Digital Commons Network^™

Subsets Of Adjacent Nodes (Soan): A Fast Method For Computing Suboptimal Paths In Protein Dynamic Networks, Thomas Dodd, Xin-Qiu Joe Yao, Donald Hamelberg, Ivaylo Lvanov

Chemistry Faculty Publications

Suboptimal path analysis in a protein structural or dynamical network becomes increasingly popular for identifying critical residues involved in allosteric communication and regulation. Several software packages have been developed for calculating suboptimal paths, including NetworkView, WISP, and CNAPATH (Bio3D). Although these packages work well for biological systems of moderate sizes, they either dramatically slow down or are subjected to accuracy issues when applied to large systems such as supramolecular complexes. In this work, we develop a new method called SOAN, which implements a modified version of Yen’s algorithm for finding loopless k-shortest paths. Instead of searching the entire protein …

Neglected Nematodes: The Neurolenin Solution, Kevin M. Shea, Steven Williams

Chemistry: Faculty Publications

Over 1 billion people worldwide are affected by Neglected Topical Diseases (NTDs). This group of pathogens encapsulates viruses, bacteria and parasites, and disproportionately affects the world’s poorest and most vulnerable communities in Africa, Asia and Latin America. Lymphatic Filariasis (LF) is an NTD caused by a parasitic nematode infection. The larvae of these filarial nematode worms are transmitted via mosquito bites and disrupt the functioning of the infected individual’s lymphatic system. LF can be caused by three types of filarial worms, Wuchereria bancrofti, Brugia malayi and Brugia timori, which are transmitted by the Culex, Anopheles and Aedes mosquito families. Symptomatic …

Cown Sustains Nitrogenase Turnover In The Presence Of The Inhibitor Carbon Monoxide, Michael S. Medina, Kevin O. Bretzing, Richard A. Aviles, Kiersten M. Chong, Alejandro Espinoza, Chloe Nicole G. Garcia, Benjamin B. Katz, Ruchita N. Kharwa, Andrea Hernandez, Justin L. Lee, Terrence M. Lee, Christine Lo Verde, Max W. Strul, Emily Y. Wong, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Nitrogenase is the only enzyme capable of catalyzing nitrogen fixation, the reduction of dinitrogen gas (N₂) to ammonia (NH₃). Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Nitrogen-fixing bacteria rely on the protein CowN to grow in the presence of CO. However, the mechanism by which CowN operates is unknown. Here, we present the biochemical characterization of CowN and examine how CowN protects nitrogenase from CO. We determine that CowN interacts directly with nitrogenase and that CowN protection observes hyperbolic kinetics with respect to CowN concentration. At a CO concentration of 0.001 atm, …

Synthesizing Laccol Based Polymers/Copolymers And Polyurethanes; Characterization And Their Applications, Imalka Marasinghe Arachchilage

USF Tampa Graduate Theses and Dissertations

In modern world research scopes are highly favored the areas of developing new polymer materials which are more integrated with the environment. Synthesizing eco-friendly, bio degradable polymer materials to replace petroleum based synthetic polymers to utilize in radiation hard applications is one of the main objectives of this study. 'Laccol' extracted from Vietnamese lacquer tree (Toxicodendron succedanea) polymerized with other monomers namely styrene and d-limonene (from citrus waste) respectively to develop copolymers via cationic polymerization. Laccol contains hydroxyl phenyl groups that act as radical scavengers, enhancing radiation resistance via their ability to convert excitation energy into non-chemistry inducing energy in …

Comprehensive Chromatographic Profiling Of Cannabis From 23 Usa States Marketed For Medical Purposes, Ramia Z. Al Bakain, Yahya S. Al-Degs, James V. Cizdziel, Mahmoud A. Elsohly

Faculty and Student Publications

In this research, cannabis varieties represent 23 USA States were assayed by GC-FID to generate their complex chemical profiles informative for plants clustering. Results showed that 45 cannabinoids and terpenoids were quantified in all plant samples, where 8 cannabinoids and 18 terpenoids were identified. Among organics, Δ9-THC, CBN (cannabinoids) and Fenchol (terpenoid) not only showed the highest levels overall contents, but also were the most important compounds for cannabis clustering. Among States, Washington, Oregon, California and Hawaii have the highest cannabis content. GC-FID data were subjected to PCA and HCA to find (1) the variations among cannabis chemical profiles as …

Blood Driven Biopower Cells: Acquiring Energy From Reverse Electrodialysis Using Sodium Concentrations From The Flow Of Human Blood, Efecan Pakkaner, Chase Smith, Christina Trexler, Jamie Hestekin, Christa Hestekin

Chemical Engineering Faculty Publications and Presentations

With the growth of the healthcare industry, small scale power sources are needed to support advancements in medical implants, artificial organs, and sensors throughout the body. However, it remains a challenge to find safe, reliable, and stable power sources for these devices. In this study, a miniaturized reverse electrodialysis (RED) biopower cell design using physiological salinity concentration differences between renal bloodstreams is explored for its potential to be used as a power supply for implantable medical devices. Two small scale RED devices produced consistent power for up to three to ten days, depending on the device design. A two-fold decrease …

Characterization Of A Broadly Specific Cadaverine N-Hydroxylase Involved In Desferrioxamine B Biosynthesis In Streptomyces Sviceus, Lesley Ann Giddings, George T. Lountos, Kang Woo Kim, Matthew Brockley, Danielle Needle, Scott Cherry, Joseph E. Tropea, David S. Waugh

Chemistry: Faculty Publications

N-hydroxylating flavin-dependent monooxygenases (FMOs) are involved in the biosynthesis of hydroxamate siderophores, playing a key role in microbial virulence. Herein, we report the first structural and kinetic characterization of a novel alkyl diamine N-hydroxylase DesB from Streptomyces sviceus (SsDesB). This enzyme catalyzes the first committed step in the biosynthesis of desferrioxamine B, a clinical drug used to treat iron overload disorders. X-ray crystal structures of the SsDesB holoenzyme with FAD and the ternary complex with bound NADP+ were solved at 2.86 Å and 2.37 Å resolution, respectively, providing a structural view of the active site environment. SsDesB crystallized as a …

College Of Natural Sciences Newsletter, March 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2. Issue 3

Contents:

Page 1 Dean's Message
Page 2-3 Awards and Recognition
Page 4 Student Club Spotlight: MICROBIOLOGY CLUB
Page 5 Research Spotlight: Dr. Chakravarty
Page 6 Open PRAIRIE Data; Grants Awarded in CNS; Research Collquia
Page 7 A Busy Month in Review; Media Coverage of the College

Soil Quality Indices As Affected By Long-Term Burning, Irrigation, Tillage, And Fertility Management, Helen C.S. Amorim, Amanda Ashworth, Kristofor R. Brye, Brian J. Wienhold, Mary C. Savin, Phillip R. Owens, Sergio Silva

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Understanding the impacts of long-term agricultural practices on soil quality (SQ) is key for sustaining agroecosystem productivity. This study investigated conventional and no-tillage (NT), residue burning and no burning, residue level (high and low), and irrigation (irrigated and dryland) effects on soil properties, SQ, and crop yields following 16 yr of a wheat (Triticum aestivum L.)–soybean [Glycine max (L.) Merr.] double-crop system via the Soil Management Assessment Framework (SMAF). A field experiment was conducted in the Lower Mississippi River Delta region on a silt-loam soil. Bulk density, soil organic C (SOC), total N (TN), pH, electrical conductivity (EC), …

The Effect Of Amino Acids And Molar Peroxide Ratio On The Oxidation Of 2,4 Dinitroanisole In An Ultraviolet Light Emitting Diode/H2O2 Advanced Oxidation Process, Jeffry P. Hart

Theses and Dissertations

2,4 Dinitroanisole (DNAN) is an organic insensitive munition that is a likely candidate to replace trinitrotoluene (TNT) for a variety of purposes. Advanced Oxidation Processes (AOPs) are a promising method that have the potential to reduce a variety of persistent chemicals, however, the performance of these systems may be degraded by co-contaminants in the influent. In this contribution, DNAN, with casamino acids as a co-contaminant, was oxidized with Ultraviolet (UV) Light Emitting Diodes (LEDs) with hydrogen peroxide (H₂O₂) in an AOP in a laboratory. The UV/ H₂O₂ AOP was capable of degrading DNAN …

Research Progress On Transition State Of Organic Electrode Materials, Xue-Qian Zhang, Zhou-Guang Lu, Wei-Wei Huang

Journal of Electrochemistry

With the increasing requirements for high energy density, long lifetime, high safety, environmentally friendly fabrication, and sustainable development of large energy storage devices, the society calls for new electrode materials in rechargeable batteries beyond traditional inorganic materials which are limited by specific capacity. Organic electrode materials have been widely used in rechargeable batteries due to their advantages of large theoretical capacity, designable structures and environmentally friendly fabrications. In this review, the radical intermediates of organic electrode materials produced in the charging-discharging process (redox reaction) and their types are systematically reviewed. The stability of radical intermediates controlled by changing the structure …

Perspective On Multi-Scale Simulation Of Thermal Transport In Solids And Interfaces (Vol 23, Pg 1785, 2021), Ming Hu, Zhonghua Yang

Faculty Publications

Correction for ‘Perspective on multi-scale simulation of thermal transport in solids and interfaces’ by Ming Hu et al., Phys. Chem. Chem. Phys., 2021, 23, 1785–1801, DOI: 10.1039/D0CP03372C.

Computationally-Efficient Spatiotemporal Correlation Analysis Super-Resolves Anomalous Diffusion, Shawn Yoshida, William Schmid, Nam Vo, William Calabrase, Lydia Kisley

Faculty Scholarship

Anomalous diffusion dynamics in confined nanoenvironments govern the macroscale properties and interactions of many biophysical and material systems. Currently, it is difficult to quantitatively link the nanoscale structure of porous media to anomalous diffusion within them. Fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) has been shown to extract nanoscale structure and Brownian diffusion dynamics within gels, liquid crystals, and polymers, but has limitations which hinder its wider application to more diverse, biophysically-relevant datasets. Here, we parallelize the least-squares curve fitting step on a GPU improving computation times by up to a factor of 40, implement anomalous diffusion and two-component …

Characterization, Immobilization, And Polymer Related Applications Of Watermelon Seed Powder, A Practical Source Of Urease Enzyme, Anthony Quan Quoc Mai

LSU Doctoral Dissertations

Urease enzyme was crystallized almost a century ago, and to this day its intrinsic stability is not ideal for everyday applications. This work introduces a new process by which a naturally encapsulated material, watermelon seed powder (WMSP), is characterized for its stability and activity. WMSP enzymatic activity has been measured for over a year at various storage conditions—exposed to ambient atmosphere for a year, WMSP retained above 90% activity. In aqueous conditions, the enzyme maintained above 60% activity after two months; with the addition of a preservative that number stays at about 90%. There is a pH shift of the …

Soil C:N:P Stoichiometry In Tropical Forests On Hainan Island Of China: Spatial And Vertical Variations, Dafeng Hui, Xitian Yang, Qi Deng, Qiang Liu, Xu Wang, Huai Yang, Hai Ren

Biology Faculty Research

Soil carbon (C), nitrogen (N), and phosphorus (P) are three important elements. The study of stoichiometric relationships of soil C, N, and P in tropical forests on Hainan Island, China could improve our understanding of nutrient cycling and provide valuable information for forest management. Soil samples were collected at five different depths from 0 to 100 cm at 100 sites among four different forest types on Hainan Island, and total C, N, and P concentrations were measured. Soil C and N concentrations and soil C:P and N:P ratios declined from the surface soil layer to the deeper soil layers and …

Changes At A Critical Branchpoint In The Anthocyanin Biosynthetic Pathway Underlie The Blue To Orange Flower Color Transition In Lysimachia Arvensis, Mercedes Sánchez-Cabrera, Francisco Javier Jiménez-López, Eduardo Narbona, Montserrat Arista, Pedro L. Ortiz, Francisco J. Romero-Campero, Karolis Ramanauskas, Boris Igić, Amelia A. Fuller, Justen B. Whittall

Chemistry and Biochemistry

Anthocyanins are the primary pigments contributing to the variety of flower colors among angiosperms and are considered essential for survival and reproduction. Anthocyanins are members of the flavonoids, a broader class of secondary metabolites, of which there are numerous structural genes and regulators thereof. In western European populations of Lysimachia arvensis, there are blue- and orange-petaled individuals. The proportion of blue-flowered plants increases with temperature and daylength yet decreases with precipitation. Here, we performed a transcriptome analysis to characterize the coding sequences of a large group of flavonoid biosynthetic genes, examine their expression and compare our results to flavonoid biochemical …

Identifying Receptors For Neuropeptides And Peptide Hormones: Challenges And Recent Progress, Md Shadman Ridwan Abid, Somayeh Mousavi, James W. Checco

Department of Chemistry: Faculty Publications

Intercellular signaling events mediated by neuropeptides and peptide hormones represent important targets for both basic science and drug discovery. For many bioactive peptides, the protein receptors that transmit information across the receiving cell membrane are not known, severely limiting these signaling pathways as potential therapeutic targets. Identifying the receptor(s) for a given peptide of interest is complicated by several factors. Most notably, cell-cell signaling peptides are generated through dynamic biosynthetic pathways, can act on many different families of receptor proteins, and can participate in complex ligand-receptor interactions that extend beyond a simple one-to-one archetype. Here, we discuss recent methodological advances …

Rotaxane Rings Promote Oblique Packing And Extended Lifetimes In Dna-Templated Molecular Dye Aggregates, Matthew S. Barclay, Simon K. Roy, Jonathan S. Huff, Olga A. Mass, Daniel B. Turner, Christopher K. Wilson, Donald L. Kellis, Jeunghoon Lee, Paul H. Davis, Bernard Yurke, William B. Knowlton, Ryan D. Pensack

Chemistry and Biochemistry Faculty Publications and Presentations

Molecular excitons play a central role in natural and artificial light harvesting, organic electronics, and nanoscale computing. The structure and dynamics of molecular excitons, critical to each application, are sensitively governed by molecular packing. Deoxyribonucleic acid (DNA) templating is a powerful approach that enables controlled aggregation via sub-nanometer positioning of molecular dyes. However, finer sub-Angstrom control of dye packing is needed to tailor excitonic properties for specific applications. Here, we show that adding rotaxane rings to squaraine dyes templated with DNA promotes an elusive oblique packing arrangement with highly desirable optical properties. Specifically, dimers of these squaraine:rotaxanes exhibit an absorption …

Using Molecular Dynamics Simulations To Understand Receptor-Complex Communication And Signaling, Hannah Margaret Hoag

Theses and Dissertations

The overarching purpose of this document is to use Computer-aided drug design and Molecular dynamic simulations to better understand elusive drug-receptor interactions, as well as various types of inter-receptor signaling. Chapter One introduces the theory and importance of Computer-aided drug design and the methodology used in both Chapters Two and Three.

Chapter Two uncovers the relationship between the well-studied ABCB1 transporter and a newly identified drug known as Xanthohumol (XN). XN is compared to a commonly used drug, Doxorubicin (DOX), in this chapter. If the ABCB1 transporter can be properly inhibited, cancer-fighting drugs will be able to stay within the …

P53 Is Potentially Regulated By Cyclophilin D In The Triple-Proline Loop Of The Dna Binding Domain, Jacques Kumutima, Xin-Qiu Joe Yao, Donald Hamelberg

Chemistry Faculty Publications

The multifunctional protein p53 is the central molecular sensor of cellular stresses. The canonical function of p53 is to transcriptionally activate target genes in response to, for example, DNA damage that may trigger apoptosis. Recently, p53 was also found to play a role in the regulation of necrosis, another type of cell death featured by the mitochondrial permeability transition (mPT). In this process, p53 directly interacts with the mPT regulator cyclophilin D, the detailed mechanism of which however remains poorly understood. Here, we report a comprehensive computational investigation of the p53–cyclophilin D interaction using molecular dynamics simulations and associated analyses. …

Corrosion Inhibition Of Mild Steel In Seawater By 2,4,6-Triamino-3-Pentadecylphenyl Acetate Derived From Cashew Nut Shell Liquid, Emanuel Ricky, Esther Lugwisha, Joseph Philip

Tanzania Journal of Science

The corrosion inhibition performance of 2,4,6-triamino-3-pentadecylphenyl acetate on mild steel in seawater at stationary condition, 30 °C and pH 8 was investigated using potentiodynamic polarization and electrochemical impedance spectroscopy. The maximum inhibition efficiency of 93% was found in the presence of 300 ppm of 2,4,6-triamino-3-pentadecylphenyl acetate for both potentiodynamic polarization and electrochemical impedance spectroscopy techniques. The potentiodynamic polarization curves show that 2,4,6-triamino-3-pentadecylphenyl acetate acts as a mixed type inhibitor which influences more the anodic processes. The Nyquist plots revealed that the polarization resistance (Rp) increases whereas the double-layer capacitance (Cdl) and corrosion current density (icorr) decrease as the concentrations of …

Physicochemical And Sensory Evaluation Of Mixed Juices From Banana, Pineapple And Passion Fruits During Storage, Victor Matabura, Oscar Kibazohi

Tanzania Journal of Science

Juices from fresh fruits offer various health benefits, including strengthening the immune system and preventing diseases. Mixed fruit juices tend to have good nutritional contents and organoleptic properties like colour, flavour, taste, and overall appeal of different fruits. This work investigated the physicochemical and sensory attributes of fruit juice of low viscosity banana juice blended with pineapple and passion juices. The prepared juices were pasteurised at 92 °C for 15 s, bottled in air-tight glass bottles, and subsequently stored in two different conditions: an ambient temperature of approximately 28 ± 2 °C and a fridge at 4 ºC for one …

Determination Of The Rydberg Constant From The Emission Spectra Of H And He+, Kyle D. Shaffer

Ramifications

Abstract

In this experiment, the Rydberg constants for the hydrogen atom and He⁺ were determined by analysis of the emission spectra of Hand He, respectively, in comparison to the principal quantum numbers of each transition. Using both a hydrogen and then a helium atomic lamp attached to a 0.5 m grating spectrometer and a photomultiplier detector (PMT), a change in voltage detected by the PMT can be paired with a corresponding wavelength passing through the spectrometer from each emission peak in the visible to ultraviolet range. The peaks acquired from this change in voltage were analyzed to find their …

Combination Therapy: Dual Drug-Loaded Superparamagnetic Iron-Oxide Nanoparticle For Targeted Drug Delivery And Treatment Of Cancer, Himanshu Polara

Electronic Theses & Dissertations

Lung cancer is the most occurring form of cancer of all ages in the United States after breast cancer. Many treatments are currently available in the market to treat cancer, but they all have some side effects. The concept of nanomedicine-based targeted drug delivery has been developed to overcome the limitations of current treatment. The advantages of this method of treatment include biocompatibility, significant toxicity towards cancer cells, immediate drug response, and fewer side effects. For the specific treatment of A549 lung cancer cells, polyacrylic acid (PAA) coated Iron Oxide Nanoparticle (IONP) were introduced for magnetic resonance imaging (MRI) of …

A Composite Textual Phenomenological Approach To Cures Versus Traditional Laboratory Experiences, Amie S. Sommers, Dana Richter-Egger, Christine E. Cutucache

The Qualitative Report

Here we present unique perspectives from undergraduate students (n=3) in STEM who have taken both a traditional laboratory iteration and a Course-based Undergraduate Research Experience (CURE) iteration of the same introductory chemistry course. CUREs can be effective models for integrating research in courses and fostering student learning gains. Via phenomenological interviews, we asked students to describe the differences in their perspectives, feelings, and experiences between a traditional lab guided by a lab manual and a CURE. We found that (i.) critical thinking/problem solving, (ii.) group work/collaboration, (iii.) student-led research questions and activities, and (iv.) time management are the top four …

A Molecular Tetrahedral Cobalt-Seleno-Based Complex As An Efficient Electrocatalyst For Water Splitting, Ibrahim Munkaila Abdullahi, Jahangir Masud, Polydoros Chrisovalantis Ioannou, Eleftherios Ferentinos, Panayotis Kyritsis, Manashi Nath

Chemistry Faculty Research & Creative Works

The cobalt-seleno-based coordination complex, [Co{(SePⁱPr₂)₂N}₂], is reported with respect to its catalytic activity in oxygen evolution and hydrogen evolution reactions (OER and HER, respectively) in alkaline solutions. An overpotential of 320 and 630 mV was required to achieve 10 mA cm^-2 for OER and HER, respectively. The overpotential for OER of this CoSe₄-containing complex is one of the lowest that has been observed until now for molecular cobalt(II) systems, under the reported conditions. In addition, this cobalt-seleno-based complex exhibits a high mass activity (14.15 A g^-1) and …

Methylation Of The D2 Dopamine Receptor Affects Binding With The Human Regulatory Proteins Par-4 And Calmodulin, Alexander Bowitch, Ansuman Sahoo, Andrea M. Clark, Christiana Ntangka, Krishna K. Raut, Paul Gollnick, Michael C. Yu, Steven M. Pascal, Sarah E. Walker, Denise M. Ferkey

Chemistry & Biochemistry Faculty Publications

No abstract provided.

Plasmodium Falciparum Cgmp-Dependent Protein Kinase – A Novel Chemotherapeutic Target, David Rotella, John Siekierka, Purnima Bhanot

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

The primary effector of cGMP signaling in Plasmodium is the cGMP-dependent protein kinase (PKG). Work in human-infective Plasmodium falciparum and rodent-infective Plasmodium berghei has provided biological validation of P. falciparum PKG (PfPKG) as a drug target for treating and/or protecting against malaria. PfPKG is essential in the asexual erythrocytic and sexual cycles as well as the pre-erythrocytic cycle. Medicinal chemistry efforts, both target-based and phenotype-based, have targeted PfPKG in the past few years. This review provides a brief overview of their results and challenges.

Cape Gooseberry Husk For The Removal Of Cecs From Wastewater: A Biosorption Study, Jehan Abdel Salam

Theses and Dissertations

Food and beverage industries produce large amounts of fruit wastes that are normally discarded every year. Meanwhile, these industries along with the pharmaceutical industries discharge wastewater effluents that are loaded with contaminants of emerging concern (CECs). Recent research is directed towards finding alternative cost effective and sustainable solutions for treating wastewater. In this regard, we investigated cape gooseberry husk as a potential biosorbent for the removal of caffeine (CA) and salicylic acid (SA), as examples of CECs, from wastewater. Three different types of husk were investigated; un-activated husk (H), and chemically activated husks (H350 and H500) prepared by acid treatment …

Effective Inhibition Of Sars-Cov-2 Entry By Heparin And Enoxaparin Derivatives, Ritesh Tandon, Joshua S. Sharp, Fuming Zhang, Vitor H. Pomin, Nicole M. Ashpole, Dipanwita Mitra, Martin G. Mccandless, Weihua Jin, Hao Liu, Poonam Sharma, Robert J. Linhardt

Faculty and Student Publications

Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has caused a pandemic of historic proportions and continues to spread globally, with enormous consequences to human health. Currently there is no vaccine, effective therapeutic, or prophylactic. As with other betacoronaviruses, attachment and entry of SARS-CoV-2 are mediated by the spike glycoprotein (SGP). In addition to its well-documented interaction with its receptor, human angiotensin-converting enzyme 2 (hACE2), SGP has been found to bind to glycosaminoglycans like heparan sulfate, which is found on the surface of virtually all mammalian cells. Here, we pseudotyped SARS-CoV-2 SGP on a third-generation lentiviral (pLV) vector and tested the …