Biochemistry Commons^™

Modulatory Effects Of Deacetylated Sialic Acids (A Sugar Residue) In Nk-Mediated Cytotoxicity And Targeted Therapy By Receptor Tyrosine Kinase Inhibitors, Mathias Tawiah Anim

Electronic Theses and Dissertations

The complex nature of the biology of cancer is still an unraveling science, yielding several biomarkers that have served as molecular targets for detection and treatment of the disease. How sugars, glycans, play a role has remained relatively uninvestigated. Sialic acid (Sia), a sugar residue on the surface of cells, has been identified as a hallmark of cancer and its progression. Sialic acid can be highly functionalized, but we became interested in acetylated Sias. This functional group is modulated by Sialate O- acetylesterase (encoded by the gene SIAE) and Sialate O-acetyltransferase (encoded by CASD1), enzymes that play a crucial role …

Approaches To Avoid Proteolysis During Protein Expression And Purification, Gary T. Henehan, Barry J. Ryan, Gemma K. Kinsella

Books/Book Chapters/ Proceedings

All cells contain proteases, which hydrolyze the peptide bonds between amino acids of a protein backbone. Typically, proteases are prevented from nonspecific proteolysis by regulation and by their physical separation into different subcellular compartments; however, this segregation is not retained during cell lysis, which is the initial step in any protein isolation procedure. Prevention of proteolysis during protein purification often takes the form of a two-pronged approach: first, inhibition of proteolysis in situ, followed by the early separation of the protease from the protein of interest via chromatographic purification. Protease inhibitors are routinely used to limit the effect of the …

Structural And Spectroscopic Study Of New Copper(Ii) And Zinc(Ii) Complexes Of Coumarin Oxyacetate Ligands And Determination Of Their Antimicrobial Activity, Muhammad Mujahid, Natasha Trendafilova, Georgina Rosair, Kevin Kavanagh, Maureen Walsh, Bernadette Creaven, Ivelina Georgieva

Articles

Tackling antimicrobial resistance is of increasing concern in a post-pandemic world where overuse of antibiotics has increased the threat of another pandemic caused by antimicrobial-resistant pathogens. Derivatives of coumarins, a naturally occurring bioactive compound, and its metal complexes have proven therapeutic potential as antimicrobial agents and in this study a series of copper(II) and zinc(II) complexes of coumarin oxyacetate ligands were synthesised and characterised by spectroscopic techniques (IR, 1H, 13C NMR, UV-Vis) and by X-ray crystallography for two of the zinc complexes. The experimental spectroscopic data were then interpreted on the basis of molecular structure modelling and subsequent spectra simulation …

Structural Files For The Etr1 Ethylene-Receptor Dimer Based On Computational Modeling, Beenish J. Azhar, Safdar Abbas, Sitwat Aman, Maria V. Yamburenko, Wei Chen, Lena Muller, Buket Uzun, David A. Jewell, Jian Dong, Samina N. Shakeel, Georg Groth, Brad M. Binder, Gevorg Grigoryan, G. Eric Schaller

Dartmouth Scholarship

Structural models for the ETR1 homodimer were generated with AlphaFold-Multimer. Coppers were modeled under two potential coordinations involving Cys65 and His69 of the ETR1 homodimer, one in which the two coppers are bound independently and do not share an interaction with each other, and another where they are closely bonded.

See the following publication for details: Azhar, B.J., Abbas, S., Aman, S., Yamburenko, M.V., Chen, W., Müller, L., Uzun, B., Jewell, D.A., Dong, J., Shakeel, S.N., Groth, G., Binder, B.M., Grigoryan, G., Schaller, G.E. (2023) Basis for high-affinity ethylene binding by the ethylene receptor ETR1 of Arabidopsis. Proc. Natl. Acad. …

Design Of Block Copolymer With Tunable Hydrophobic/Hydrophilic/Fluorophilic Interactions, Tatiane De Fatima Dutra

Theses, Dissertations and Culminating Projects

Block copolymers (BCP) with balanced interactions and their resultant bulk-phase self-assembly have become increasingly important in advancing nanotechnology, separation, and energy applications. However, a few reports have addressed the synthesis challenge and bulk-phase self-assembly of such triblock copolymers. This thesis presents a facile route for preparing triblock copolymer via controlled radical and organocatalytic ring-opening polymerization that allows precise control over the incorporation of individual moieties in resultant polymer, responsible for balanced hydrophilic, hydrophobic/lipophilic, and fluorophilic interactions. Synthesized polymer with suggested self-assembled 2D lamellar nanostructure exhibits high-temperature stability. The long-term goal of this work is to selectively use this polymer class …

A Computational Study Of The Copper-Catalyzed Trifluoromethylation Of Boronic Acids, Kevin Nyhuis

Theses, Dissertations and Culminating Projects

This work is a computational study of a reaction mechanism for the trifluoromethylation of boronic acids. Three steps of the proposed reaction mechanism are studied, •CF₃ addition to a copper catalyst center, base promoted transmetalation between copper and aryl boronic acid, and bond forming reductive elimination in which the CF₃ and aryl substituent form a bond. Limited information is known about this mechanism. This study uses computational methods to attempt to elucidate the mechanism and provide the groundwork for potential improvement. Quantum chemical methods in conjunction with tight-binding based conformational sampling methods are used to investigate the possible …

Investigating The Roles Of Active Site Residues K59, K119 And E168 In M. Tuberculosis Indole-3-Glycerol Phosphate Synthase, Maryum M. Bhatti

Theses, Dissertations and Culminating Projects

Tuberculosis (TB) is a disease that is caused by a bacteria called Mycobacterium tuberculosis and primarily attacks the lungs but can spread to other areas of the body as well. TB can develop resistance to drugs that may be used to cure the disease. Multidrug resistant TB is especially a growing issue as it does not respond to the two most powerful anti-TB drugs, isoniazid and rifampicin. For this reason, finding new ways to target TB are critically needed. One possible way to do this is to target the enzymes in the tryptophan biosynthetic pathway of M. tuberculosis. Studies have …

Arginine-178 Is An Essential Residue For Itpa Function, Nicholas E. Burgis, Caitlin April, Kandise Vanwormer

Chemistry and Biochemistry Faculty Publications

The inosine triphosphate pyrophosphatase (ITPA) enzyme plays a critical cellular role by removing noncanonical nucleoside triphosphates from nucleotide pools. One of the first pathological ITPA mutants identified is R178C (rs746930990), which causes a fatal infantile encephalopathy, termed developmental and epileptic encephalopathy 35 (DEE 35). The accumulation of noncanonical nucleotides such as inosine triphosphate (ITP), is suspected to affect RNA and/or interfere with normal nucleotide function, leading to development of DEE 35. Molecular dynamics simulations have shown that the very rare R178C mutation does not significantly perturb the overall structure of the protein, but results in a high level of structural …

Role Of Grb2 Intracellular Localization In Progesterone Receptor Positive Breast Cancer, Nattamolphan Wittayavimol

Chulalongkorn University Theses and Dissertations (Chula ETD)

Progesterone receptor (PR) extranuclear signaling mediates mainly through PR polyproline domain (PPD) interaction with SH3 domain of cytoplasmic signaling molecules. PR-PPD interfered with Grb2-SOS binding through SH3 interaction resulting in decreased cell proliferation and correlates with a good prognosis in PR positive breast cancer. Grb2 is a key adaptor molecule and expressed in both nucleus and cytoplasm. We hypothesized that change in Grb2 localization alters PR transcription resulting in better clinical outcomes in PR positive breast cancer. BT-474 breast cancer cells expressing inducible Grb2-SV402x (nuclear Grb2, nuGrb2) or Grb2-MYR (membrane Grb2, memGrb2) were constructed. MemGrb2-BT-474 showed higher levels of PR …

Roles Of Progesterone Signaling On Dna Repair And Cell Survival In Ovarian Cancer Cells, Pattarasiri Rangsrikitphoti

Chulalongkorn University Theses and Dissertations (Chula ETD)

Every year over 300,000 women worldwide are diagnosed with ovarian cancer and half of these patients die from this disease. The symptoms of ovarian cancer are very general and often confused with other common female diseases making ovarian cancer a challenging disease to diagnose and treat. Platinum-based chemotherapy, including cisplatin, stands as the first-line treatment for ovarian cancer. However, chemotherapy resistance remains a continuing problem, contributing to a high mortality rate. Progesterone receptor (PR) signaling has been implicated in various aspects of ovarian cancer biology. Clinical studies show a positive correlation between PR expression, improved patient survival and cisplatin response, …

Cisplatin - Loaded Calcium Citrate Nanoparticlesfor Inhibition Of Lung Cancer Cell Growthand Quantum Mechanical Study Of Cisplatin And Citrate, Lipika Oopkaew

Chulalongkorn University Theses and Dissertations (Chula ETD)

The International Organization for Research on Cancer (International Agency for Research on Cancer (IARC) issued a statement saying lung cancer is a cancer with high incidence rates of new cases and deaths. Although there are current therapeutic approaches such as surgery, radiation therapy, and chemotherapy. However, these treatments exhibit ineffectiveness; the main limitation is severe side effects to normal cells or non-target organs. To address this challenge, the development of targeted therapy by nanoparticle-based drug delivery system is applied to increase drug stability and control the specificity to cancer cells with target-specific proteins that play an important role in intracellular …

The Molecular Mechanisms Of Ifn-Γ Promoted Necroptosis In Macrophages, Meghan R. Vogt

Biotechnology Theses

Necroptosis, a form of programmed lytic cell death, has emerged as a driving factor in the pathogenesis of acute lung injury. One specific inflammatory mediator that is of interest is interferon-γ (IFN-γ). Our laboratory has reported that IFN-γ is the most potent enhancer of necroptosis in primary lung epithelial cells and macrophages by upregulating MLKL expression. How IFN-γ enhances necroptosis and MLKL upregulation is currently unknown. In this research, we utilized multiple approaches to study the potential molecular mechanisms of IFN-γ promoted necroptosis in macrophages. We found that MLKL and ZBP1 are significantly upregulated by IFN-γ through an unknown pathway …

Investigating The Relationship Between Metabolic Reprogramming And Peripheral Cd4+ T-Cell Inflammation In Human Type 2 Diabetes Pathogenesis, Gabriella Kalantar

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Chronic, low-grade systemic inflammation rises in obesity and promotes type 2 diabetes (T2D). Circulating immune cells are key indicators of obesity and T2D pathogenesis. T cells outnumber monocytes, in blood, suggesting that T cells might fuel peripheral inflammation in obesity/T2D. Our lab’s work supports this idea by identification of a Th17 cytokine profile in T2D from T-cell stimulated peripheral blood mononuclear cells. Work described herein further supported this work by demonstrating that T cells dominate peripheral inflammation over monocytes across the spectrum of obesity and glycemic control. Our lab has also recently shown that inflammation changes during prediabetes (preT2D), identified …

Developing A Biocatalytic Toolbox To Aid In Understanding Nucleoside Antibiotics, Jasmine Brianna Woods

Theses and Dissertations--Pharmacy

Antibiotic resistance happens when bacteria develop the ability to survive medications that normally terminate them. Instead, these super germs are able to survive in the body and produce a community of antibiotic resistance germs which can cause human fatalities. It is important to discover and develop new compounds and molecules that will improve this clinical obstacle. This research focused on analyzing the biosynthesis that incorporates distinctive chemical characteristic of various nucleoside antibiotics, ß-hydroxy amino acids and α-methyl-amino acids. ß-hydroxy amino acids and α-methyl-amino acids are considered an important class of industrially useful compounds, particularly for pharmaceutical development, and are found …

Impact Of Sample Conditions On Dna Phosphodiester Backbone Bi/Bii Conformational Equilibrium Dynamics, Autumn C. Pilarski

Graduate Theses/Dissertations

DNA damage, such as single base lesions and mismatches, is highly prevalent within cells. If these DNA damage events are not repaired, they could lead to mutations and thus disease and cancer. Intricate repair mechanisms are in place to fix these damage events, one such being Base Excision Repair (BER) and associated enzyme: Thymine DNA Glycosylase (TDG). The first step of this repair process, recognition of the lesion by TDG, is not well understood. The following thesis presents results to better understand the fundamental biophysical question of how a DNA lesion within a mismatch context is recognized in a million …

Investigation Of Mechanical Regulation On Stat3 Activity And Mmp Production, Jaxson R. Libby

Honors Theses and Capstones

Transcription factor, STAT3, is inappropriately expressed in cancer cells, and has contrasting activation in 2D versus 3D microenvironments. 2D plates are often used for drug screening and do not always recapitulate in vivo responses. To combat inaccurate 2D drug studies, a 3D hydrogel was created to support the growth of cancer cells into a tumor-like environment. The hydrogel consists of a biocompatible dextran homopolysaccharide, cell adhesion RGD sequences, and crosslinker MMP labile peptides. A pH dependent reaction couples the RGD sequences to dextran then the polymers are crosslinked into a gel. Crosslinking is accomplished using terminal cysteine peptide sequences, allowing …

Molecular Mechanisms Of Wild-Type And Mutant Prion Formation, Daniel J. Walsh

Dartmouth College Ph.D Dissertations

Prion diseases are a class of infectious neurodegenerative disorders which affect humans and many other mammalian species. The causative agent is a unique pathogen known as a prion or PrPSc, a misfolded form of a host-encoded glycoprotein which replicates by templated conformational change. Distinct strains of prions with unique phenotypic and pathologic presentations appear to be encoded by subtle conformational changes within the misfolded protein. While the general manner of prion transmission is known, our detailed understanding of these mechanisms remains incomplete, limiting efforts for the discovery or design of therapeutic treatments for these fatal diseases. In vitro synthesis of …

Mitochondrial Division: Synergizing In Mitochondrial Divisome, Ao Liu

Dartmouth College Ph.D Dissertations

Mitochondria are the energy factories of the cell. The dynamic nature of cells demands routine changes in mitochondrial morphology by fusion and division. The dynamin GTPase Drp1 is a central mitochondrial division protein, driving constriction of the outer mitochondrial membrane via oligomerization. At least four regulatory factors control Drp1 activity on the outer mitochondrial membrane (OMM): 1) receptor proteins (Mff, MiD49, MiD51, and Fis1); 2) actin filaments; 3) the mitochondrial phospholipid cardiolipin (CL); and 4) Drp1 post-translational modifications, of which two phosphorylation sites (S579 and S600) are the most well studied. However, the molecular mechanism of how these factors work …

Biogeography Of Special Metabolites Produced By Ant-Associated Bacteria, Katherine Hansen

Scripps Senior Theses

There is an urgent and growing need for novel antibiotics with the growing prevalence of antibiotic-resistant pathogens. Ecologically-guided discovery is a strategy that focuses on how and where specially evolved metabolites such as antibiotics are used in nature. This strategy reveals unique active molecules with potential for human use. An unexplored niche with great potential for antibiotic discovery exists with Southwestern fungus-farming Trachymyrmex ants and their Actinobacteria symbionts. In exchange for nutrients from the ant, the ants’ bacterial symbiont produces antifungal molecules that protect the ants’ fungal cultivar from invasion by pathogenic microorganisms. They also produce antibacterial molecules to protect …

Determination Of The Effects Of Added Methionine On The Toxicity Of Platinum Drugs In Saccharomyces Cerevisiae, Kassidy Owens, Jonathan White

Longwood Senior Thesis Proposal

Platinum (Pt) drugs are used in about half of all anticancer treatments. A common way to study Pt drugs is by using S. cerevisiae (brewer’s yeast) as a model cellular organism. One of the most commonly-used strains of yeast is BY4741, which is auxotrophic for (cannot synthesize) several small-molecule nutrients, including the amino acid methionine. Therefore, methionine must be supplemented in the cell culture medium. Interestingly, it is known that methionine can react with Pt compounds, including Pt drugs. Methionine-supplemented media continues to be used to study Pt drugs in yeast, especially BY4741, yet the potential for methionine to interfere …

Investigating Visinin-Like Protein 1 And Ubiquitinated Visinin-Like Protein 1 As Mild Traumatic Brain Injury Biomarkers, Yueming Wu

Theses and Dissertations--Chemistry

Traumatic brain injury (TBI) continues to be a significant cause of morbidity and mortality worldwide. Despite significant progress in understanding the complex pathophysiology of TBI, the underlying mechanisms remain poorly understood. The primary brain damage is acute and irreversible. However, secondary brain injuries often develop gradually over months to years, creating an opportunity for critical therapeutic interventions. In the past decade, research on TBI biomarkers has seen significant progress. This progress has been driven by the diverse nature of TBI pathologies and the challenges they present for evaluation, management, and prognosis. TBI biomarker proteins resulting from axonal, neuronal, or glial …

Extension Of The Ergot Alkaloid Gene Cluster, Samantha Joy Fabian

Graduate Theses, Dissertations, and Problem Reports (ETD)

Specialized metabolites produced by fungi impact human health. A large portion of the pharmaceuticals currently on the market are derived from metabolites biosynthesized by microbes. Ergot alkaloids are a class of fungal metabolites that are important in the interactions of environmental fungi with insects and mammals and also are used in the production of pharmaceuticals. In animals, ergot alkaloids can act as partial agonists or antagonists at receptors for 5-hydroxytryptamine (serotonin), dopamine, and noradrenaline as ergot alkaloids have chemical structures similar to those neurotransmitters. Therefore, they affect insects and mammals that consume them and can be used to produce drugs …

Identification And Functional Characterization Of Mads-Box Proteins And Ccos Involved In Carotenoid Metabolism In Durian Durio Zibethinus L. Pulps, Kittiya Tantisuwanichkul

Chulalongkorn University Theses and Dissertations (Chula ETD)

Durian (Durio zibethinus L.), known as the "King of fruits," holds significant economic importance in Thailand. Apart from its unique odor and sweet taste, durian pulp exhibits a yellow color, which is an important aspect of fruit quality. Carotenoids are essential compounds responsible for the yellow, orange, and red coloration in many fruits and vegetables. During durian fruit development and ripening processes, its pulp changes from white to yellow due to increased carotenoid accumulation. The carotenoid biosynthetic pathway, responsible for carotenoid production, is controlled by ethylene. However, the mechanism underlying this process in durian fruit is still unknow. Notably, the …

Producing Grnas For Use In Crispr-Cas9 Dna Editing Applications Via In Vivo T7 Rna Polymerase Transcription In Escherichia Coli., Christian A. Santiago

Honors Program Theses

The development of the CRISPR-Cas9 system is widely considered to be a breakthrough advancement in gene editing. Compared to traditional technologies, CRISPR is generally regarded as the most accessible, effective, and precise tool for inducing stable and inheritable gene edits in vivo. The CRISPR-Cas9 gene editing complex relies on the complementary binding of guide RNAs to specifically target a DNA sequence for endonuclease cleavage and mutagenesis. The production of gRNAs for use in CRISPR applications can become exceedingly complex and costly, as in vivo methodologies generally require the use of RNA polymerases that interfere with gRNA sequence identity and in …

Lead Induced Differences In Bone Properties In Osteocalcin +/+ And −/− Female Mice, G. Yildirim, W. C. Budell, O. Berezovska, S. Yagerman, S. S. Maliath, P. Mastrokostas, S. Tommasini, T. L. Dowd

Publications and Research

Lead (Pb) toxicity is a major health problem and bone is the major reservoir. Lead is detrimental to bone, affects bone remodelingand is associated with elderly fractures. Osteocalcin (OC) affects bone remodeling, improves fracture resistance and decreases with age and in some diseases. The effect of lead in osteocalcin depleted bone is unknown and of interest. We compared bone mineral properties of control and Pb exposed (from 2 to 6 months) femora from female adult C57BL6 OC+/+ and OC−/− mice using Fourier Transform Infrared Imaging (FTIRI), Micro-computed tomography (uCT), bone biomechanical measurements and serum turnover markers (P1NP, CTX). Lead significantly …

Characterizing Cellular Injury And Inflammation With Aldob-/-Mouse Model Of Mafld, Andy Rashid

All Master's Theses

Metabolic-associated fatty liver disease (MAFLD) affects 1 in 3 people in the US and is a healthcare burden on the order of billions of dollars. MAFLD is characterized by pathological lipid accumulation in the liver, excess production of triglycerides and cholesterol, and export of LDL particles that raise serum lipid levels. These metabolic perturbations can lead to the development of liver fibrosis, chronic inflammation, and insulin resistance. Diagnosing MAFLD prior to fibrosis is crucial for successful intervention and prevention of advanced liver disease and other metabolic complications. Fructose-1Phospahte (F1P) accumulation from fructose overconsumption can drive hepatic lipogenesis and MAFLD progression. …

Under Ice Photosynthetic Primary Production And Dark Carbon Fixation In A Temperate Freshwater System, Vanessa Cubillos Tellez

Dissertations, Master's Theses and Master's Reports

Ice-covered lakes are vulnerable to environmental change, especially those in the Northern Hemisphere where ice cover is rapidly declining due to global warming. These changes can alter metabolic processes and disrupt carbon cycling driven by primary producers who form the base of the food chain and are key to sustaining ecosystem function. Photosynthetic primary production and dark carbon fixation under the ice in the Keweenaw Waterway, a temperate freshwater system that is ice-covered for ~3 months out of the year, were studied using a carbon isotopic labeling (14C-bicarbonate) technique. Water samples were collected weekly during ice cover and monthly during …

Development Of Novel Cellular Assay Model And Therapeutic Deep Eutectic Solvents To Optimize The Activity Of Anticancer Agents, Nizam Uddin

Electronic Theses and Dissertations

Multidrug resistance (MDR) is the major burden behind chemotherapeutic treatment failure. It is the principal mechanism by which cancer cells evade chemotherapeutic treatment. As a result, aggressive cancer cells survive and continue uncontrolled cell division. Multidrug resistance affects survival rate of almost all types of cancer patients and death toll rises at an alarming rate. There are seven different mechanisms for evolving MDR. The most common mechanism in efflux activity of overexpressed ABC transporters. MRP1 is a prominent ABC transporter that pumps out a wide variety of anticancer drugs from the cells and thereby reduces intracellular drug concentrations and develops …

Modulatory Effects Of Deacetylated Sialic Acids On Breast Cancer Resistance Protein-Mediated Multidrug Resistance And Receptor Tyrosine Kinase-Targeted Therapy, Isaac Tuffour

Electronic Theses and Dissertations

Multidrug resistance (MDR) remains a major challenge in cancer treatment, accounting for over 90% of chemotherapeutic failures. Cancers utilize sugar residues to engage in multidrug resistance. The underlying mechanism of action involving glycans, specifically the glycan sialic acid (Sia) and its various functional group alterations, has not been explored. ATP-binding cassette (ABC) transporter proteins, key proteins utilized by cancers to engage in MDR pathways, contain Sias in their extracellular domains. Modulating the expression of acetylated-Sias on Breast Cancer Resistance Protein (BCRP), a significant ABC transporter implicated in MDR, in lung and colon cancer cells directly impacted the ability of cancer …

Specialized Metabolism In Retina, Retinal Pigmented Epithelium, And Testis, Siyan Zhu

Graduate Theses, Dissertations, and Problem Reports (ETD)

The retina and its neighboring retinal pigmented epithelium (RPE) are high energy-demanding and metabolically active tissues with specialized and complementary metabolism. They are metabolically interdependent and impact each other’s viability. Interestingly, many of the metabolic features in the retina and RPE are shared with the testis. For example, testis is also energy costly due to continuous sperm differentiation and it has similar metabolic inter-dependence between different testis cells. Both the retina and testis are vulnerable to mitochondrial metabolic impairments.

We conducted three research projects to understand 1) the nutrient utilization and communication in retina and RPE; 2) The profiling of …