Biochemistry Commons^™

Air-Jet Bioprinting Of Stem Cell-Encapsulated Alginate Micro-Droplets For Organoid Biomanufacturing, Mirabella B. Stump

Electronic Theses and Dissertations

Biomanufactured 3D-organoids show promise for modeling and treating various conditions, particularly insulin-dependent diabetes mellitus (type-1 diabetes). Pancreatic islet organoids serve as sustainable sources of insulin-producing β-cells, potentially restoring insulin regulation in patients and providing a long-term solution for diabetes. Hydrogel droplet printing is an emerging technique in regenerative medicine due to its advantageous tunability and biocompatibility; however, challenges of consistency, quality control, and scalability persist. To address these issues, we developed a novel air-jetting based droplet bioprinting system for the generation of monodispersed alginate micro-droplets. The objective of this project was to incorporate human induced pluripotent stem cells (hiPSCs) into …

Mutational Analysis Of The Nitrogenase Carbon Monoxide Protective Protein Cown Reveals That A Conserved C‑Terminal Glutamic Acid Residue Is Necessary For Its Activity, Dustin L. Willard, Joshuah J. Arellano, Mitch Underdahl, Terrence M. Lee, Avinash S. Ramaswamy, Gabriella Fumes, Agatha Kliman, Emily Y. Wong, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Nitrogenase is the only enzyme that catalyzes the reduction of nitrogen gas into ammonia. Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Many nitrogen fixing bacteria protect nitrogenase from CO inhibition using the protective protein CowN. This work demonstrates that a conserved glutamic acid residue near the C-terminus of Gluconacetobacter diazotrophicus CowN is necessary for its function. Mutation of the glutamic acid residue abolishes both CowN’s protection against CO inhibition and the ability of CowN to bind to nitrogenase. In contrast, a conserved C-terminal cysteine residue is not important for CO protection by CowN. Overall, this work …

Role Of Prmt5 In Ulk1-Mediated Autophagy And Breast Cancer Therapy, Charles Brobbey

MUSC Theses and Dissertations

PRMT5 (Protein arginine methyltransferase 5) is the predominant type II PRMT that monomethylates and symmetrically dimethylates arginine residues of histone and none- histone proteins to regulate diverse cellular processes. PRMT5 overexpression has been implicated in tumorigenesis and other diseases and has gained trac1on as a poten1al an1tumor target with some of its inhibitors being tested in clinical trials. Despite the well- established an1tumor effect of PRMT5 inhibitors, how the efficacy of these inhibitors is regulated is unexplored. We show in this study that autophagy blockage enhances cellular sensi1vity to PRMT5 inhibitor in triple nega1ve breast cancer cells. Both gene1c deple1on …

Heterotypic Interaction Of Α-Synuclein And Tdp-43 In Neurodegenerative Diseases, Shailendra Dhakal

Dissertations

Amyloid aggregates of specific proteins form important pathological hallmarks in many neurodegenerative diseases, defining neuronal degeneration and disease onset. Recently, increasing numbers of patients show co-morbidities and exhibit clinical and pathological overlaps between multiple neurodegenerative diseases including α-synucleinopathies and TDP-43 proteinopathies. These overlaps are often accompanied by co-localization of α-synuclein (αS) and TDP-43 enhancing the possibility of direct interactions to generate heterotypic amyloids with distinct cellular consequences. To understand this, we investigate the interaction of α-synuclein (αS) and prion-like domain of TDP-43 (TDP-43 PrLD) in both homogenous and inhomogeneous phases. Firstly, we show that monomeric TDP-43 PrLD and αS interact …

Structural Features Of Hiv-1 Integrase In The Late Stage Of Viral Replication, Tolga Catmakas

Dissertations

HIV-1 integrase (IN) is an essential enzyme for the viral life cycle as it integrates viral genomic material into the host cell genome. In addition to its’ essential catalytic function, IN has another important non-catalytic role where it binds the viral RNA to facilitate successful particle maturation during the viral life cycle. A significant number of IN mutants, addressed as class II IN mutants, show various defects, affecting different steps of the viral life cycle. Class II IN mutants exhibit aberrant morphology where viral ribonucleoprotein particles are mislocalized outside of the capsid core. This phenomenon can be observed in the …

Biophysical Factors Affecting Habitat Suitability For Crassostrea Virginica, Jason D. Tilley

Dissertations

Oyster reefs provide a variety of important ecosystem services. However, the mortality rate of eastern oyster, Crassostrea virginica, the dominant species that produces oyster reefs in the northern Gulf of Mexico, is increasing at an alarming rate due to a variety of abiotic and biological factors. I examined how biophysical factors, including the less-studied fatty acid profiles of the suspended particulate matter on which oysters feed, influenced morphometric condition of C. virginica.

I sampled suspended particulate matter (SPM) and oysters in-situ in the western Mississippi Sound, which historically supported the majority of oyster production in Mississippi waters. Sampling …

Effects Of Dimerization On The Deacylase Activities Of Human Sirt2., Jie Yang, Nathan I Nicely, Brian P Weiser

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Human sirtuin isoform 2 (SIRT2) is an NAD+-dependent enzyme that functions as a lysine deacetylase and defatty-acylase. Here, we report that SIRT2 readily dimerizes in solution and in cells and that dimerization affects its ability to remove different acyl modifications from substrates. Dimerization of recombinant SIRT2 was revealed with analytical size exclusion chromatography and chemical cross-linking. Dimerized SIRT2 dissociates into monomers upon binding long fatty acylated substrates (decanoyl-, dodecanoyl-, and myristoyl-lysine). However, we did not observe dissociation of dimeric SIRT2 in the presence of acetyl-lysine. Analysis of X-ray crystal structures led us to discover a SIRT2 double mutant (Q142A/E340A) that …

Diaryl Oxazoles As Cleavable Linkers For Drug Discovery Platforms, Elizabeth Taggart

Honors Theses

Within the field of medicine and pharmacology, discovering small molecule or biologic based molecules with therapeutic potential is a difficult task. Current methods involve individually screening hundreds of compounds on a potential target biomolecule, and recent technologies have explored peptide encoded libraries (PELs) as a means of making this screening process more high-throughput. These libraries produce a large number of small molecule drug candidates each conjugated to a unique peptide fragment, functioning as a barcode. Analysis of PELs requires the capture of hit small molecules and the subsequent release of their peptide tags; however, current approaches are limited in their …

Liquid Chromatography Mass Spectrometry Method Development For The Determination Of Β–Defensins In Bovine Milk, Elisha Ogbebor

Masters Theses & Specialist Projects

Bovine mastitis is caused by a wide range of pathogens which results in a substantial economic loss for the dairy cattle livestock industry. β-defensins are a part of the innate immune system and act as the first line of defense against mastitis in bovine. β-defensins (~6- 10kDa) are antimicrobial peptides that contain about 28 to 67 amino acids, the presence of six cysteine residues results in their three disulfide bonds and a β-sheet structure. A few β- defensins have been identified in cows based on the site of occurrence and time of expression in tissue, but not in milk. A …

Design Of An Fgf-1-Fgf-2 Heterodimer Variant With Enhanced Stability And Cell Proliferation Activity, Nicholas Alan Pohlman

Chemistry & Biochemistry Undergraduate Honors Theses

The FGF-1 subfamily, composed of FGF-1 and FGF-2, assists in broad health-related processes such as cell proliferation and angiogenesis respectively.^1,2 The subfamily shows promising signs as a therapeutic, however, the inherent thermal instability leads to a low half-life in vivo.³ To assist in improving the stability, FGF-1 and FGF-2 were connected via a 12-residue glycine linker ultimately producing a heterodimer. This heterodimer was further examined to discover its novel properties. Inspiration for this project was drawn from previous research which performed five mutations on FGF-1 ultimately improving stability in the protein complex. In addition to these five …

Biochemical Analyses Of Udgx-A Crosslinking Uracil-Dna Glycosylase, Chuan Liang

All Dissertations

DNA base damage is common due to exposure to various endogenous and exogenous factors. To repair the base lesions, such as uracil from cytosine deamination, enzymes from the uracil-DNA glycosylase (UDG) superfamily are critical, which can recognize the damaged base and initiate the base excision repair (BER) pathway. There used to be six families of proteins identified in the UDG superfamily until a new member, UDGX, was found in Mycobacterium smegmatis, which is a unique DNA-crosslinking UDG. In this dissertation work, a series of biochemical analyses of the newly found UDGX are performed, including the analyses of structures, functions, …

The Discovery Of Diverse Picophytoplankton Populations In The Columbia And Willamette Rivers Using Flow Cytometry, Kylee M. Lamberson

Chemistry Undergraduate Departmental Honors Theses

As important primary producers, picophytoplankton determine the flow of carbon and energy in aquatic ecosystems. Picocyanobacteria are one picophytoplankton group known to be dominant in oceans and lakes, but they are still poorly understood in river systems. This project examined picophytoplankton communities in two distinct river systems: the Columbia and Willamette Rivers in Portland, Oregon. I aimed to characterize and quantify the picophytoplankton populations in the context of the environmental conditions of the two rivers. I used flow cytometry to detect cells based on their relative size and pigment fluorescence. I sampled nearly weekly for ten months to capture population …

Exploring The Impact Of High-Temperature Stress On Physiological, Anatomical, Molecular, Productive, And Quality Parameters In Diverse Olive Cultivars, Bassam F. Alowaiesh, Taghreed S. Alnusaire

The Philippine Agricultural Scientist

Olive (Olea europaea L.) is one of the most important horticultural crops in Saudi Arabia. High temperatures are typical in most regions during the summer season. This study explored the effect of high temperatures on diverse olive cultivars (Manzanillo, Chemlali, and Picual) grown in three different geographical locations in Saudi Arabia (Sakaka, Basita, and Al-Qurayyat). Sakaka region was classified as a hot region, while the Basita and Al-Qurayyat regions were characterized by relatively mild or low temperatures. Genotypic components were assessed by studying Amplified Fragment Length Polymorphism (AFLP) molecular markers and physiological, anatomical, productive, and oil quality parameters. The …

Growth, Yield, And Photosynthetic Dry Matter Remobilization Response Of Barley To Plant Growth Promoting Rhizobacteria (Pgpr) And Nitrogen, Abazar Abbasi, Shahram Mehri, Hossein Solimanzadeh, Saeid Alipour

The Philippine Agricultural Scientist

A two-year factorial experiment based on a randomized complete block design with three replicates was carried out on barley cultivar LB-IRAN at the research farm of the Islamic Azad University, Ardabil, Iran, during the cropping years of 2019–2021, in order to survey the impact of plant growth-promoting rhizobacteria (PGPR) and nitrogen fertilizer on growth, yield, and remobilization of photosynthetic dry matter in barley. The first factor included five nitrogen levels: 0 (control), 25, 50, 75, 100 kg/ha net nitrogen; the second factor contained grain inoculations with four bacteria: no inoculation (control), Azotobacter chroococcum race 5, Azospirillum lipoferum race of, and …

Crispr-Cas Enabled Dna Nanotechnology For Advanced Pathogen Detection, Mahera J. Kachwala

Legacy Theses & Dissertations (2009 - 2024)

The ever-growing list of carcinogens, toxicants, pathogens, and other disease-causing agents necessitates the development of new and improved mechanisms of disease detection. A better understanding of events leading up to the diseased state and early diagnosis is imperative for the timely management and targeted treatment of diseases affecting the biological world. Recent achievements in DNA nanotechnology have led to the prominence of DNA-based technologies for multiplexed biological sensing, high-throughput analysis, and improved diagnostics. Typical methods of disease detection employ complex multi-step procedures and advanced equipment, which significantly reduces their accessibility while elevating their cost. DNA functionalized sensing systems that examine …

Cell Aggregation Activates Small Gtpase Rac1 And Induces Cd44 Cleavage By Maintaining Lipid Raft Integrity, Dong Li, Younhee Park, Hami Hemati, Xia Liu

Markey Cancer Center Faculty Publications

Lipid rafts are highly ordered membrane domains that are enriched in cholesterol and glycosphingolipids and serve as major platforms for signal transduction. Cell detachment from the extracellular matrix (ECM) triggers lipid raft disruption and anoikis, which is a barrier for cancer cells to metastasize. Compared to single circulating tumor cells (CTCs), our recent studies have demonstrated that CD44-mediatd cell aggregation enhances the stemness, survival and metastatic ability of aggregated cells. Here, we investigated whether and how lipid rafts are involved in CD44-mediated cell aggregation. We found that cell detachment, which mimics the condition when tumor cells detach from the ECM …

A Cancer-Specific Study On The Differentially Expressed Protein-Protein Interactions Of Fumarate Hydratase, Sydney Lac

Dissertations and Theses (Open Access)

Fumarate hydratase (FH) is an enzyme used in the Krebs Cycle to convert fumarate to malate, and it is controlled by the FH gene. In this paper, we will investigate its role in Uterine Corpus Endometrial Carcinoma (UCEC) and how FH-deficient cells affect tumorigenesis. It is well-established that FH has been extensively studied in connection with renal cell carcinoma, skin and uterine leiomyomas, pheochromocytoma, and paraganglioma. However, we aim to construct an interaction network of significant genes related to the FH gene under conditions of FH deficiency in the Kreb Cycle. Creating an interactive network that illustrates the interconnectedness of …

Amyloid Fibrils Of Human Fgf-1 Induced By Different Detergents, Zeina Ismael Ibrahem Alraawi

Graduate Theses and Dissertations

Nature achieves molecular self-assembly through the ordered growth of nanoscale building blocks with high efficiency to fabricate macromolecular architectures. One example of self- assembly is peptides folding onto protein is one of the most astounding biological self-assembly processes. When proteins aggregate to form amyloid fibers, the secondary structure of the protein converts from its native state to a cross-beta-sheet. Fibroblast growth factors (FGFs) possess an essential role in neuronal survival during development. In addition, they are involved in neural stem cell (NSC) proliferation. Fibroblast growth factors (FGFs) are well known to be synthesized in the central nervous system (CNS) and …

Characterization Of Human Fibroblast Growth Factor 2 Variant To Determine Effects On Structure, Stability, And Cell Proliferation, Ryan Layes

Graduate Theses and Dissertations

Fibroblast growth factors (FGFs) are a family of cell signaling proteins conserved across multiple species. Each individual FGF elicits different cellular functions including, but not limited to, proliferation, migration, differentiation, angiogenesis, and wound healing. One of the most studied members, fibroblast growth factor 2 (FGF2), has demonstrated substantial wound healing capacity in a wide range of tissues including skeletal, muscular, neural, respiratory, epithelial, and cardiovascular. This ability makes FGF2 a potential therapeutic for a wide range of conditions and injuries. However, due to a short half-life at room temperature, therapeutic use of FGF2 is limited. It has been demonstrated that …

Structural Studies Of The Human Hsp60 And Bacteriophage Phiel Chaperonins, Daniel Han Von Salzen

Open Access Theses & Dissertations

Chaperonins are large protein complexes responsible for the refolding of misfoldedsubstrate. Many mechanisms of the folding process have not been completely elucidated. Here we perform biochemical and structural analysis on two chaperonins, the human mitochondrial Hsp60 and the bacteriophage EL encoded PhiEL, to better understand key structural components and their purpose to the chaperonin function. Hsp60 plays an essential role in maintaining protein within the mitochondrial matrix. Despite its importance, the detailed mechanism of ATP hydrolysis and the role of the C-terminal tail remains unresolved. Here we show that the C-terminal tail not only acts as a sensor for the …