Other Biochemistry, Biophysics, and Structural Biology Commons^™

Serving Justice Case By Case, Michael Becker

WRIT: Journal of First-Year Writing

Forensic Science is an integral part of serving justice in today's society, and majority of the world has little understanding of what forensics is. Read this article on forensic science and how it relates to writing in today's world.

Therapies For Mitochondrial Disorders, Kayli Sousa Smyth, Anne Mulvihill

SURE Journal: Science Undergraduate Research Experience Journal

Mitochondria are cytoplasmic, double-membrane organelles that synthesise adenosine triphosphate (ATP). Mitochondria contain their own genome, mitochondrial DNA (mtDNA), which is maternally inherited from the oocyte. Mitochondrial proteins are encoded by either nuclear DNA (nDNA) or mtDNA, and both code for proteins forming the mitochondrial oxidative phosphorylation (OXPHOS) complexes of the respiratory chain. These complexes form a chain that allows the passage of electrons down the electron transport chain (ETC) through a proton motive force, creating ATP from adenosine diphosphate (ADP). This study aims to explore current and prospective therapies for mitochondrial disorders (MTDS). MTDS are clinical syndromes coupled with abnormalities …

The Effects Of Tubulin Post-Translational Modifications On The Flagellar Motility Of Trypanosoma Brucei, Katherine Wentworth

All Theses

Trypanosoma brucei is a parasitic kinetoplastid that causes African trypanosomiasis and is transmitted to a mammalian host by the tsetse fly (Glossina spp.). T. brucei relies on its flagellar motility to carry out its morphological changes from the procyclic form (predominant in the fly vector) to the bloodstream form (infectious form in mammals) and navigate the bloodstream of its host. The driving structure within the flagellum is the axoneme, which is composed of microtubules and dynein motor proteins. The tubulin code hypothesis suggests that cells regulate microtubule motor protein activity through post-translational modifications (PTMs) of alpha and beta …

Functional Analysis Of Legionella Pneumophila Effector Protein, Shreya Neupane

Masters Theses & Specialist Projects

Legionella pneumophila is a gram-negative bacterium that causes Legionnaire’s disease (a severe form of pneumonia) in humans. L. pneumophila can cause infection by utilizing its Type IV secretion system, a protein secretion system that transports proteins from the bacterial cytosol into the infected macrophage. Effectors released from the Type Iv secretion system allow L. pneumophila to create a safe environment to survive, replicate and cause infection. One such effector, RavQ, inhibits cell proliferation of mammalian HEK 293T cells and localizes to the cell’s nucleus, leading us to hypothesize that RavQ interferes with cellular activity in the nucleus. To detect its …

Chemosensory Receptors In Berghia Stephanieae: Bioinformatics And Localization, Kelsi L. Watkins

Masters Theses

Chemosensation is achieved through the binding of chemical signals to chemoreceptor proteins embedded in the membranes of sensory neurons. The molecular identity of these receptors, as well as the downstream processing of chemosensory signals, has been well studied in arthropods and vertebrates. However, very little is known about molluscan chemosensation. The identity of chemoreceptor proteins in the nudibranch mollusc Berghia stephanieae are unknown. Data from other protostome and molluscan studies suggest Berghia may use ionotropic receptors for some forms of chemoreception. This study used a bioinformatics approach to identify potential chemosensory ionotropic receptors in the transcriptome of Berghia. A …

Hsp- 70 Mediated Nervous System Enhancement By Etas, Taylor Carter

Theses (2016-Present)

Neurodegenerative disease in the CNS is usually a product of increased oxidative stress in the brain. In this study we tested the ability of an asparagus supplement ETAS to help reduce oxidative stress in the normal brains of Balb C mice. Oxidative stress pathways (Heat shock proteins) are usually cumulative in the damage they cause when disrupted. We treated normal Balb C mice with ETAS and had control groups with no ETAS supplementation in their regular diet. We then sacrificed the mice and conducted microarray studies to compare oxidative stress pathway genes. We also characterized the effects of regular oxidative …

Modulation Of Kras Structure And Dynamics By Kras Ubiquitination And Membrane Depolarization, Vinay Nair

Dissertations & Theses (Open Access)

KRAS, a 21 kDa small GTPase protein, functions as a molecular switch playing a key role in regulating cell proliferation. Dysregulation of KRAS signaling by oncogenic mutations leads to uncontrolled cell proliferation, a hallmark of cancer cells. Attempts to therapeutically target oncogenic KRAS have led to limited success resulting in a need to identify new mechanisms to targeting KRAS. The interaction of KRAS with its regulators, effectors, and the membrane present one such avenue. In this study, we investigated how post-translational covalent and environmental modifications could modulate these interactions of KRAS. Using computational molecular dynamics simulations, nuclear magnetic resonance spectroscopy …

Annual Faculty Research Symposium 2022, Oakwood University

Proceedings

No abstract provided.

The Structural And Functional Role Of Photosensing In Rgs-Lov Proteins, Zaynab Jaber

Dissertations, Theses, and Capstone Projects

Light provides organisms with energy and spatiotemporal information. To survive and adapt, organisms have developed the ability to sense light to drive biochemical effects that underlie vision, entrainment of circadian rhythm, stress response, virulence, and many other important molecularly driven responses. Blue-light sensing Light-Oxygen-Voltage (LOV) domains are ubiquitous across multiple kingdoms of life and modulate various physiological events via diverse effector domains. Using a small molecule flavin chromophore, the LOV domain undergoes light-dependent structural changes leading to activation or repression of these catalytic and non-catalytic effectors. In silico analyses of high-throughput genomic sequencing data has led to the marked expansion …

Fine-Tuning Of Alanyl-Trna Synthetase Quality Control Alleviates Global Dysregulation Of The Proteome, Paul Kelly, Arundhati Kavoor, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

One integral step in the transition from a nucleic acid encoded-genome to functional proteins is the aminoacylation of tRNA molecules. To perform this activity, aminoacyl-tRNA synthetases (aaRSs) activate free amino acids in the cell forming an aminoacyl-adenylate before transferring the amino acid on to its cognate tRNA. These newly formed aminoacyl-tRNA (aa-tRNA) can then be used by the ribosome during mRNA decoding. In Escherichia coli, there are twenty aaRSs encoded in the genome, each of which corresponds to one of the twenty proteinogenic amino acids used in translation. Given the shared chemicophysical properties of many amino acids, aaRSs have …

High Concentrations Of Trimethylamines In Slime Glands Inhibit Skein Unraveling In Pacific Hagfish, Gaurav Jain, Marie Starksen, Kashika Singh, Christopher Hoang, Paul Yancey, Charlene Mccord, Douglas S. Fudge

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Hagfish defend themselves from fish predators by producing large volumes of gill-clogging slime when they are attacked. The slime consists of seawater and two major components that are ejected from the slime glands: mucus and threads. The threads are produced within specialized cells and packaged into intricately coiled bundles called skeins. Skeins are kept from unraveling via a protein adhesive that dissolves when the skeins are ejected from the slime glands. Previous work revealed that hagfish slime glands have high concentrations of methylamines including trimethylamine N-oxide (TMAO), trimethylglycine (betaine) and dimethylglycine (DMG); however, the function of these compounds in the …

Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an …

Molecular Fossils From Phytoplankton Reveal Secular Pco2 Trend Over The Phanerozoic, Caitlyn R. Witkowski, Johan W. H. Weijers, Brian S. Blais, Stefan Schouten, Jaap S. Sinninghe Damsté

Science and Technology Department Faculty Journal Articles

Past changes in the atmospheric concentration of carbon dioxide (PCO2) have had a major impact on earth system dynamics; yet, reconstructing secular trends of past PCO2 remains a prevalent challenge in paleoclimate studies. The current long-term PCO2reconstructions rely largely on the compilation of many different proxies, often with discrepancies among proxies, particularly for periods older than 100 million years (Ma). Here, we reconstructed Phanerozoic PCO2 from a single proxy: the stable carbon isotopic fractionation associated with photosynthesis (Ɛp) that increases as PCO2 increases. This concept has been widely applied to alkenones, but here, we …

Curcumin Potentiates The Function Of Human Α7-Nicotinic Acetylcholine Receptors Expressed In Sh-Ep1 Cells, Eslam El Nebrisi, Lina T. Al Kury, Keun-Hang Susan Yang, Petrilla Jayaprakash, Frank Christopher Howarth, Nadine Kabbani, Murat Oz

Mathematics, Physics, and Computer Science Faculty Articles and Research

Effects of curcumin, a biologically active ingredient of turmeric, were tested on the Ca²⁺transients induced by the activation of α₇ subunit of the human nicotinic acetylcholine (α₇nACh) receptor expressed in SH-EP1 cells. Curcumin caused a significant potentiation of choline (1 mM)-induced Ca²⁺ transients with an EC₅₀ value of 133 nM. The potentiating effect of curcumin was not observed in Ca²⁺ transients induced by high K⁺ (60 mM) containing solutions or activation of α₄β₂ nACh receptors and the extent of curcumin potentiation was not altered in the presence of …

Itraq-Based Proteomics Analysis And Network Integration For Kernel Tissue Development In Maize, Long Zhang, Yongbin Dong, Qilei Wang, Chunguang Du, Wenwei Xiong, Xinyu Li, Sailan Zhu, Yuling Li

Department of Biology Faculty Scholarship and Creative Works

Grain weight is one of the most important yield components and a developmentally complex structure comprised of two major compartments (endosperm and pericarp) in maize (Zea mays L.), however, very little is known concerning the coordinated accumulation of the numerous proteins involved. Herein, we used isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative proteomic method to analyze the characteristics of dynamic proteomics for endosperm and pericarp during grain development. Totally, 9539 proteins were identified for both components at four development stages, among which 1401 proteins were non-redundant, 232 proteins were specific in pericarp and 153 proteins were specific in …

Approaching Undergraduate Research With Students Who Are Deaf And Hard-Of-Hearing, Austin U. Gehret, Jessica W. Trussell, Lea V. Michel

Journal of Science Education for Students with Disabilities

An undergraduate research experience can provide a unique opportunity for students to learn and grow as scientists; when positive, this experience is often transformative and motivates students to pursue science, technology, engineering and mathematics (STEM) graduate degrees or careers. Conversely, negative research experiences can sour a student’s opinion of research, propagate misconceptions of graduate school, and lead to attrition from STEM fields. Negative research experiences can be equally devastating for faculty mentors and may result in reluctance to mentor future research students. Using a mentoring approach that has traditionally translated to positive research experiences for hearing students may not be …

Inquiry Into Perilipin-5a Expression In Triacylglycerol Rich Vs Normal Fed Mouse Tissue, Kobi Agyepong

Undergraduate Honors Thesis Projects

The steep rise in both childhood and adult obesity over the past three decades has moved to the forefront of public consciousness in recent years. This development has generated a marked increase in general health awareness and lifestyle changes for a vast number of individuals, most notably in the form of increased physical activity and diet alterations. The latter point is especially salient in a biochemical context, because of the myriad factors that can result in “fat accumulation”. Chief among these factors is the Perilipin 5A gene, (known as PLIN5A) which encodes the protein Perilipin 5A of the Perilipin family …

Expression Of Glycine-Rich Proteins Found In Salivary Glands Of The Lone Star Tick (Amblyomma Americanum) Using A Mammalian Cell Line, Annabelle Clark

Honors Theses

Ticks play an important ecological role as well as a growing role in human health and veterinary care. Ticks are hosts to a plethora of microbial pathogens that can be transferred during feeding to cause tick-borne diseases in humans and many animals. Ticks may in large part owe the success of the transfer of these pathogens between hosts to their complex saliva. The saliva secreted upon a tick’s attachment to a host serves the following, among other, functions: anti-hemostasis of the blood pool, preventing an inflammatory response at the bite site, and serving as a natural anti-microbial substance. An important …

Promoting Extracellular Matrix Crosslinking In Synthetic Hydrogels, Marcos M. Manganare

Masters Theses

The extracellular matrix (ECM) provides mechanical and biochemical support to tissues and cells. It is crucial for cell attachment, differentiation, and migration, as well as for ailment-associated processes such as angiogenesis, metastases and cancer development. An approach to study these phenomena is through emulation of the ECM by synthetic gels constructed of natural polymers, such as collagen and fibronectin, or simple but tunable materials such as poly(ethylene glycol) (PEG) crosslinked with short peptide sequences susceptible to digestion by metalloproteases and cell-binding domains. Our lab uses PEG gels to study cell behavior in three dimensions (3D). Although this system fosters cell …

Isotopic Discrimination In The Double-Crested Cormorant (Phalacrocorax Auritus), Elizabeth C. Craig, Brian S. Dorr, Katie C. Hanson-Dorr, Jed P. Sparks, Paul D. Curtis

Brian S Dorr

The diet-tissue discrimination factor is the amount by which a consumer’s tissue varies isotopically from its diet, and is therefore a key element in models that use stable isotopes to estimate diet composition. In this study we measured discrimination factors in blood (whole blood, red blood cells and plasma), liver, muscle and feathers of Double- crested Cormorants (Phalacrocorax auritus) for stable isotope ratios of carbon, nitrogen and sulfur. Cormorants exhibited discrimination factors that differed significantly among tissue types (for carbon and nitrogen), and differed substantially (in the context of the isotopic variation among relevant prey species) from those observed in …

Fishing For A Sustainable Future: Aquaponics As A Method Of Food Production, Richard Ramsundar

Student Theses 2015-Present

This thesis compares and explains the advantages aquaponics farming has over modern industrial intensive farming. Through a comparison natural capital usage, conservation, recycling and cost, the thesis advocates for the expansion of aquaponics usage in urban settings. The thesis also explains the history of intensive farming and aquaponics in America, the science of how aquaponics operates, the economic and environmental costs of modern intensive farming versus aquaponics farming, and the social implications of aquaponics. Lastly, I propose a policy that reallocates farm subsidies by modifying the Farm Bill. Then I propose policies that support creating a new standard of farm …

Shifting The Stress Curve: Using "Stress Inoculation" And Exercise To Promote Resilience, Mikyung Kim

Master's Theses

Problem

Stress influences an organism’s physiological systems via an inverted u-shaped curve: An optimum amount of stress will optimize body functions, but too little stress or too much stress for long periods of time can impair body functions. Researchers have been very interested in exploring the mechanisms that may “delay the tipping point” between the positive and negative effects of stress. A rightward shift in the stress curve would allow one to maintain optimal performance even at higher or more prolonged stress levels. The molecular and cellular mechanisms that underlie this rightward shift could result in resilience, clinically defined as …

A High Omega-3 Fatty Acid Diet Has Different Effects On Early And Late Stage Myeloid Progenitors, Melinda Varney, James Buchanan, Yulia Dementieva, W. Hardman, Vincent Sollars

Yulia Dementieva

The effects of the polyunsaturated omega-3 (n-3) and omega-6 (n-6) fatty acids (FA) on hematopoiesis are complex in that both FA forms are processed into leukotrienes, eicosanoids, and prostaglandins, which can have independent effects. These FA have antagonistic effects in that n-6 FA prostaglandins tend to be pro-proliferative and pro-inflammatory, while the effects of n-3 FA prostaglandins are the opposite. We have previously shown that diets high in n-3 FA reduce the size of the middle to later stage myeloid progenitor compartment in FVB X sv129 F1hybrid mice. To assay the effects of high n-3 FA diets on earlier stages …

Global Analysis Of Gene Expression Changes During Retinoic Acid-Induced Growth Arrest And Differentiation Of Melanoma: Comparison To Differentially Expressed Genes In Melanocytes Vs Melanoma, Mary H. Estler, Goran Boskovic, James Denvir, Sarah Miles, Donald A. Primerano, Richard M. Niles

Goran Boskovic

BACKGROUND: The incidence of malignant melanoma has significantly increased over the last decade. Some of these malignancies are susceptible to the growth inhibitory and pro-differentiating effects of all-trans-retinoic acid (RA). The molecular changes responsible for the biological activity of RA in melanoma are not well understood. RESULTS: In an analysis of sequential global gene expression changes during a 4-48 h RA treatment of B16 mouse melanoma cells, we found that RA increased the expression of 757 genes and decreased the expression of 737 genes. We also compared the gene expression profile (no RA treatment) between non-malignant melan-a mouse melanocytes and …

Effects Of Canola And Corn Oil Mimetic On Jurkat Cells, Gabriela Ion, Kayla Fazio, Juliana A. Akinsete, W. Elaine Hardman

Gabriela Ion

BACKGROUND: The Western diet is high in omega-6 fatty acids and low in omega-3 fatty acids. Canola oil contains a healthier omega 3 to omega 6 ratio than corn oil. Jurkat T leukemia cells were treated with free fatty acids mixtures in ratios mimicking that found in commercially available canola oil (7% α-linolenic, 30% linoleic, 54% oleic) or corn oil (59% linoleic, 24% oleic) to determine the cell survival or cell death and changes in expression levels of inflammatory cytokines and receptors following oil treatment. METHODS: Fatty acid uptake was assessed by gas chromatography. Cell survival and cell death were …

Maternal Consumption Of Canola Oil Suppressed Mammary Gland Tumorigenesis In C3(1) Tag Mice Offspring, Gabriela Ion, Juliana A. Akinsete, W. Elaine Hardman

Gabriela Ion

Background: Maternal consumption of a diet high in omega 6 polyunsaturated fats (n-6 PUFA) has been shown to increase risk whereas a diet high in omega 3 polyunsaturated fats (n-3 PUFA) from fish oil has been shown to decrease risk for mammary gland cancer in female offspring of rats. The aim of this study was to determine whether increasing n-3 PUFA and reducing n-6 PUFA by using canola oil instead of corn oil in the maternal diet might reduce the risk for breast cancer in female offspring. Methods: Female SV 129 mice were divided into two groups and placed on …

Consumption Of High Ω-3 Fatty Acid Diet Suppressed Prostate Tumorigenesis In C3(1) Tag Mice, Juliana Akinsete, Gabriela Ion, Theodore Witte, W. Hardman

Gabriela Ion

Prostate cancer incidence and mortality are high in the Western world and high ω-6/ω-3 PUFA in the Western diet may be a contributing factor. We investigated whether changing from a diet that approximates ω-6 fat content of the Western diet to a high ω-3 fat diet at adulthood might reduce prostate cancer risk. Female SV 129 mice that had consumed a high ω-6 diet containing corn oil for 2 weeks were bred with homozygous C3(1)Tag transgenic male mice. All male offspring were weaned to the corn oil diet (CO) until postpuberty when half of the male offspring were transferred to …

Serotyping Group B Streptococci In A Small Community Hospital: An Analysis Of Distribution And Site Of Isolation, Jennifer M. Smith, Jason A. Rexroth, David G. Chaffin, Susan H. Jackman

Susan H. Jackman

Objective: To determine the prevalence and site of isolation of different serotypes of group B streptococcus (GBS) colonization or infection at a small community hospital. Methods: GBS isolates were obtained from a small community hospital and were then serotyped as la, Ib, II, III, IV, V or non-typeable. Hospital records were reviewed for patient sex, age and pregnancy status as well as the site of GBS isolation. Results: GBS serotypes Ia, III and V were most common and accounted for over 60% of the total number of isolates. Serotype Ia was most prevalent in reproductive-age females, while serotypes V and …

Murine Epidermal Cell Antigen (Skn)-Directed Autoimmunity Induced By Transfer Of Cd4+ T Cells, Susan H. Jackman, Shivaleela Keerthy, Giselle Perry

Susan H. Jackman

While pathogenic T cells have been identified for several diseases with epithelial cell damage, an autoimmune T cell-mediated response targeted against a known keratinocyte antigen has not been reported. Previously we described an autoimmune response directed to the mouse epidermal cell antigens, Skn. For our murine model, primed Skn-immune lymphocytes are adoptively transferred to recipients, which develop lesions at the site of mild skin trauma. In this study we investigated the nature of the autoimmune component of the Skn response. A time-course study demonstrated a relationship between the number of primed Sknimmune cells injected and the severity of skin lesions …

Serotyping Group B Streptococci In A Small Community Hospital: An Analysis Of Distribution And Site Of Isolation, Jennifer M. Smith, Jason A. Rexroth, David G. Chaffin, Susan H. Jackman

David G. Chaffin

Objective: To determine the prevalence and site of isolation of different serotypes of group B streptococcus (GBS) colonization or infection at a small community hospital. Methods: GBS isolates were obtained from a small community hospital and were then serotyped as la, Ib, II, III, IV, V or non-typeable. Hospital records were reviewed for patient sex, age and pregnancy status as well as the site of GBS isolation. Results: GBS serotypes Ia, III and V were most common and accounted for over 60% of the total number of isolates. Serotype Ia was most prevalent in reproductive-age females, while serotypes V and …