Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Biochemistry, Biophysics, and Structural Biology (64)
- Molecular Biology (37)
- Biochemistry (35)
- Biology (29)
- Cell and Developmental Biology (21)
-
- Physical Sciences and Mathematics (20)
- Bioinformatics (15)
- Chemistry (15)
- Cell Biology (14)
- Medicine and Health Sciences (14)
- Animal Sciences (12)
- Microbiology (10)
- Physiology (10)
- Genetics and Genomics (9)
- Cancer Biology (8)
- Cellular and Molecular Physiology (8)
- Pharmacology, Toxicology and Environmental Health (8)
- Analytical Chemistry (7)
- Immunology and Infectious Disease (7)
- Systems Biology (7)
- Marine Biology (6)
- Integrative Biology (5)
- Medical Sciences (5)
- Plant Sciences (5)
- Agriculture (4)
- Genomics (4)
- Neuroscience and Neurobiology (4)
- Virology (4)
- Chemicals and Drugs (3)
- Institution
-
- California Polytechnic State University, San Luis Obispo (17)
- Western University (12)
- University of South Florida (11)
- University of Tennessee, Knoxville (8)
- Virginia Commonwealth University (8)
-
- University of Texas at El Paso (7)
- University of Arkansas, Fayetteville (6)
- University of the Pacific (6)
- Brigham Young University (5)
- University of Kentucky (5)
- University of Vermont (5)
- City University of New York (CUNY) (3)
- Dartmouth College (3)
- Georgia State University (3)
- University of Denver (3)
- Wayne State University (3)
- Old Dominion University (2)
- South Dakota State University (2)
- The Texas Medical Center Library (2)
- University of Louisville (2)
- University of Nebraska Medical Center (2)
- Clemson University (1)
- DePaul University (1)
- Dominican University of California (1)
- East Tennessee State University (1)
- Edith Cowan University (1)
- Louisiana State University (1)
- Missouri State University (1)
- Portland State University (1)
- University of Mississippi (1)
- Publication Year
- Publication
-
- Master's Theses (16)
- Theses and Dissertations (13)
- Electronic Thesis and Dissertation Repository (12)
- USF Tampa Graduate Theses and Dissertations (11)
- Electronic Theses and Dissertations (8)
-
- Doctoral Dissertations (7)
- Open Access Theses & Dissertations (7)
- Graduate Theses and Dissertations (6)
- University of the Pacific Theses and Dissertations (6)
- Graduate College Dissertations and Theses (5)
- Biology Dissertations (4)
- Dartmouth College Ph.D Dissertations (3)
- Dissertations & Theses (Open Access) (2)
- Student Theses (2)
- Theses & Dissertations (2)
- Theses and Dissertations--Animal and Food Sciences (2)
- Wayne State University Dissertations (2)
- All Theses (1)
- Arts & Sciences Electronic Theses and Dissertations (1)
- Biological Sciences (1)
- Browse all Theses and Dissertations (1)
- College of Science and Health Theses and Dissertations (1)
- Computational Modeling & Simulation Engineering Theses & Dissertations (1)
- Dissertations, Masters Theses, Capstones, and Culminating Projects (1)
- Dissertations, Theses, and Capstone Projects (1)
- Graduate Student Theses, Dissertations, & Professional Papers (1)
- Graduate Theses, Dissertations, and Problem Reports (1)
- Honors Theses (1)
- LSU Doctoral Dissertations (1)
- MSU Graduate Theses (1)
Articles 1 - 30 of 131
Full-Text Articles in Life Sciences
Quantitative Proteomic Strategies To Determine Substrate Specificities Of Phosphoprotein Phosphatases, Hieu Trung Nguyen
Quantitative Proteomic Strategies To Determine Substrate Specificities Of Phosphoprotein Phosphatases, Hieu Trung Nguyen
Dartmouth College Ph.D Dissertations
Reversible phosphorylation is a crucial regulatory mechanism of cellular signaling pathways. Being the most prevalent post-translational modification (PTM) in the cells, with over 75% of all proteins detected to be phosphorylated, phosphorylation regulates a significant number of important cellular processes that have implications in various diseases. Phosphorylation is carried out by protein kinases, which have been extensively studied. However, the opposite reaction, carried out by protein phosphatases, has lagged significantly, exposing a gap of knowledge that is required to be investigated to delineate the kinase-substrate-phosphatase relationship. Phosphoprotein phosphatase family (PPPs), containing seven members of phospho-Serine (pS) and phospho-Threonine (pT) phosphatases, …
Molecular Mechanisms Of Opioid Use Disorder In Human Brain Models, Emily Mendez
Molecular Mechanisms Of Opioid Use Disorder In Human Brain Models, Emily Mendez
Dissertations & Theses (Open Access)
Opioid use disorder (OUD) is a national and global public health crisis with no end in sight. While studies from animal models hint at widespread epigenetic and transcriptomic alterations of opioid drugs, the molecular consequences of long-term exposure to opioid drugs in human brain is still unclear, and human-centered translational models are necessary to discern the human cell type-specific effects of OUD.
Using postmortem brain Brodmann area 9 (BA9) from the UTHealth Brain Collection for Research on Psychiatric Disorders, I identified angiogenic gene networks perturbed in the RNA and protein of OUD subjects, as well as downregulation of many neuron-correlated …
Quantum Dots' Toxicity: A Multi-Level Investigation On The Impact Of Quantum Dots On The Actin Cytoskeleton, Nhi Le
MSU Graduate Theses
Quantum dots (QDs) are fluorescence nanomaterials with unique optical and physical properties. As such, they are highly sought after for their potential use in several biomedical and industrial applications. Despite their vast potential, recent studies have suggested that quantum dots are toxic to cells. Yet, the mechanism of quantum dots’ toxicity remains unclear. As such, my thesis aims to comprehensively examine the mechanism of quantum dots’ toxicity, emphasizing how quantum dots disrupt the actin cytoskeleton. In this study, I used RNA sequencing and mass spectrometry to investigate the influence of CdSe/ZnS QDs on the transcriptomic proteomic level of Saccharomyces cerevisiae …
Quantitative Shotgun Proteomic Analysis Of Bacteria After Overexpression Of Recombinant Spider Miniature Spidrion, Masp1, Kathryn P. Randene
Quantitative Shotgun Proteomic Analysis Of Bacteria After Overexpression Of Recombinant Spider Miniature Spidrion, Masp1, Kathryn P. Randene
University of the Pacific Theses and Dissertations
Spider silk has extraordinary mechanical properties, displaying high tensile strength, elasticity, and toughness. Given the high performance of natural fibers, one of the long-term goals of the silk community is to manufacture large-scale synthetic spider silk. This process requires vast quantities of recombinant proteins for wet-spinning applications. Attempts to synthesize large amounts of native size recombinant spidroins in diverse cell types have been unsuccessful. In these studies, we design and express recombinant miniature black widow (Latrodectus hesperus) MaSp1 spidroins in bacteria that incorporate the NTD and CTD, along with varying numbers of codon-optimized internal block repeats. Following spidroin overexpression, we …
Personalized Molecular Therapies For Advanced Non-Small Cell Lung Cancer: Overcoming Heterogeneity To Optimize Treatment Response And Clinical Outcomes, Zuan-Fu Lim
Graduate Theses, Dissertations, and Problem Reports
Lung cancer remains one of the deadliest cancers. Novel, paradigm shifting treatments including immunotherapy and targeted therapies have recently been developed to cull the deadly effects of lung cancer, but many challenges remain. There remains a significant unmet need to accurately predict and optimally select for patients who will respond to immune checkpoint inhibitors (ICI) treatment. In Chapter 2 of this dissertation, we investigated a novel live single cell cytokine profiling lab-on-chip platform, IsoLight, using peripheral CD4+ and CD8+ T-cells for ICI biomarker development. A total of 55,175 single T-lymphocytes were analyzed in this proof-of-concept study. We found that an …
Proteomic Approaches To Identify Unique And Shared Substrates Among Kinase Family Members, Charles Lincoln Howarth
Proteomic Approaches To Identify Unique And Shared Substrates Among Kinase Family Members, Charles Lincoln Howarth
Dartmouth College Ph.D Dissertations
Protein phosphorylation is a reversible post-translational modification that is a critical component of almost all signaling pathways. Kinases regulate substrate proteins through phosphorylation, and nearly all proteins are phosphorylated to some extent. Crucially, breakdown in phosphorylation signaling is an underlying factor in many diseases, including cancer. Understanding how phosphorylation signaling mediates cellular pathways is crucial for understanding cell biology and human disease.
Targeted protein degradation (TPD) is a strategy to rapidly deplete a protein of interest (POI) and is applicable to any gene that is amenable to CRISPR-Cas9 editing. One TPD approach is the auxin-inducible degron (AID) system, which relies …
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. …
Soluble Epoxide Hydrolase Inhibition: A Novel Therapeutic Strategy For Alcohol-Associated Liver Disease., Jeffrey Warner
Soluble Epoxide Hydrolase Inhibition: A Novel Therapeutic Strategy For Alcohol-Associated Liver Disease., Jeffrey Warner
Electronic Theses and Dissertations
Introduction Alcohol-associated liver disease (ALD) is a common chronic liver disease and healthcare burden, and a spectrum of pathologies ranging from steatosis to steatohepatitis, fibrosis, and alcohol-associated hepatitis (AH). Despite its prevalence, there are limited effective therapeutic options for the treatment of ALD/AH. Previous evidence suggested that inhibition of soluble epoxide hydrolase (sEH), a lipid metabolism enzyme which degrades beneficial metabolites of dietary polyunsaturated fatty acids, may be a beneficial strategy. The central hypothesis of the current dissertation is that sEH inhibition will ameliorate alcohol-associated liver injury and inflammation in mouse models of ALD. Methods To determine the efficacy of …
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 …
Leveraging Mass Spectrometry-Based Proteomics And Post-Translational Modifications For System-Wide Understanding Of Bioenergy Plants And Their Environment, Him K. Shrestha
Doctoral Dissertations
Bioenergy research focuses on utilizing renewable biomass feedstocks to produce biofuels and bioproducts to address growing concerns about energy security and climate change. To better understand the details of bioenergy crop production and conversion to bioproducts, it is essential to characterize bioenergy plants and their environments at a molecular systems level. Mass spectrometry has emerged as a promising technique for detailed proteomic information, including post-translational modifications (PTMs), of molecular processes and cellular functions of biological systems. In this dissertation, proteomic approaches have been optimized and implemented to deepen our understanding of the interaction of plants and their environment in a …
Eluication Of Lipid Metabolic Pathways In Differentiating Giardia Lamblia Using High Resolution Mass Spectrometry, Cameron Ellis
Eluication Of Lipid Metabolic Pathways In Differentiating Giardia Lamblia Using High Resolution Mass Spectrometry, Cameron Ellis
Open Access Theses & Dissertations
Giardia lamblia is an intestinal protozoan found worldwide, including the U.S. This parasite exists in two morphologic stages - a replicative trophozoite and a relatively dormant yet viable cyst. While exposures of cysts to gastric acid during passage through the human stomach induces excystation, factors in the small intestine, where trophozoites colonize trigger encystation or cyst formation. Transformation into cyst stage is essential for Giardia to survive in the environment for months before infecting new hosts. Because of its small genome size (11.7 Mb), metabolic pathways in Giardia are highly reduced. As far as lipid metabolism is concerned, only limited …
Identification Of Genomic, Proteomic, And Metabolomic Signatures Associated With Pulmonary Hypertension Syndrome In Broilers, Duaa Almansaf
Identification Of Genomic, Proteomic, And Metabolomic Signatures Associated With Pulmonary Hypertension Syndrome In Broilers, Duaa Almansaf
Graduate Theses and Dissertations
The present dissertation contains a collection of studies that examine the genomic, proteomic, and metabolomic association to pulmonary hypertension or ascites phenotype in fast-growing broilers. Pulmonary hypertension is a multifactorial metabolic disease influenced by physiological, environmental, and nutritional factors. It is characterized by a number of structural changes including, thrombosis and adverse pulmonary vascular remodeling. Thus, the atrial pressure is increased, and the right ventricle becomes hypertrophied, resulting in heart failure and the death of the bird. Pulmonary hypertension or ascites is a global problem that has negatively impacted the economy. The increased mortality rate of broilers (25%) is estimated …
Deciphering Phosphoprotein Phosphatase Signaling Networks Using Proteomics Approaches, Brooke Brauer
Deciphering Phosphoprotein Phosphatase Signaling Networks Using Proteomics Approaches, Brooke Brauer
Dartmouth College Ph.D Dissertations
Protein phosphorylation is a highly regulated mechanism of cell signaling control and its deregulation is implicated in disease. The kinases that catalyze the addition of phosphate groups onto their substrate proteins have been well studied, their signaling pathways mapped, and their effects on cell and organismal health observed. Knowledge of the phosphatases that reverse the reaction only recently began to come into focus. Phosphoprotein phosphatases (PPPs), long thought to be housekeeping enzymes, are now known to be exquisitely specific towards their substrates, but the exact nature of phosphatase regulation—both upstream and downstream of the phosphatase—is unclear.
PPPs recognize substrates through …
Signature Peptide Identification For Body Fluids In Sexual Assault Cases By Liquid Chromatography Tandem Mass Spectrometry (Lc-Ms/Ms), Kelci Somers
Student Theses
Body fluids contain proteins that perform functions specific to different types of body fluids. Therefore, the detection of signature peptides for these proteins can potentially identify a body fluid in a forensic investigation. This project aimed to validate a method to detect signature peptides in body fluids commonly found in sexual assault cases by LC-MS/MS. Signature peptides for semen and saliva fluids were combined with two signature peptides for vaginal fluids. Samples created using two donors each for saliva, semen, and vaginal fluids were extracted using a trypsin digest, with separation of the protein and DNA fractions. The LC-MS/MS was …
Evaluation Of Postmortem Protein Expression In Determining Cause Of Death, Zoe Robinson
Evaluation Of Postmortem Protein Expression In Determining Cause Of Death, Zoe Robinson
University Honors Theses
Cause of death differentiation during a medicolegal autopsy can be complicated by several factors, including sample conditions which can create uncertainty. Postmortem protein analysis has potential to be used as an additional evidentiary tool in determining cause of death. Proteomic biomarkers offer a method to directly measure physiological conditions at time of death that are stable in a postmortem state. Specific protein expression levels have been studied for their postmortem application in significantly differentiating many different causes of death. Work done in regard to asphyxial, toxicological, and traumatic deaths will be specifically discussed here. Proteins will be reviewed for potential …
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, …
Elucidating The Cellular Physiology Of Glyphosate Resistance In Palmer Amaranth (Amaranthus Palmeri) Using Integrated Omics Approaches, Pawanjit Kaur Sandhu
Elucidating The Cellular Physiology Of Glyphosate Resistance In Palmer Amaranth (Amaranthus Palmeri) Using Integrated Omics Approaches, Pawanjit Kaur Sandhu
All Theses
The evolution of resistance to herbicides in weeds poses a major threat to agricultural production systems. To date, herbicide resistance has been reported against 21 modes of action in 266 weed species across 71 countries. More than 50 weed species have developed resistance against glyphosate, the most widely used herbicide worldwide. Although several mechanisms of glyphosate resistance have been discovered, our understanding of alterations in the cellular physiology of glyphosate-resistant weed biotypes, and the induction of the resistance mechanisms remains limited. This knowledge is critical to developing sustainable weed management practices and for a comprehensive understanding of plant stress adaptations. …
Extending Plasma Proteome Coverage To Enable Biomarker Discovery, Jordan Bruce Burton
Extending Plasma Proteome Coverage To Enable Biomarker Discovery, Jordan Bruce Burton
Wayne State University Dissertations
Two features make plasma a valued source of health information: First, plasma contains secreted proteins from all tissues in the body and can, therefore, provide information about the health status of all tissues. Second, plasma is available in large quantity using a minimally invasive procedure that is well tolerated. The status of plasma as a valued source of health information is matched by the difficulty in extracting proteome information from the samples. Using state of the art instrumentation a standard analysis of plasma yields quantitative information on approximately 300 proteins. Extreme fractionation strategies coupled with increased mass spectrometry time extends …
Beyond Cortisol: Indicators Of Stress And Negative Feedback In Plasma And Blubber Of Marine Mammals, Jessica Avalos
Beyond Cortisol: Indicators Of Stress And Negative Feedback In Plasma And Blubber Of Marine Mammals, Jessica Avalos
University of the Pacific Theses and Dissertations
Marine mammals play an important role in ecosystem stability. However, anthropogenic activity is compounding pressure on many already vulnerable populations. A potential consequence of anthropogenic disturbance is physiological stress, which can impact metabolism, immunity, and reproduction, especially if it occurs repeatedly. Previous studies on marine mammals have focused on acute stress, but the impacts of repeated stress are poorly understood. Due to its accessibility on land during haul-outs, the northern elephant seal (Mirounga angustirostris) is a good system in which to study the effects of stress in marine mammals. Stress stimulates the release of glucocorticoid hormones, primarily cortisol. Elevated cortisol …
How Do They Do It? Using Omics Approaches To Explore Metabolic Responses Associated With Hypoxia And Exercise Tolerance In The Deepest Diving Pinniped, Elizabeth R. Piotrowski
How Do They Do It? Using Omics Approaches To Explore Metabolic Responses Associated With Hypoxia And Exercise Tolerance In The Deepest Diving Pinniped, Elizabeth R. Piotrowski
University of the Pacific Theses and Dissertations
Marine mammals such as northern elephant seals (NES) routinely experience hypoxemia and ischemia-reperfusion events to many tissues during deep dives with no apparent adverse effects. Adaptations to diving include increased antioxidants and elevated oxygen storage capacity associated with high hemoprotein content in blood and muscle. Despite experiencing decreased oxygen tensions during diving, NES likely rely on the mobilization of large lipids stores and catabolism of fatty acids to provide energy to exercising muscle while diving. To identify potential regulatory mechanisms that may underly hypoxia and exercise tolerance in diving mammals, this study used system-wide approaches to characterize changes in genes …
The Rotator Cuff Tendon-To-Bone Interface: Maturation, Aging, And 3d Bioprinting For Regeneration, Xiping Jiang
The Rotator Cuff Tendon-To-Bone Interface: Maturation, Aging, And 3d Bioprinting For Regeneration, Xiping Jiang
Theses & Dissertations
Rotator cuff tendon injuries often occur at the tendon-to-bone interface (i.e., enthesis) area with a high prevalence for the elderly population. In addition, regeneration of the gradient structure of the enthesis is still a significant clinical challenge. Our studies aim to identify the histological, molecular, and biomechanical alterations of the rotator cuff enthesis with maturation and aging, and develop a novel therapeutic method using three-dimensional (3D) bioprinting technique to regenerate a functional enthesis. Striking variations of the entheses were observed both histologically and biomechanically during the maturation process. The histological features did not show many differences at the insertion site …
Probing The Role Of Astrocytes In The Pathology Of Fragile X Syndrome With Human Stem Cells, Baiyan Ren
Probing The Role Of Astrocytes In The Pathology Of Fragile X Syndrome With Human Stem Cells, Baiyan Ren
Theses & Dissertations
Fragile X syndrome (FXS) is an X-linked neurodevelopmental disorder related to intellectual disability and the most common monogenic cause of autism spectrum disorder. FXS is mainly caused by an expansion of CGG repeats in the 5’-untranslated region of fragile X mental retardation 1 (FMR1) gene, leading to the loss of expression of fragile X mental retardation protein (FMRP). Astrocytes are the most abundant glial cells in the central nervous system (CNS). Loss of FMRP in astrocytes has been found to contribute to structural and functional synaptic deficits in the Fmr1-KO mouse model. The contribution of human astrocytes, however, to the …
Development Of High-Throughput Methods For Screening Venom Peptides, Tanya Napolitano
Development Of High-Throughput Methods For Screening Venom Peptides, Tanya Napolitano
Dissertations, Theses, and Capstone Projects
Bioactive venom peptides are increasingly being explored as drug leads in pharmaceutical research because of their immense therapeutic potential, however there is a need to more efficiently screen and characterize these peptides to discover medicinal leads more quickly.1,2 The Holford lab has leveraged recent technological achievements in genomics, transcriptomics, and proteomics to produce a leap in the discovery of venom peptides from previously hard to characterize small and neglected venomous animals such as Terebridae, an understudied lineage of the Conoidea Superfamily.4, 5–7 With the rise of -omic technologies the floodgates have opened and venom researchers are awash with large datasets …
Mapping Ku70 Protein Interactions Using Proximity-Dependent Biotin Identification, Sanna Abbasi
Mapping Ku70 Protein Interactions Using Proximity-Dependent Biotin Identification, Sanna Abbasi
Electronic Thesis and Dissertation Repository
The Ku heterodimer, composed of subunits Ku70 and Ku80, is a highly abundant protein complex, known for its affinity for double-stranded DNA ends. Accordingly, Ku is most well-studied for repairing double-stranded DNA breaks through the non-homologous end-joining (NHEJ) DNA repair pathway. Aside from NHEJ, Ku has also been implicated and studied in various other cellular processes including V(D)J recombination and telomere maintenance.
Numerous protein interactions have been mapped to the C-terminal region of Ku70, although few have been mapped to its N-terminal von Willebrand A-like (vWA) domain. Here, we used the high-throughput proteomic technique, proximity-dependent biotin identification (BioID, BioID2) to …
Uncovering The Ubiquitin Ligase Activity And Substrates Of The Human C-Terminal To Lish (Ctlh) Complex, Matthew E.R. Maitland
Uncovering The Ubiquitin Ligase Activity And Substrates Of The Human C-Terminal To Lish (Ctlh) Complex, Matthew E.R. Maitland
Electronic Thesis and Dissertation Repository
Ubiquitination is the transfer of a ubiquitin molecule to protein substrates by the sequential actions of E1 activating enzymes, E2 conjugating enzymes, and E3 ligases. It is a post-translational modification that controls the fate and function of the substrate protein. Substrate specificity in the ubiquitination reaction is conferred by the E3 ligases. Sequence homology suggests the human C-terminal to LisH (CTLH) complex could be an E3 ligase; however, very little is known about this complex. In this thesis, I characterize the human CTLH complex as a multi-subunit E3 ligase and define its activity, structure, and substrates. I demonstrate that the …
Characterization And Discovery Of Short Linear Motifs Mediating Protein Nuclear Import, Tanner M. Tessier
Characterization And Discovery Of Short Linear Motifs Mediating Protein Nuclear Import, Tanner M. Tessier
Electronic Thesis and Dissertation Repository
Protein-protein interactions (PPI) mediated through short linear motifs (SLiMs) are ubiquitous throughout the human proteome and are involved in many essential cellular processes. One such type of SLiM is the classical nuclear localization sequence (cNLS), which facilitates nuclear import by binding importin-α (Imp-α). This pathway is indispensable to many cellular processes and is extensively used by viral proteins that function within the nucleus of infected cells. Based on this, I demonstrated that the classical nuclear import pathway inhibitor, ivermectin, can inhibit replication of human adenovirus. Treatment with ivermectin blocks nuclear localization of the E1A protein, an essential viral nuclear protein …
Lymphocyte Proteomics For Monitoring Long Term Immune System Dynamics, Michaela Mccown
Lymphocyte Proteomics For Monitoring Long Term Immune System Dynamics, Michaela Mccown
Undergraduate Honors Theses
Time dependent change in lymphocytes provides a necessary background for monitoring the development of Chronic Lymphocytic Leukemia from asymptomatic to malignant. Several bulk proteomics studies characterize differences between tumor cells and healthy B cells, yet the transition to symptomatic disease is not well understood. This could be shown by a longitudinal study beginning with asymptomatic patients if the rare tumor cells in early stages can be isolated from small volume blood draws and effectively characterized with few cells, such as was done here using healthy B cells to provide a baseline for such studies to discriminate routine fluctuation from pathogenic …
Molecular Responses To Catastrophic Molting In A Wild Marine Mammal, Anna Keith
Molecular Responses To Catastrophic Molting In A Wild Marine Mammal, Anna Keith
University of the Pacific Theses and Dissertations
While most mammals shed their hair and skin either continuously or seasonally, northern elephant seals (Mirounga angustirostris) undergo an annual catastrophic molt, in which they shed their entire fur and underlying skin layer in the span of just three weeks. Due to the energetic and thermoregulatory constraints of molting and the large distances between their coastal rookeries and foraging grounds, elephant seals must remain on land and fast for the duration of their molt. Previous studies of molting northern elephant seals have examined endocrine and metabolic adjustments to fasting, but not the molecular processes underlying molting. We examined changes in …
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 …