Biochemistry Commons^™

Attempted Identification Of The Calcium-Dependent Sodium Channel Gene In Paramecium Tetraurelia Using Rnai, Gwendolyn Kuzmishin

Senior Independent Study Theses

Ion channels play an important role in the swimming behavior of Paramecium tetraurelia. Electrophysiological experiments indicate that a calcium-dependent sodium channel exists in Paramecium, but a gene has not been identified for this channel. It is hypothesized that this channel evolved from a voltage-dependent sodium channel after a whole genome duplication event. In this paper, 13 candidate genes were identified from the Paramecium genome based on their similarity to a reference human voltage-dependent sodium channel. Bioinformatics analysis of the selectivity filter of these putative ion channel genes suggested that at least 8 of the candidate genes were sodium channels …

High Borate Glasses For The Controlled Release Of Therapeutic Metal Ions, Kathleen O'Connell

Theses

Within the biomaterial community significant effort has been directed towards engineering materials that induce precise host responses, which are tailored to specific applications. However, this has also seen an increase in the complexity of some biomaterials, which is being increasingly criticised within the literature, as it is attributed to hindering their clinical utility. In this context the release of therapeutic metal ions from glass-based biomaterials have been shown to promote hard tissue repair and regeneration through angiogenesis and osteogenesis processes. Within this thesis project two separate quaternary high borate glass systems were prepared containing the therapeutic metal ions strontium and …

A Five Residue Insertion Between Codons 28 And 29 Of The Hiv-1 Protease Gene Reduces The Replicative Capacity Of The Virus, Cathy Mcleod

Wayne State University Theses

HIV-1 protease (PR) is a 99 amino acid protein responsible for cleavage of the viral polyprotein. We have identified a novel clinical isolate, MDR/28, which contains a five residue insertion between codons 28 and 29 of a multi-drug resistant (MDR) PR. This clinical isolate displays reduced viral replicative capacity compared to the wild-type. As opposed to drug-resistance mutations, studies on insertions remain largely underrepresented in the literature, and the consequences of such insertions are largely unknown. To understand the mechanism leading to reduced replicative capacity, three PR models were created and subjected to 40ns molecular dynamics simulations: MDR/28, wild type, …

Probing Allosteric, Partial Inhibition Of Thrombin Using Novel Anticoagulants, Stephen S. Verespy Iii

Theses and Dissertations

Thrombin is the key protease that regulates hemostasis; the delicate balance between procoagulation and anticoagulation of blood. In clotting disorders, like deep vein thrombosis or pulmonary embolism, procoagulation is up-regulated, but propagation of clotting can be inhibited with drugs targeting the proteases involved, like thrombin. Such drugs however, have serious side effects (e.g., excessive bleeding) and some require monitoring during the course of treatment. The reason for these side effects is the mechanism by which the drugs’ act. The two major mechanisms are direct orthosteric and indirect allosteric inhibition, which will completely abolish the protease’s activity. Herein we sought an …

Celecoxib Enhances Sorafenib/Sildenafil Lethality In Cancer Cells And Reverts Platinum Chemotherapy Resistance, Timothy A. Webb

Theses and Dissertations

The present studies sought to determine whether the lethality of the drug combination [sorafenib + sildenafil] could be enhanced by the anti-inflammatory agent celecoxib, using ovarian cancer and other tumor cell lines as models. Also, in a dose dependent fashion celecoxib enhanced [sorafenib + sildenafil] lethality in multiple ovarian cancer cell lines. In a dose dependent fashion celecoxib enhanced the ability of [sorafenib + sildenafil] to reduce expression of multiple chaperone proteins in parallel with lower levels of the drug efflux pumps ABCB1 and ABCG2. Over-expression of GRP78 and HSP27 maintained pump expression in the presence of drugs. Cell killing …

The Study Of The Regulon Of Oxyr In Escherichia Coli And Porphyromonas Gingivalis, Christopher K. Pham

Theses and Dissertations

The facultative anaerobe, Escherichia coli and the obligate anaerobe, Porphyromonas gingivalis are two bacteria that reside in our body. Although they reside in separate environments, they are both subject to hydrogen peroxide stress and have mechanisms to regulate the stress. OxyR is the primary transcriptional regulator/sensor of oxidative stress response caused by hydrogen peroxide. OxyR in P. gingivalis is not well-characterized compared to OxyR in E. coli. We sought to characterize and compare the two forms of OxyR in order to gain a better understanding of the protein. We determined the oligomeric state of both proteins: primarily a tetramer for …

Conditional Cardiac-Specific Akap13 Knockout Induces Sex Dependent Biventricular Dilated Cardiomyopathy With Sarcomeric And Mitochondrial Defects, Kimberlyn M. Baig-Ward

Theses and Dissertations

Heart disease is a complex and heterogeneous disease. Notably, studies have demonstrated gender differences in the expression and types of cardiovascular disease, such as dilated cardiomyopathy (DCM), a major underlying cause of heart failure. Previously we showed that loss of A-Kinase Anchoring Protein 13 (Akap13), a unique proto-oncogene and estrogen receptor modulator, resulted in enlarged embryonic hearts, defective cardiac sarcomere formation, and embryonic lethality in mice. Data have also shown cAMP-dependent Protein Kinase A (PKA) to be involved in DCM pathophysiology. Given the established role of AKAP13 in cell signaling, its ability to bind and modulate ligand-activated nuclear hormone …

Atm Phosphorylates Subunit A Of Pp2a Resulting In Its Nuclear Export And Spatiotemporal Regulation Of The Dna Damage Response, Amrita D. Sule

Theses and Dissertations

Ataxia telangiectasia mutated (ATM) is a serine-threonine protein kinase and major regulator of the DNA damage response (DDR). One critical ATM target is protein phosphatase 2A (PP2A) known to regulate diverse cellular processes such as mitosis and cell growth as well as dephosphorylation of many proteins during the recovery from the DDR while returning the cell to normalcy. Interestingly, ATM and PP2A are known to form an auto-regulatory yin-yang kinase-phosphatase relationship. Herein, we show that the phosphorylation of the PP2A-Aα structural subunit at S401 by ATM results in nuclear export, which regulates the DDR at multiple levels and affects genomic …

Deep Models For Brain Em Image Segmentation: Novel Insights And Improved Performance, Ahmed Fakhry, Hanchuan Peng, Shuiwang Ji

Computer Science Faculty Publications

Motivation: Accurate segmentation of brain electron microscopy (EM) images is a critical step in dense circuit reconstruction. Although deep neural networks (DNNs) have been widely used in a number of applications in computer vision, most of these models that proved to be effective on image classification tasks cannot be applied directly to EM image segmentation, due to the different objectives of these tasks. As a result, it is desirable to develop an optimized architecture that uses the full power of DNNs and tailored specifically for EM image segmentation.

Results: In this work, we proposed a novel design of DNNs for …

The Role Of Oxidative Stress In The Mechanisms Of Ammonia-Induced Brain Swelling And Tolerance In The Goldfish (Carassius Auratus), David F. Jones Lisser Mr.

Theses and Dissertations (Comprehensive)

Toxic build-ups of ammonia can cause potentially fatal brain swelling in mammals, but such swelling is reversible in the anoxia- and ammonia-tolerant goldfish (Carassius auratus). The mechanisms of ammonia-induced brain swelling and tolerance remain elusive, but several studies have suggested a role for reactive oxygen species (ROS), which may damage proteins and lipids in the plasma membrane of astrocytes in the brain. As a result, osmotic gradients across cell membranes may be altered leading to water uptake by astrocytes and swelling. While a role for ROS has been proposed in mammals, no studies have addressed this question in …

The Kinetic Characterization Of Two Putative Galactosidases, Bt2857 And Sco6594, And The Preliminary Analyses Of Sco6595-97, Maria Ngo

Theses and Dissertations (Comprehensive)

Bacteroides thetaiotaomicron is a prolific bacterium found in the distal intestinal tract of humans that possesses the ability to breakdown complex polysaccharides through the release of carbohydrate-active enzymes (CAZymes). Overall, the saccharolytic prowess of B. thetaiotaomicron presents an intriguing model for understanding microbial-host nutrient exchange within the gut and to identify novel mechanisms for accessing carbohydrates. The successful expression, purification, and preliminary kinetic characterization of BT2857 are reported. BT2857 was found to be enzymatically active against the artificial substrate, 4-nitrophenyl β-D-galactopyranoside (pNP-Gal); suggesting its role as a putative β-galactosidase and allowed for the quantification of BT2857 activity by the determination …

Characterization Of A Phosphonate-Specific Cytidylyltransferase, Kissa Batul

Theses and Dissertations (Comprehensive)

Antibiotic resistance is a major global health concern that requires new therapeutic approaches. Furthermore, a lack of narrow spectrum antibiotics on the market produces unintended consequences with respect to changes in our microbial make up. Phosphonates are reduced versions of phosphates that possess a C-P bond which is more resistant to enzymatic and chemical degradation. The role of phosphonate containing macromolecules (e.g. cell surface polysaccharides) remains enigmatic, however their presence suggests that they may confer an advantage. The biosynthesis of phosphonate-containing macromolecules is unknown, but a pathway is proposed involving aLicC type cytidylyltransferase-catalyzed conjugation to a phosphonate followed by a …

Superior Inhibitory Control And Resistance To Mental Fatigue In Professional Road Cyclists, Kristy Martin, Walter Staiano, Paolo Mensaspa, Tom Hennessey, Samuele M. Marcora, Richard J. Keegan, Kevin G. Thompson, David T. Martin, Shona R. Halson, Ben Rattray

Research outputs 2014 to 2021

Purpose:

Given the important role of the brain in regulating endurance performance, this comparative study sought to determine whether professional road cyclists have superior inhibitory control and resistance to mental fatigue compared to recreational road cyclists.

Methods:

After preliminary testing and familiarization, eleven professional and nine recreational road cyclists visited the lab on two occasions to complete a modified incongruent colour-word Stroop task (a cognitive task requiring inhibitory control) for 30 min (mental exertion condition), or an easy cognitive task for 10 min (control condition) in a randomized, counterbalanced cross-over order. After each cognitive task, participants completed a 20-min time …

Metabolomics Enables Precision Medicine: “A White Paper, Community Perspective”, Richard D. Beger, Warwick B. Dunn, Michael A. Schmidt, Steven S. Cross, Jennifer A. Kirwan, Marta S. Cascante, Lorraine Brennan, David S. Wishart, Matej Orešič, Thomas Hankemeier, David Broadhurst, Andrew N. Lane, Karsten Suhre, Gabi Kastenmüller, Susan J. Sumner, Ines Thiele, Oliver E. Fiehn, Rima Kaddurah- Daouk

Research outputs 2014 to 2021

Introduction:Background to metabolomics:

Metabolomics is the comprehensive study of the metabolome, the repertoire of biochemicals (or small molecules) present in cells, tissues, and body fluids. The study of metabolism at the global or “-omics” level is a rapidly growing field that has the potential to have a profound impact upon medical practice. At the center of metabolomics, is the concept that a person’s metabolic state provides a close representation of that individual’s overall health status. This metabolic state reflects what has been encoded by the genome, and modified by diet, environmental factors, and the gut microbiome. The metabolic profile provides …

The Effect Of Posttranslational Modifications On Protein Aggregation, Morphology, And Toxicity, Mu Yang

Dissertations, Master's Theses and Master's Reports

Proteins are one of the most versatile macromolecules in the biological system. The function or activity of a protein highly depends on its 3D native structure. However, under stress, they are at risk of misfolding/aggregation, leading to formation of structures that can indicate loss of function or gain of toxicity. In severe cases, protein aggregation can result in many diseases, including neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, Huntington’s, and amyotrophic lateral sclerosis. Due to the heterogeneous nature of cellular environment and protein molecules, mechanism of in vivo folding and related toxicity still remains elusive. To have a better understanding of …

A Biophysical Study Of The Ion Transport Mechanism In Uncoupling Protein 2 By Investigating The Role Of Lysine Residues In Its Matrix Network, Stephanie O. Uwumarenogie

Theses and Dissertations (Comprehensive)

ABSTRACT

Uncoupling protein 2 (UCP2) is one of five UCP homologues found in the inner mitochondrial membrane that transports protons from the intermembrane space to the mitochondrial matrix. In turn, the proton motive force is dissipated and less ATP is produced in the mitochondria. UCP2 is proposed to influence insulin secretion in type II diabetes, and decrease the amount of reactive oxygen species produced in the mitochondria, however the detailed mechanism of ion (proton and anions) transport in UCP2 and other UCP homologues are not fully understood. Sequence alignment analysis performed on proteins in the mitochondrial carrier family (MCF) including …

Reduction Of Oxidative Stress And Storage Lesions (Rcsl) In Red Blood Cells - Analysis Of Ascorbic Acid (Aa), N-Acetylcysteine Amide (Ad4), And Serotonin (5-Ht), Shanmuka Gadiraju

Undergraduate Research Posters

Oxidative stress is a common occurrence in red blood cell (RBC) storage in blood banks throughout the world. Typically RBC units stored under routine standard protocol (stored in SAGM-CPD additive solution) can only be kept up to 42 days for transfusion usage before being discarded. I am studying the effects of Ascorbic Acid (AA), N-acetylcysteine amide (AD4), and Serotonin (5-HT) as additives in blood bank storage because I want to find out if these additives can reduce storage-induced oxidative stress on red blood cells (RBCs), in order to help my reader understand how potential blood storage additives can affect the …

Confirmation Of Emx2 Protein Binding Partners, Cody Gillman

All Master's Theses

The neocortex is a structure within mammalian brains that processes sensory input from eyes, ears, and touch receptors and mediates the conscious use of skeletal muscles. The processing of information related to each of these types of functions is localized within discrete areas of the neocortex, which are separated by sharp borders. Proper development of these functional areas is regulated during embryogenesis by several transcription factors that are expressed in distinct gradients across the progenitor layer of the neocortex, the ventricular zone. Despite the vast amount of progress that has been made in describing how these transcription factors impact the …

Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion In Protein Lysine Methyltransferase Smyd2, Nicholas Spellmon, Xiaonan Sun, Nualpun Sirinupong, Brian Fp Edwards, Chunying Li, Zhe Yang

Biochemistry and Molecular Biology Faculty Publications

SMYD proteins are an exciting field of study as they are linked to many types of cancer- related pathways. Cardiac and skeletal muscle development and function also depend on SMYD proteins opening a possible avenue for cardiac-related treatment. Previous crystal structure studies have revealed that this special class of protein lysine methyltransferases have a bilobal structure, and an open–closed motion may regulate substrate specificity. Here we use the molecular dynamics simulation to investigate the still-poorly-understood SMYD2 dynamics. Cross-correlation analysis reveals that SMYD2 exhibits a negative cor- related inter-lobe motion. Principle component analysis suggests that this correlated dynamic is contributed to …

Alternative Use Of Dna Binding Domains By The Neurospora White Collar Complex Dictates Circadian Regulation And Light Responses, Bin Wang, Xiaoying Zhou, Jennifer J. Loros, Jay C. Dunlap

Dartmouth Scholarship

In the Neurospora circadian system, the White Collar complex (WCC) of WC-1 and WC-2 drives transcription of the circadian pacemaker gene frequency (frq), whose gene product, FRQ, as a part of the FRQ-FRH complex (FFC), inhibits its own expression. The WCC is also the principal Neurospora photoreceptor; WCC-mediated light induction of frq resets the clock, and all acute light induction is triggered by WCC binding to promoters of light-induced genes. However, not all acutely light-induced genes are also clock regulated, and conversely, not all clock-regulated direct targets of WCC are light induced; the structural determinants governing the shift …

Period-1 Encodes An Atp-Dependent Rna Helicase That Influences Nutritional Compensation Of The Neurospora Circadian Clock, Jillian M. Emerson, Bradley M. Bartholomai, Carol S. Ringelberg, Scott E. Baker, Jennifer Loros, Jay Dunlap

Dartmouth Scholarship

Mutants in the period-1 (prd-1) gene, characterized by a recessive allele, display a reduced growth rate and period lengthening of the developmental cycle controlled by the circadian clock. We refined the genetic location of prd-1 and used whole genome sequencing to find the mutation defining it, confirming the identity of prd-1 by rescuing the mutant circadian phenotype via transformation. PRD-1 is an RNA helicase whose orthologs, DDX5 [DEAD (Asp-Glu-Ala-Asp) Box Helicase 5] and DDX17 in humans and DBP2 (Dead Box Protein 2) in yeast, are implicated in various processes, including transcriptional regulation, elongation, and termination, ribosome biogenesis, and mRNA decay. …

Characterization Of Cytidylyltransferase Enzyme Activity Through High Performance Liquid Chromatography, James Brault

Theses and Dissertations

The cytidylyltransferases are a family of enzymes that utilize cytidine 5â?? triphosphate (CTP) to synthesize molecules that are precursors to membrane phospholipids. There are four well known enzymes: CTP: phosphoethanolamine cytidylyltransferase (ECT), CTP: glycerol-3-phosphate cytidylyltransferase (GCT), 2-C-methyl-D-erythritol-4-phosphate cytidylyltransferase synthetase (CMS), and CTP: phosphocholine cytidylyltransferase (CCT). Previously, a radioisotope tagging method was employed to study cytidylyltransferase catalysis. Using CCT as a model, a method utilizing high performance liquid chromatography (HPLC) was developed to replace the radioisotope scintillation technique. The development of this new HPLC method is cheaper, more efficient, and more accurate than the previously established method.

The targets of separation …

Regulation Of The Transmembrane Mucin Muc4 By Wnt/Β-Catenin In Gastrointestinal Cancers, Priya Pai

Theses & Dissertations

The transmembrane mucin MUC4 is a high molecular weight glycoprotein that is expressed de novo in pancreatic ductal adenocarcinoma (PDAC). MUC4 has been shown to play a tumor-promoting role in malignancies such as PDAC, ovarian cancer and breast cancer. Unlike the normal pancreas, MUC4 is ordinarily expressed by goblet and absorptive cells in the normal colonic epithelium. However, its expression/role in colorectal cancer (CRC) is not well studied.

In this dissertation, the goal was to identify factor(s) that may differentially regulate MUC4 in these two disparate malignancies. Furthermore, in light of its pro-tumorigenic role in other malignancies, we analyzed the …

Ubiquitin Goes Green, Zhihua Hua, Richard D. Vierstra

Biology Faculty Research

Chloroplasts depend on the nucleus for much of their proteome. Consequently, strong transcriptional coordination exists between the genomes, which is attuned to the developmental and physiological needs of the organelle. Recent studies highlight that the post-translational modifier ubiquitin adds another layer to plastid homeostasis and even helps eliminate damaged chloroplasts.

Microsolvation Of Anions By Molecules Forming Ch∙∙X- Hydrogen Bonds, Steve Scheiner, Binod Nepal

Chemistry and Biochemistry Faculty Publications

Various anions were surrounded by n molecules of CF₃H, which was used as a prototype CH donor solvent, and the structures and energies studied by M06-2X calculations with a 6-31+G∗∗ basis set. Anions considered included the halides F^-, Cl^-, Br^- and I^-, as well as those with multiple proton acceptor sites: CN^-, NO₃ ^-, HCOO^-, CH₃COO^-, HSO₄ ^-, H₂PO₄ ^-, and anions with higher charges SO₄ ^2-, HPO₄ ^2- and PO_{4 …}

Aggregation Characterization Of Wild-Type P53 And Six Common P53 Mutants, Taylor A. Arhar

Honors Thesis

P53 is a tumor suppressor protein, which functions in maintaining the cell cycle. When p53 loses its function, cells may multiply at an uncontrolled rate and form tumors. This loss of function is linked to over fifty percent of human cancers. This investigation aims to explore the possible link between p53 aggregation and tumorigenesis. There is a possibility that p53, especially in mutant form, will aggregate beyond its normal tetrameric conformation and lose its function, leading to tumor formation. Wild-type p53 and six mutants, R175H, R175C, R248Q, R248W, R273C, and R273H (six of the most common mutations found in human …

Reactive Oxygen Species Homeostasis And Proline Catabolism, Lu Zhang

Department of Biochemistry: Dissertations, Theses, and Student Research

The role of proline metabolism in regulating cellular redox status was first proposed three decades ago. Proline catabolism was then later found to induce programmed cell death and cell apoptosis by regulating ROS signaling. Proline oxidation was also found to promote cell survival under oxidative stress. Proline catabolism-mediated reactive oxygen species (ROS) were suggested to be involved in both cases by serving as a regulatory signal. In this work, the sources of proline oxidation-induced ROS production were explored in both bacteria and animal cells. Proline oxidation-induced ROS was found to be shared by bacteria (Escherichia coli) and animals …

Investigation Of The Inherent Chemical, Structural, And Mechanical Attributes Of Bio-Engineered Composites Found In Nature: Alligator Gar’S Exoskeleton Fish Scales, Wayne Derald Hodo

Graduate Theses and Dissertations

The U.S. Army has determined a huge cost savings of up to 51% can be accomplished by reducing the gross vehicle weight, for their personnel carrier, by 33%. To cut cost, composite materials are needed. Man-made composites can have superior material properties (high-strength, high-fracture toughness, and lightweight), but they are prone to delamination at the glued-layered interface. In contrast, fish scale is a natural composite that has the same material properties and, additionally, tend not to delaminate.

The focus of this study was to learn how nature integrates hard and soft materials at each length scale to form a layered …

Effect Of Raised Body Fat On Vitamin D, Leptin And Bone Mass, Syeda Sadia Fatima, Saad Farooq, Maaida Asif Tauni, Omar Irfan, Faiza Alam

Department of Biological & Biomedical Sciences

Objective: To estimate leptin, vitamin D and bone mineral density levels in individuals with high fat mass, and to assess any correlation.Methods: The cross-sectional study was conducted at the Basic Medical Sciences Institute, Jinnah Post Graduate Medical Centre, Karachi, and Aga Khan University, Karachi, from August 2012 to July 2014, and comprised healthy male volunteers between the ages of 18-60 years. Body fat percentage was determined using bioelectrical impedance analysis and the participants were classified as: Group A (15-21.9); Group B (22-27.9); and Group C ( > 28). Bone mineral density was calculated by ultrasound bone densitometer (T-score between +1 and …

Fsh/Lh Ratio In Females And Intracytoplasmic Sperm Injection, Rehana Rehman, Hareem Syed, Najeeha Talat Iqbal, Sara Arif, Saeeda Sheharyar

Department of Biological & Biomedical Sciences

Objective: To observe the effect of follicle stimulating hormone-luteinizing hormone ratio on oocyte parameters, quality of embryo, implantation and clinical pregnancy rate after intracytoplasmic sperm injection.
Methods: The retrospective study was conducted at a fertility clinic in Islamabad, Pakistan, and comprised data of primary infertile females who underwent intracytoplasmic sperm injection from June 2011 to March 2013. All subjects had duration of infertility more than two years, and age range was 20-40 years. Follicle stimulating hormone and luteinizing hormone were estimated by enzyme-linked immunosorbent assay on day 3 of the cycle and the ratio was calculated. Groups were stratified on …