Biochemistry Commons^™

The Effect Of Pure Infrared Light On The Growth Of Rhodospirrilum Rubrum, Jordan Lee Wilkes

Undergraduate Honors Capstone Projects

Scientists who study aquatic ecosystems quickly notice a diversity of pathways that different microbes and organisms can use to metabolize nutrients found in common ponds or pools. Competition for vital resources, such as light and inorganic minerals, allow only certain organisms to grow in certain niches within these ecosystems. Rhodospirillum rubrum is a gram negative, photosynthetic bacteria that competes for light within aquatic ecosystems in order to survive. R. rubrum is believed to specifically absorb light for photosynthesis at wavelengths in the range of infrared light. It was found that R. rubrum indeed can grow in "dark", anaerobic environments by …

Spa47 Is An Oligomerization - Activated Type Three Secretion System (T3ss) Atpase From Shigella Flexneri, Jamie Lee Kingsford

Undergraduate Honors Capstone Projects

Gram-negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa4 7 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 …

Effects Of Streptozotocin-Induced Diabetes On Gene And Protein Expression In Sinoatrial Node Of Rat Heart, Zannatul Ferdous

Theses

Diabetes mellitus is one of the most common endocrine disorders and its global prevalence is increasing at an alarming rate. Cardiovascular disease is the major cause of morbidity and mortality among diabetic patients. In addition to defects in contraction, the diabetic heart also frequently suffers from disturbances to the electrical conduction system. This study investigates the effects of diabetes on the sinoatrial node (SAN) of the rat heart. Previous in vivo and in vitro experiments have demonstrated reduced heart rate, longer SAN action potential duration, prolonged pacemaker cycle length and Sino-atrial conduction time in streptozotocin (STZ) - induced diabetic rat …

Placental ‘€˜Omics’€™ Study To Understand The Pathogenesis Of Preeclampsia, Komal Kedia

Theses and Dissertations

Preeclampsia (PE) is a potentially fatal complication of pregnancy characterized by an increase in blood pressure (>140/90 mmHg) and proteinuria (>300 mg/24 hrs), often accompanied by edema. Symptoms of PE start after 20 weeks of gestation. If PE remains untreated, it can lead to eclampsia, grand-mal seizures responsible for most fatalities. PE is believed to affect 2-10% of pregnancies worldwide, and claims the lives of over 75,000 mothers and 500,000 newborns yearly. No therapeutic agents have been developed to prevent or cure PE. Part of the reason for this is the absence of a complete understanding of the …

Investigation Of Novel Functions For Dna Damage Response And Repair Proteins In Escherichia Coli And Humans, Benjamin A. Hilton

Electronic Theses and Dissertations

Endogenous and exogenous agents that can damage DNA are a constant threat to genome stability in all living cells. In response, cells have evolved an array of mechanisms to repair DNA damage or to eliminate the cells damaged beyond repair. One of these mechanisms is nucleotide excision repair (NER) which is the major repair pathway responsible for removing a wide variety of bulky DNA lesions. Deficiency, or mutation, in one or several of the NER repair proteins is responsible for many diseases, including cancer. Prokaryotic NER involves only three proteins to recognize and incise a damaged site, while eukaryotic NER …

Modulation Of Cell Death Signaling And Cell Proliferation By The Interaction Of Homoserine Lactones And Paraoxonase 2., Aaron Mackallan Neely

Electronic Theses and Dissertations

Pseudomonas aeruginosa produces N-(3-oxododecanoyl)-homoserine lactone (C12) as a quorum-sensing molecule that functions to facilitate bacteria-bacteria communication. C12 has also been reported to affect many aspects of human host cell physiology, including evoking cell death in various types of cells. However, the signaling pathway(s) leading to C12-triggerred cell death remains unclear. To clarify cell death signaling induced by C12, we examined mouse embryonic fibroblasts (MEFs) deficient in one or more caspases. Our data indicate that, unlike most apoptotic inducers, C12 evokes a novel form of apoptosis in cells, probably through the direct induction of mitochondrial membrane permeabilization. Previous studies indicate that …

Mechanisms Of Regulation Of Tau Ires Mediated Translation, Niza Nemkul

Dissertations and Theses (Open Access)

The translation of most eukaryotic mRNAs occurs in a cap-dependent manner. However, a subset of mRNAs are capable of initiating translation in a cap-independent manner by utilizing sequences in their 5’ UTR called IRES. It was previously shown that the 5’ UTR of the tau mRNA contains an IRES. In this study I show that IRES dependent translation of tau IRES is regulated at multiple levels in order to regulate the expression of the tau protein.

Tau protein is ubiquitously expressed but is concentrated in the brain. In this study, I utilized neural and non-neural cell lines to show that …

The Roles Of Malt1 In Nf-Κb Activation And Solid Tumor Progression, Deng Pan

Dissertations and Theses (Open Access)

The transcription factor NF-κB plays a central role in many aspects of biological processes and diseases, such as inflammation and cancer. Although it has been suggested thatNF-κB is critical in tumorigenesis and tumor progression, the molecular mechanism by which NF-κB is activated in solid tumor remains largely unknown. In the current work, we focus on growth factor receptor-induced NF-κB activation and tumor progression, including epidermal growth factor receptor (EGFR)-induced NF-κB in lung cancer and heregulin receptor (HER2)-induced NF-κB in breast cancer. We found that Mucosa-associated lymphoma translocation protein 1 (MALT1), also known as paracaspase, is required for EGFR-induced NF-κB activation …

Cll Metabolism Is Regulated By Prognostic Factors, Modulated By Stroma And Abrogated By Pi3k Inhibition, Hima Vangapandu

Dissertations and Theses (Open Access)

Metabolism of chronic lymphocytic leukemia (CLL), a disease characterized by the relentless accumulation of mature B cells has been little explored. Bone marrow stromal cells provide a survival benefit to CLL cells, in part through PI3K/AKT pathway. Compared with proliferative B-cell lines, metabolic fluxes of oxygen and lactate were low in quiescent malignant B lymphocytes from CLL patients. Glycolysis (extracellular acidification rate, ECAR) was consistently low in CLL samples, but oxygen consumption (OCR) varied considerably. Higher OCR was associated with poor prognostic factors such as ZAP 70 positivity, unmutated IgVH, high β2M levels, and higher Rai stage. Co-culture with the …

Preeclampsia: The Roles Of Acute Inflammation And Intrauterine Stress, Nicholas Parchim

Dissertations and Theses (Open Access)

Preeclampsia (PE) is a severe, acute disease of pregnancy affecting approximately 8% of pregnant women after week 20 of gestation. PE is characterized by hypertension and renal damage reflected by proteinuria and has significant morbidity to both mother and fetus. Maternal symptoms range from headaches, nausea, edema, to visual changes, but once maternal symptoms present, damage to the fetus has begun. Mothers who progress untreated through the disease can also experience a condition called eclampsia characterized by seizure, coma, and, ultimately, death. PE-affected newborns experience features similar to prematurity—abnormal lung and renal development, intrauterine growth retardation (IUGR), and, possibly, fetal …

Quantum Mechanical Studies Of Charge Assisted Hydrogen And Halogen Bonds, Binod Nepal

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Like cement bridges one brick to another, noncovalent forces also bridge two or more molecules together to form a molecular crystal or molecular cluster. Although weaker than the covalent bond, the existence of noncovalent forces can be seen everywhere from liquid water to construction of complex biomolecules like DNA, RNA, proteins etc. An introduction of suitable charge; positive or negative, on the binding units can increase the strength of noncovalent interaction by several orders of magnitude. The primary aim of this dissertation is to explore some fundamental properties of such charge assisted noncovalent interactions which will be helpful for the …

Structural And Biochemical Characterization Of The Frequency-Interacting Rna Helicase Frh, Jacqueline M. Johnson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Cells function through a variety of regulatory pathways intricately communicating with one another. These pathways ensure that cellular functions happen at the appropriate times and keep the natural balance within the cell. When pathways do not communicate appropriately, this can lead to disease states and cell death. Two such connected pathways in Neurospora crassa involve the regulation of RNA levels and the circadian rhythms essential for these cells to maintain homeostasis. These pathways are connected by a unique helicase called the Frequency-interacting RNA Helicase (FRH), named for its discovery with the frequency protein involved in the circadian oscillation of the …

Investigation Of Parasympathetic Effects Of Lavender Essential Oil In Humans, Haakon Robert Nelson, Rachel Ann Burkhart, Daniel Morin, Nicole Grace Weissenfluh, Michael R. Korn

Montview Journal of Research & Scholarship

The purpose of this study will be to investigate the claim that administration of lavender (Lavandula angustifolia) essential oil (topically, orally, and/or respiratorily) produces a relaxative effect in human subjects. This investigation will theoretically be conducted in two stages. Stage one will focus primarily on determining the presence of therapeutic effects and the relative effectiveness of lavender in several application modalities. Stage two will proceed based on findings from stage one. If significant parasympathetic effects are observed in relation to one or more of the lavender oil modalities described above, a more focused investigation will be conducted in stage two …

Characterization And Target Identification Of Ak301: A Novel Mitotic Arrest Agent, Michael J. Bond, Avijeet S. Chopra, Marina Bleiler, Michelle Yeagley, Eric Scocchera

University Scholar Projects

The Giardina Laboratory has recently identified AK301 as a novel mitotic arrest agent. This work aimed to characterize the arrest state induced by AK301 (EC₅₀ ~ 150nM) and identify the cellar targets responsible for the arrest. It was found that AK301 arrest is readily reversible upon withdrawal of AK301. Cells that slip from mitosis after removal of AK301 are sensitized to apoptosis. This was found to be unique for AK301 when compared to other mitotic arrest agents like colchicine, vincristine, and BI2536. Arrested cells were found to have increased ATM activity as well as an upregulation of p53 and …

Alternative Pathway For Provision Of Acyl Coa Precursors For Fatty Acid Biosynthesis: Purification And Kinetic Characterization Of Phosphotransbutyrylase And Butyrate Kinase From Listeria Monocytogenes, Sirisha Sirobhushanam

Theses and Dissertations

Listeria monocytogenes is a foodborne pathogen that causes listeriosis, a disease characterized by gastroenteritis, meningitis, spontaneous miscarriages and high mortality rate among infected individuals. L. monocytogenes is a major concern in the food industry, due to its ability to grow at refrigeration temperatures and the zero tolerance policy of the FDA, resulting in expensive food recalls. Growth at low temperatures is aided in part by the high membrane content of branched-chain fatty acids (BCFAs) which imparts greater fluidity to the membrane. Mutants of L. monocytogenes impaired in BCFA biosynthesis display diminished growth at normal and low temperatures, exhibit lower tolerance …

Binding Of Oxygen To Human Hemoglobin Within The Erythrocyte Using Icam Spectrophotometry, Kyle K. Hill

Department of Chemistry: Dissertations, Theses, and Student Research

Many of the spectrophotometric techniques used to determine the properties of intracellular human hemoglobin cannot be utilized due to the turbidity of erythrocyte suspensions. An Integrating Cavity Absorption Meter, or ICAM, allows for absorption measurements of strongly scattering samples in the visible-light region of the spectrum. The spectrum of oxygenated hemoglobin within erythrocytes is significantly different from the absorption spectrum of oxygenated hemoglobin in solution. Studies of the oxygen binding to hemoglobin in erythrocytes allowed the four sequential binding constants (Adair constants) to be determined and compared with those of hemoglobin in solution. The Adair constants for hemoglobin in solution …

Effects Of Creatine, Leucine, And Ethanol On Glial Cell Line-Derived Neurotrophic Factor In C2c12 Skeletal Muscle Cells, Daniel Waters

Honors Theses

Glial Cell Line-Derived Neurotrophic Factor (GDNF) is a protein expressed throughout the mammalian nervous system that serves several protective functions. Originally discovered in the brain, where it supports the survival of dopaminergic neurons, GDNF has since been shown to be expressed in skeletal muscle and is vital for the maintenance of motor neurons. The relationship between muscle hypertrophy, and GDNF is not well understood. The purpose of this study was to examine the relationship between hypertrophy and GDNF by inducing hypertrophy in C2C12 skeletal muscle cells using leucine and creatine, inhibiting hypertrophy using ethanol and measuring GDNF content. As measured …

A Guided Inquiry To The Bromination Of Alkenes: An Effort To Foster Student Understanding Of Thin Layer Chromatography In The Organic Chemistry Laboratory, Casey Wright

Honors Theses

Many of the chemistry laboratories taught at Western Michigan University are “cookbook” labs, meaning that students are given an instruction manual with a prescribed set of instructions and a predicted outcome. Therein we present an introductory organic chemistry laboratory experiment to reinforce the student understanding of Thin Layer Chromatography which utilizes a guided inquiry format as part of an effort to move toward discovery based learning in our organic chemistry curriculum. Educational research was performed on classroom artifacts collected from the laboratory. We were able to gain an understanding of the struggles students face in applying general chemistry content knowledge …

The Pcna-Associated Protein Pari Negatively Regulates Homologous Recombination Via The Inhibition Of Dna Repair Synthesis, Peter Burkovics, Lili Dome, Szilvia Juhasz, Veronika Altmannova, Marek Sebesta, Martin Pacesa, Kasper Fugger, Claus Storgaard Sorensen, Marietta Y W T Lee, Lajos Haracska, Lumir Krejci

NYMC Faculty Publications

Successful and accurate completion of the replication of damage-containing DNA requires mainly recombination and RAD18-dependent DNA damage tolerance pathways. RAD18 governs at least two distinct mechanisms: translesion synthesis (TLS) and template switching (TS)-dependent pathways. Whereas TS is mainly error-free, TLS can work in an error-prone manner and, as such, the regulation of these pathways requires tight control to prevent DNA errors and potentially oncogenic transformation and tumorigenesis. In humans, the PCNA-associated recombination inhibitor (PARI) protein has recently been shown to inhibit homologous recombination (HR) events. Here, we describe a biochemical mechanism in which PARI functions as an HR regulator after …

Novel Compound Heterozygous Mutations Expand The Recognized Phenotypes Of Fars2-Linked Disease, Melissa A. Walker, Kyle Mohler, Kyle W. Hopkins, Derek H. Oakley, David A. Sweetser, Michael Ibba, Matthew P. Frosch, Ronald L. Thibert

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Mutations in mitochondrial aminoacyl-tRNA synthetases are an increasingly recognized cause of human diseases, often arising in individuals with compound heterozygous mutations and presenting with system-specific phenotypes, frequently neurologic. FARS2 encodes mitochondrial phenylalanyl transfer ribonucleic acid (RNA) synthetase (mtPheRS), perturbations of which have been reported in 6 cases of an infantile, lethal disease with refractory epilepsy and progressive myoclonus. Here the authors report the case of juvenile onset refractory epilepsy and progressive myoclonus with compound heterozygous FARS2 mutations. The authors describe the clinical course over 6 years of care at their institution and diagnostic studies including electroencephalogram (EEG), brain magnetic resonance …