Life Sciences Commons^™

Comparative Thermal Ecology Of Coastal And Inland Pacific Rattlesnakes (Crotalus Oreganus), Hayley Layne Crowell

Master's Theses

Global biodiversity is declining as a direct result of anthropogenic climate change. Ectothermic species have become focal organisms for studying the ecological effects of altered climates due to the clear relationship between environmental temperatures and ectotherms’ basic physiological functions. Historically, examinations of these effects have focused heavily on heliothermic lizards, and most others have tended to focus on single populations or sympatric species within a single community. Addressing the longterm energetic implications of environmental temperature variation will provide valuable insight into the cascading physiological effects that certain populations or species may experience as a result of altered climates.

In this …

Evaluating Alternate Management Strategies For Spotted Seatrout (Cynoscion Nebulosus) In The North-Central Gulf Of Mexico, Nathaniel Wallace Jermain

Master's Theses

Spotted Seatrout (Cynoscion nebulosus) receive considerable fishing pressure as the most popular saltwater target species in the north-central Gulf of Mexico. The potential for alternate management strategies, including stock enhancement and reducing discard mortality, to support the sustainability of the stocks and the desires of stakeholders is unknown. The purpose of this study was to provide an objective evaluation of the efficacy of alternate management strategies for Spotted Seatrout in Louisiana, Mississippi, and Alabama. I used a management strategy evaluation (MSE) to measure the performance of 18 alternate management scenarios relative to control scenarios. Scenarios with a high …

Scl: A Lattice-Based Approach To Infer Three-Dimensional Chromosome Structures From Single-Cell Hi-C Data, Hao Zhu

Master's Theses

In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.

We developed SCL (Single-Cell Lattice), a computational method to reconstruct three-dimensional (3D) structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3D cubic lattice. Metropolis-Hastings simulation and simulated annealing are used …

Gogo: An Improved Algorithm To Measure The Semantic Similarity Between Gene Ontology Terms, Chenguang Zhao

Master's Theses

Measuring the semantic similarity between Gene Ontology (GO) terms is an essential step in functional bioinformatics research. We implemented a software named GOGO for calculating the semantic similarity between GO terms. GOGO has the advantages of both information-content-based and hybrid methods, such as Resnik’s and Wang’s methods. Moreover, GOGO is relatively fast and does not need to calculate information content (IC) from a large gene annotation corpus but still has the advantage of using IC. This is achieved by considering the number of children nodes in the GO directed acyclic graphs when calculating the semantic contribution of an ancestor node …

Investigating Diel Periodicity In Export Flux In The Gulf Of Mexico Using A Particulate Imaging System, Justin Edward Blancher

Master's Theses

To estimate the diurnal periodicity in the biological pump, a floating array with a marine snow camera system at 150 m depth was used, and particles were imaged at a 40 second interval for a 24 to 30 hour period at five sites in the Gulf of Mexico in June 2017. Each image was processed to identify and size all the particles within the frame, which was then processed to determine diameter, an estimated volume, and settling speed for each particle. Using these parameters, particle mass was estimated using algebraically rearranged calculations for settling speed. Each hour during the deployment …

The Effects Of Salinity On Zootechnical Performance Of Spotted Seatrout (Cynoscion Nebulosus) In Recirculating Aquaculture Systems, Eric Gigli

Master's Theses

The spotted seatrout (Cynoscion nebulosus) is a euryhaline finfish candidate for marine aquaculture in the northern Gulf of Mexico. Aquaculture of this species currently uses salinities of 25 psu or greater making production challenging in areas where high salinity water is not available. This study aimed to document the effects of salinity on zootechnical performance of spotted seatrout embryos, early larvae, and juveniles in recirculating aquaculture systems to assist with the development of protocols for low salinity culture.

Embryos obtained from a volitional spawn at 29 psu were incubated at three salinities (12.5, 18.75, or 25 psu) until …

Methylation-Specific Differentiation Of Vaginal Epithelial Cells For Forensic Tissue Typing By Bisulfite Conversion And Pyrosequencing, Elise Pood

Master's Theses

The identification of bodily fluids and tissues is often applied to criminal investigations to clarify events that may or may not have taken place. Current forensic techniques can identify blood, saliva, seminal fluid, and spermatozoa, but there is a clear absence of reliable testing to identify vaginal epithelial tissue. Though there are serological tests available for this purpose, tissue-specific methylation markers have recently been investigated as a candidate for the identification of blood, saliva, and spermatozoa.

In this study, tissue-specific methylation markers were analyzed to identify a set of markers for the differentiation of vaginal fluid from blood, saliva, and …

Attenuated Responses To Inflammatory Cytokines In Mouse Embryonic Stem Cells: Biological Implications And The Molecular Basis, Bohan Chen

Master's Theses

Embryonic stem cells (ESCs) have attracted intense interest due to their great potential for regenerative medicine. However, their immune property is an overlooked but a significant issue that needs to be thoroughly investigated not only to resolve the concern for therapeutic applications but also for further understanding the early stage of organismal development. Recent studies demonstrated that ESCs are deficient in innate immune responses to viral/bacterial infections and inflammatory cytokines. Inflammatory conditions generally inhibit cell proliferation, which could be detrimental to ESCs, since cell proliferation is their dedicated task during early embryogenesis. Thus, I hypothesize that the attenuated innate immunity …

Dna Methylation Methods For Donor Age Prediction Using Touch Dna, Emily Neverett

Master's Theses

The International Labor Organization (ILO) estimated over 30 million individuals fall victim to human trafficking each year, of which, 50% are children below the age of 16. In 2012, the ILO reported there to be 168 million child laborers worldwide, with many trafficked into hazardous conditions to manufacture consumer products that are sold in developed countries. This is a modern form of slavery with poor working conditions, no access to education, and low wages. The hidden nature of this crime, however, makes it extremely difficult to identify and locate victims of forced child labor, and thus making it challenging to …

Naatm1: Examining The Mechanism Of A Heavy-Metal Abc Exporter, Dennis Hicks

Master's Theses

ATP-Binding Cassette (ABC) Transporters are a superfamily of integral membrane proteins that have been found embedded in both the cellular membranes and internal organelles of all species yet analyzed (1). This extreme conservation throughout the tree of life is due to their vitally critical and broad task of transporting all manner of things into and out of the cell and related organelles. This broadness of responsibility has led to an abundant diversity of this family, which in turn, has allowed life to adapt to the many environments found on Earth. While the importance and variability of this family is abundantly …

The Effect Of Alcohol And Bitterness Levels On Brewing Yeast Viability, Nichole Elizabeth Bryant

Master's Theses

Two of the most popular beer styles within the craft brewing industry are India Pale Ales (IPA’s) and those with high alcohol by volume (ABV). Production of these styles requires high gravity fermentation and high amounts of bittering hops in order to reach the required values for ABV and International Bitterness units (IBU) respectively. The aim of this study was to determine the impact of high gravity fermentation and high IBU levels on yeast viability and repitching cycles.

An initial experiment on high gravity fermentations was done in order to assess the effects this variable had alone. Successive five day …

Effectiveness Of Windrow Composting Methodology In Killing A Thermo-Tolerant Species Of Salmonella During Mortality Composting, Spencer Gabriel Myers

Master's Theses

In a large agricultural operation, such as the one at Cal Poly San Luis Obispo, disposal of deceased animals is an immense issue. The cost of transporting and rendering every dead animal is inhibitory to the general function of the agricultural operations and their thin budget. Therefore, we propose that composting mortalities could be an economical alternative. Composting is a recognized method for taking animal waste products along with carbon waste and turning it into a pathogen-free, nutrient-rich topsoil. Carcass composting is in fact performed in other countries and states to varying degrees of success. However, the California EPA limits …

Assay Development For The Identification Of Species And Bioactive Compounds Of Morinda Citrifolia (Noni) In Dietary Supplements By Rt-Qpcr, Dna Sanger Sequencing And Spectroscopy (Uv-Vis/Ftir), Ricardo L. Fernandez Walker

Master's Theses

Regulation standards for dietary supplements lack greatly. Due to this, fraud during the manufacturing of these products might be committed. Previous investigations on herbal dietary supplements have shown that the main ingredient was not present in most of the herbal supplements tested and that these products also contained other substances not stated in the label The purpose of this study was to develop a fluorescent qPCR assay for the identification of Morinda citrifolia herbal species in dietary supplements. Primers for genetic regions rbcL and matK of M. citrifolia were designed. The potential of novel matK primer showed discrimination potential …

Adolescent Binge Alcohol Exposure Effects On Heart Structure And Function, Lizhuo Ai

Master's Theses

More than 5 million underage Americans report binge drinking at least once per month. While the effects of alcohol consumption on the adult heart have been well studied, the impact to the adolescent heart is almost entirely unknown. Adolescents primarily consume alcohol in a binge pattern, which elevates blood alcohol content (BAC) to 0.08 g/dL within 2 hours. During adolescence the body grows rapidly, and the heart must also grow by cellular hypertrophy to meet this increasing demand. Our goal was to determine the impact of adolescent binge alcohol exposure on the heart, using an outbred rat model. This thesis …

Mllt3 Regulates Expression Of Genes Critical To Liver Metabolic Homeostasis, Jonathan Richard Dixit

Master's Theses

Hepatic steatosis (fatty liver) is increasingly prevalent in the US, and is characterized by triglyceride accumulation within hepatocytes. This is a direct result of an imbalance between lipid import, export, de novo lipogenesis, and beta oxidation. Hepatic steatosis can also progress to nonalcoholic steatohepatitis (NASH) which is characterized by increased hepatocyte damage, inflammation, and fibrosis. Further progression can lead to liver failure or hepatocellular carcinoma, requiring liver transplant or causing death. Our lab recently created Mllt3 conditional whole body knockout mice. These mice developed hepatic steatosis and NASH following Mllt3 deletion. MLLT3 is a master gene regulator that is part …

Testosterone Replacement Therapy For The Recovery From Chronic Vestibular Dysfunction Following Repeat Mild Traumatic Brain Injury In Male Long-Evans Hooded Rats, Arthur Segismundo

Master's Theses

Repeat mild traumatic brain injury (rmTBI) is a major public health concern leading to both chronic hypogonadism and vestibular impairment. Following rmTBI, vestibular symptoms are one of the most common complaints and hypogonadism occurs in a majority of patients. Gonadal hormones have a well-established role in neuroplasticity and axonal regeneration. The loss of gonadal hormones due to rmTBI may delay recovery. A clinically relevant closed-headed rmTBI male rodent model was utilized to examine the role of testosterone replacement therapy on chronic vestibular dysfunction. This is the first study to demonstrate both hypogonadism and vestibular dysfunction in the acute and chronic …

The Role Of Polyamines In Enteroviral Attachment, Thomas Mckenzie Kicmal

Master's Theses

Polyamines are small polycationic molecules with flexible carbon chains that are found in all eukaryotic cells. Polyamines are involved in the regulation of many host processes and have been shown to be implicated in viral replication. Depletion of polyamine pools in cells with FDA approved drugs restricts replication of diverse RNA viruses. Viruses can exploit host polyamines to facilitate packaging, transcription, translation, and protease activity but other mechanisms remain largely unknown. Picornaviruses, including Coxsackievirus B3 (CVB3), are sensitive to depletion of polyamines and remain a significant public health threat. We employed CVB3 as a model system to investigate a potential …

A Possible Role Of Clostridium Difficile Association With The Gi Tract In Relapsing Clostridium Difficile Infection, Asiyya Ashraf

Master's Theses

Clostridium difficile infection (CDI), caused by the anaerobic spore-former C. difficile, is a major cause of health-care associated morbidity. CDI occurs in individuals that have a disrupted GI tract microbiota, typically in patients who are on antibiotic therapy. After recovery from an episode of CDI, approximately, 15-30% of patients experience relapse of disease. The mechanism of relapse is not well understood. It is plausible for relapse to occur if C. difficile cells and spores associate with the GI tract mucosa during infection and persist after infection. However, little is known about the association of cells and spores with the GI …

Role Of Daxx As A Predictive Biomarker In Breast Cancer, Michelle Lucia Fernandez

Master's Theses

Breast cancer is the most commonly diagnosed form of cancer in women, besides skin cancer, and second only to lung cancer for cause of mortality. It is divided into three subtypes, depending on different molecular or pathologic characteristics, including estrogen or progesterone receptor-positive (ER/PR+), human epidermal growth factor receptor-2-positive (HER2+) and triple negative breast cancer (TNBC). There are several therapies used to target these subtypes, but there is still a chance that the cancer will recur into a more aggressive, resistant form even if the therapies were successful before. This recurrence is believed to be due to the Cancer Stem …

Assessing The Role Of A Putative Peptidase In The Processing And Transport Of Aip In The Agr Quorum Sensing System Of Staphylococcus Aureus, Chance Joseph Cosgriff

Master's Theses

Staphylococcus aureus infections are a global burden on human health. The wide rangeof infectious diseases caused by S. aureus stem from the production of myriad virulence factors that manipulate host immune responses and promote bacterial survival. These virulence traits, coupled with the rise in antibiotic resistance, demonstrate a need for novel therapeutics to control infection. Many current therapeutic initiatives focus on targeting the virulence factors produced by S. aureus or the regulatory systems that control their expression such as the Accessory gene regulatory system, Agr.Initial characterization of a putative S. aureus peptidase MroQ indicates a major role in regulation of …

Longitudinal Urinary Microbiome Studies: A Need To Transition To Voided Urine, Baylie Hochstedler

Master's Theses

It is now established that the bladder is not sterile; it contains communities of microbes (microbiota). While the healthy bladder microbiota have been defined using expanded quantitative urine culture (EQUC) and urines obtained by transurethral catheterization (TUC), longitudinal and population studies have not previously been possible. These studies cannot be done using TUC urines, as it would be impractical to catheterize participants daily. Instead, we must transition to using voided urines.In order to make this switch, we have addressed three main issues raised by using voided urine. First, we showed that EQUC out performs standard urine culture on voided urines …

Molecular And Biochemical Phenotypes Underlying Reactive Astrocytosis In Primary Optic Nerve Head Astrocytes, Anita Kirti Ghosh

Master's Theses

Glaucoma is a progressive optic neuropathy that manifests in a pathological triad of optic nerve head remodeling, damage to optic nerve axons, and retinal ganglion cell death. Optic nerve head astrocytes (ONHAs) are the primary cell type in the optic nerve head. ONHAs undergo reactive astrocytosis, an activated phenotype characterized by altered gene and protein expression and increased cell migration and proliferation, early in the disease pathology. Reactive astrocytosis is thought to underlie optic nerve head remodeling. The first goal of this thesis was to determine if exposure of primary adult rat ONHAs to hyperbaric pressure (25-30 mm Hg above …

California Livestock Owners: An Assessment Of Familiarity With New Antimicrobial Rules And Access To Educational Outreach, Philip Theodor Paulson

Master's Theses

The purpose of this research is to support the California Department of Food & Agriculture (CDFA) with education and outreach about recent changes regarding antimicrobial use in livestock, and to enhance their emergency communications network. This was done by characterizing a population of small-scale livestock owners underserved with regards to educational outreach about animal health issues, such as antimicrobial use rules. The project also seeks to enhance public understanding of the importance of responsible antimicrobial use in animal and human health.

To accomplish this, the study used a survey administered in person at local farm supply stores and online to …

Dissecting A Role For Polyamines In Rift Valley Fever Virus Infection, Vincent Mastrodomenico

Master's Theses

Bunyaviruses are emerging viral pathogens that cause encephalitis, hemorrhagic fevers, and meningitis. Rift Valley fever virus is a particularly devastating bunyavirus, infecting both humans and livestock with significant morbidity and mortality. By coordinating several host and viral processes Rift Valley fever virus is able to produce infectious virions. Polyamines are small, positively-charged host-derived molecules that play diverse roles in human cells and in infection. We previously demonstrated that polyamines are crucial for RNA viruses; however, the mechanisms by which polyamines function remain unknown. Here, we investigated polyamines' role in the replication of the Rift Valley fever virus (vaccine strain MP-12). …

Habitat Associations And Community Interactions Of Non-Native Species In The Southern Basin Of Lake Michigan, Erin O'Shaughnessey

Master's Theses

Non-native crayfishes, mollusks, and macrophytes can have large impacts on biodiversity and damage ecosystem services in freshwaters. In 2015 we discovered an established population of the globally widespread invader red swamp crayfish (Procambarus clarkii) in the North Shore Channel of the Chicago Area Waterway System. This population overlaps with a population of rusty crayfish (Faxonius rusticus), a previous invader that is widely distributed and usually the dominant crayfish species across the Great Lakes region. I studied the interactions between these two species while directly competing over shelter and food. In the field, each species was studied to determine the rate …

Modulation Of Coxsackievirus Protease Activity By Polyamines, Courtney Noelle Dial

Master's Theses

Coxsackievirus type B (CVB3) is one of the six serotypes of the Coxsackievirus family of non-enveloped, linear, and positive-sense single-stranded RNA viruses. It is a pathogenic enterovirus that belongs to the same genus as the notable pathogen poliovirus. CVB3 can cause a range of illnesses from a fever to gastrointestinal distress but is most noteworthy for the ability to cause viral myocarditis, a swelling of the heart muscle. Coxsackievirus, like all RNA viruses, tends to develop mutations rapidly due to its error prone polymerase and lack of proofreading activity. These mutations can be advantageous for the virus, allowing it to …

Seasonal Diet Variation In Thirteen-Lined Ground Squirrel (Ictidomys Tridecemlineatus) In Southernwestern Michigan, Austin Menzmer

Master's Theses

Thirteen-lined ground squirrels (Ictidomys tridecemlineatus) are omnivorous ground squirrels that range from Texas to Alberta and from Michigan to Utah. The amount and type of both animal and plant matter in their diet may vary both geographically and seasonally. The present study was motivated by prior work, based on δ13C analysis of incisor enamel of thirteen-lined ground squirrels from a colony in southwestern Michigan, suggesting that these animals underwent a pronounced, late-season shift in diet from predominantly C3 to C4 plants. However, this inferred dietary shift was not directly demonstrated. Here, I tracked diet of thirteen-lined ground squirrels in southwestern …

Investigating The Anti-Cancer Properties Of Novel Hybrid 1,4-Dihydropyridine Derivatives In U-87mg Glioblastoma Cell, Tendai Hunyenyiwa

Master's Theses

Glioblastoma is the most devastating of brain cancers with a very high death rate and a low survival rate of less than 15 months after diagnosis. Glioblastoma is a cancer of astrocytes which are the majority of the brain glial cells that support neurons and help create the blood-brain barrier among other functions. The current approach to treating this disease is surgical removal of the main tumor, followed by radiotherapy and limited chemical intervention by the use of temozolomide (TMZ). This disease is characterized by high invasion and recurrence after surgical removal of the main tumor as a result of …

Assessment Of Eastern Massasauga Rattlesnakes (Sistrurus Catenatus) In Berrien County Historical Sites, Roshelle M. Hall

Master's Theses

The Eastern Massasauga rattlesnake (Sistrurus catenatus; EMR) is a small robust pit viper currently found in nine states and the province of Ontario, Canada. Wetland habitats have experienced significant destruction and fragmentation by humans; as a result, the current distribution of the EMR is a fraction of its historic distribution. For this reason, the EMR has been federally listed as threatened. In general, little is known about the current distribution of this rattlesnake (in the southwest corner of Michigan, the size of local populations or their stability and genetic diversity. Much of this knowledge is based upon historical data. My …

Synthesis And Screening Of Novel Hybrid Benzothiazoles In U-87 Mg Glioblastoma Cell Line, Priscilla Kyi

Master's Theses

Benzothiazole is a heteroaromatic compound known for its wide range of bioactivities including anti-cancer, anti-viral, anti-microbial, anti-inflammatory, anti-convulsant, anti-diabetic, anti-helminthic, and anti-tubercular activities. Research has shown that derivatives of benzothiazole exhibit inhibition of proliferation via apoptosis in various human cancer cell lines, such as liver cancer (Wang, et. al., 2011). In this study, a series of novel hybrid benzothiazole α-cyanostilbene derivatives and styrylbenzothiazole derivatives containing boronic acid and non-boronic acid pharmacophores were synthesized. The anti-cancer and anti-invasive properties of selected benzothiazole α-cyanostilbene derivatives on U-87MG glioblastoma cells were investigated in vitro.

U-87MG cells were incubated with synthesized novel hybrid compounds …