Matching Items (229)
Description
Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative diseases are commonly misdiagnosed in live human subjects. Postmortem histopathological examination of a donor's brain, combined with premortem clinical criteria, is often the most robust approach to correctly classify an individual as a disease-specific case or unaffected control. We describe the establishment of primary dermal fibroblasts cells lines from 28 autopsy donors. These fibroblasts were used to examine the proliferative effects of establishment protocol, tissue amount, biopsy site, and donor age. As proof-of-principle, iPSCs were generated from fibroblasts from a 75-year-old male, whole body donor, defined as an unaffected neurological control by both clinical and histopathological criteria. To our knowledge, this is the first study describing autopsy donor-derived somatic cells being used for iPSC generation and subsequent neural differentiation. This unique approach also enables us to compare iPSC-derived cell cultures to endogenous tissues from the same donor. We utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of in vitro-differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed in vitro progression towards the reference brain tissue, supported by (i) a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) (P < 0.05), consistent with the transcriptional complexity of the brain, (ii) an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue, and (iii) a significant decreasing monotonic correlation between the days of our timecourse and the percent of in vitro to brain-tissue differences (P < 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. These studies support the utility of autopsy donors' somatic cells for iPSC-based neurological disease models, and provide evidence that in vitro neural differentiation can result in physiologically progression.
ContributorsHjelm, Brooke E (Author) / Craig, David W. (Thesis advisor) / Wilson-Rawls, Norma J. (Thesis advisor) / Huentelman, Matthew J. (Committee member) / Mason, Hugh S. (Committee member) / Kusumi, Kenro (Committee member) / Arizona State University (Publisher)
Created2013
Description
The body is capable of regulating hunger in several ways. Some of these hunger regulation methods are innate, such as genetics, and some, such as the responses to stress and to the smell of food, are innate but can be affected by body conditions such as BMI and physical activity. Further, some hunger regulation methods stem from learned behaviors originating from cultural pressures or parenting styles. These latter regulation methods for hunger can be grouped into the categories: emotion, environment, and physical. The factors that regulate hunger can also influence the incidence of disordered eating, such as eating in the absence of hunger (EAH). Eating in the absence of hunger can occur in one of two scenarios, continuous EAH or beginning EAH. College students are at a particularly high risk for EAH and weight gain due to stress, social pressures, and the constant availability of energy dense and nutrient poor food options. The purpose of this study is to validate a modified EAH-C survey in college students and to discover which of the three latent factors (emotion, environment, physical) best predicts continual and beginning EAH. To do so, a modified EAH-C survey, with additional demographic components, was administered to students at a major southwest university. This survey contained two questions, one each for continuing and beginning EAH, regarding 14 factors related to emotional, physical, or environmental reasons that may trigger EAH. The results from this study revealed that the continual and beginning EAH surveys displayed good internal consistency reliability. We found that for beginning and continuing EAH, although emotion is the strongest predictor of EAH, all three latent factors are significant predictors of EAH. In addition, we found that environmental factors had the greatest influence on an individual's likelihood to continue to eat in the absence of hunger. Due to statistical abnormalities and differing numbers of factors in each category, we were unable to determine which of the three factors exerted the greatest influence on an individual's likelihood to begin eating in the absence of hunger. These results can be utilized to develop educational tools aimed at reducing EAH in college students, and ultimately reducing the likelihood for unhealthy weight gain and health complications related to obesity.
ContributorsGoett, Taylor (Author) / Johnston, Carol (Thesis advisor) / Lee, Chong (Committee member) / Lespron, Christy (Committee member) / Arizona State University (Publisher)
Created2013
Description
In October, 2009, participants of the Arizona Special Supplemental Nutrition Program for Women, Infants and Children (WIC) began receiving monthly Cash Value Vouchers (CVV) worth between six and 10 dollars towards the purchase of fresh fruits and vegetables. Data from the Arizona Department of Health Services (ADHS) showed CVV redemption rates in the first two years of the program were lower than the national average of 77% redemption. In response, the ADHS WIC Food List was expanded to also include canned and frozen fruits and vegetables. More recent data from ADHS suggest that redemption rates are improving, but variably exist among different WIC sub-populations. The purpose of this project was to identify themes related to the ease or difficulty of WIC CVV use amongst different categories of low-redeeming WIC participants. A total of 8 focus groups were conducted, four at a clinic in each of two Valley cities: Surprise and Mesa. Each of the four focus groups comprised one of four targeted WIC participant categories: pregnant, postpartum, breastfeeding, and children with participation ranging from 3-9 participants per group. Using the general inductive approach, recordings of the focus groups were transcribed, hand-coded and uploaded into qualitative analysis software resulting in four emergent themes including: interactions and shopping strategies, maximizing WIC value, redemption issues, and effect of rule change. Researchers identified twelve different subthemes related to the emergent theme of interactions and strategies to improve their experience, including economic considerations during redemption. Barriers related to interactions existed that made their purchase difficult, most notably anger from the cashier and other shoppers. However, participants made use of a number of strategies to facilitate WIC purchases or extract more value out of WIC benefits, such as pooling their CVV. Finally, it appears that the fruit and vegetable rule change was well received by those who were aware of the change. These data suggest a number of important avenues for future research, including verifying these themes are important within a larger, representative sample of Arizona WIC participants, and exploring strategies to minimize barriers identified by participants, such as use of electronic benefits transfer-style cards (EBT).
ContributorsBertmann, Farryl M. W (Author) / Wharton, Christopher (Christopher Mack), 1977- (Thesis advisor) / Ohri-Vachaspati, Punam (Committee member) / Johnston, Carol (Committee member) / Hampl, Jeffrey (Committee member) / Dixit-Joshi, Sujata (Committee member) / Barroso, Cristina (Committee member) / Arizona State University (Publisher)
Created2013
Description
Random peptide microarrays are a powerful tool for both the treatment and diagnostics of infectious diseases. On the treatment side, selected random peptides on the microarray have either binding or lytic potency against certain pathogens cells, thus they can be synthesized into new antimicrobial agents, denoted as synbodies (synthetic antibodies). On the diagnostic side, serum containing specific infection-related antibodies create unique and distinct "pathogen-immunosignatures" on the random peptide microarray distinct from the healthy control serum, and this different mode of binding can be used as a more precise measurement than traditional ELISA tests. My thesis project is separated into these two parts: the first part falls into the treatment side and the second one focuses on the diagnostic side. My first chapter shows that a substitution amino acid peptide library helps to improve the activity of a recently reported synthetic antimicrobial peptide selected by the random peptide microarray. By substituting one or two amino acids of the original lead peptide, the new substitutes show changed hemolytic effects against mouse red blood cells and changed potency against two pathogens: Staphylococcus aureus and Pseudomonas aeruginosa. Two new substitutes are then combined together to form the synbody, which shows a significantly antimicrobial potency against Staphylococcus aureus (<0.5uM). In the second chapter, I explore the possibility of using the 10K Ver.2 random peptide microarray to monitor the humoral immune response of dengue. Over 2.5 billion people (40% of the world's population) live in dengue transmitting areas. However, currently there is no efficient dengue treatment or vaccine. Here, with limited dengue patient serum samples, we show that the immunosignature has the potential to not only distinguish the dengue infection from non-infected people, but also the primary dengue infection from the secondary dengue infections, dengue infection from West Nile Virus (WNV) infection, and even between different dengue serotypes. By further bioinformatic analysis, we demonstrate that the significant peptides selected to distinguish dengue infected and normal samples may indicate the epitopes responsible for the immune response.
ContributorsWang, Xiao (Author) / Johnston, Stephen Albert (Thesis advisor) / Blattman, Joseph (Committee member) / Arntzen, Charles (Committee member) / Arizona State University (Publisher)
Created2013
Description
Vaccinia virus (VACV) is the current vaccine for the highly infectious smallpox disease. Since the eradication of smallpox, VACV has been developed extensively as a heterologous vaccine vector for several pathogens. However, due to the complications associated with this replication competent virus, the safety and efficacy of VACV vaccine vector has been reevaluated. To evaluate the safety and efficacy of VACV, we study the interactions between VACV and the host innate immune system, especially the type I interferon (IFN) signaling pathways. In this work, we evaluated the role of protein kinase R (PKR) and Adenosine Deaminase Acting on RNA 1(ADAR1), which are induced by IFN, in VACV infection. We found that PKR is necessary but is not sufficient to activate interferon regulatory factor 3 (IRF3) in the induction of type I IFN; and the activation of the stress-activated protein kinase/ c-Jun NH2-terminal kinase is required for the PKR-dependent activation of IRF3 during VACV infection. Even though PKR was found to have an antiviral effect in VACV, ADAR1 was found to have a pro-viral effect by destabilizing double stranded RNA (dsRNA), rescuing VACVΔE3L, VACV deleted of the virulence factor E3L, when provided in trans. With the lessons we learned from VACV and host cells interaction, we have developed and evaluated a safe replication-competent VACV vaccine vector for HIV. Our preliminary results indicate that our VACV vaccine vector can still induce the IFN pathway while maintaining the ability to replicate and to express the HIV antigen efficiently. This suggests that this VACV vector can be used as a safe and efficient vaccine vector for HIV.
ContributorsHuynh, Trung Phuoc (Author) / Jacobs, Bertram L (Thesis advisor) / Hogue, Brenda (Committee member) / Chang, Yung (Committee member) / Ugarova, Tatiana (Committee member) / Arizona State University (Publisher)
Created2013
Description
There are several visual dimensions of food that can affect food intake, example portion size, color, and variety. This dissertation elucidates the effect of number of pieces of food on preference and amount of food consumed in humans and motivation for food in animals. Chapter 2 Experiment 1 showed that rats preferred and also ran faster for multiple pieces (30, 10 mg pellets) than an equicaloric, single piece of food (300 mg) showing that multiple pieces of food are more rewarding than a single piece. Chapter 2 Experiment 2 showed that rats preferred a 30-pellet food portion clustered together rather than scattered. Preference and motivation for clustered food pieces may be interpreted based on the optimal foraging theory that animals prefer foods that can maximize energy gain and minimize the risk of predation. Chapter 3 Experiment 1 showed that college students preferred and ate less of a multiple-piece than a single-piece portion and also ate less in a test meal following the multiple-piece than single-piece portion. Chapter 3 Experiment 2 replicated the results in Experiment 1 and used a bagel instead of chicken. Chapter 4 showed that college students given a five-piece chicken portion scattered on a plate ate less in a meal and in a subsequent test meal than those given the same portion clustered together. This is consistent with the hypothesis that multiple pieces of food may appear like more food because they take up a larger surface area than a single-piece portion. All together, these studies show that number and surface area occupied by food pieces are important visual cues determining food choice in animals and both food choice and intake in humans.
ContributorsBajaj, Devina (Author) / Phillips, Elizabeth D. (Thesis advisor) / Cohen, Adam (Committee member) / Johnston, Carol (Committee member) / Bimonte-Nelson, Heather A. (Committee member) / Arizona State University (Publisher)
Created2013
Description
Well-established model systems exist in four out of the seven major classes of vertebrates. These include the mouse, chicken, frog and zebrafish. Noticeably missing from this list is a reptilian model organism for comparative studies between the vertebrates and for studies of biological processes unique to reptiles. To help fill in this gap the green anole lizard, Anolis carolinensis, is being adapted as a model organism. Despite the recent release of the complete genomic sequence of the A. carolinensis, the lizard lacks some resources to aid researchers in their studies. Particularly, the lack of transcriptomic resources for lizard has made it difficult to identify genes complete with alternative splice forms and untranslated regions (UTRs). As part of this work the genome annotation for A. carolinensis was improved through next generation sequencing and assembly of the transcriptomes from 14 different adult and embryonic tissues. This revised annotation of the lizard will improve comparative studies between vertebrates, as well as studies within A. carolinensis itself, by providing more accurate gene models, which provide the bases for molecular studies. To demonstrate the utility of the improved annotations and reptilian model organism, the developmental process of somitogenesis in the lizard was analyzed and compared with other vertebrates. This study identified several key features both divergent and convergent between the vertebrates, which was not previously known before analysis of a reptilian model organism. The improved genome annotations have also allowed for molecular studies of tail regeneration in the lizard. With the annotation of 3' UTR sequences and next generation sequencing, it is now possible to do expressional studies of miRNA and predict their mRNA target transcripts at genomic scale. Through next generation small RNA sequencing and subsequent analysis, several differentially expressed miRNAs were identified in the regenerating tail, suggesting miRNA may play a key role in regulating this process in lizards. Through miRNA target prediction several key biological pathways were identified as potentially under the regulation of miRNAs during tail regeneration. In total, this work has both helped advance A. carolinensis as model system and displayed the utility of a reptilian model system.
ContributorsEckalbar, Walter L (Author) / Kusumi, Kenro (Thesis advisor) / Huentelman, Matthew (Committee member) / Rawls, Jeffery (Committee member) / Wilson-Rawls, Norma (Committee member) / Arizona State University (Publisher)
Created2012
Description
Cancer is one of the most serious global diseases. We have focused on cancer immunoprevention. My thesis projects include developing a prophylactic primary and metastatic cancer vaccines, early cancer detection and investigation of genes involved in tumor development. These studies were focused on frame-shift (FS) antigens. The FS antigens are generated by genomic mutations or abnormal RNA processing, which cause a portion of a normal protein to be translated out of frame. The concept of the prophylactic cancer vaccine is to develop a general cancer vaccine that could prevent healthy people from developing different types of cancer. We have discovered a set of cancer specific FS antigens. One of the FS candidates, structural maintenance of chromosomes protein 1A (SMC1A) FS, could start to accumulate at early stages of tumor and be specifically exposed to the immune system by tumor cells. Prophylactic immunization with SMC1A-FS could significantly inhibit primary tumor development in different murine tumor models and also has the potential to inhibit tumor metastasis. The SMC1A-FS transcript was detected in the plasma of the 4T1/BALB/c mouse tumor model. The tumor size was correlated with the transcript ratio of the SMC1A-FS verses the WT in plasma, which could be measured by regular RT-PCR. This unique cancer biomarker has a practical potential for a large population cancer screen, as well as clinical tumor monitoring. With a set of mimotope peptides, antibodies against SMC1A-FS peptide were detected in different cancer patients, including breast cancer, pancreas cancer and lung cancer with a 53.8%, 56.5% and 12.5% positive rate respectively. This suggested that the FS antibody could be a biomarker for early cancer detection. The characterization of SMC1A suggested that: First, the deficiency of the SMC1A is common in different tumors and able to promote tumor initiation and development; second, the FS truncated protein may have nucleolus function in normal cells. Mis-control of this protein may promote tumor development. In summary, we developed a systematic general cancer prevention strategy through the variety immunological and molecular methods. The results gathered suggest the SMC1A-FS may be useful for the detection and prevention of cancer.
ContributorsShen, Luhui (Author) / Johnston, Stephen Albert (Thesis advisor) / Chang, Yung (Committee member) / Miller, Laurence (Committee member) / Sykes, Kathryn (Committee member) / Jacobs, Bertram (Committee member) / Arizona State University (Publisher)
Created2012
Description
Dietary protein is known to increase postprandial thermogenesis more so than carbohydrates or fats, probably related to the fact that amino acids have no immediate form of storage in the body and can become toxic if not readily incorporated into body tissues or excreted. It is also well documented that subjects report greater satiety on high- versus low-protein diets and that subject compliance tends to be greater on high-protein diets, thus contributing to their popularity. What is not as well known is how a high-protein diet affects resting metabolic rate over time, and what is even less well known is if resting metabolic rate changes significantly when a person consuming an omnivorous diet suddenly adopts a vegetarian one. This pilot study sought to determine whether subjects adopting a vegetarian diet would report decreased satiety or demonstrate a decreased metabolic rate due to a change in protein intake and possible increase in carbohydrates. Further, this study sought to validate a new device called the SenseWear Armband (SWA) to determine if it might be sensitive enough to detect subtle changes in metabolic rate related to diet. Subjects were tested twice on all variables, at baseline and post-test. Independent and related samples tests revealed no significant differences between or within groups for any variable at any time point in the study. The SWA had a strong positive correlation to the Oxycon Mobile metabolic cart but due to a lack of change in metabolic rate, its sensitivity was undetermined. These data do not support the theory that adopting a vegetarian diet results in a long-term change in metabolic rate.
ContributorsMoore, Amy (Author) / Johnston, Carol (Thesis advisor) / Appel, Christy (Thesis advisor) / Gaesser, Glenn (Committee member) / Arizona State University (Publisher)
Created2012
Description
Objective: Vinegar consumption studies have demonstrated possible therapeutic effects in reducing HbA1c and postprandial glycemia. The purpose of the study was to closely examine the effects of a commercial vinegar drink on daily fluctuations in fasting glucose concentrations and postprandial glycemia, and on HbA1c, in individuals at risk for Type 2 Diabetes Mellitus (T2D). Design: Thirteen women and one man (21-62 y; mean, 46.0±3.9 y) participated in this 12-week parallel-arm trial. Participants were recruited from a campus community and were healthy and not diabetic by self-report. Participants were not prescribed oral hypoglycemic medications or insulin; other medications were allowed if use was stable for > 3 months. Subjects were randomized to one of two groups: VIN (8 ounces vinegar drink providing 1.5 g acetic acid) or CON (1 vinegar pill providing 0.04 g acetic acid). Treatments were taken twice daily immediately prior to the lunch and dinner meals. Venous blood samples were drawn at trial weeks 0 and 12 to measure insulin, fasting glucose, and HbA1c. Subjects recorded fasting glucose and 2-h postprandial glycemia concentrations daily using a glucometer. Results: The VIN group showed significant reductions in fasting capillary blood glucose concentrations (p=0.05) that were immediate and sustained throughout the duration of the study. The VIN group had reductions in 2-h postprandial glucose (mean change of −7.6±6.8 mg/dL over the 12-week trial), but this value was not significantly different than that for the CON group (mean change of 3.3±5.3 mg/dL over the 12-week trial, p=0.232). HbA1c did not significantly change (p=0.702), but the reduction in HbA1c in the VIN group, −0.14±0.1%, may have physiological relevance. Conclusions: Significant reductions in HbA1c were not observed after daily consumption of a vinegar drink containing 1.5 g acetic acid in non-diabetic individuals. However, the vinegar drink did significantly reduce fasting capillary blood glucose concentrations in these individuals as compared to a vinegar pill containing 0.04 g acetic acid. These results support a therapeutic effect for vinegar in T2D prevention and progression, specifically in high-risk populations.
ContributorsQuagliano, Samantha (Author) / Johnston, Carol (Thesis advisor) / Appel, Christy (Committee member) / Dixon, Kathleen (Committee member) / Arizona State University (Publisher)
Created2013