Biochemistry Commons^™

Disease-Associated Mutation A554v Disrupts Normal Autoinhibition Of Dnmt1, Rebecca L. Switzer, Zach J. Hartman, Geoffrey R. Hewett, Clara F. Carroll

Faculty Journal Articles

DNA methyltransferase 1 (DNMT1) is the enzyme primarily responsible for propagation of the methylation pattern in cells. Mutations in DNMT1 have been linked to the development of adult-onset neurodegenerative disorders; these disease-associated mutations occur in the regulatory replication foci-targeting sequence (RFTS) domain of the protein. The RFTS domain is an endogenous inhibitor of DNMT1 activity that binds to the active site and prevents DNA binding. Here, we examine the impact of the disease-associated mutation A554V on normal RFTS-mediated inhibition of DNMT1. Wild-type and mutant proteins were expressed and purified to homogeneity for biochemical characterization. The mutation increased DNA binding affinity …

High-Resolution Cryo-Em Structure Of The Pseudomonas Bacteriophage E217, Fenglin Li, Chun-Feng Hou, Ravi K. Lokareddy, Ruoyu Yang, Francesca Forti, Federica Briani, Gino Cingolani

Department of Biochemistry and Molecular Biology Faculty Papers

E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after DNA ejection at 3.1 Å and 4.5 Å resolution, respectively, determined using cryogenic electron microscopy (cryo-EM). We identify and build de novo structures for 19 unique E217 gene products, resolve the tail genome-ejection machine in both extended and contracted states, and decipher the complete architecture of the baseplate formed by 66 polypeptide chains. We also determine that E217 recognizes the host O-antigen as a receptor, and we resolve the N-terminal portion …

Fibrosis-The Tale Of H3k27 Histone Methyltransferases And Demethylases, Morgan D. Basta, Svetlana Petruk, Alexander Mazo, Janice L. Walker

Department of Biochemistry and Molecular Biology Faculty Papers

Fibrosis, or excessive scarring, is characterized by the emergence of alpha-smooth muscle actin (αSMA)-expressing myofibroblasts and the excessive accumulation of fibrotic extracellular matrix (ECM). Currently, there is a lack of effective treatment options for fibrosis, highlighting an unmet need to identify new therapeutic targets. The acquisition of a fibrotic phenotype is associated with changes in chromatin structure, a key determinant of gene transcription activation and repression. The major repressive histone mark, H3K27me3, has been linked to dynamic changes in gene expression in fibrosis through alterations in chromatin structure. H3K27-specific homologous histone methylase (HMT) enzymes, Enhancer of zeste 1 and 2 …

A Novel Method Of Rapid Detection For Heavy Metal Copper Ion Via A Specific Copper Chelator Bathocuproinedisulfonic Acid Disodium Salt, Yali Wang, Tinglin Ma, Joseph Brake, Zhaoyue Sun, Jiayu Huang, Jing Li, Xiaobin Wu

Department of Biochemistry: Faculty Publications

The extensive usage and production of copper may lead to toxic effects in organisms due to its accumulation in the environment. Traditional methods for copper detection are time consuming and infeasible for field usage. It is necessary to discover a real-time, rapid and economical method for detecting copper to ensure human health and environmental safety. Here we developed a colorimetric paper strip method and optimized spectrum method for rapid detection of copper ion based on the specific copper chelator bathocuproinedisulfonic acid disodium salt (BCS). Both biological assays and chemical methods verified the specificity of BCS for copper. The optimized reaction …

Invited Review: Adrenocortical Function In Avian And Non-Avian Reptiles: Insights From Dispersed Adrenocortical Cells., Rocco V. Carsia, Patrick J. Mcilroy, Henry B John-Alder

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Herein we review our work involving dispersed adrenocortical cells from several lizard species: the Eastern Fence Lizard (Sceloporus undulatus), Yarrow's Spiny Lizard (Sceloporus jarrovii), Striped Plateau Lizard (Sceloporus virgatus) and the Yucatán Banded Gecko (Coleonyx elegans). Early work demonstrated changes in steroidogenic function of adrenocortical cells derived from adult S. undulatus associated with seasonal interactions with sex. However, new information suggests that both sexes operate within the same steroidogenic budget over season. The observed sex effect was further explored in orchiectomized and ovariectomized lizards, some supported with exogenous testosterone. Overall, a suppressive effect of testosterone was evident, especially in cells …

Long-Term Monitoring Of Clodronate In Equine Hair Using Liquid Chromatography-Tandem Mass Spectrometry, Heather K. Knych, D. S. Mckemie, S. Yim, S. D. Stanley, R. M. Arthur

UK CARES Faculty Publications

Given the potential for long-term inhibition of bone remodeling/healing and detrimental effects to horses in training, bisphosphonates are tightly regulated in horseracing. Hair has proven to be an effective matrix for detection of drug administration to horses and has been particularly effective in detecting drugs for a long period of time post administration. Thus, hair may prove to be a useful matrix for detection of administration of this class of drugs. The objective of the current study was to develop an assay and assess the usefulness of hair as a matrix for long-term detection of clodronate to horses. Seven horses …

The Sound Of Geological Targets On Mars From The Absolute Intensity Of Laser-Induced Sparks Shock Waves, C. Alvarez-Llamas, J. Laserna, J. Moros, P. Purohit, L. García-Gómez, S. M. Angel Ph.D., P. Bernardi, B. Bousquet, A. Cadu, E. Dauson, O. Forni, T. Fouchet, O. Gasnault, X. Jacob, G. Lacombe, N. L. Lanza, C. Larmat, J. Lasue, R. D. Lorenz, P. Y. Meslin, D. Mimoun, F. Montmessin, N. Murdoch, A. M. Ollila, P. Pilleri, N. Randazzo, A. L. Reyes-Newell, S. Schröder, A. Stott, J. Ten Cate, A. Udry, D. Vogt

Faculty Publications

Inspection of geological material is one of the main goals of the Perseverance rover during its journey across the landscape of the Jezero crater in Mars. NASA's rover integrates SuperCam, an instrument capable of performing standoff characterization of samples using a variety of techniques. Among those tools, SuperCam can perform laser-induced breakdown spectroscopy (LIBS) studies to elucidate the chemical composition of the targets of interest. Data from optical spectroscopy can be supplemented by simultaneously-produced laser-produced plasma acoustics in order to expand the information acquired from the probed rocks thanks to the SuperCam's microphone (MIC) as it can be synchronized with …

Analysis Of The Paraventricular Nucleus Of The Hypothalamus After Exposure To Decabromodiphenyl Ether In Mice, Tia Blossomgame, Hermei Herman, Sharlenn La, Jocelyn Saquisili, Annabella Vargas, Grace Martinichio, Vincent P. Markowski

McNair Scholars Program

No abstract provided.

Sympatric Soil Microbe Interactions Between Streptomyces And Fusarium Isolates, Lehren A. Olk-Szost

All NMU Master's Theses

Interkingdom interactions between soil bacteria and fungi may play a critical role in occurrence of disease suppressive soils, yet our understanding of these interactions remains limited. Streptomyces are well-known producers of antimicrobial compounds important to medicine and agriculture. Production of these secondary metabolites is often mediated by quorum sensing. Most Streptomyces research occurs in single species experiments, yet new metabolites have been discovered in interspecies co-culture experiments. Interspecies, intergenic, and interkingdom co-culture research will likely reveal many valuable compounds, and strengthen our understanding of complex ecological interactions in soil microbiomes. Interactions between sympatric Streptomyces and Fusarium isolates from disease suppressive …

The Role Of Tc-Ptp-Mediated Suppression Of Autophagy During Skin Carcinogenesis, Obed Asare

Theses and Dissertations

Ultraviolet B (UVB) radiation can distort cellular homeostasis and predispose the skin to carcinogenesis. Amongst the deteriorating effects of the sun’s UVB radiation on cellular homeostasis is the formation of DNA photoproducts such as cyclobutene pyrimidine dimers. These photoproducts can cause significant changes in the structure and conformation of the DNA, inducing gene mutations which may accumulate to trigger the formation of skin cancer. Photoproducts are typically repaired by nucleotide excision repair. Notwithstanding, when the repair mechanism fails, apoptosis ensues to prevent the accumulation of mutations and to restore cellular homeostasis. We have identified T-cell protein tyrosine phosphatase (TC-PTP) as …

Enhanced Bypass Of Pd-L1 Translation Reduces The Therapeutic Response To Mtor Kinase Inhibitors, Yanan Cao, Qing Ye, Murong Ma, Qing-Bai She

Markey Cancer Center Faculty Publications

Increased PD-L1 expression in cancer cells is known to enhance immunosuppression, but the mechanism underlying PD-L1 upregulation is incompletely characterized. We show that PD-L1 expression is upregulated through internal ribosomal entry site (IRES)-mediated translation upon mTORC1 inhibition. We identify an IRES element in the PD-L1 50-UTR that permits cap-independent translation and promotes continuous production of PD-L1 protein despite effective inhibition of mTORC1. eIF4A is found to be a key PD-L1 IRES-binding protein that enhances PD-L1 IRES activity and protein production in tumor cells treated with mTOR kinase inhibitors (mTORkis). Notably, treatment with mTORkis in vivo elevates PD-L1 levels and reduces …

Messes: Software For Transforming Messy Research Datasets Into Clean Submissions To Metabolomics Workbench For Public Sharing, P. Travis Thompson, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

In recent years, the FAIR guiding principles and the broader concept of open science has grown in importance in academic research, especially as funding entities have aggressively promoted public sharing of research products. Key to public research sharing is deposition of datasets into online data repositories, but it can be a chore to transform messy unstructured data into the forms required by these repositories. To help generate Metabolomics Workbench depositions, we have developed the MESSES (Metadata from Experimental SpreadSheets Extraction System) software package, implemented in the Python 3 programming language and supported on Linux, Windows, and Mac operating systems. MESSES …

The Metabolomics Workbench File Status Website: A Metadata Repository Promoting Fair Principles Of Metabolomics Data, Christian D. Powell, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

Background: An updated version of the mwtab Python package for programmatic access to the Metabolomics Workbench (MetabolomicsWB) data repository was released at the beginning of 2021. Along with updating the package to match the changes to MetabolomicsWB’s ‘mwTab’ file format specification and enhancing the package’s functionality, the included validation facilities were used to detect and catalog file inconsistencies and errors across all publicly available datasets in MetabolomicsWB.

Results: The MetabolomicsWB File Status website was developed to provide continuous validation of MetabolomicsWB data files and a useful interface to all found inconsistencies and errors. This list of detectable issues/errors include format …

Amyloid-Beta Protein Concentration Dependence Of Reversible Aggregation Using Gold Colloid Particles, Renee Spencer, Lila Kocieniewski, Bryan Martinez, Kazushige Yokoyama

McNair Scholars Program

Although Alzheimer’s and COVID-19 are different diseases, the commonality between them is during the process of them developing in a person by fibrillogenesis. The product of fibrillogenesis results in the development of these diseases. We study the first stage of fibrillogenesis where the amyloid-beta peptide monomers are assembled into an oligomer. We want to isolate this oligomer using gold colloids because this step can be reversed. Utilizing gold colloids allows us to freeze fibrillogenesis in the first step by folding and unfolding the protein repeatedly through a series of pH changes from 4 or below to 10 or higher. At …

Linking The Metabolic And Ecological Fate Of Caribbean Ciguatoxins And Related Neurotoxins In Reef Herbivores, Jessica K. Gwinn

Graduate Theses and Dissertations (2019 - present)

Ciguatera poisoning (CP) is one of the most prominent seafood-borne illnesses worldwide, affecting between 25,000–500,000 people annually. Ciguatera is caused by the ingestion of seafood contaminated with algal-derived ciguatoxins (CTX), the precursors of which are produced by benthic and toxigenic dinoflagellates in the genera Gambierdiscus and Fukuyoa. These compounds enter marine food webs through herbivory and are subsequently transferred to higher trophic levels, undergoing complex metabolic biotransformations, which produce structurally related CTX derivatives. Consumption of CTX induces a variety of severe neurological, gastrointestinal, and/or cardiovascular symptoms beginning within hours and lasting for weeks to months following exposure. Despite the impact …

Impact Of Sediment Diversion For Coastal Restoration On Nitrogen And Phosphorus Biogeochemical Cycling In Coastal Louisiana, Usa, Mercedes M. Pinzon Delgado

LSU Master's Theses

Wetlands provide essential ecosystem services and functions, including improving surface water quality through nutrient removal. Louisiana experienced ~4,800 km² of coastal wetland loss between 1932 and 2016 due to high relative sea level rise and reduced sediment input from the Mississippi River (MR). The 2023 Louisiana Coastal Master Plan aims to restore Louisiana's degraded coastline through restoration projects, including sediment diversions. The Mid-Barataria Sediment Diversion project will reconnect MR sediment-laden water with Barataria Basin degrading marshes. The diversion will also deliver nitrate (NO₃^-) and soluble reactive phosphorus (SRP) to this basin, potentially negatively impacting water quality. …

Effects Of Roasting Conditions On The Proximate Composition And Functional Properties Of Common Bean (Phaseolus Vulgaris) Flours, Rachel Byarugaba, Agnes Nabubuya, John Muyonga, Ali Mwakha

Tanzania Journal of Science

Roasting of dry beans presents the possibility of a value-added product with improved nutritional quality and potential use in different food systems. The effect of roasting on the proximate composition and functional properties of dry beans (Phaseolus vulgaris L.) was determined. Beans were roasted at 140, 170, and 200 °C for 5, 10, and 15 minutes. The moisture, carbohydrate, protein, dietary fibre, total ash and fat contents of the flours ranged from 4.58 to 6.72%, 56.21 to 60.51%, 23.09 to 26.74%, 4.12 to 7.01%, 3.94 to 4.58% and 1.28 to 2.10%, respectively. An increase in roasting temperature and time significantly …

Biochemical Markers Of Liver Toxicity Among Coal Mine Workers Of Punjab, Pakistan Suffering From Hcv, Aima Iram Batool, Asma Noreen, Naima Huma Naveed, Iram Inayat, Muhammad Fayyaz Ur Rehman, Fariha Idrees, Muhammad Ali Kanwal, Syeda Humaira Jabeen, Hakim Bibi

Journal of Bioresource Management

Hepatitis C is among the leading hepatic disorders in current period through which about 3 % world population has been anguish among them 170 million were diagnosed as persistent carriers. A great range of alteration in liver biochemical parameters were found to be allied with HCV infestation. Current study was designed to evaluate the extent of HCV mediated abnormalities in liver biochemical markers which includes ALT (alanine aminotransferase), AST (Aspartate transaminase), ALP (Alkaline Phosphatase) and serum bilirubin. The study was conducted on coal miners of Punjab province, Pakistan. HCV was primarily diagnosed through one step rapid test device after which …

Putrescine Detected In Strains Of Staphylococcus Aureus, Javier Seravalli, Frank Portugal

Department of Biochemistry: Faculty Publications

Most forms of life, including the archaea, bacteria, and eukaryotes synthesize the polyamine putrescine. Although putrescine is widely distributed, several Gram-positive bacteria, including Staphylococcus aureus (S. aureus), appear to be the exceptions. We report here that strains of S. aureus can produce the polyamine putrescine, as well as the derivative N-acetyl-putrescine. Three strains of S. aureus from the American Type Culture Collection (ATCC), one strain listed in the National Center for Biotechnology Information (NCBI) database, whose genomic sequence is well defined, and well as eight strains from S. aureus-induced brain abscesses of individual patients from multiple …

Investigating The Activity Of Alternative Warheads For Targeted Covalent Inhibition Of The Inhibitor Vertebrate Lysozyme Protein From Pseudomonas Aeruginosa, Katie Hambrick

Master of Science in Chemical Sciences Theses

Pseudomonas aeruginosa (P. aeruginosa) is a Gram-negative bacterium that causes blood and lung infections in hospital environments due to its ability to survive on improperly sterilized medical equipment. P. aeruginosa has developed several multi-drug resistance mechanisms that make it very difficult to treat with current antibiotics.¹ This presents the need for a new class of antibiotics that cannot be overcome by P. aeruginosa’s mechanisms of resistance.

The primary goal of this project was to develop a small library of inhibitors that could later be incorporated into lead compounds for novel antibiotic drug discovery. One of P. …

Type Iv Pilus-Mediated Inhibition Of Acinetobacter Baumannii Biofilm Formation By Phenothiazine Compounds, Nam Vo, Benjamin S. Sidner, Yafan Yu, Kurt H. Piepenbrink

Department of Biochemistry: Faculty Publications

Infections by pathogenic Acinetobacter species represent a significant burden on the health care system, despite their relative rarity, due to the difficulty of treating infections through oral antibiotics. Multidrug resistance is commonly observed in clinical Acinetobacter infections and multiple molecular mechanisms have been identified for this resistance, including multidrug efflux pumps, carbapenemase enzymes, and the formation of bacterial biofilm in persistent infections. Phenothiazine compounds have been identified as a potential inhibitor of type IV pilus production in multiple Gram-negative bacterial species. Here, we report the ability of two phenothiazines to inhibit type IV pilus-dependent surface (twitching) motility and biofilm formation …

Effect Of Dual Inhibition Of Atypical Pkc Signaling And Pi3k/Akt Signaling On Cell Viability And Apoptosis In Clear Cell Renal Cell Carcinoma (Ccrcc)., Khandker M. Khalid

USF Tampa Graduate Theses and Dissertations

Renal Cell Carcinoma (RCC) is the most common type of kidney cancer (85%); 75% of the cases involve conventional clear cell RCC (ccRCC). The choice of treatments recommended for clear cell carcinoma and non-clear cell carcinoma include partial nephrectomy (Stage I), radical nephrectomy (Stages II and III), and chemotherapy (stage IV). Phosphatidylinositol-3-kinase (PI3K) inhibitors can be a viable candidate in the chemotherapy of ccRCC because the PI3K/Akt pathway is frequently activated in RCC. Hence, PI3K inhibitors like Alpelisib (BYL719) can be chosen as a treatment. In addition, aPKCs (PKC-ί and PKC ζ) are overexpressed in most cancer cells, and they …

Institutional And Individual Approaches To Change In Undergraduate Stem Education: Two Framework Analyses, Stephanie B. Feola

USF Tampa Graduate Theses and Dissertations

The overarching goal of this dissertation is to examine institutional change initiatives in STEM and to understand the impact of engaging with a specific change strategy on a biochemistry educator’s instructional practice. Institutional change initiatives involve executing an intentional strategy to influence teaching practices within a specific institution. This research investigates NSF-funded change initiatives at three public research universities that were focused on encouraging the adoption of evidenced-based instructional practices (EBIPs) by STEM faculty. As part of an effort to understand how the three institutions approached this task, framework analysis was performed using the initiative’s annual reports to NSF. Further …

Raw Diffraction Data For 1tel-Aa-Vwa (Sumo), Wwpdb Id: 7n1o, Moriah H. Mathis, Braydan D. Bezzant, Diana T. Ramírez, Supeshala D. Nawarathnage, Tzanko I. Doukov, James Moody

ScholarsArchive Data

This X-ray diffraction dataset was collected on October 21Oct2020 at SSRL Beamline BL9-2. The crystal was of Batch 1 1TEL-AA-vWa (SUMO) The solved structure used frames 1-999 and has been deposited in the wwPDB under the PDB ID 7N1O. This data can be readily processed using XDS, AutoProc, CCP4, HKL2000/3000, or other crystallographic X-ray diffraction data processing software. The files have a human-readable header but are otherwise binary.

Raw Diffraction Data For 3tel-Hlx-Darpin (Sumo), Wwpdb Id: 7n2b, Supeshala D. Nawarathnage, Parag Laljibhai Gajjar, Derick R. Bunn, Cameron Stewart, Tzanko I. Doukov, James Moody

ScholarsArchive Data

This X-ray diffraction dataset was collected on October 21Oct2020 at SSRL Beamline BL9-2. The crystal was of 3TEL-hlx-DARPin (SUMO) The solved structure used frames 1-1799 and has been deposited in the wwPDB under the PDB ID 7N2B. This data can be readily processed using XDS, AutoProc, CCP4, HKL2000/3000, or other crystallographic X-ray diffraction data processing software. The files have a human-readable header but are otherwise binary.

Examining Parent-Of-Origin Effects On Transcription And Rna Methylation In Mediating Aggressive Behavior In Honey Bees (Apis Mellifera), Sean T. Bresnahan, Ellen Lee, Lindsay Clark, Rong Ma, Michael P. Markey, Juliana Rangel, Christina M. Grozinger, Hongmei Li-Byarlay

Biochemistry and Molecular Biology Faculty Publications

Conflict between genes inherited from the mother (matrigenes) and the father (patrigenes) is predicted to arise during social interactions among offspring if these genes are not evenly distributed among offspring genotypes. This intragenomic conflict drives parent-specific transcription patterns in offspring resulting from parent-specific epigenetic modifications. Previous tests of the kinship theory of intragenomic conflict in honey bees (Apis mellifera) provided evidence in support of theoretical predictions for variation in worker reproduction, which is associated with extreme variation in morphology and behavior. However, more subtle behaviors – such as aggression – have not been extensively studied. Additionally, the canonical epigenetic mark …

Chemical And Genetic Composition Analysis Of Organic And Nonorganic Tortilla Chips, Aubrey White-Day

Honors Theses

The aim of this study was to explore the chemical and genetic differences between organic and nonorganic tortilla chips using GC-MS and PCR. Twenty chip brands were selected: 10 organic and 10 nonorganic. A survey on shopping preferences was created and distributed to compare results of public opinion to experimental data. It yielded 212 responses. All organic chip brands, and one out of ten nonorganic chip brands, tested negative for GMOs. This study concluded that there are minimal chemical differences based on Jaccard similarity indicies and stark genetic differences between organic and nonorganic tortilla chips. In comparing statistical analyses to …

Investigating The Role Of Tethering In Exosomal Secretion, Zdeněk Otruba

Undergraduate Theses, Capstones, and Recitals

Exosomes are a type of membrane vesicles utilized in intercellular communication. Exosomes are first packaged into larger membrane vesicles called multivesicular bodies (MVBs). When exosomes are secreted, the membrane of the MVBs fuses with the cellular membrane, and then the exosomes are released. Experimental observations suggest that the movement of the exosomes is hindered during this process; they require much longer time to leave the fusion site than they would if they were diffusing freely. A prevalent hypothesis is that the cause of this hindrance is attachment of the exosomes to the cell surface. Recent work suggests that tetherin, a …

Protein Folding Kinetics Analysis Using Fluorescence Spectroscopy, Dhanya Dhananjayan

USF Tampa Graduate Theses and Dissertations

The conformational changes that occur during the folding of a protein is an intensely researched area because of the impact that it has on human health and cellular functions. Protein stability is crucial in the context of protein misfolding and aggregation due to its implications on misfolding diseases such as amyloid fibril degenerative diseases (Alzheimer’s, Parkinson’s). By examining the kinetics of protein folding, we can gain valuable information about the folding mechanism and help us identify potential targets for many of the protein misfolding diseases.

In this study, we present the folding and unfolding kinetics of TEM-1 β-lactamase from Escherichia …

Hematopoietic Stem Cells And Betaherpesvirus Latency, Lindsey B. Crawford

Department of Biochemistry: Faculty Publications

The human betaherpesviruses including human cytomegalovirus (HCMV), human herpesvirus (HHV)-6a and HHV-6b, and HHV-7 infect and establish latency in CD34+ hematopoietic stem and progenitor cells (HPCs). The diverse repertoire of HPCs in humans and the complex interactions between these viruses and host HPCs regulate the viral lifecycle, including latency. Precise manipulation of host and viral factors contribute to preferential maintenance of the viral genome, increased host cell survival, and specific manipulation of the cellular environment including suppression of neighboring cells and immune control. The dynamic control of these processes by the virus regulate inter- and intra-host signals critical to the …