Biochemistry, Biophysics, and Structural Biology Commons^™

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 …

Silver Ions Inhibit Bacterial Movement And Stall Flagellar Motor, Benjamin Russell, Ariel Rogers, Ryan Yoder, Matthew Kurilich, Venkata Rao Krishnamurthi, Jingy Chen, Yong Wang

Physics Faculty Publications and Presentations

Silver (Ag) in different forms has been gaining broad attention due to its antimicrobial activities and the increasing resistance of bacteria to commonly prescribed antibiotics. However, various aspects of the antimicrobial mechanism of Ag have not been understood, including how Ag affects bacterial motility, a factor intimately related to bacterial virulence. Here, we report our study on how Ag⁺ ions affect the motility of E. coli bacteria using swimming, tethering, and rotation assays. We observed that the bacteria slowed down dramatically by >70% when subjected to Ag⁺ ions, providing direct evidence that Ag⁺ ions inhibit the motility …

Exploring The Interactions Between Sars-Cov-2 And Host Proteins, Sojan Shrestha

School of Biological Sciences: Dissertations, Theses, and Student Research

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current pandemic, Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 is considered to be of zoonotic origin; it originated in non-human animals and was transmitted to humans. Since the early stage of the pandemic, however, the evidence of transmissions from humans to animals (reverse zoonoses) has been found in multiple animal species including mink, white-tailed deer, and pet and zoo animals. Furthermore, secondary zoonotic events of SARS-CoV-2, transmissions from animals to humans, have been also reported. It is suggested that non-human hosts can act as SARS-CoV-2 reservoirs where accumulated …

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 …

Cadmium And Salinity Stressor Antagonism On Vallisneria Neotropicalis, Christopher P. Mikolaitis

Graduate Theses and Dissertations (2019 - present)

Submerged macrophytes form the foundation of freshwater ecosystems. These organisms are sessile and are very susceptible to shifts in their environment. Heavy metals are of particular concern as they can be sequestered indefinitely in sediments and are readily taken up by rooted vegetation. In the presence of saltwater intrusions, these metals can interact with salt ions potentially changing their availability to submerged vegetation. In this study a freshwater macrophyte, Vallisneria neotropicalis, was used as a test species for interactive effects between Cd, a non-essential heavy metal, and salt stress. The metrics used to establish the individual as well as …

Suitability Of Double-Stranded Dna As A Molecular Standard For The Validation Of Analytical Ultracentrifugation Instruments, Maduni Ranasinghe, Jonathan M Fogg, Daniel J Catanese, Lynn Zechiedrich, Borries Demeler

Faculty, Staff and Students Publications

To address the current lack of validated molecular standards for analytical ultracentrifugation (AUC), we investigated the suitability of double-stranded DNA molecules. We compared the hydrodynamic properties of linear and circular DNA as a function of temperature. Negatively supercoiled, nicked, and linearized 333 and 339 bp minicircles were studied. We quantified the hydrodynamic properties of these DNAs at five different temperatures, ranging from 4 to 37 °C. To enhance the precision of our measurements, each sample was globally fitted over triplicates and five rotor speeds. The exceptional stability of DNA allowed each sample to be sedimented repeatedly over the course of …

Characterization Of Atrial And Ventricular Remodeling In An Improved Minimally Invasive Mouse Model Of Transverse Aortic Constriction, Jose Alberto Navarro-Garcia, Satadru K Lahiri, Yuriana Aguilar-Sanchez, Anilkumar K Reddy, Xander H T Wehrens

Faculty, Staff and Students Publications

INTRODUCTION: Heart failure (HF) is the leading cause of death worldwide. Most large and small animal disease models of HF are based on surgical procedures. A common surgical technique to induce HF is transverse aortic constriction (TAC), which induces pressure overload. The conventional TAC (cTAC) procedure is a highly invasive surgery that is associated with severe inflammation and excessive perioperative deaths.

AIM: To establish an improved, minimally invasive TAC (mTAC) procedure that does not require thoracotomy.

METHODS AND RESULTS: Following anesthesia, mice were intubated, and a small incision was made at the neck and chest. After cutting the sternum about …

Testis-Specific Serine Kinase 3 Is Required For Sperm Morphogenesis And Male Fertility, Kaori Nozawa, Thomas X Garcia, Katarzyna Kent, Mei Leng, Antrix Jain, Anna Malovannaya, Fei Yuan, Zhifeng Yu, Masahito Ikawa, Martin M Matzuk

Faculty, Staff and Students Publications

BACKGROUND: The importance of phosphorylation in sperm during spermatogenesis has not been pursued extensively. Testis-specific serine kinase 3 (Tssk3) is a conserved gene, but TSSK3 kinase functions and phosphorylation substrates of TSSK3 are not known.

OBJECTIVE: The goals of our studies were to understand the mechanism of action of TSSK3.

MATERIALS AND METHODS: We analyzed the localization of TSSK3 in sperm, used CRISPR/Cas9 to generate Tssk3 knockout (KO) mice in which nearly all of the Tssk3 open reading frame was deleted (ensuring it is a null mutation), analyzed the fertility of Tssk3 KO mice by breeding mice for 4 months, …

Advancing Asms With Lc-Ms/Ms For The Discovery Of Novel Pdcl2 Ligands From Dna-Encoded Chemical Library Selections, Qiuji Ye, Hassane Belabed, Yong Wang, Zhifeng Yu, Murugesan Palaniappan, Jian-Yuan Li, Stacey A Kalovidouris, Kevin R Mackenzie, Mingxing Teng, Damian W Young, Yoshitaka Fujihara, Martin M Matzuk

Faculty, Staff and Students Publications

BACKGROUND: A safe, effective, and reversible nonhormonal male contraceptive drug is greatly needed for male contraception as well as for circumventing the side effects of female hormonal contraceptives. Phosducin-like 2 (PDCL2) is a testis-specific phosphoprotein in mice and humans. We recently found that male PDCL2 knockout mice are sterile due to globozoospermia caused by impaired sperm head formation, indicating that PDCL2 is a potential target for male contraception. Herein, our study for the first time developed a biophysical assay for PDCL2 allowing us to screen a series of small molecules, to study structure-activity relationships, and to discover two PDCL2 binders …

Targeting Aav Vectors To The Central Nervous System By Engineering Capsid-Receptor Interactions That Enable Crossing Of The Blood-Brain Barrier, Qin Huang, Albert T Chen, Ken Y Chan, Hikari Sorensen, Andrew J Barry, Bahar Azari, Qingxia Zheng, Thomas Beddow, Binhui Zhao, Isabelle G Tobey, Cynthia Moncada-Reid, Fatma-Elzahraa Eid, Christopher J Walkey, M Cecilia Ljungberg, William R Lagor, Jason D Heaney, Yujia A Chan, Benjamin E Deverman

Faculty, Staff and Students Publications

Viruses have evolved the ability to bind and enter cells through interactions with a wide variety of cell macromolecules. We engineered peptide-modified adeno-associated virus (AAV) capsids that transduce the brain through the introduction of de novo interactions with 2 proteins expressed on the mouse blood-brain barrier (BBB), LY6A or LY6C1. The in vivo tropisms of these capsids are predictable as they are dependent on the cell- and strain-specific expression of their target protein. This approach generated hundreds of capsids with dramatically enhanced central nervous system (CNS) tropisms within a single round of screening in vitro and secondary validation in vivo …

Safety Endpoints With Vadadustat Versus Darbepoetin Alfa In Patients With Non- Dialysis-Dependent Ckd: A Post Hoc Regional Analysis Of The Pro2tect Randomized Clinical Trial Of Esa-Treated Patients, Patrick S Parfrey, Steven K Burke, Glenn M Chertow, Kai-Uwe Eckardt, Alan G Jardine, Eldrin F Lewis, Wenli Luo, Kunihiro Matsushita, Peter A Mccullough, Todd Minga, Wolfgang C Winkelmayer

Faculty, Staff and Students Publications

RATIONALE & OBJECTIVE: In the PRO

STUDY DESIGN: Phase 3, global, open-label, randomized, active-controlled clinical trial.

SETTING & PARTICIPANTS: A total of 1,725 erythropoiesis-stimulating agent (ESA)-treated patients with anemia and NDD-CKD.

INTERVENTION: 1:1 randomization to receive vadadustat or darbepoetin alfa.

OUTCOMES: The primary safety end point was the time to first MACE.

RESULTS: At baseline, patients in Europe (n=444) were primarily treated with darbepoetin alfa, showed higher proportions on low ESA doses (/kg/wk epoetin alfa equivalents) with a hemoglobin concentration of ≥10 g/dL compared with patients in the US (n=665) and non-US/non-Europe (n=614) regions. The MACE rates per 100 person-years …

Covet: A Covariation-Evolutionary Trace Method That Identifies Protein Structure-Function Modules, Daniel M Konecki, Spencer Hamrick, Chen Wang, Melina A Agosto, Theodore G Wensel, Olivier Lichtarge

Faculty, Staff and Students Publications

Measuring the relative effect that any two sequence positions have on each other may improve protein design or help better interpret coding variants. Current approaches use statistics and machine learning but rarely consider phylogenetic divergences which, as shown by Evolutionary Trace studies, provide insight into the functional impact of sequence perturbations. Here, we reframe covariation analyses in the Evolutionary Trace framework to measure the relative tolerance to perturbation of each residue pair during evolution. This approach (CovET) systematically accounts for phylogenetic divergences: at each divergence event, we penalize covariation patterns that belie evolutionary coupling. We find that while CovET approximates …

Outersphere Approach To Increasing The Persistance Of Oxygen-Sensitive Europium(Ii)-Containing Contrast Agents For Magnetic Resonance Imaging With Perfluorocarbon Nanoemulsions Toward Imaging Of Hypoxia, Jacob C Lutter, Andrea L Batchev, Caitlyn J Ortiz, Alexander G Sertage, Jonathan Romero, S A Amali S Subasinghe, Steen E Pedersen, Md Abul Hassan Samee, Robia G Pautler, Matthew J Allen

Faculty, Staff and Students Publications

Radiographic mapping of hypoxia is needed to study a wide range of diseases. Complexes of EuII are a promising class of molecules to fit this need, but they are generally limited by their rapid oxidation rates in vivo. Here, a perfluorocarbon-nanoemulsion perfused with N2, forms an interface with aqueous layers to hinder oxidation of a new perfluorocarbon-soluble complex of EuII. Conversion of the perfluorocarbon solution of EuII into nanoemulsions results in observable differences between reduced and oxidized forms by MRI both in vitro and in vivo. Oxidation in vivo occurrs over a period of ~30 min compared to <5 min for a comparable EuII-containing complex without nanoparticle interfaces. These results represent a critical step toward delivery of EuII-containing complexes in vivo for the study of hypoxia.

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 …

Novel Roles Of The Blm Syndrome Dna Helicase In Genome Maintenance And Mitochondrial Regulation, Brian B. Rodemoyer

USF Tampa Graduate Theses and Dissertations

Bloom syndrome (BS) is an extremely rare autosomal recessive genetic disorder caused by defects in the BLM gene. Patients with BS display a broad phenotypic spectrum including abnormally short stature, microcephaly, sun sensitivity, insulin resistance, perpetual oxidative stress, and a ~300-fold greater propensity for developing cancer than the general population. As such, BS patients typically do not live past their 20’s. The BLM gene encodes the BLM helicase, a member of the highly conserved RecQ family of 3’ to 5’ DNA helicases. Most of our cellular understanding of BLM is through its role in DNA damage repair through the homologous …

Twenty-Year Survival Following Lung Transplantation, John James Miggins, Ross M Reul, Spencer Barrett, Abbas Rana, Ahmed Alnajar, Jordan Dunson, Alexis Shafii, Puneet Garcha, John Goss, Gabriel Loor

Faculty, Staff and Students Publications

BACKGROUND: Lung transplantation median survival has seen improvements due to recognition of short-term survival factors but continues to trail behind other solid organs due to limited understanding of long-term survivorship. Given the creation of the United Network for Organ Sharing (UNOS) database in 1986, it was difficult to accrue data on long-term survivors until recently. This study characterizes factors impacting lung transplant survival beyond 20 years, conditional to 1-year survival.

METHODS: Lung transplant recipients listed in UNOS from 1987 to 2002 who survived to 1 post-transplant year were reviewed. Kaplan-Meier and adjusted Cox regression analyses were performed at 20 and …

Withaferin A And Immune Checkpoint Blocker Therapy For The Treatment Of Non-Small Cell Lung Cancer, Roukiah Khalil

USF Tampa Graduate Theses and Dissertations

Lung cancer is the first cause of cancer-related deaths in both men and women with an overall five-year survival rate of 28%. Although immune checkpoint blockers (ICBs) are currently FDA-approved for the treatment of non-small cell lung cancer (NSCLC), only 17-20% of patients achieve durable responses by the induction of immunologic memory. The lack of response in most patients can be attributed to the tumor-intrinsic or tumor-extrinsic immune resistance mechanisms. A biomarker of importance is the Programmed Death Ligand-1 (PD-L1), as higher PD-L1 expression is usually associated with a better response to ICBs. Although studies have attempted to combine ICBs …