Matching Items (4)
Filtering by
- All Subjects: Diabetes
- Language: English
- Creators: LaBaer, Joshua
- Resource Type: Text
Description
This dissertation investigates the condition of skeletal muscle insulin resistance using bioinformatics and computational biology approaches. Drawing from several studies and numerous data sources, I have attempted to uncover molecular mechanisms at multiple levels. From the detailed atomistic simulations of a single protein, to datamining approaches applied at the systems biology level, I provide new targets to explore for the research community. Furthermore I present a new online web resource that unifies various bioinformatics databases to enable discovery of relevant features in 3D protein structures.
ContributorsMielke, Clinton (Author) / Mandarino, Lawrence (Committee member) / LaBaer, Joshua (Committee member) / Magee, D. Mitchell (Committee member) / Dinu, Valentin (Committee member) / Willis, Wayne (Committee member) / Arizona State University (Publisher)
Created2013
Description
The pathogenesis of type 1 diabetes (T1D) is still not fully understood in the scientific community. Evidence has shown that viral infections are one of the important environmental factors associated with the disease development. Seven of the top T1D related viruses were selected to study the prevalence of viral humoral response in T1D patients using our innovative protein array platform called Nucleic Acid Programmable Protein Array (NAPPA). In this study, each viral gene was individually captured using various PCR based techniques, cloned into a protein expression vector, and assembled as the first version of T1D viral protein array. Humoral responses of IgG, IgA, and IgM were examined. Although each class of immunoglobulin generated a wide-range of reactivity, responses to various viral proteins from different proteins were observed. In summary, we captured most of the T1D related viral genes, established viral protein expression on the protein array, and displayed the serum response on the viral protein array. The successful progress will help to fulfill the long term goal of testing the viral infection hypothesis in T1D development.
ContributorsDavis, Amy Darlene (Author) / LaBaer, Joshua (Thesis director) / Qiu, Ji (Committee member) / Desi, Paul (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2013-05
Description
Type 2 diabetes mellitus (T2DM) is a life-long disease that affects over 27 million individuals in the United States alone. There are many different risk factors and pre-indicators of T2DM. One of them is insulin resistance. Insulin resistance occurs when the body is unable to appropriately respond to insulin. This in turn leads to increased levels of glucose and insulin in the bloodstream. Unlike T2DM, insulin resistance is a reversible diagnosis. The purpose of this project was to identify the most influential genetic and dietary factors of insulin resistance and to see if individuals have some extent of control to possibly avoid the diagnosis of insulin resistance and possibly T2DM entirely.
A total of 26 human subjects were used in this study. Each subject was classified as either lean or obese, according to their BMI measurement. First, the subjects underwent an oral glucose tolerance test. Blood samples were taken to measure glucose levels in the blood. After the test subject characteristics for each subject was obtained. These included age, BMI, body fat percentage, fat free mass (FFM), height, total mass, waist circumference, hip circumference, and waist to hip ratio. After the subject characteristics and blood glucose were measured the blood samples taken previously were then centrifuged, and the blood plasma was extracted. The blood plasma was then used to undergo an Insulin ELISA test. After extensive analysis, the Matsuda Index of each subject was obtained. Subjects with a Matsuda value of 6.0 or under were considered insulin resistant while subjects with a Matsuda value higher than 6.0 were considered insulin sensitive. Subjects were also required to submit a dietary record over the course of three days. The food intake was then put into a food processing software which gave a daily average of the macro and micro nutrients for each subject. Both the subject and dietary values were put into a multiple regression with a significance factor of p < 0.5 to see which factors contributed most to the Matsuda value.
It was found that BMI, height, total mass, insulin and fat free mass, all of which were subject characteristics, were considered to be significant. Some of these factors an individual has no control over, such as height and insulin. However other factors such as BMI, total mass and fat free mass can be affected by both a healthy diet and frequent exercise. This study validated that diet and physical activity can greatly influence an individual’s susceptibility to insulin resistance and ultimately T2DM.
A total of 26 human subjects were used in this study. Each subject was classified as either lean or obese, according to their BMI measurement. First, the subjects underwent an oral glucose tolerance test. Blood samples were taken to measure glucose levels in the blood. After the test subject characteristics for each subject was obtained. These included age, BMI, body fat percentage, fat free mass (FFM), height, total mass, waist circumference, hip circumference, and waist to hip ratio. After the subject characteristics and blood glucose were measured the blood samples taken previously were then centrifuged, and the blood plasma was extracted. The blood plasma was then used to undergo an Insulin ELISA test. After extensive analysis, the Matsuda Index of each subject was obtained. Subjects with a Matsuda value of 6.0 or under were considered insulin resistant while subjects with a Matsuda value higher than 6.0 were considered insulin sensitive. Subjects were also required to submit a dietary record over the course of three days. The food intake was then put into a food processing software which gave a daily average of the macro and micro nutrients for each subject. Both the subject and dietary values were put into a multiple regression with a significance factor of p < 0.5 to see which factors contributed most to the Matsuda value.
It was found that BMI, height, total mass, insulin and fat free mass, all of which were subject characteristics, were considered to be significant. Some of these factors an individual has no control over, such as height and insulin. However other factors such as BMI, total mass and fat free mass can be affected by both a healthy diet and frequent exercise. This study validated that diet and physical activity can greatly influence an individual’s susceptibility to insulin resistance and ultimately T2DM.
ContributorsBrinkerhoff, Catalina Marie (Author) / Katsanos, Christos (Thesis director) / Shaffer, Zachary (Committee member) / College of Health Solutions (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by progressive autoimmune destruction of insulin-producing pancreatic β-cells. Genetic, immunological and environmental factors contribute to T1D development. The focus of this dissertation is to track the humoral immune response in T1D by profiling autoantibodies (AAbs) and anti-viral antibodies using an innovative protein array platform called Nucleic Acid Programmable Protein Array (NAPPA).
AAbs provide value in identifying individuals at risk, stratifying patients with different clinical courses, improving our understanding of autoimmune destructions, identifying antigens for cellular immune response and providing candidates for prevention trials in T1D. A two-stage serological AAb screening against 6,000 human proteins was performed. A dual specificity tyrosine-phosphorylation-regulated kinase 2 (DYRK2) was validated with 36% sensitivity at 98% specificity by an orthogonal immunoassay. This is the first systematic screening for novel AAbs against large number of human proteins by protein arrays in T1D. A more comprehensive search for novel AAbs was performed using a knowledge-based approach by ELISA and a screening-based approach against 10,000 human proteins by NAPPA. Six AAbs were identified and validated with sensitivities ranged from 16% to 27% at 95% specificity. These two studies enriched the T1D “autoantigenome” and provided insights into T1D pathophysiology in an unprecedented breadth and width.
The rapid rise of T1D incidence suggests the potential involvement of environmental factors including viral infections. Sero-reactivity to 646 viral antigens was assessed in new-onset T1D patients. Antibody positive rate of EBV was significantly higher in cases than controls that suggested a potential role of EBV in T1D development. A high density-NAPPA platform was demonstrated with high reproducibility and sensitivity in profiling anti-viral antibodies.
This dissertation shows the power of a protein-array based immunoproteomics approach to characterize humoral immunoprofile against human and viral proteomes. The identification of novel T1D-specific AAbs and T1D-associated viruses will help to connect the nodes in T1D etiology and provide better understanding of T1D pathophysiology.
AAbs provide value in identifying individuals at risk, stratifying patients with different clinical courses, improving our understanding of autoimmune destructions, identifying antigens for cellular immune response and providing candidates for prevention trials in T1D. A two-stage serological AAb screening against 6,000 human proteins was performed. A dual specificity tyrosine-phosphorylation-regulated kinase 2 (DYRK2) was validated with 36% sensitivity at 98% specificity by an orthogonal immunoassay. This is the first systematic screening for novel AAbs against large number of human proteins by protein arrays in T1D. A more comprehensive search for novel AAbs was performed using a knowledge-based approach by ELISA and a screening-based approach against 10,000 human proteins by NAPPA. Six AAbs were identified and validated with sensitivities ranged from 16% to 27% at 95% specificity. These two studies enriched the T1D “autoantigenome” and provided insights into T1D pathophysiology in an unprecedented breadth and width.
The rapid rise of T1D incidence suggests the potential involvement of environmental factors including viral infections. Sero-reactivity to 646 viral antigens was assessed in new-onset T1D patients. Antibody positive rate of EBV was significantly higher in cases than controls that suggested a potential role of EBV in T1D development. A high density-NAPPA platform was demonstrated with high reproducibility and sensitivity in profiling anti-viral antibodies.
This dissertation shows the power of a protein-array based immunoproteomics approach to characterize humoral immunoprofile against human and viral proteomes. The identification of novel T1D-specific AAbs and T1D-associated viruses will help to connect the nodes in T1D etiology and provide better understanding of T1D pathophysiology.
ContributorsBian, Xiaofang (Author) / LaBaer, Joshua (Thesis advisor) / Mandarino, Lawrence (Committee member) / Chang, Yung (Committee member) / Arizona State University (Publisher)
Created2015