Matching Items (361)
Description
Heterochromatin is a repressive chromatin compartment essential for maintaining genomic integrity. A hallmark of heterochromatin is the presence of specialized nonhistone proteins that alter chromatin structure to inhibit transcription and recombination. It is generally assumed that heterochromatin is highly condensed. However, surprisingly little is known about the structure of heterochromatin or its dynamics in solution. In budding yeast, formation of heterochromatin at telomeres and the homothallic silent mating type loci require the Sir3 protein. Here, we use a combination of sedimentation velocity, atomic force microscopy and nucleosomal array capture to characterize the stoichiometry and conformation of Sir3 nucleosomal arrays. The results indicate that Sir3 interacts with nucleosomal arrays with a stoichiometry of two Sir3 monomers per nucleosome. We also find that Sir3 fibres are less compact than canonical magnesium-induced 30 nm fibres. We suggest that heterochromatin proteins promote silencing by ‘coating’ nucleosomal arrays, stabilizing interactions between nucleosomal histones and DNA.
ContributorsSwygert, Sarah G. (Author) / Manning, Benjamin J. (Author) / Senapati, Subhadip (Author) / Kaur, Parminder (Author) / Lindsay, Stuart (Author) / Demeler, Borries (Author) / Peterson, Craig L. (Author) / Biodesign Institute (Contributor) / Single Molecule Biophysics (Contributor)
Created2014-08-01
Description
We studied the microbial community structure of pilot two-stage membrane biofilm reactors (MBfRs) designed to reduce nitrate (NO[subscript 3]–) and perchlorate (ClO[subscript 4]–) in contaminated groundwater. The groundwater also contained oxygen (O[subscript 2]) and sulfate (SO[2 over 4]–), which became important electron sinks that affected the NO[subscript 3]– and ClO[subscript 4]– removal rates. Using pyrosequencing, we elucidated how important phylotypes of each “primary” microbial group, i.e., denitrifying bacteria (DB), perchlorate-reducing bacteria (PRB), and sulfate-reducing bacteria (SRB), responded to changes in electron-acceptor loading. UniFrac, principal coordinate analysis (PCoA), and diversity analyses documented that the microbial community of biofilms sampled when the MBfRs had a high acceptor loading were phylogenetically distant from and less diverse than the microbial community of biofilm samples with lower acceptor loadings. Diminished acceptor loading led to SO[2 over 4]– reduction in the lag MBfR, which allowed Desulfovibrionales (an SRB) and Thiothrichales (sulfur-oxidizers) to thrive through S cycling. As a result of this cooperative relationship, they competed effectively with DB/PRB phylotypes such as Xanthomonadales and Rhodobacterales. Thus, pyrosequencing illustrated that while DB, PRB, and SRB responded predictably to changes in acceptor loading, a decrease in total acceptor loading led to important shifts within the “primary” groups, the onset of other members (e.g., Thiothrichales), and overall greater diversity.
ContributorsOntiveros-Valencia, Aura (Author) / Tang, Youneng (Author) / Zhao, Heping (Author) / Friese, David (Author) / Overstreet, Ryan (Author) / Smith, Jennifer (Author) / Evans, Patrick (Author) / Rittmann, Bruce (Author) / Krajmalnik-Brown, Rosa (Author) / Biodesign Institute (Contributor) / Swette Center for Environmental Biotechnology (Contributor) / Julie Ann Wrigley Global Institute of Sustainability (Contributor) / School of Sustainability (Contributor)
Created2014-07-01
Description
The Combined Activated Sludge-Anaerobic Digestion Model (CASADM) quantifies the effects of recycling anaerobic-digester (AD) sludge on the performance of a hybrid activated sludge (AS)-AD system. The model includes nitrification, denitrification, hydrolysis, fermentation, methanogenesis, and production/utilization of soluble microbial products and extracellular polymeric substances (EPS). A CASADM example shows that, while effluent COD and N are not changed much by hybrid operation, the hybrid system gives increased methane production in the AD and decreased sludge wasting, both caused mainly by a negative actual solids retention time in the hybrid AD. Increased retention of biomass and EPS allows for more hydrolysis and conversion to methane in the hybrid AD. However, fermenters and methanogens survive in the AS, allowing significant methane production in the settler and thickener of both systems, and AD sludge recycle makes methane formation greater in the hybrid system.
ContributorsYoung, Michelle (Author) / Marcus, Andrew (Author) / Rittmann, Bruce (Author) / Biodesign Institute (Contributor) / Swette Center for Environmental Biotechnology (Contributor)
Created2013-08-13
Description
The main purpose of this investigation is to determine the intensity, economic costs, and potential solutions to HIV/AIDS stigma in the United States and Tanzania. In order to accomplish this goal, a literature review was conducted, and an economic model was created to determine how HIV/AIDS treatment deterrence manifests and affects these countries. The results of the economic model suggested that Tanzania suffers greater economic loss due to HIV treatment deterrence than the United States, however, both countries lose a significant portion of GDP due to HIV treatment deterrence. Stigma materializes differently in each country based on a variety of sociocultural factors. These include the demographic groups most affected, the perception of those living with HIV, and how sexually transmitted infections are perceived within communities. The solutions to HIV stigma must be tailored to the country, culture, and context that it arises for interventions to be effective. To further prevent HIV/AIDS stigma and its economic consequences, the etiology of stigma and how it presents in different communities must be understood.
ContributorsSangha, Pooja (Co-author) / Hopewell, Sophia (Co-author) / Baldwin, Marjorie (Thesis director) / Hruschka, Daniel (Committee member) / Department of Psychology (Contributor) / Department of Economics (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
This paper explores the impacts of dam-induced displacement on the health of populations. By the start of the 21st century, an estimated 40-80 million people worldwide were forced to resettle due to the construction of large dams. The process of displacement and resettlement is connected to numerous social impacts on communities such as decreases in household income, natural resources, and social connectivity, but less seems to be known about specific health impacts. Analyzing literature in a formal review allowed for increased understanding about what information already exists in published research regarding the connections between dams, displacement, and health. Some negative health impacts as a result of forced displacement were identified, including increases in infectious disease transmission, depression, and mortality rates as well as losses of food and water sources. However, the small amount of cases found in the literature review when compared to the massive scale of dam development worldwide indicates a gap in knowledge in the dam industry and research field specifically about the health of the vast majority of populations forcibly displaced by dams. Health impacts must be considered and systematically studied in dam projects involving displacement to fully understand the needs of resettled populations and move towards equitable processes in development projects worldwide.
ContributorsWalker, Erika (Author) / Hruschka, Daniel (Thesis director) / Brian, Jennifer (Committee member) / Drake, Alexandria (Committee member) / School of Human Evolution & Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Callithrix penicillata, also known as the Black-tufted marmoset primarily lives in the Brazilian highlands and has had little research conducted on it. For this project I performed a genome curation on the newly assembled genome of this species. The scaffolds obtained by the Dovetail Genomics reads were organized and labeled into chromosomes using the 2014 Callithrix jacchus genome as a reference. Then, using that same genome as a reference, 13 of the chromosomes were reverse complimented to be continuous with the 2014 Callithrix jacchus genome. The N50 statistics of the assembly were calculated and found to be 124 Mb. Quality scores were run for the final genome using referee and visualized with a bar plot, with 99% of sites scoring above 0. Heterozygosity was also calculated and found to be 0.3%. Finally, the final version of the genome was visually compared to the 2017 Callithrix jacchus genome and the GRCh38 human genome. This genome was submitted to the NCBIs database to await further approval.
ContributorsJohnson, Joelle Genevieve (Author) / Cartwright, Reed (Thesis director) / Stone, Anne (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-12
Description
Dielectrophoresis has been shown in the recent past to successfully separate bioparticles of very subtle differences at high resolutions using biophysical forces. In this study, we test the biophysical differences of methicillin resistant and susceptible Staph. aureus that are known to have very similar genomes by using a modified gradient insulator-based dielectrophoresis device (g-iDEP). MRSA is commonly seen in hospitals and is the leading killer of infectious bacteria, claiming the lives of around 10,000 people annually. G-iDEP improves many capabilities within the DEP field including sample size, cost, ease of use and analysis time. This is a promising foundation to creating a more clinically optimized diagnostic tool for both separation and detection of bacteria in the healthcare field. The capture on-set potential for fluorescently tagged MRSA (801 ± 34V) is higher than fluorescently tagged MSSA (610 ± 32V), resulting in a higher electrokinetic to dielectrophoretic mobility ratio for MRSA. Since the strains have proven to be genomically similar through sequencing, it is reasonable to attribute this significant biophysical difference to the added PBP2a enzyme in MRSA. These results are consistent with other bacterial studied within in this device and have proven to be reproducible.
ContributorsSmithers, Jared (Author) / Hayes, Mark (Thesis director) / Woodbury, Neal (Committee member) / School of Criminology and Criminal Justice (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
In Western medicine, the hard sciences have generally been understood as the sole guiding force in patient care and treatment. However, both history and the present day suggest another strong influence on Western medicine: folklore. The term folklore can easily be dismissed as a term representing beliefs and stories of the past, but its relevance transcends time and continues to impact people daily. It “involves values, traditions, ways of thinking and behaving. It’s about art. It’s about people and the way people learn. It helps us learn who we are and how to make meaning in the world around us” (Sims & Stephens, 2011, pp. 1-2). With its wide range of influence, folklore exists as the umbrella term encompassing several categories. Folk beliefs are one of these categories and can develop from “observation, memory, testimony or inference” (Hutton, 1942, p. 83). Given that each of these forms are subject to some sort of error, folk beliefs become “a jumble of the true and the erroneous” (p. 84). Similarly, contemporary legends are narratives that often combine the physical and supernatural world to explain nuances or uncertainty present in the relevant experiences of a people. Folk beliefs can result in the formation of contemporary legends and they can also stem from contemporary legends. These two categories are often associated with subjects that promote fear and uncertainty, and thus play an essential role in navigating folklore’s application to biomedicine. This paper explores the historical and modern effects that folklore has had on two separate maladies: Hansen’s Disease (leprosy) and Major Depressive Disorder (depression). While these conditions do not resemble each other in physical presentations, Hansen’s Disease and Major Depressive Disorder patients both have faced and continue to face discrimination. Andrea Wiley and John Allen’s three-part definition of a malady: society’s perception (sickness), the individual’s experience (illness), and medical professionals’ diagnosis and treatment (disease); was utilized as a tool for analyzing the application of folklore to modern medicine. The way that a society views a particular malady often dictates the sick role expected of a diagnosed individual. Additionally, the public’s view can directly affect medical professionals’ understanding of a malady. This then can drastically shape a patient’s diagnosis, treatment, and prognosis. This anthropological analysis acts as an interdisciplinary bridge between medicine and the humanities.
ContributorsPeake, Ashley E (Co-author) / Peake, Ashley (Co-author) / Ellis, Lawrence (Thesis director) / Hoyt, Heather (Committee member) / Hruschka, Daniel (Committee member) / School of Molecular Sciences (Contributor) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Diabesity is a global epidemic affecting millions worldwide. Diabesity is the term given to the link between obesity and Type II diabetes. It is estimated that ~90% of patients diagnosed with Type II diabetes are overweight or have struggled with excess body fat in the past. Type II diabetes is characterized by insulin resistance which is an impaired response of the body to insulin that leads to high blood glucose levels. Adipose tissue, previously thought of as an inert tissue, is now recognized as a major endocrine organ with an important role in the body's immune response and the development of chronic inflammation. It is speculated that adipose tissue inflammation is a major contributor to insulin resistance particular to Type II diabetes. This literature review explores the popular therapeutic targets and marketed drugs for the treatment of Type II diabetes and their role in decreasing adipose tissue inflammation. rAGE is currently in pre-clinical studies as a possible target to combat adipose tissue inflammation due to its relation to insulin resistance. Metformin and Pioglitazone are two drugs already being marketed that use unique chemical pathways to increase the production of insulin and/or decrease blood glucose levels. Sulfonylureas is one of the first FDA approved drugs used in the treatment of Type II diabetes, however, it has been discredited due to its life-threatening side effects. Bariatric surgery is a form of invasive surgery to rid the body of excess fat and has shown to normalize blood glucose levels. These treatments are all secondary to lifestyle changes, such as diet and exercise which can help halt the progression of Type II diabetes patients.
ContributorsRobles, Alondra Maria (Author) / Woodbury, Neal (Thesis director) / Redding, Kevin (Committee member) / Allen, James (Committee member) / Hendrickson, Kirstin (Committee member) / Sanford School of Social and Family Dynamics (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Menstruation - a stigmatized topic and a social taboo- has led to a lack of menstrual hygiene awareness and improper practices impacting women’s health adversely over generations in India. Akshara aims to increase menstrual hygiene education and reduce stigma in India. A creative children’s illustrated book, and interactive workshop curriculum about menstruation were designed and published in Hindi and English. Menstrual hygiene workshops, utilizing the designed tools, were conducted in Delhi and Ghaziabad, India to over 230 students through NGO partnerships in December 2018. The response to the menstrual hygiene and stigma workshops was overwhelmingly positive, and a significant increase in the knowledge and awareness survey scores was observed after the curriculum teachings and classroom discussions. This evaluation highlights and provides a potential solution path to eradicate the root cause of the menstruation stigma in underprivileged women through education and open conversations on the topic starting at a pivotal young age. The main aim of the workshop was to help eradicate the stigma associated with menstruation and menstrual health in India through education.
ContributorsBhalla, Jahnavi (Co-author) / Dani, Advika (Co-author) / Schuster, Roseanne (Thesis director) / Hruschka, Daniel (Thesis director) / School of Molecular Sciences (Contributor) / School of Human Evolution & Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05