Life Sciences Commons^™

The Classification Of Basket Neural Cells In The Mammalian Neocortex, Sreya Pudi

Senior Theses

Basket neuronal cells of the mammalian neocortex have been classically categorized into two or more groups. Originally, it was thought that the large and small types are the naturally occurring groups that emerge from reasons that relate to neurobiological function and anatomical position. Later, a study based on anatomical and physiological features of these neurons introduced a third type, the net basket cell which is intermediate in size as compared to the large and small types. In this study, multivariate analysis was used to test the hypothesis that the large and small types are morphologically distinct groups. The results of …

Ahr Expression On Rorc-Expressing Immune Cells Is Essential For I3c-Mediated Protection Against Colitis, Michal C. Williams

Senior Theses

Colitis is an inflammatory bowel disorder (IBD) whose etiology is attributed to modification in the luminal microbiota and dysregulation in the immune response. Indole is a signaling molecule which is naturally produced by gut luminal microbiota. Indole-3- carbinol (I3C) is a compound commonly found in vegetables and a ligand for the aryl hydrocarbon receptor (AhR). Previous studies have detected decreased expression and activation on the AhR receptor in colitis patients, thought to possibly alter gut microbiota metabolism, subsequently promoting colitis. 1 AhR, expressed in a variety of immune and epithelial cells, contributes to gut homeostasis by affecting vital mediators such …

Construction And Analysis Of Three Multi-Partite Synthetic Microbial Communities, Alexander J. Lazzara, Jacob K. Fanning

Honors Theses

Microbial Communities are of interest to molecular biologists hoping to understand the nature of metabolic interactions between co-existing, or possibly mutualistic, organisms. These interactions are ubiquitous in nature, but understanding the molecular mechanisms involved remains challenging and not well understood. Here, we design three tri-partite microbial circuits based on possible interactions among involved microbes, which are discussed and may suggest mutualistic interactions. Carbon and nitrogen molecular pathways and the intracellular metabolism of each microbe is discussed. We present minimal growth media that will ensure that organisms utilize available resources, which may originate from metabolic processes in neighboring microbes, simulating a …

Pectin And Alginate Extraction To Treat Liquid Cafo Manure, Clare Sunderman

Honors Projects

For this project, various extraction methods were used to extract pectin from Pastinaca Sativa and alginate from Macrocystis. These extractions were then dried and used in treating 250mL of manure along with a CaCl₂ or FeCl₃ coagulant. It was found that CaCl₂ was not as effective as FeCl₃ in coagulating manure. But the results obtained suggest that pectin and alginate obtained with a simpler extraction method is just as effective as the highly purified and refined pectin and alginate produced for the food industry, in the treatment of CAFO manure. The liquid portion of the …

Competitive Interactions Among Co-Infecting Symbionts In A Model Animal-Associated Microbiome, Justin L. Pritchett

Chancellor’s Honors Program Projects

No abstract provided.

Density Dependent Growth Of Pseudomonas Fluorescens In The Presence And Absence Of C. Elegans Predation In Liquid Media, Jack Landmann

Honors Theses

The purpose of this study was to understand the predator-prey relationship between C. elegans worms and P. fluorescens bacteria in liquid media. We were aiming to create a predation model of the relationship between these two species.

This study was performed through three experiments. Using 96-well plates, we were able to measure the change in optical density (OD) of these wells and calculate the growth rate. This growth rate was then graphed and analyzed. The first experiment contained P. fluorescens and KB liquid media, this study demonstrated that the bacterial population has a carrying capacity. We were also able to …

Cyclic Fluctuations Of Zooplankton Dynamics In A Tidal Salt-Marsh Basin, Jamaal Jacobs

Senior Theses

Zooplankton are pelagic aquatic animals that are limited in their movements by the water currents around them and are major links in aquatic food webs between primary producers and higher trophic levels. Their populations are temporally and spatially variable, as they are sensitive to changes in salinity, temperature, and dissolved oxygen. This is especially true in highly dynamic environments, like estuaries, where environmental conditions are highly variable across seasonal and daily cycles. In order to examine the variability in zooplankton populations across a tidal cycle, we collected zooplankton samples from North Inlet Estuary at 30-minute intervals over a half tidal …

Evolution And Development Of Staminodes In Paronychia (Caryophyllaceae), Andrea D. Appleton

Honors College Theses

Staminodes are infertile stamens that have evolved numerous times in flowering plants and exhibit a vast array of forms and functions. Variation in staminodes suggests that numerous evolutionary processes underlie their origins, but to understand their how and why they evolved, comparative studies are needed in groups of closely related species. Identifying structures as staminodes is not always straightforward and sometimes requires corroborating phylogenetic and developmental evidence. Staminodial structures in Paronychia (Caryophyllaceae), for example, vary in shape and size and have been referred to as both petals and staminodes, rendering their homology uncertain. The development of staminodes was compared across …

Examining The Mechanistic Roles Of Integrin Alpha-6 In Cancer Metastasis., Chase T. Clark

Honors College Theses

Metastasis- the spread of cancer cells from the primary tumor to the surrounding tissues- is responsible for 90% of cancer deaths. Integrin alpha-6 (ITGA6) is a specific transmembrane cell surface protein that functions in cell surface adhesion and signaling. ITGA6 is upregulated in many types of cancers and promotes the migration and invasion of cancer cells to surrounding tissues. It is my objective to determine the mechanism through which ITGA6 facilitates the migration of cancer cells through the extracellular matrix (ECM). These experiments helped to establish the role of ITGA6 in tumor development and provide focus for possible chemotherapeutic treatment. …

Microsatellites And Their Association With Break Induced Replication, French J. Damewood Iv

Browse all Theses and Dissertations

To study microsatellites instability and their repair pathways a dual fluorescent (DF2) and selectable (ganciclovir sensitive/ thymidine kinase (TK) expressing) cell system was assayed using replication fork stalling agents hydroxyurea and telomestatin. These cell lines carried ectopically integrated microsatellites derived from the Dystrophia Myotonica Protein Kinase (DMPK) gene ((CTG)102 microsatellite), or an 88 bp polypurine/ polypyrimidine (Pu/Py) repeat from the PKD-1 locus, inserted into a FLP recombinase target site. These microsatellites form non-B DNA structures in -vivo and in-vitro causing replication fork stalling and double strand breaks. DF2 myc (CTG)102 -TK cells treated with hydroxyurea were assayed for mutagenesis of …

Analyses Of Coyote (Canis Latrans) Consumption Of Anthropogenic Material And Dietary Composition In Urban And Non-Urban Habitats, Audrey A. Hayes

Browse all Theses and Dissertations

Coyotes are a generalist species that have adapted to nearly every terrestrial habitat in the United States. The species’ success is heavily attributed to their omnivorous diets and tolerance for environments that are regularly disturbed. Because the larger predator species that typically act as apex predators are sensitive to highly fragmented landscapes, the coyote is the functioning apex predator in many ecosystems where large predators, such as wolves, have been extirpated. The coyotes’ ecological role in urban ecosystems has received much attention in the last few decades as the species’ presence in cities and suburbs has increased, along with human-coyote …

Will There Be Changes In Sexually Differentiated Behaviors In Mice Manipulated For The Sry Gene As They Mature Into Adultood?, Subin Joo

CMC Senior Theses

Sexually differentiated behavior has been shown to be affected by both genes and hormones. The discovery of the SRY gene, which codes for the development of testes, lead to the development of the Four Core Genotypes model of mice, and the separation of sex chromosomes and its resulting gonadal hormones. Using the FCG model, this study aims to look at the development of sexually differentiated behavior in mice, and track how it changes throughout their life. FCG mice will be divided into individual and social housing, and repeated experiments carried out to test their reaction to both intact female and …

Cultivating A Stem Investigation: Reading And Task Expectations For Introductory Biology Courses, Tina M. Ballard

Graduate Research Theses & Dissertations

College completion is an important discussion in today’s world with only about 30% of community college students completing their degrees within three years of starting their programs. Especially in the Science, Technology, Engineering, and Math (STEM) fields, students are changing their majors or not completing their degrees for a variety of reasons. Previous research has established that there are high attrition and failure rates for introductory biology courses which may be causing some students to change their majors or not complete their degrees. This multicase study investigated the reading and task demands for introductory biology courses designed for STEM majors …

The Role Of Software Engineering In Bioinformatics, Brendan Sean Lawlor

Theses

This thesis proposes that by applying state-of-the-art software engineering tools, techniques and frameworks to currently recognised challenges in bioinformatics, improved outcomes can be attained in that field. It begins by decomposing software engineering into two categories, namely process and architecture, and choosing two key challenges in the practice of bioinformatics: reproducibility and scalability. The body of the thesis is an exploration of the intersection between these two software engineering categories and these two bioinformatics challenges. The question is asked: Can best practices in professional software engineering be applied to address key issues in the bioinformatics domain, creating positive outcomes? And …

Changes In The Vertical Stratification Of Neotropical Nymphalidae At Forest Edges In Relation To Light And Temperature Conditions, Brian Koji Oye

University of the Pacific Theses and Dissertations

The composition of neotropical fruit-feeding nymphalid butterflies assemblages often varies by location and stratum within a forest. Recent work has shown that vertical stratification in particular may serve as barrier to gene flow, indicating the potential role vertical stratification may play in evolution. At forest edges, the distinction between assemblages has been described to decrease, with species considered to be canopy specialists descending to the forest understory. The similarity in light conditions between the canopy and understory strata at edges or disturbed habitat is hypothesized to be responsible for this phenomenon. We conducted a study using standardized sampling to document …

Examining A Functional Interaction Between Chromatin Remodeler Chd1 And Histone H1 In D. Melanogaster, Breanna Kim

Scripps Senior Theses

Chromodomain-helicase-DNA-binding-protein-1 (CHD1) is a highly conserved ATP- dependent remodeling protein. It is localized to active genes and directs nucleosome spacing, while its loss has been linked to various human diseases, such as human prostate cancer. In Drosophila, CHD1 is important for fertility and wing development, and overexpression of CHD1 leads to severe wing vein defect phenotypes. The Linker Histone H1, which is known for maintaining heterochromatin and is associated with inactive genes, had been previously identified as a possible functional partner of CHD1, though the exact nature of their interaction is unclear. I undertook a genetic approach to examining the …

Determining Environmental Changes Using Time Lapse Photography, Emily Lemasters

Williams Honors College, Honors Research Projects

This paper aims to use photographs throughout several years to observe, examine, and make conclusions on changes occurring at different areas of the Bath Nature Preserve. Throughout the years 2013-2021, photographs have been captured at roughly the same angle at multiple locations in the preserve. These photographs will be placed into a time lapse video and examined to physically see how the environment is changing. Changes to the environment could be natural or as a result of outside factors. By examining these changes, it can be determined if alterations need to be made to help the environment thrive. Two specific …

Composition And Homology In The Taxonomic Classification Of Escherichia Coli, Tanya Irani

Theses and Dissertations (Comprehensive)

As new techniques have been introduced, specifically the possibility of complete genome sequencing, better methods of defining bacterial species have also been proposed. One of the most recently proposed methods, using bioinformatic techniques, is to calculate the average nucleotide identity (ANI) between the homologous genome segments of different isolates. Another method for species discrimination that has been tested successfully is the similarity of DNA compositional signatures. However, in a recent update, DNA signatures split the available Escherichia coli complete genomes into three groups. To check if this result was consistent with such genomes belonging to different species, we tested methods …

Microsatellites And Their Association With Break Induced Replication, French J. Damewood Iv

Browse all Theses and Dissertations

To study microsatellites instability and their repair pathways a dual fluorescent (DF2) and selectable (ganciclovir sensitive/ thymidine kinase (TK) expressing) cell system was assayed using replication fork stalling agents hydroxyurea and telomestatin. These cell lines carried ectopically integrated microsatellites derived from the Dystrophia Myotonica Protein Kinase (DMPK) gene ((CTG)102 microsatellite), or an 88 bp polypurine/ polypyrimidine (Pu/Py) repeat from the PKD-1 locus, inserted into a FLP recombinase target site. These microsatellites form non-B DNA structures in -vivo and in-vitro causing replication fork stalling and double strand breaks. DF2 myc (CTG)102 -TK cells treated with hydroxyurea were assayed for mutagenesis of …

Interleukin-2 Receptor Alpha Nuclear Localization Impacts Vascular Smooth Muscle Cell Function And Phenotype, Kristie Nhi Dinh

Browse all Theses and Dissertations

Atherosclerosis is responsible for 50% of all deaths in western society and is the main cause of cardiovascular diseases (Pahwa et al. 2020). Vascular smooth muscle cells (VSMC) play a vital role in the development of atherosclerotic plaques; this is due to their ability to proliferate and migrate in response to inflammation and damage to arteries’ inner linings. To further understand what causes these cells to proliferate and migrate, our lab has previously found that VSMC express all three subunits of the IL-2 receptor (IL-2R). Out of these three subunits, IL-2Rα appeared to change the most depending on the phenotype …

Characterizing The Effects Of 14-3-3 Isoforms On Alpha-Synuclein Toxicity In A Yeast Model, Angela Marie Braunschweiger

Browse all Theses and Dissertations

The presynaptic protein alpha-synuclein encoded by SNCA is the primary component of Lewy bodies and Lewy neurites which are the histopathological hallmarks of Parkinson’s disease. While the etiology of Parkinson’s remains unclear, SNCA mutations and copy number variations are one of several genes linked to Parkinson’s. The family of highly conserved chaperone proteins 14-3-3 have been shown to co-aggregate and share regions of 40% homology with alpha-synuclein. Mitochondrial dysfunction also plays a role in Parkinson’s disease with abnormalities in mitochondrial respiration due to interference of complex I in the electron transport chain being found in Parkinson’s patients. Alpha-synuclein increases fragmentation …