Biochemistry, Biophysics, and Structural Biology Commons^™

Extraction Of Transcriptional Regulators For The Polyhydroxyalkanoate Depolymerase Gene From Streptomyces Nymphaeiformis, Kara B. Eppard, Stephen F. Baron

Honors Projects

Plastic waste has become an increasingly prevalent environmental pollutant. This problem is exacerbated by the inability of plastic to degrade under most natural conditions. In contrast, polyhydroxyalkanoates (PHAs) are biologically produced, plastic-like polymers that can be broken down and metabolized by bacteria. The bacterium Streptomyces nymphaeiformis can degrade the PHA, polyhydroxybutrate (PHB), using an extracellular PHB depolymerase, which is encoded by the phaZ gene. PHB depolymerase is synthesized only in the presence of PHB or its monomer, but not glucose, suggesting that transcription of phaZ is regulated, presumably by transcriptional regulatory proteins that bind to its promoter region. The DNA …

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 …

A Novel Role Of Tgfbi In Macrophage Polarization And Macrophage-Induced Pancreatic Cancer Growth And Therapeutic Resistance, Jing Zhou, Nan Lyu, Qiongling Wanga, Ming Yang, Eric T. Kimchi, Kun Chenge, Trupti Joshi, Adama R. Tukulif, Kevin F. Staveley-O’Carroll, Guangfu Li

Biomedical Sciences

Tumor-associated macrophages (TAMs), as a major and essential component of tumor microenvironment (TME), play a critical role in orchestrating pancreatic cancer (PaC) tumorigenesis from initiation to angiogenesis, growth, and systemic dissemination, as well as immunosuppression and resistance to chemotherapy and immunotherapy; however, the critical intrinsic factors responsible for TAMs reprograming and function remain to be identified. By performing single-cell RNA sequencing, transforming growth factor-beta-induced protein (TGFBI) was identified as TAM-producing factor in murine PaC tumors. TAMs express TGFBI in human PaC and TGFBI expression is positively related with human PaC growth. By inducing TGFBI loss-of-function in macrophage (MΦs) in vitro …

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 …

Identification Of Genes Conferring Resistance To 2-Amino-3-Methylimidazo [4,5-F] Quinoline Genotoxicity In Budding Yeast Using High-Throughput And Targeted Approaches, Michael J. Dolan

Legacy Theses & Dissertations (2009 - 2024)

Heterocyclic aromatic amines (HAAs) are potent carcinogenic agents found in charred read meat and cigarette smoke. We hypothesize that HAAs may contribute to red meat being a risk factor for colorectal cancer (CRC). At present, few eukaryotic genes conferring resistance to HAAs have been identified. In this research, the genome of Saccharomyces cerevisiae (budding yeast) was profiled using next-generation sequencing to identify genes conferring resistance to one such HAA, 2-amino-3-methylimidazo[4,5-f] quinoline (IQ).CYP1A2 and NAT2 activate IQ to become a mutagenic nitrenium compound. Deletion libraries expressing human CYP1A2 and NAT2 or no human genes were exposed to either 400 or 800 …

Identification And Characterization Of Geotrichum Candidum Isolates From Peach With Reduced Sensitivity To Propiconazole, Sara Price

All Theses

Geotrichum candidum Link (1809) is a yeast-like fungus that causes sour rot of stone fruits, including peach (Prunus persica). The disease caused damage between 2021 and 2023 to the peach crop kept in cold storage at a commercial farm in South Carolina despite preharvest and postharvest applications of fungicides. Isolates from 41 symptomatic fruit, from a South Carolina (SC) commercial packing house, as well as other isolates obtained from South Carolina were identified to be G. candidum based on species-specific PCR amplifications of the β tubulin gene. Commonly used postharvest fungicide fludioxonil had no effect on G. candidum mycelial growth …

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 …

Understanding The Kinetics Of Laser-Induced Nanowelding Of Nanoparticles And The Motility Of Bacteria When Faced With Obstacles, Ariel Rogers

Graduate Theses and Dissertations

This dissertation has two focus areas: nanoparticle nanowelding and bacteria motility in the presence of micrometer sized structures. There are two main projects for the nanoparticle nanowelding studies: “Real-time imaging of laser-induced nanowelding in solution” and “Two-color laser-induced nanostructure shape modulation.” For the real-time imaging project, I used a fluorescence microscope, a 405 nm laser, and various python packages to quantify the average size of nanowelded nanostructures as a function of time and found that the average nanostructure growth over time fit the parameters of A¯(t) ∝ c0(1−e−t/τ), where c0 represents the initial concentration of nanoparticles in the solution and …

Deficiency Of Acute-Phase Serum Amyloid A Exacerbates Sepsis-Induced Mortality And Lung Injury In Mice, Ailing Ji, Andrea C. Trumbauer, Victoria P. Noffsinger, Luke W. Meredith, Brittany Dong, Qian Wang, Ling Guo, Xiangan Li, Frederick C. De Beer, Nancy R. Webb, Lisa R. Tannock, Marlene E. Starr, Christopher M. Waters, Preetha Shridas

Saha Cardiovascular Research Center Faculty Publications

Serum amyloid A (SAA) is a family of proteins, the plasma levels of which may increase >1000-fold in acute inflammatory states. We investigated the role of SAA in sepsis using mice deficient in all three acute-phase SAA isoforms (SAA-TKO). SAA deficiency significantly increased mortality rates in the three experimental sepsis mouse models: cecal ligation and puncture (CLP), cecal slurry (CS) injection, and lipopolysaccharide (LPS) treatments. SAA-TKO mice had exacerbated lung pathology compared to wild-type (WT) mice after CLP. A bulk RNA sequencing performed on lung tissues excised 24 h after CLP indicated significant enrichment in the expression of genes associated …

Loss Of Carnitine Palmitoyltransferase 1a Reduces Docosahexaenoic Acid-Containing Phospholipids And Drives Sexually Dimorphic Liver Disease In Mice, Mikala M. Zelows, Corissa Cady, Nikitha Dharanipragada, Anna E. Mead, Zachary A. Kipp, Evelyn A. Bates, Venkateshwari Varadharajan, Rakhee Banerjee, Se-Hyung Park, Nathan R. Shelman, Harrison A. Clarke, Tara R. Hawkinson, Terrymar Medina, Ramon C. Sun, Todd A. Lydic, Terry D. Hinds, Jr., J. Mark Brown, Samir Softic, Gregory A. Graf, Robert N. Helsley

Saha Cardiovascular Research Center Faculty Publications

Background and aims: Genome and epigenome wide association studies identified variants in carnitine palmitoyltransferase 1a (CPT1a) that associate with lipid traits. The goal of this study was to determine the role of liver-specific CPT1a on hepatic lipid metabolism.

Approach and results: Male and female liver-specific knockout (LKO) and littermate controls were placed on a low-fat or high-fat diet (60% kcal fat) for 15 weeks. Mice were necropsied after a 16 h fast, and tissues were collected for lipidomics, matrix-assisted laser desorption ionization mass spectrometry imaging, kinome analysis, RNA-sequencing, and protein expression by immunoblotting. Female LKO mice had increased serum alanine …

On The Origin And Evolution Of The Mosquito Male-Determining Factor Nix, James K. Biedler, Azedah Aryan, Yumin Qi, Aihua Wang, Ellen O. Martinson, Daniel A. Hartman, Fan Yang, Atashi Sharma, Katherine S. Morton, Mark Potters, Chujia Chen, Stephen L. Dobson, Gregory D. Ebel, Rebekah C. Kadling, Sally Paulson, Rui-De Xue, Michael R. Strand, Zhijian Tu

Entomology Faculty Publications

The mosquito family Culicidae is divided into 2 subfamilies named the Culicinae and Anophelinae. Nix, the dominant male-determining factor, has only been found in the culicines Aedes aegypti and Aedes albopictus, 2 important arboviral vectors that belong to the subgenus Stegomyia. Here we performed sex-specific whole-genome sequencing and RNAseq of divergent mosquito species and explored additional male-inclusive datasets to investigate the distribution of Nix. Except for the Culex genus, Nix homologs were found in all species surveyed from the Culicinae subfamily, including 12 additional species from 3 highly divergent tribes comprising 4 genera, suggesting Nix originated at least 133 to …

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 …

Interfacial Interactions Between Engineered Nanoplastics And Biological Systems: Towards An Atomic And Molecular Understanding Of Plastics- Driven Cellular Dyshomeostasis, Afroz Karim

Open Access Theses & Dissertations

The persistent presence of micro (nano) plastics in our environment has raised concerns regarding potential health risks associated with human exposure. With the extensive use of plastic materials and the widespread consumption of plastic-contaminated food items, two types of microplastics, polystyrene (PS) and polymethylmethacrylate (PMMA), have attracted increased attention. While the adverse effects of microplastics on animals and marine life have been extensively studied, their potential impact on human health remains largely unexplored. Specifically, the interaction between microplastics and biomolecules within the human body and their effect on human health have yet to be comprehensively investigated. This dissertation study focuses …