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Full-Text Articles in Physical Sciences and Mathematics
Linking Decomposition Reactions In Arctic Soils To Microbial Enzyme Production, Jane Karen Martinez
Linking Decomposition Reactions In Arctic Soils To Microbial Enzyme Production, Jane Karen Martinez
Open Access Theses & Dissertations
Microbial processes such as soil enzyme production are a major driver of decomposition and a current topic of interest in arctic soils due to the effects of climate warming. Despite the advances in understanding soil enzymes, there are still knowledge gaps regarding the role of enzymes in decomposition. In this dissertation, I addressed three of those gaps in the following chapters: (Ch.2) to explore the location of enzymes within the soil matrix, (Ch.3) to identify peptides matched to soil enzymes produced by microorganisms for organic matter decomposition, and (Ch.4) understand the longevity of enzymes in the soil after microbial production. …
Mass Spectrometry-Based Proteomic Analysis To Characterise Barley Breeding Lines, Mahya Bahmani
Mass Spectrometry-Based Proteomic Analysis To Characterise Barley Breeding Lines, Mahya Bahmani
Theses: Doctorates and Masters
Barley is a key ingredient in the malting and brewing industry, and it is the fourth most important crop being cultivated worldwide. The protein content of the barley grain is one of the main components determining the quality and nutritive value of the food and beverages prepared from barley. Mass spectrometry-based proteomic analysis is a valuable tool that can guide and inform plant breeding strategies and crop improvement programs. Understanding the proteome changes in barley grain under different growing locations, the impact of different environmental conditions and its relationship with malting characteristics have the potential to inform breeding programs to …
Lipid Rafts, Exosomal Vesicles And Anti-Giardial Therapies, Brian Ivan Grajeda
Lipid Rafts, Exosomal Vesicles And Anti-Giardial Therapies, Brian Ivan Grajeda
Open Access Theses & Dissertations
Giardia lamblia, a protozoan parasite, is a major cause of waterborne infection, worldwide. While the trophozoite form of this parasite induces pathological symptoms in the gut, the cyst forms transmit the infection via contaminated water. Since Giardia is a non-invasive parasite, the actual mechanism by which it causes infection remains elusive. We have previously reported that Giardia assembles cholesterol and GM1 glycolipid-enriched lipid rafts (LRs) that participate in encystation and cyst production. To further delineate the role of LRs in pathogenesis, we isolated LRs from Giardia and subjected them to proteomic analysis. Various cellular proteins including the virulent proteinsâe.g., giardins, …
Validation Of A Deployable Proteomic Assay For The Serological Screening Of Sexual Assault Samples, Catherine O'Sullivan Brown
Validation Of A Deployable Proteomic Assay For The Serological Screening Of Sexual Assault Samples, Catherine O'Sullivan Brown
Electronic Theses and Dissertations
Protein mass spectrometry (MS) has emerged as a technique to supplant traditional serological tests for body fluid identification. It was hypothesized that proteomic techniques would surpass the sensitivity and specificity of traditional serological techniques. An automated workflow coupled with protein MS has been developed for the confirmatory identification of five biological fluids. A developmental validation was completed, assessing parameters such as reproducibility, sensitivity, ion suppression, and limit of detection. Implementation was determined through tandem sample processing by MS, traditional serological tests, and standard DNA profiling methods. The MS approach offered superior detection limits while also providing true confirmatory results, producing …
Ensemble Protein Inference Evaluation, Kyle Lee Lucke
Ensemble Protein Inference Evaluation, Kyle Lee Lucke
Graduate Student Theses, Dissertations, & Professional Papers
The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …
Intrinsic Buffer Hydroxyl Radical Dosimetry For Hydroxyl Radical Protein Footprinting, Addison Roush
Intrinsic Buffer Hydroxyl Radical Dosimetry For Hydroxyl Radical Protein Footprinting, Addison Roush
Honors Theses
Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry is a powerful technique for the analysis of protein topography as it generates covalent mass labels that can survive downstream sample handling, and it is sensitive to the solvent accessibility of amino acid sidechains. Of the multiple platforms for HRPF, fast photochemical oxidation of proteins (FPOP) utilizes a pulsed 248 nm KrF excimer laser to label proteins by photolyzing hydrogen peroxide. FPOP is the most widely used HRPF platform because it labels proteins faster than unfolding can occur. Variations in FPOP sample conditions make it difficult to compare results between experiments …
An Exploration Of Protein And Dna Components In Fingerprint Residue, Ashley Borrego
An Exploration Of Protein And Dna Components In Fingerprint Residue, Ashley Borrego
Student Theses
The main focus of this project was to investigate the protein and DNA components in both sebaceous and eccrine fingerprints. This study investigated the relative content of DNA and proteins in eccrine fingerprints to sebaceous fingerprints. All volunteers were instructed to wash and dry their hands prior to depositing parallel thumbprints. Twenty volunteers were instructed to touch their face to produce sebaceous prints, and 5 volunteers were instructed to wear gloves over a heat source to produce sweaty or eccrine prints. Microscopy was used to score the cellular debris of the right fingerprint on a scale of 1-4 based on …
Nbpmf: Novel Network-Based Inference Methods For Peptide Mass Fingerprinting, Zhewei Liang
Nbpmf: Novel Network-Based Inference Methods For Peptide Mass Fingerprinting, Zhewei Liang
Electronic Thesis and Dissertation Repository
Proteins are large, complex molecules that perform a vast array of functions in every living cell. A proteome is a set of proteins produced in an organism, and proteomics is the large-scale study of proteomes. Several high-throughput technologies have been developed in proteomics, where the most commonly applied are mass spectrometry (MS) based approaches. MS is an analytical technique for determining the composition of a sample. Recently it has become a primary tool for protein identification, quantification, and post translational modification (PTM) characterization in proteomics research. There are usually two different ways to identify proteins: top-down and bottom-up. Top-down approaches …
Oxidative Stress And Proteomic Studies Of Mammalian Models Of Age-Related Metabolic Dysfunction In Neurodegenerative Disorders, Aaron M. Swomley
Oxidative Stress And Proteomic Studies Of Mammalian Models Of Age-Related Metabolic Dysfunction In Neurodegenerative Disorders, Aaron M. Swomley
Theses and Dissertations--Chemistry
Expression proteomics is the field of science wherein proteins that make up the cellular proteome are identified both by name and by fold-change. Depending on the application of proteomics, this change in level could be due to internal cellular stressors or introduction of xenobiotics. Global oxidative stress measures use immunohistochemistry to determine the relative level of oxidative stress of macromolecules within the cell. In this dissertation, both global oxidative stress measures and expression proteomics were used in a variety of mammalian models in order to determine the effects of protein upregulation, intranasal insulin administration, and resveratrol supplementation on the cellular …
Nanoceria Exposure To Kidney Beans (Phaseolus Vulgaris): Implications On Plant Physiology, Nutrition And Their Transfer To Next Trophic Level, Sanghamitra Majumdar
Nanoceria Exposure To Kidney Beans (Phaseolus Vulgaris): Implications On Plant Physiology, Nutrition And Their Transfer To Next Trophic Level, Sanghamitra Majumdar
Open Access Theses & Dissertations
Previous studies investigating the effects of cerium oxide nanoparticles (nanoceria, nCeO2) on plants have primarily focused on the physiological and biochemical changes at early growth stages. Comprehensive information on the effects of nCeO2 through the entire life cycle of plants and the nutritional quality of the edible tissues is limited. No studies have been reported on the interactions between nCeO2 and common beans (Phaseolus vulgaris). Common beans are leguminous crops, which are societally important due to their nutritional benefits. The beans are rich in proteins and essential nutrients like folate, iron, zinc, molybdenum and magnesium, and are consumed worldwide. This …
Identification And The Significance Of Selective Proteins In Bile And Plasma Of Normal And Health-Compromised Chickens, Balamurugan Packialakshmi
Identification And The Significance Of Selective Proteins In Bile And Plasma Of Normal And Health-Compromised Chickens, Balamurugan Packialakshmi
Graduate Theses and Dissertations
During the last 50 years, animal breeding programs in commercial poultry have made significant progress in the bodyweight gain of broilers but led to several metabolic and skeletal disorders. Lameness associated with proximal femur known as femoral head separation (FHS) or femoral head necrosis (FHN) is one of the major metabolic disorders in poultry industry. In order to select for healthy chickens, markers that can distinguish between healthy and affected birds are required. Biomarkers from blood represent an ideal and rich source of markers which can be obtained using minimally invasive methods. The biomarkers were explored in an experimental model …
Bioinformatic Solutions To Complex Problems In Mass Spectrometry Based Analysis Of Biomolecules, Ryan M. Taylor
Bioinformatic Solutions To Complex Problems In Mass Spectrometry Based Analysis Of Biomolecules, Ryan M. Taylor
Theses and Dissertations
Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation. The complexity and volume of data produced by modern MS-omic instrumentation challenges biological interpretation, while the complexity of the instrumentation, sample noise, and complexity of data analysis present difficulties in maintaining and ensuring data quality, validity, and relevance. We present a corpus of tools which improves …
Demonstration Of A Targeted Proteome Characterization Approach For Examining Specific Metabolic Pathways In Complex Bacterial Systems, Adam Justin Martin
Demonstration Of A Targeted Proteome Characterization Approach For Examining Specific Metabolic Pathways In Complex Bacterial Systems, Adam Justin Martin
Masters Theses
Multiple Reaction Monitoring (MRM) is a powerful tandem mass spectrometry (MS/MS) tool frequently implemented in proteomic studies to provide targeted analysis of proteins and peptides. The selectivity that MRM delivers is so strong that it provides the quadrupole mass spectrometers (QQQ), on which it is commonly employed, with pertinence to proteomic studies that they would otherwise lack for their relatively low resolution. Additionally, this increased level of selectivity is sufficient enough to supplant complicated fractionation techniques, additional dimensions of chromatography, and 24 hour long MS/MS experiments in simplistic biological samples. But there is a deficiency of evidence to determine the …
Methods In Metallomics, Proteomics, And Toxicology: Development And Applications Of Laser Ablation Inductively Coupled Plasma Mass Spectrometry And Native Sds-Page, William John Wobig
Methods In Metallomics, Proteomics, And Toxicology: Development And Applications Of Laser Ablation Inductively Coupled Plasma Mass Spectrometry And Native Sds-Page, William John Wobig
Theses and Dissertations
Polyacrylamide gel electrophoresis (PAGE) is a bio-analytical method used to separate proteins in solution into an array of individual bands of proteins in a gel matrix. Current PAGE methods, however, have severe limitations in simultaneously maintaining a protein's native structure and association with transition metals while providing adequate resolution. Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) provides a means to perform trace to ultra-trace level inorganic analysis of solid samples such as dried PAGE gels containing metallo-protein arrays. Current LA-ICP-MS methods involving the analysis of PAGE gels, however, have been limited in their effective use by inadequate limits of …
Endocrine Disrupting Compound 4-Nonylphenol And Neurodegeneration, Jessica Martinez Jurado
Endocrine Disrupting Compound 4-Nonylphenol And Neurodegeneration, Jessica Martinez Jurado
Open Access Theses & Dissertations
Neurodegeneration, a progressive loss of nerve cells (neurons), occurs in many neurological disorders including Alzheimer's disease, Parkinson's disease, Schizophrenia, and drug addiction. Cytoskeletal disruption in neurons and aggregation of proteins associated with these disorders is the hallmark of neurodegeneration. However, the cause of neurodegenerative disorders is unknown and currently there are no effective drug treatments. Aging is the most consistent risk factor for developing a neurodegenerative disorder, and recent evidence suggests that environmental factors, which act as endocrine disruptors, pose a risk in the disease process. 4- nonylphenol (4-NP), an endocrine-disrupting compound (EDC), has been shown to affect brain development …
Protein Profiling Of Adenine Nucleoside And Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-Azidoadenosine Analogs As Affinity Based Protein Profiling Probes, Shikha Mahajan
USF Tampa Graduate Theses and Dissertations
Identification of differential expressions of proteins in proteomic profiles of biological samples shows great potential as a valuable technique for the early diagnosis of various diseases. An important challenge in modern protein profiling approaches is to reduce the complexity of the samples by limiting the number of proteins that need to be evaluated for distinction in the expression between normal and deceased cells. In this research, an affinity based approach for the enrichment of nucleotide and nucleoside binding proteins from a complex cell proteome has been developed. To achieve this goal, new N6-biotinylated-8-azido-adenosine probes (AdoRs) have been designed and synthesized …
A Top-Down Proteomic Approach For The Discovery Of Novel Serum Biomarkers Of Pregnancy-Related Disease, Karen Merrell
A Top-Down Proteomic Approach For The Discovery Of Novel Serum Biomarkers Of Pregnancy-Related Disease, Karen Merrell
Theses and Dissertations
The serum fraction of blood is an ideal material in which to search for novel biomarkers for disease. It is easily obtained through relatively non-invasive means, routinely collected, and a rich treasure-trove of information about the health of an individual. Cells react to signal molecules, take up nutrients, and release waste products, fragments that are the result of proteolysis, and other molecules out into the bloodstream. If these components are unique to the cells in question, that part of the complex mixture that is the blood stream can potentially characterize the health of the tissue or organ those cells are …
Study Of The Reproducibility Of Proteomics Methods And Variability Of Fruit Fly Proteomes., Thomas Franklin Culwell
Study Of The Reproducibility Of Proteomics Methods And Variability Of Fruit Fly Proteomes., Thomas Franklin Culwell
Theses and Dissertations
The reliability of biomarker discovery by means of proteomics has been called into question. It was speculated that "background noise" variation resulting from differences in preparation and handling of samples and proteome dynamics may mask subtle, yet important, differences due to the biological condition. Little is understood about complex proteomes and their variability. A critical aspect of proteomic biomarker research that is largely unexplored is the comparative reproducibility of certain methods such as two-dimensional gel electrophoresis and liquid chromatography/mass spectrometry. In particular, with liquid chromatography/mass spectrometry, it is not known whether variability in peptide quantitation is dependent on any of …
Biochemical Investigations Of Macular Degeneration: The Significance Of Protein Oxidation Including Novel Methods For Its Study, Sarah Warburton
Biochemical Investigations Of Macular Degeneration: The Significance Of Protein Oxidation Including Novel Methods For Its Study, Sarah Warburton
Theses and Dissertations
The retinal pigment epithelium (RPE) is a monolayer of cells located directly behind the photoreceptor cells in the retina. These cells are involved in a variety of functions that support the visual process in the eye, namely 1) they form a blood-retina barrier which separates the neural retina from the choroid's blood supply, 2) the apical processes of RPE cells diurnally phagocytose the outer segments of photoreceptor cells, and 3) they participate in the renewal of the photopigment 11-cis retinal. Age-related macular degneration (AMD) is the leading cause of blindness in people over the age of 50 years in North …