Mass Spectrometry-based Metabolomics: Considerations for Laboratory Testing

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Description
Metabolomics focuses on the study of metabolic changes occurring in varioussystems and utilizes quantitative and semi-quantitative measurements of multiple metabolites in parallel. Mass spectrometry (MS) is the most ubiquitous platform in this field, as it provides superior sensitivity regarding measurements

Metabolomics focuses on the study of metabolic changes occurring in varioussystems and utilizes quantitative and semi-quantitative measurements of multiple metabolites in parallel. Mass spectrometry (MS) is the most ubiquitous platform in this field, as it provides superior sensitivity regarding measurements of complex metabolic profiles in biological systems. When combined with MS, multivariate statistics and advanced machine learning algorithms provide myriad opportunities for bioinformatics insights beyond simple univariate data comparisons. In this dissertation, the application of MS-based metabolomics is introduced with an emphasis on biomarker discovery for human disease detection. To advance disease diagnosis using MS-based metabolomics, numerous statistical techniques have been implemented in this research including principal component analysis, factor analysis, partial least squares-discriminant analysis (PLS-DA), orthogonal PLS-DA, random forest, receiver operating characteristic analysis, as well as functional pathway/enzyme enrichment analyses. These approaches are highly useful for improving classification sensitivity and specificity related to disease-induced biological variation and can help identify useful biomarkers and potential therapeutic targets. It is also shown that MS-based metabolomics can distinguish between clinical and prodromal disease as well as similar diseases with related symptoms, which may assist in clinical staging and differential diagnosis, respectively. Additionally, MS-based metabolomics is shown to be promising for the early and accurate detection of diseases, thereby improving patient outcomes, and advancing clinical care. Herein, the application of MS methods and chemometric statistics to the diagnosis of breast cancer, coccidioidomycosis (Valley fever), and senile dementia (Alzheimer's disease) are presented and discussed. In addition to presenting original research, previous efforts in biomarker discovery will be synthesized and appraised. A Comment will be offered regarding the state of the science, specifically addressing the inefficient model of repetitive biomarker discovery and the need for increased translational efforts necessary to consolidate metabolomics findings and formalize purported metabolic markers as laboratory developed tests. Various factors impeding the translational throughput of metabolomics findings will be carefully considered with respect to study design, statistical analysis, and regulation of biomedical diagnostics. Importantly, this dissertation will offer critical insights to advance metabolomics from a scientific field to a practical one including targeted detection, enhanced quantitation, and direct-to-consumer considerations.
Date Created
2022
Agent

Discovering Autoantibodies to Nitrated Proteins in Type 1 Diabetes

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Description
Type 1 diabetes (T1D) is the result of an autoimmune attack against the insulin-producing β-cells of the pancreas causing hyperglycemia and requiring the individual to rely on life-long exogenous insulin. With the age of onset typically occurring in childhood, there

Type 1 diabetes (T1D) is the result of an autoimmune attack against the insulin-producing β-cells of the pancreas causing hyperglycemia and requiring the individual to rely on life-long exogenous insulin. With the age of onset typically occurring in childhood, there is increased physical and emotional stress to the child as well as caregivers to maintain appropriate glucose levels. The majority of T1D patients have antibodies to one or more antigens: insulin, IA-2, GAD65, and ZnT8. Although antibodies are detectable years before symptoms occur, the initiating factors and mechanisms of progression towards β-cell destruction are still not known. The search for new autoantibodies to elucidate the autoimmune process in diabetes has been slow, with proteome level screenings on native proteins only finding a few minor antigens. Post-translational modifications (PTM)—chemical changes that occur to the protein after translation is complete—are an unexplored way a self-protein could become immunogenic. This dissertation presents the first large sale screening of autoantibodies in T1D to nitrated proteins. The Contra Capture Protein Array (CCPA) allowed for fresh expression of hundreds of proteins that were captured on a secondary slide by tag-specific ligand and subsequent modification with peroxynitrite. The IgG and IgM humoral response of 48 newly diagnosed T1D subjects and 48 age-matched controls were screened against 1632 proteins highly or specifically expressed in pancreatic cells. Top targets at 95% specificity were confirmed with the same serum samples using rapid antigenic protein in situ display enzyme-linked immunosorbent assay (RAPID ELISA) a modified sandwich ELISA employing the same cell-free expression as the CCPA. For validation, 8 IgG and 5 IgM targets were evaluated with an independent serum sample set of 94 T1D subjects and 94 controls. The two best candidates at 90% specificity were estrogen receptor 1 (ESR1) and phosphatidylinositol 4-kinase type 2 beta (PI4K2B) which had sensitivities of 22% (p=.014) and 25% (p=.045), respectively. Receiver operating characteristic (ROC) analyses found an area under curve (AUC) of 0.6 for ESR1 and 0.58 for PI4K2B. These studies demonstrate the ability and value for high-throughput autoantibody screening to modified antigens and the frequency of Type 1 diabetes.
Date Created
2022
Agent

Relationships Between Erythrocyte Osmotic Fragility and Vitamin C Nutriture in Adults with or without Type 2 Diabetes

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Description
Diabetes is the 7th leading cause of death globally. In 2018, 34.2 million Americans had type 2 diabetes. Many symptoms of diabetes are similar to those of scurvy or vitamin C deficiency. Vitamin C marginality and inadequacy are more prevalent

Diabetes is the 7th leading cause of death globally. In 2018, 34.2 million Americans had type 2 diabetes. Many symptoms of diabetes are similar to those of scurvy or vitamin C deficiency. Vitamin C marginality and inadequacy are more prevalent in Type 2 Diabetes/prediabetes than with normal glucose tolerance. Intracellular vitamin C inadequacy is suspected due to competition between dehydroascorbic acid and glucose at GLUT 1 and 3 cellular receptors. Erythrocyte osmotic fragility is noted in Gulo -/- knockout mice unable to synthesize endogenous vitamin C. The ascorbate deficient red blood cells presented with low cytoskeletal B-spectrin, spherocyte appearance, and impaired deformability. This cross-sectional study investigated the relationships between diabetes status, erythrocyte osmotic fragility, and serum vitamin C status. Participants were aged 18-65, non-smoking, reported no unresolved health complications, and denied prior vitamin C supplementation. Those with T2D indicated diagnosis of >1 year. All participants provided written informed consent and the study was approved by the local Institutional Review Board in January 2021. Participants provided one fasted blood sample. Erythrocyte osmotic fragility was measured via UV/Vis spectrophotometry with various concentrations of sodium chloride (0.85% - 0.10%) to induce osmotic stress. In addition, plasma was extracted and mixed 1:1 with 10% (w/v) metaphosphoric acid in 2 mmol/L disodium EDTA and centrifuged. The supernatant was stored at -80°C until analysis with isocratic reverse-phase UV-HPLC separation. Participant characteristics did not differ significantly between groups apart from age (p< 0.01) and HbA1c (p=0.002). Data are presented for adults with T2D (n=14; 36% female; 55.5±8.2 y; 31.5±9.0 kg/m2; HbA1c: 7.4±1.9%; plasma vitamin C: 36.0±12.2 uM) and without T2D (n=16; 69% female; 38.7±13.5 y; 26.8±6.6 kg/m2; A1c: 5.4±0.3%; plasma vitamin C: 34.8±10.9uM). Erythrocyte osmotic fragility was significantly elevated (+4.4% hemolysis) in adults without T2D at 0.35% saline (p=0.039). Greater VC status (>30 uM) was associated with lower hemolysis at 0.35% NaCl (p=0.031). Erythrocyte osmotic stability was linked to greater vitamin C intake at 0.20% saline in those without T2D (p =0.019). In this pilot study, vitamin C status did not differ significantly by diabetes status. Vitamin C status was directly linked to erythrocyte osmotic stability in adults without T2D.
Date Created
2022
Agent

Nitrogen Balance and Protein Intake at the RDA in Inactive Male Vegans

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Description
Background: Vegan and vegetarian diets have gained in popularity in recent years. Stated reasons for this include some possible health benefits and concerns of animal welfare. Though considered to be nutritionally adequate, questions remain over whether current protein recommendations of

Background: Vegan and vegetarian diets have gained in popularity in recent years. Stated reasons for this include some possible health benefits and concerns of animal welfare. Though considered to be nutritionally adequate, questions remain over whether current protein recommendations of 0.8 g/kg/d are sufficient to maintain body processes and growth. Protein is unique in that it is the only macronutrient that contains nitrogen. Its status can be determined through nitrogen balance analysis of the urine if protein content of the diet is known. Nitrogen balance is considered the gold standard for determining protein intake requirements. A negative balance indicates a catabolic state, whereas a positive nitrogen balance is seen during anabolism. In healthy people, nitrogen equilibrium is desired under normal circumstances. This equilibrium reflects the net synthesis and breakdown of proteins. While nitrogen balance techniques have been used for decades, currently, there are no known studies measuring nitrogen balance and protein intake in strict vegans. Methods: Twenty vegan, inactive, male participants were recruited and received a 5-day eucaloric diet with a known protein content held constant at 0.8 g/kg/d. On day five, 24-hour urine was collected by participants and aliquoted for future analysis. Nitrogen content of the urine was determined through photometric assay and compared to the known nitrogen content of the diet to calculate nitrogen balance status. Results: Mean absolute nitrogen balance (-1.38 ± 1.22 g/d, effect size = -1.13) was significantly lower than zero (equilibrium) (p < .001). Mean relative nitrogen balance (-18.60 ± 16.96 mg/kg/d, effect size = -1.10) was significantly lower than zero (p < .001). There were no correlations seen between nitrogen balance and age, years as vegan, or fat- free mass. Conclusion: Consuming 0.8 g/kg/d of protein is insufficient to produce nitrogen balance in long-term vegans.
Date Created
2022
Agent

Variation in Plasma Protein Levels in House Finches (Haemorhous mexicanus): Effects of Season, Disease State, and Urbanization

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Description

Bioindicators of wildlife health are useful tools for studying the viability of various organisms and populations, and can include a range of phenotypic variables, such as behavior, body size, and physiological parameters, such as circulating hormones and nutrients. Few studies

Bioindicators of wildlife health are useful tools for studying the viability of various organisms and populations, and can include a range of phenotypic variables, such as behavior, body size, and physiological parameters, such as circulating hormones and nutrients. Few studies have investigated the utility of total plasma protein as a predictor of environmental or nutritional variation among birds, as well as variation across different seasons and life-history stages. Here I examined relationships between plasma protein and season, urbanization, sex, body condition, molt status, and disease state in house finches (Haemorhous mexicanus). I sampled blood from house finches across three seasons (winter, summer and fall 2021) and measured plasma protein levels using a Bradford assay. I also collected data including condition, sex, and poxvirus infection state at capture, as well as fecal samples to assess gut parasitism (coccidiosis). During the fall season I also estimated molt status, as number of actively growing feathers. I found circulating plasma protein concentration to be lower in the fall during molt than during winter or summer. I also found a significant relationship between circulating protein levels and capture site, as well as novel links to molt state and pox presence, with urban birds, those infected with pox, and those in more intense molt having higher protein levels. My results support the hypotheses that plasma protein concentration can be indicative of a bird’s body molt (which demands considerable protein for feather synthesis) and degree of habitat urbanization, although future work is needed to determine why protein levels were higher in virus-infected birds.

Date Created
2022-05
Agent

Differential Expression Profile of Sphingosine-1-Phosphate Receptors in Human Brain Vascular Smooth Muscle Cells and Endothelial Cells Following Hypoxia Plus Glucose Deprivation

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Description

Sphingosine-1-phosphate receptors (S1PRs) and their signaling pathways play an important role in mediating vascular health and function. Upon ligand mediated activation, S1PRs 1-5 couple with diverse heterotrimeric G-protein subunits (Gαi, Gαq/11, Gα12/13), initiating multimodal downstream signaling pathways which result in

Sphingosine-1-phosphate receptors (S1PRs) and their signaling pathways play an important role in mediating vascular health and function. Upon ligand mediated activation, S1PRs 1-5 couple with diverse heterotrimeric G-protein subunits (Gαi, Gαq/11, Gα12/13), initiating multimodal downstream signaling pathways which result in various physiological outcomes in the vasculature, including cell proliferation and migration, barrier integrity preservation or loss, contraction, and inflammation. Specifically, S1PR2 activation has been linked to endothelial activation, barrier integrity loss, and inflammation, whereas S1PR1 activation contributes to barrier integrity preservation, vasodilation, and anti-inflammatory properties. Although the role of S1PRs during pathophysiological conditions such as acute ischemic stroke is under current investigation, the complete S1PR expression profile in the cerebrovasculature following acute ischemic injury has not yet been investigated. Therefore, the present study was aimed to characterize the expression profiles of S1PRs 1-5 in human brain microvascular endothelial cells (HBMECs) and human brain vascular smooth muscle cells (HBVSMCs) following 3h hypoxia plus glucose deprivation (HGD; in vitro ischemic injury) exposure. At the mRNA level, we observed expression of S1PRs 1-5 in HBVSMCs and S1PRs 1-4 in HBMECs. Under basal conditions, we employed real-time RT-PCR and observed that mRNA levels of S1PR1 were highest in expression followed by S1PR3 then S1PR2 in HBMECs. On the other hand, S1PR3 mRNA was the highest followed by S1PR2 then S1PR1 in HBVSMCs. In HBMECs, HGD exposure increased S1PR1 mRNA and protein levels, but decreased S1PR1 mRNA in HBVSMCs. Similarly, HGD induced increased S1PR3 mRNA in HBMECs and decreased S1PR3 mRNA in HBVSMCs. For S1PR2, HGD did not alter mRNA or protein expression in HBMECs but increased mRNA levels in HBVSMCs. These data suggest that acute exposure to HGD appears to differentially regulate expression of S1PRs in HBMECs and HBVSMCs. The differential expression in S1PRs both basally and following HGD exposure may suggest distinct signaling mechanisms at play within the two cerebrovascular cell types, implicating these receptors as potential therapeutic targets following ischemic injury.

Date Created
2022-05
Agent

Back to the future: does previously grown ornamental coloration in male house finches reveal mate quality at the time of pair formation?

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Description

Animals use diverse signal types (e.g. visual, auditory) to honestly advertise their genotypic and/or phenotypic quality to prospective mates or rivals. Behavioral displays and other dynamically updateable signals (e.g. songs, vibrations) can reliably reveal an individual’s quality in real-time, but

Animals use diverse signal types (e.g. visual, auditory) to honestly advertise their genotypic and/or phenotypic quality to prospective mates or rivals. Behavioral displays and other dynamically updateable signals (e.g. songs, vibrations) can reliably reveal an individual’s quality in real-time, but it is unclear whether more fixed traits like feather coloration, which is often developed months before breeding, still reveal an individual’s quality at the time of signal use. To address this gap, we investigated if various indices of health and condition – including body condition (residual body mass), poxvirus infection, degree of habitat urbanization, and circulating levels of ketones, glucose, vitamins, and carotenoids – were related to the expression of male plumage coloration at the start of the spring breeding season in wild male house finches (Haemorhous mexicanus), a species in which many studies have demonstrated a link between plumage redness and the health and condition of individuals at the time the feathers are grown in late summer and autumn. We found that, at the time of pair formation, plumage hue was correlated with body condition, such that redder males were in better condition (i.e. higher residual mass). Also, as in previous studies, we found that rural males had redder plumage; however, urban males had more saturated plumage. In sum, these results reveal that feather coloration developed long before breeding still can be indicative to choosy mates of a male’s current condition and suggest that females who prefer to mate with redder males may also gain proximate material benefits (e.g. better incubation provisioning) by mating with these individuals in good current condition.

Date Created
2021-12
Agent

Where Have the Carotenoids Gone? Physiology of Carotenoid Absorption And Distribution in Birds

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Description
Organisms regularly face the challenge of having to accumulate and allocate limited resources toward life-history traits. However, direct quantification of how resources are accumulated and allocated is rare. Carotenoids are among the best systems for investigating resource allocation, because they

Organisms regularly face the challenge of having to accumulate and allocate limited resources toward life-history traits. However, direct quantification of how resources are accumulated and allocated is rare. Carotenoids are among the best systems for investigating resource allocation, because they are diet-derived and multi-functional. Birds have been studied extensively with regard to carotenoid allocation towards life-history traits, but direct quantification of variation in carotenoid distribution on a whole-organism scale has yet to be done. Additionally, while we know that scavenger receptor B1 (SCARB1) is important for carotenoid absorption in birds, little is known about the factors that predict how SCARB1 is expressed in wild populations. For my dissertation, I first reviewed challenges associated with statistically analyzing tissue distributions of nutrients (nutrient profiles) and tested how tissue carotenoid distributions (carotenoid profiles) varied by sex, season, health state, and coloration in two bird species, house finches (Haemorhous mexicanus) and zebra finches (Taeniopygia guttata). Then, I investigated the relationship between dietary carotenoid availability, relative expression of SCARB1, and extent of carotenoid-based coloration in a comparative study of wood-warblers (Parulidae). In my review of studies analyzing nutrient profiles, I found that multivariate analyses were the most common, but studies rarely reported intercorrelations among nutrient types. In house finches, all tissue carotenoid profiles varied by sex, season, and coloration. For example, males during autumn (molt) had higher concentrations of 3-hydroxyechinenone (the major red carotenoid in sexually attractive male feathers) in most but not all tissues compared to other season and sex combinations. However, the relationship between color and carotenoid profiles depended on the color metric. In zebra finches, only muscle and spleen carotenoid profiles varied between immune-challenged and control birds. In wood-warblers, I found that capacity to absorb carotenoids was positively correlated with the evolution of carotenoid-based coloration but negatively associated with liver carotenoid accumulation. Altogether, my dissertation illustrates (a) the context-dependence of tissue carotenoid profile variation, (b) that carotenoid-based integumentary coloration is a reflection of tissue carotenoid profiles, and (c) that digestive physiology (e.g., carotenoid absorption) is an important consideration in the study of diet and coloration in wild birds.
Date Created
2021
Agent

The Pursuit of Parenthood: Expanding Horizons of Reproductive Physiology and Assisted Reproductive Technologies

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Description
The desire to start a family is something millions of people around the globe strive to achieve. However, many factors such as the societal changes in family planning due to increasing maternal age, use of birth control, and ever-changing lifestyles

The desire to start a family is something millions of people around the globe strive to achieve. However, many factors such as the societal changes in family planning due to increasing maternal age, use of birth control, and ever-changing lifestyles have increased the number of infertility cases seen in the United States each year. Infertility can manifest as a prolonged inability to conceive, or inability to carry a pregnancy full-term. Modern advancements in the field of reproductive medicine have begun to promote the use of Assisted Reproductive Technologies (ART) to circumvent reduced fertility in both men and women. Implementation of techniques such as In Vitro Fertilization, Intracytoplasmic Sperm Injection, and Pre-Implantation Genetic Testing have allowed many couples to conceive. There is continual effort being made towards developing more effective and personalized fertility treatments. This often begins in the form of animal research—a fundamental step in biomedical research. This dissertation examines infertility as a medical condition through the characterization of normal reproductive anatomy and physiology in the introductory overview of reproduction. Specific pathologies of male and female-factor infertility are described, which necessitates the use of ARTs. The various forms of ARTs currently utilized in a clinical setting are addressed including history, preparations, and protocols for each technology. To promote continual advancement of the field, both animal studies and human trials provide fundamental stepping-stones towards the execution of new techniques and protocols. Examples of research conducted for the betterment of human reproductive medicine are explored, including an animal study conducted in mice exploring the role of tyramine in ovulation. With the development and implementation of new technologies and protocols in the field, this also unearths ethical dilemmas that further complicate the addition of new technologies in the field. Combining an extensive review in assisted reproduction, research and clinical fieldwork, this study investigates the history and development of novel research conducted in reproductive medicine and explores the broader implications of new technologies in the field.
Date Created
2021
Agent

Protein Regulators of Lipid and Energy Metabolism

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Description
Lipolysis or hydrolysis of triglyceride (TG) stored within intracellular lipid droplets (LD), is vital to maintaining metabolic homeostasis in mammals. Regulation of lipolysis and subsequent utilization of liberated fatty acids impacts cellular and organismal functions including body fat accumulation and

Lipolysis or hydrolysis of triglyceride (TG) stored within intracellular lipid droplets (LD), is vital to maintaining metabolic homeostasis in mammals. Regulation of lipolysis and subsequent utilization of liberated fatty acids impacts cellular and organismal functions including body fat accumulation and thermogenesis. Adipose triglyceride lipase (ATGL) is the intracellular rate-limiting enzyme responsible for catalyzing hydrolysis of TG to diacylglycerol (DAG), the initial step of the lipolytic reaction. G0/G1 switch gene-2 (G0S2) and hypoxia-inducible gene-2 (HIG2) are selective inhibitors of ATGL. G0S2 facilitates accumulation of TG in the liver and adipose tissue, while HIG2 functions under hypoxic conditions. Sequence analysis and mutagenesis were used to confirm the presence of conserved domains between these proteins, and that these domains are required for efficient binding and inhibition of ATGL. Further analysis revealed a Positive sequence (Pos-Seq)-LD binding motif in G0S2 but not HIG2. The Pos-Seq mediated ATGL-independent localization to LD and was required for achieving maximal inhibition of ATGL activity by G0S2. Identification and mutational analysis of this motif revealed distinct mechanisms for HIG2 and G0S2 LD association. In addition to molecular characterization of known protein inhibitors of lipolysis, an intracellular member of the apolipoprotein L (ApoL) family, ApoL6, was also identified as a LD and mitochondria associated protein expressed in adipose tissue. Brown adipose tissue uses fatty acids as fuel for increasing its energy output as heat during acute responses to cold exposure. A Comprehensive Lab Animal Monitoring System was used to compare heat production at room temperature (RT) and 4oC in transgenic animals overexpressing ApoL6 in brown adipose tissue. Overexpression of ApoL6 delayed utilization of long-chain fatty acids (LCFAs) as a fuel source while promoting an enhanced thermogenic response during initial cold exposure. ApoL6 mediated inhibition of LCFA utilization results from binding of ApoL6 to Mitochondrial Trifunctional Protein (MTP/TFP), which catalyzes mitochondrial β-oxidation. Indirect calorimetry and fasting acute cold exposure experiments suggest the augmented thermogenic profile of ApoL6 transgenic animals is a result of enhanced utilization of medium-chain fatty acids (MCFAs), glucose, and amino acids as fuel sources. Cumulatively these results indicate multiple mechanisms for regulation lipolysis and fatty acid utilization.
Date Created
2021
Agent