Matching Items (152)
Description
Dire wolves have recently risen to fame as a result of the popular television program Game of Thrones, and thus many viewers know dire wolves as the sigil and loyal companions of the Stark house. Far fewer recognize dire wolves by their scientific name, Canis dirus, or understand the population history of this ‘fearsome wolf’ species that roamed the Americas until the megafaunal mass extinction event of the Late Pleistocene. Although numerous studies have examined the species using morphological and geographical methods, thus far their results have been either inconclusive or contradictory. Remaining questions include the relationships dire wolves share with other members of the Canis genus and the internal structure of their populations. Advancements in ancient DNA recovery methods may make it possible to study dire wolf specimens at the molecular level for the first time and may therefore prove useful in clarifying the answers to these questions. Eighteen dire wolf specimens were collected from across the United States and subjected to ancient DNA extraction, library preparation, amplification and purification, bait preparation and capture, and next-generation sequencing. There was an average of 76.9 unique reads and 5.73% coverage when mapped to the Canis familiaris reference genome in ultraconserved regions of the mitochondrial genome. The results indicate that endogenous ancient DNA was not successfully recovered and perhaps ancient DNA recovery methods have not advanced to the point of retrieving informative amounts of DNA from particularly old, thermally degraded specimens. Nevertheless, the ever-changing nature of ancient DNA research makes it vital to continually test the limitations of the field and suggests that ancient DNA recovery methods will prove useful in illuminating dire wolf population history at some point in the future.
ContributorsSkerry, Katherine Marie (Author) / Stone, Anne (Thesis director) / Amdam, Gro (Committee member) / Larson, Greger (Committee member) / School of Human Evolution and Social Change (Contributor) / School of Nutrition and Health Promotion (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The effect of an anaerobic reductive environment produced by the oxidation of zero valent iron (ZVI) on the microbial reductive dechlorination of trichloroethylene and its applicability to in-situ bioremediation processes was investigated using microcosms and soil column studies. I learned that microbial dechlorination requires a highly reductive environment, as represented by negative values for oxidation-reduction potential (ORP), which can be maintained through the addition of reducing agents such as ZVI, or to a lesser extent, the fermentation of added substrates such as lactate. Microcosm conditions represented distance from an in-situ treatment injection well and contained different types of iron species and dechlorinating bioaugmentation cultures. Diminishing efficacy of microbial reductive dechlorination along a gradient away from the injection zone was observed, characterized by increasing ORP and decreasing pH. Results also suggested that the use of particular biostimulation substrates is key to prioritizing the dechlorination reaction against competing microbial and abiotic processes by supplying electrons needed for microbial dechlorination.
ContributorsMouti, Aatikah (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Delgado, Anca (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Hydrogen is a key indicator of microbial activity in soils/sediments and groundwater because of its role as an electron donor for reducing sulfate and nitrate and carrying out other metabolic processes. The goal of this study was to quantitatively measure the total biological hydrogen demand (TBHD) of soils and sediments in anaerobic environments. We define the total biological hydrogen demand as the sum of all electron acceptors that can be used by hydrogen-oxidizing microorganisms. Three sets of anaerobic microcosms were set up with different soils/sediments, named Carolina, Garden, and ASM. The microcosms included 25g of soil/sediment and 75 mL of anaerobic medium. 10 mL of hydrogen were pulse-fed for 100 days. Hydrogen consumption and methane production were tracked using gas chromatography. Chemical analysis of each soil was performed at the beginning of the experiment to determine the concentration of electron acceptors in the soils/sediments, including nitrate, sulfate, iron and bicarbonate. An analysis of the microbial community was done at t = 0 and at the end of the 100 days to examine changes in the microbial community due to the metabolic processes occurring as hydrogen was consumed. Carolina consumed 9810 43 mol of hydrogen and produced 19,572 2075 mol of methane. Garden consumed 4006 33 mol of hydrogen and produced 7,239 543 mol of methane. Lastly, ASM consumed 1557 84 mol of hydrogen and produced 1,325 715 mol of methane. I conclude that the concentration of bicarbonate initially present in the soil had the most influence over the hydrogen demand and microbial community enrichment. To improve this research, I recommend that future studies include a chemical analysis of final soil geochemistry conditions, as this will provide with a better idea of what pathway the hydrogen is taking in each soil.
ContributorsLuna Aguero, Marisol (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Delgado, Anca (Committee member) / Civil, Environmental and Sustainable Engineering Programs (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Vitellogenin (vg) is a precursor protein of egg yolk in honeybees, but it is also known to have immunological functions. The purpose of this experiment was to determine the effect of vg on the viral load of deformed wing virus (DWV) in worker honey bees (Apis mellifera). I hypothesized that a reduction in vg expression would lead to an increase in the viral load. I collected 180 worker bees and split them into four groups: half the bees were subjected to a vg gene knockdown by injections of double stranded vg RNA, and the rest were injected with green fluorescent protein (gfp) double stranded RNA. Half of each group was thereafter injected with DWV, and half given a sham injection. The rate of mortality in all four groups was higher than expected, leaving only 17 bees total. I dissected these bees' fat bodies and extracted their RNA to test for vg and DWV. PCR results showed that, out of the small group of remaining bees, the levels of vg were not statistically different. Furthermore, both groups of virus-injected bees showed similar viral loads. Because of the high mortality rate bees and the lack of differing levels of vg transcript between experimental and control groups, I could not draw conclusions from these results. The high mortality could be caused by several factors: temperature-induced stress, repeated stress from the two injections, and stress from viral infection. In addition, it is possible that the vg dsRNA batch I used was faulty. This thesis exemplifies that information cannot safely be extracted when loss of sampling units result in a small datasets that do not represent the original sampling population.
ContributorsCrable, Emma Lewis (Author) / Amdam, Gro (Thesis director) / Wang, Ying (Committee member) / Dahan, Romain (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
In Apis mellifera, gustatory responsiveness to sucrose is a good indicator of learning ability \u2014 in that individuals with high sucrose responsiveness will typically form faster, longer-lasting associations with conditioned stimulus than individuals with a low sucrose responsiveness. The purpose of this study was to determine whether experience with olfactory conditioning had lasting effects on gustatory responsiveness. Groups were placed in an environment that would facilitate association of an odor to a sucrose reward, tested for retention, then tested for gustatory responsiveness. Control groups underwent the same testing schedule, but were not exposed to odor in the first environment. There was no significant difference in gustatory responsiveness between the two groups. Mann-Whitney tests were used to analyze the results, and though the mean GRS score was lower among the treatment group there was no significant trend, possibly due to small sample sizes.
ContributorsSeemann, J. H. (Author) / Amdam, Gro (Thesis director) / Smith, Brian (Committee member) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Genetic counseling is a medical field that was established in the 1970s, but whose demand is now growing exponentially due to modern genetic technology. We now have the ability to look into the human genetic code, detect the genotype of individuals, and use this knowledge to our benefit. However, Genetic testing results in a need for new ethical boundaries to be drawn. The idea of the "best possible conditions" of conceiving a child and whether this child has a right to not know are the two major ethical issues that will be focused on in order to analyze the ethical boundary that needs to be drawn for genetic counseling. In order to analyze these ethical issues, a focus group of Arizona State University students was organized. After producing results for the focus group, there are no true conclusions that can be drawn that applied to all of society. The focus group sample size was too small to produce a broad range of results and the participants were all Arizona State University Undergraduate students. However, it did become apparent that knowledge on these ethical issues is crucial in order to ensure they do not hinder the field of genetic counseling. It is predicted that in order to have the best outcome for the field of genetic counseling, genetic counselors themselves need to draw the ethical boundaries for the issues studied.
ContributorsBarker, Samantha (Author) / Amdam, Gro (Thesis director) / Bang, Christofer (Committee member) / Wang, Ying (Committee member) / Barrett, The Honors College (Contributor)
Created2016-05
Description
In the United States, the prevalence of pediatric obesity has increased to 17% in the general population and even more so in the Hispanic pediatric population to 22.4%. These children are at a higher risk for associated comorbidities, including cardiovascular disease and insulin resistance. The purpose of the following study is to determine the effectiveness of the Nutrition and Health Awareness curriculum at reducing childhood obesity by evaluating alterations in the gut microbial composition, diet, and overall health of the students throughout the five-week program. Nutrition and Health Awareness (NHA) is a student organization that strives to reduce the prevalence of obesity, diabetes, and cardiovascular diseases, specifically in children, by providing active nutrition education services through peer mentoring in elementary schools and community programs. This study went through ASU's Institutional Review Board process and all forms were translated into Spanish. The control group maintained their normal routines and the experimental group received the 5 week NHA program and then continued with their normal routines. Anthropometric measures (Body Mass Index, waist-to-hip ratio, and blood pressure), diet measures (Hispanic food frequency questionnaire), fecal swabs, and content surveys were collected on weeks 0, 5, and 8. Contrary to expected, alpha diversity, kilocalorie intake, and macronutrient intake decreased as the study progressed for both the control and experimental groups. Anthropometric measurements were relatively stable. Though not statistically significant, the greatest difference in time points is between weeks 1 and 8. This decrease in alpha diversity and kilocalorie intake could be due to a change in environment since the children started school on week 8. Future implications of this study are that parental involvement is necessary for an effective, sustainable change in these children. More research in different settings is necessary to determine NHA's effectiveness
ContributorsPatel, Kapila Cristina (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Whisner, Corrie (Committee member) / School of Nutrition and Health Promotion (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Microorganisms can produce metabolites in the gut including short chain fatty acids, vitamins, and amino acids. Certain metabolites produced in the gut can affect the brain through changes in neurotransmitter concentrations. Serotonin, a neurotransmitter, is associated with mood, appetite, and sleep. Up to 90% of serotonin synthesis is located in the gut, by human enterochromaffin cells. Bacteria known to biosynthesize tryptophan, precursor to serotonin, include Escherichia coli, Enterococcus and Streptococcus. Tryptophan is synthesized by bacteria with the enzyme tryptophan synthase and requires Vitamin B6 (Pyridoxal). We hypothesize that gut isolates from surgical weight loss patients can enhance tryptophan production, which relies on vitamin B6 availability. Our goal was to isolate bacteria in order to test for tryptophan production and to determine how Vitamin B6 concentrations could affect tryptophan production. We isolated gut bacteria was from successful surgical weight loss patient with selective pressures for Enterobacter isolates and Enterococcus isolates. We tested the isolates were tested to determine if they could biosynthesize tryptophan in-vitro. Bacterial cultures were enriched with yeast and enriched with serine and indole, substrates necessary for tryptophan biosynthesis. We analyzed the supernatant samples for tryptophan production using GC-FID. Bacterial isolates most closely related to E. coli and Klebsiella based on 16S rRNA gene sequences, produced tryptophan in vitro. While under serine & indole media conditions, R1, the isolate most similar to Klebsiella produced more tryptophan than R14, the isolate most similar to E. coli. We tested the R1 isolate with a gradient of vitamin B6 concentrations from 0.02 µg/mL to 0.2 µg/mL to determine its effect on tryptophan production. When less than 0.05 µg/mL of Vitamin B6 was added, tryptophan production at 6 hours was higher than tryptophan production with Vitamin B6 concentrations at 0.05 µg/mL and above. The production and consumption of tryptophan by Klebsiella under 0 µg/mL and 0.02 µg/mL concentrations of Vitamin B6 occurred at a faster rate when compared to concentrations 0.05 µg/mL or higher of Vitamin B6.
ContributorsYee, Emily L. (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Ilhan, Zehra (Committee member) / W. P. Carey School of Business (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Under current climate conditions northern peatlands mostly act as C sinks; however, changes in climate and environmental conditions, can change the soil carbon decomposition cascade, thus altering the sink status. Here I studied one of the most abundant northern peatland types, poor fen, situated along a climate gradient from tundra (Daring Lake, Canada) to boreal forest (Lutose, Canada) to temperate broadleaf and mixed forest (Bog Lake, MN and Chicago Bog, NY) biomes to assess patterns of microbial abundance across the climate gradient. Principal component regression analysis of the microbial community and environmental variables determined that mean annual temperature (MAT) (r2=0.85), mean annual precipitation (MAP) (r2=0.88), and soil temperature (r2=0.77), were the top significant drivers of microbial community composition (p < 0.001). Niche breadth analysis revealed the relative abundance of Intrasporangiaceae, Methanobacteriaceae and Candidatus Methanoflorentaceae fam. nov. to increase when MAT and MAP decrease. The same analysis showed Spirochaetaceae, Methanosaetaceae and Methanoregulaceae to increase in relative abundance when MAP, soil temperature and MAT increased, respectively. These findings indicated that climate variables were the strongest predictors of microbial community composition and that certain taxa, especially methanogenic families demonstrate distinct patterns across the climate gradient. To evaluate microbial production of methanogenic substrates, I carried out High Resolution-DNA-Stable Isotope Probing (HR-DNA-SIP) to evaluate the active portion of the community’s intermediary ecosystem metabolic processes. HR-DNA-SIP revealed several challenges in efficiency of labelling and statistical identification of responders, however families like Veillonellaceae, Magnetospirillaceae, Acidobacteriaceae 1, were found ubiquitously active in glucose amended incubations. Differences in metabolic byproducts from glucose amendments show distinct patterns in acetate and propionate accumulation across sites. Families like Spirochaetaceae and Sphingomonadaceae were only found to be active in select sites of propionate amended incubations. By-product analysis from propionate incubations indicate that the northernmost sites were acetate-accumulating communities.
These results indicate that microbial communities found in poor fen northern peatlands are strongly influenced by climate variables predicted to change under current climate scenarios. I have identified patterns of relative abundance and activity of select microbial taxa, indicating the potential for climate variables to influence the metabolic pathway in which carbon moves through peatland systems.
ContributorsSarno, Analissa Flores (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Childers, Daniel (Committee member) / Arizona State University (Publisher)
Created2022
Description
Dyslexia is a learning disability that negatively affects reading, writing, and spelling development at the word level in 5%-9% of children. The phenotype is variable and complex, involving several potential cognitive and physical concomitants such as sensory dysregulation and immunodeficiencies. The biological pathogenesis is not well-understood. Toward a better understanding of the biological drivers of dyslexia, we conducted the first joint exome and metabolome investigation in a pilot sample of 30 participants with dyslexia and 13 controls. In the metabolite analysis, eight metabolites of interest emerged (pyridoxine, kynurenic acid, citraconic acid, phosphocreatine, hippuric acid, xylitol, 2-deoxyuridine, and acetylcysteine). A metabolite-metabolite interaction analysis identified Krebs cycle intermediates that may be implicated in the development of dyslexia. Gene ontology analysis based on exome variants resulted in several pathways of interest, including the sensory perception of smell (olfactory) and immune system-related responses. In the joint exome and metabolite analysis, the olfactory transduction pathway emerged as the primary pathway of interest. Although the olfactory transduction and Krebs cycle pathways have not previously been described in the dyslexia literature, these pathways have been implicated in other neurodevelopmental disorders including autism spectrum disorder and obsessive-compulsive disorder, suggesting the possibility of these pathways playing a role in dyslexia as well. Immune system response pathways, on the other hand, have been implicated in both dyslexia and other neurodevelopmental disorders.
ContributorsNandakumar, Rohit (Author) / Dinu, Valentin (Thesis director) / Peter, Beate (Committee member) / Barrett, The Honors College (Contributor) / College of Health Solutions (Contributor)
Created2022-05