa Fahie Jan 2017

Pore Forming Protein Assembly And The Use In Nanopore Sensing: A Study On E. Coli Proteins Clya And Ompg, Monifa Fahie

Doctoral Dissertations

Pore forming proteins are typically the proteins that form channels in membranes. They have several roles ranging from molecule transport to triggering the death of a cell. This work focuses on two E. coli pore forming proteins that have vastly differing roles in nature. Outer membrane protein G (OmpG) is an innocuous β-barrel porin while Cytolysin A (ClyA) is an α-helical pore forming toxin. For OmpG we probed its potential to be a nanopore sensor for protein detection and quantification. A small high affinity ligand, biotin, was covalently attached to loop 6 of OmpG and used to capture biotin-binding proteins ...


Modification Of Carbohydrate Active Enzymes In Switchgrass (Panicum Virgatum L.) To Improve Saccharification And Biomass Yields For Biofuels, Jonathan Duran Willis Aug 2016

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 ...


Electron Transport To Photosystem I By Soluble Carriers: Evolution Of The Interacting Pair, Khoa Dang Nguyen Aug 2016

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 ...


Nanocomposite Adhesive Of English Ivy (Hedera Helix): Bioproduction, Nanoparticle Isolation, And Molecular Analysis, Jason Neil Burris Aug 2016

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 ...


Novel Advancements For Improving Sprout Safety, Kyle S. Landry Jan 2016

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 ...


Engineering Photosystem I Complexes For Use In Bio-Hybrid Dye-Sensitized Solar Cells, Richard Franklin Simmerman Aug 2015

Engineering Photosystem I Complexes For Use In Bio-Hybrid Dye-Sensitized Solar Cells, Richard Franklin Simmerman

Doctoral Dissertations

Increasing global population, growing per capita energy needs, diminishing fossil fuels, and climate change collectively will require new, innovative, and sustainable alternatives to meet the world’s growing energy needs. One of the most promising yet simple approaches are dye-sensitized solar cells (DSSCs). However, conventional DSSCs use semi-conductor anodes sensitized with complex synthetic organometallic dyes. Most dyes utilize ruthenium complexes to absorb photons, which upon excitation, inject electrons into the anode, while holes migrate to the cathode via liquid electrolyte. However, these dyes are expensive, difficult to make, and resource-limited. This dissertation focuses on replacing synthetic dyes with the naturally ...


Design And Synthesis Of Polymeric Nanoparticles For Drug And Protein Delivery, Judy A. Ventura Jan 2015

Design And Synthesis Of Polymeric Nanoparticles For Drug And Protein Delivery, Judy A. Ventura

Doctoral Dissertations

Nanoparticles are emerging as carriers in biological applications due to advances in their preparation, size control, surface modification and encapsulation capabilities. In addition, nanomaterials improve bioavailability by enhancing aqueous solubility of the guest molecule and increasing resistance time in the body. However, the delivery of guest molecules is still challenging due to the intrinsic characteristics of the guest molecule including large size and propensity to denature or degradation in the case of biomolecules and the encapsulation stability of the small guest molecules.

Our group recently reported the preparation of self-cross-linked polymeric nanogels possessing surface functionalization capabilities. In this dissertation we ...


Applications And Improvements In The Molecular Modeling Of Protein And Ligand Interactions, Jason Bret Harris Aug 2014

Applications And Improvements In The Molecular Modeling Of Protein And Ligand Interactions, Jason Bret Harris

Doctoral Dissertations

Understanding protein and ligand interactions is fundamental to treat disease and avoid toxicity in biological organisms. Molecular modeling is a helpful but imperfect tool used in computer-aided toxicology and drug discovery. In this work, molecular docking and structural informatics have been integrated with other modeling methods and physical experiments to better understand and improve predictions for protein and ligand interactions. Results presented as part of this research include:

1.) an application of single-protein docking for an intermediate state structure, specifically, modeling an intermediate state structure of alpha-1-antitrypsin and using the resulting model to virtually screen for chemical inhibitors that can ...


Toward Direct Biosynthesis Of Drop-In Ready Biofuels In Plants: Rapid Screening And Functional Genomic Characterization Of Plant-Derived Advanced Biofuels And Implications For Coproduction In Lignocellulosic Feedstocks, Blake Lee Joyce Aug 2013

Toward Direct Biosynthesis Of Drop-In Ready Biofuels In Plants: Rapid Screening And Functional Genomic Characterization Of Plant-Derived Advanced Biofuels And Implications For Coproduction In Lignocellulosic Feedstocks, Blake Lee Joyce

Doctoral Dissertations

Advanced biofuels that are “drop-in” ready, completely fungible with petroleum fuels, and require minimal infrastructure to process a finished fuel could provide transportation fuels in rural or developing areas. Five oils extracted from Pittosporum resiniferum, Copaifera reticulata, and surrogate oils for Cymbopogon flexuosus, C. martinii, and Dictamnus albus in B20 blends were sent for ASTM International biodiesel testing and run in homogenous charge combustion ignition engines to determine combustion properties and emissions. All oils tested lowered cloud point. Oils derived from Copaifera reticulata also lowered indicated specific fuel consumption and had emissions similar to the ultra-low sulfur diesel control. Characterization ...


Characterization Of Field Evolved Resistance To Transgenic Cry1fa Maize In Spodoptera Frugiperda (J. E. Smith), Siva Rama Krishna Jakka May 2013

Characterization Of Field Evolved Resistance To Transgenic Cry1fa Maize In Spodoptera Frugiperda (J. E. Smith), Siva Rama Krishna Jakka

Doctoral Dissertations

Transgenic Bt crops expressing Cry and Vip toxins from Bacillus thuringiensis (Bt) have been increasingly planted to manage insect pest damage on agricultural crops. The high adoption of Bt-based insecticidal technologies suggests an increase selection pressure for the evolution of resistance in insect populations. So far, nine insect species have developed field evolved resistance to Bt crops, yet the mechanisms involved in field evolved resistance are unknown. In the present study, the resistance mechanism in field evolved resistance to maize producing Cry1Fa in Spodoptera frugiperda collected in fields from Puerto Rico was characterized. High levels of resistance to Cry1Fa have ...


Synthesis, Characterization And Self-Assembly Of Amphiphilic Block Copolymers, Xiaojun Wang May 2012

Synthesis, Characterization And Self-Assembly Of Amphiphilic Block Copolymers, Xiaojun Wang

Doctoral Dissertations

This dissertation presents a review on state-of-the-art research of well-defined charged block copolymers, including synthesis, characterization, bulk morphology and self-assembly in aqueous solution of amphiphilic block polyelectrolytes. In Chapter 1, as a general introduction, experimental observations and theoretical calculations devoted towards understanding morphological behavior in charged block copolymer systems are reviewed along with some of the new emerging research directions. Further investigation of charged systems is urged in order to fully understand their morphological behavior and to directly target structures for the tremendous potential in technological applications. Following this background, in Chapters 2, 3, 4 and 5 are presented the ...


Protein Engineering For The Enhanced Photo-Production Of Hydrogen By Cyanobacterial Photosystem I, Ifeyinwa Jane Iwuchukwu May 2011

Protein Engineering For The Enhanced Photo-Production Of Hydrogen By Cyanobacterial Photosystem I, Ifeyinwa Jane Iwuchukwu

Doctoral Dissertations

Photosystem I (PSI) from plants, algae, and cyanobacteria can mediate H2 evolution in vivo and in vitro. A simple, self-platinization procedure that permits stable PSI-mediated H2 evolution in vitro has been developed. The H2 evolution capabilities of PSI from Thermosynechococcus elongatus have been characterized. This organism utilizes cytochrome c6 (cyt c6) as the e- donor to P700. Using a solution-based, self-organized platinization of the PSI nanoparticles, this study demonstrates a sodium ascorbate-cyt-PSI-Pt-H2 electron transport and proton reduction system that yields light-dependent H2. The system was thermostable with H2 evolution increasing up to 55°C. In addition, stability studies have shown ...


Microscopy Techniques For Investigating Interactions In Microbial Systems, Amanda Nicole Edwards May 2011

Microscopy Techniques For Investigating Interactions In Microbial Systems, Amanda Nicole Edwards

Doctoral Dissertations

Biological interactions occur on multiple length scales, ranging from molecular to population wide interactions. This work describes the study of two specific areas of biological interactions in microbial systems: intracellular protein-protein interactions and cell-to-cell interactions. The implementation of optical and atomic force microscopy and the methodologies developed during this study proved to be invaluable tools for investigating these systems.

Identifying and characterizing protein interactions are fundamental steps toward understanding complex cellular networks. We have developed a unique methodology which combines an imaging-based protein interaction assay with a fluorescence recovery after photobleaching technique (FRAP). Protein interactions are readily detected by co-localization ...