Chemistry Commons^™

Methionyl-Trna Synthetase Synthetic And Proofreading Activities Are Determinants Of Antibiotic Persistence, Whitney N. Wood, Miguel Angel Rubio, Lorenzo Eugenio Leiva, Gregory J. Phillips, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bacterial antibiotic persistence is a phenomenon where bacteria are exposed to an antibiotic and the majority of the population dies while a small subset enters a low metabolic, persistent, state and are able to survive. Once the antibiotic is removed the persistent population can resuscitate and continue growing. Several different molecular mechanisms and pathways have been implicated in this phenomenon. A common mechanism that may underly bacterial antibiotic persistence is perturbations in protein synthesis. To investigate this mechanism, we characterized four distinct metG mutants for their ability to increase antibiotic persistence. Two metG mutants encode changes near the catalytic site …

In Silico Analysis Of C-Type Lectins As Co-Infection Receptors Of Dengue And Chikungunya Viruses In Aedes Aegypti, Munawir Sazali, R. C. Hidayat Soesilohadi, Nastiti Wijayanti, Tri Wibawa, Arif Nur Muhammad Ansori

Makara Journal of Science

Aedes aegypti is a primer vector of dengue virus (DENV) and chikungunya virus (CHIKV). The susceptibility of mosquitoes to DENV and CHIKV depends on their recognition receptor of pathogens. C-type lectins (CTLs) are an important mediator of virus infection in A. aegypti. This study aims to identify potential receptors and determine the binding affinity between ligand–receptor interaction, CTLs and virus envelopes (DENV-1, 2, 3, and 4 and CHIKV) interaction based on in silico analysis. Sample sequences were obtained from GenBank (NCBI), and 10 CTLs were acquired from VectorBase. Homology modeling based on a minimum standard of 20% was processed …

The Polyglutamine Domain Is The Primary Driver Of Seeding In Huntingtin Aggregation, Adam Skeens, Chathuranga Siriwardhana, Sophia E. Massinople, Michelle M. Wunder, Zachary L. Ellis, Kaitlyn M. Keith, Tyler Girman, Shelli L. Frey, Justin Legleiter

Chemistry Faculty Publications

Huntington’s Disease (HD) is a fatal, neurodegenerative disease caused by aggregation of the huntingtin protein (htt) with an expanded polyglutamine (polyQ) domain into amyloid fibrils. Htt aggregation is modified by flanking sequences surrounding the polyQ domain as well as the binding of htt to lipid membranes. Upon fibrillization, htt fibrils are able to template the aggregation of monomers into fibrils in a phenomenon known as seeding, and this process appears to play a critical role in cell-to-cell spread of HD. Here, exposure of C. elegans expressing a nonpathogenic N-terminal htt fragment (15-repeat glutamine residues) to preformed htt-exon1 fibrils induced …

Β-Sheets Mediate The Conformational Change And Allosteric Signal Transmission Between The Aslov2 Termini, Sian Xiao, Mayar Terek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

Avena sativa phototropin 1 light-oxygen-voltage 2 domain (AsLOV2) is a model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change begins with the unfolding of the N-terminal A'α helix in the dark state followed by the unfolding of the C-terminal Jα helix. The light state is characterized by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β-sheets are identified as crucial components for mediating allosteric signal transmission between the two termini. Through combined experimental and computational investigations, the Hβ …

Novel Inhibitors To Mmpl3 Transporter Of Mycobacterium Tuberculosis By Structure-Based High-Throughput Virtual Screening And Molecular Dynamics Simulations, Hetanshi Choksi, Justin Carbone, Nicholas J. Paradis, Lucas Bennett, Candice Bui-Linh, Chun Wu

College of Science & Mathematics Departmental Research

Tuberculosis (TB)-causing bacterium Mycobacterium tuberculosis (Mtb) utilizes mycolic acids for building the mycobacterial cell wall, which is critical in providing defense against external factors and resisting antibiotic action. MmpL3 is a secondary resistance nodulation division transporter that facilitates the coupled transport of mycolic acid precursor into the periplasm using the proton motive force, thus making it an attractive drug target for TB infection. In 2019, X-ray crystal structures of MmpL3 from M. smegmatis were solved with a promising inhibitor SQ109, which showed promise against drug-resistant TB in Phase II clinical trials. Still, there is a pressing need to discover more …

Induction Of Neuroinflammation And Brain Oxidative Stress By Brain-Derived Extracellular Vesicles From Hypertensive Rats, Xinqian Chen, Xin Yan, Leah Gingerich, Qing Hui Chen, Lanrong Bi, Zhiying Shan

Michigan Tech Publications

Neuroinflammation and brain oxidative stress are recognized as significant contributors to hypertension including salt sensitive hypertension. Extracellular vesicles (EVs) play an essential role in intercellular communication in various situations, including physiological and pathological ones. Based on this evidence, we hypothesized that EVs derived from the brains of hypertensive rats with salt sensitivity could trigger neuroinflammation and oxidative stress during hypertension development. To test this hypothesis, we compared the impact of EVs isolated from the brains of hypertensive Dahl Salt-Sensitive rats (DSS) and normotensive Sprague Dawley (SD) rats on inflammatory factors and mitochondrial reactive oxygen species (mtROS) production in primary neuronal …

Dna-Pkcs Rnaseq Data: Dna-Pkcs Wilde-Type Or Kinase-Dead Protein Regulate Basal And Etoposide-Induced Gene Expression Changes, Amanda Ashley

Chemistry & Biochemistry: Datasets

No abstract provided.

Antioxidant Properties Of Kombucha Beverage Infused With Ganoderma Lucidum And Green Tea From Camellia Sinensis (L.) Kuntze With Several Fermentation Times, Rizki Rabeca Elfirta, Pamungkas Rizki Ferdian, Iwan Saskiawan, Tri Hadi Handayani, Kayla Faza Gustafri Mandalika, Rini Riffiani, Kasirah Kasirah, Ukhradiya Magharaniq Safira Purwanto

Karbala International Journal of Modern Science

Kombucha is a functional beverage produced through the fermentation of infused tea or Camelia sinensis (L.) Kuntze (CS) by a symbiotic culture of bacteria and yeast. Apparently, the substrate of kombucha can be substituted to enhance its functional properties. Ganoderma lucidum (GL) is a potential substrate reported to have health benefits. This study aims to evaluate antioxidant properties by comparing different formulations and fermentation times. The formulations prepared in the present study varied in the compositions of GL and CS substrates, namely F1 (100% GL), F2 (75% GL: 25% CS), F3 (50% GL: 50% CS), F4 (25% GL: 75% CS), …

Raw Nmr Data For Tripeptides, David J. Michaelis, Scott R. Burt, Mariur Rodriguez Moreno, Nye C. Johnson, Christopher B. Stewart, Mary L. Setelin, Adam X. Wayment, Braxton M. Felix

ScholarsArchive Data

This data set contains primary data for 50 tripeptides that were generated as part of an advanced undergraduate laboratory experience in solid phase peptide synthesis. The raw data can be processed sing NMR interpretation software and can be used as problems for exams and quizzes or as supplementary materials for a laboratory experience

Toward A Coordinated Understanding Of Hydro-Biogeochemical Root Functions In Tropical Forests For Application In Vegetation Models, Daniela F. Cusack, Bradley Christoffersen, Chris M. Smith-Martin, Kelly M. Andersen, Amanda L. Cordeiro, Katrin Fleischer, S. Joseph Wright, Nathaly R. Guerrero-Ramírez, Laynara F. Lugli, Lindsay A. Mcculloch, Mareli Sanchez-Julia, Sarah A. Batterman, Caroline Dallstream, Claire Fortunel, Laura Toro, Lucia Fuchslueger, Michelle Y. Wong, Daniela Yaffar, Joshua B. Fisher, Marie Arnaud, Lee H. Dietterich, Shalom D. Addo-Danso, Oscar J. Valverde-Barrantes, Monique Weemstra, Jing Cheng Ng, Richard J. Norby

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest–climate feedbacks for these carbon-rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics …

3-Chloropropylbis(Catecholato)Silicate As A Bifunctional Reagent For The One-Pot Synthesis Of Tetrahydroquinolines From O-Bromosulfonamides, Noah Brodsky, Nidheesh Phadnis, Mohamed Ibrahim, Isabel M. Andino, Inés Blanc Giro, John A. Milligan

College of Life Sciences Faculty Papers

Bis(catecholato)silicate salts are easily accessible reagents that can be used to install alkyl fragments through photoredox-enabled cross-coupling. These reagents can incorporate various functional groups including pendant alkyl halides. A halogenated organosilicate reagent was leveraged to develop a one-pot synthesis of tetrahydroquinolines from o-bromosulfonamides, where the bifunctional reagent participates in a nickel/photoredox cross-coupling followed by intramolecular nucleophilic substitution. The functional group tolerance of this cross-coupling strategy allowed for the preparation of a series of substituted tetrahydroquinolines.

Investigations Of The Eutectic Formation And Skin Rejuvenation By Hyaluronan - Kojic Acid Dipalmitate System, Syed Waqar Hussain Shah, Sumbal Imran, Iram Bibi, Kashif Ali, Nadia Bashir

Karbala International Journal of Modern Science

Eutectic phenomenon has been investigated in binary system based on biopolymer hyaluronan (HN) and kojic acid dipalmitate (KAD). Solid-liquid phase diagram showed a significant dependence of melting points on weight fraction of KAD up to KAD < 0.5. A negligible regain to melting temperature of pure KAD occurred later. Simulations of molecular mechanics using a four-unit segment of HN and KAD revealed the interaction between carbonyl of KAD with 4-OH on N-acetylglucosamine unit of oligomer. Infrared vibrational spectroscopy also endorsed the existence of a weakly interacting system. Such behavior was expected due to steric hinderance and rigidity of biopolymer. The thermal decomposition temperature of HN (i.e., 215 °C) was increased to 322 °C in HK50 having HN and KAD in 1:50 w/w. Bioelectric impedance analysis revealed that these green materials could promote skin health in humans.

Synthesis And Characterization Of Renewable Heterogeneous Catalyst Zno Supported Biogenic Silica From Pineapple Leaves Ash For Sustainable Biodiesel Conversion, Nadila Pratiwi, Suriati Eka Putri, Yulia Shinta, Arya Ibnu Batara, Diana Eka Pratiwi, Abd Rahman, Nur Ahmad, Heryanto Heryanto

Karbala International Journal of Modern Science

This study reports on the first case of the low-cost and environmentally friendly ZnO/SiO2 heterogeneous catalyst from pineapple leaves ash (PLA). Catalyst shows excellent performance in catalyzing the transesterification of waste cooking oil (WCO) with methanol for biodiesel conversion. This study focuses on assessing the influence of Zn content on physicochemical characteristics, using XRD, FTIR, SEM, and N2 adsorption-desorption methods. In addition, three different Zn content levels (20, 25, and 30 %wt) were applied. The results showed that all ZnO/SiO2 samples exhibited characteristics suitable for use as catalyst with an average crystallite size of 31.83-34.15 nm, and a surface area …

Butterworth Filter To Reduce Reactivity Fluctuations, Daniel Suescún-Díaz, Geraldyne Ule-Duque, Luis E. Cardoso-Páez

Karbala International Journal of Modern Science

In this study, we introduce the calculation of reactivity in nuclear reactors. The proposed method uses the Euler-Maclaurin series to approximate the integral in the inverse equation of point kinetics. The approximation is done with the first three terms, the first term represents the approximation of a zero-order sum, the second term the trapezoidal rule and the third term the first Bernoulli number. These three terms improve the approximation, along with an estimate of the neutron density using the prompt jump approximation. To reduce neutron density fluctuations, a second-order Butterworth filter for the reactivity calculation was implemented, which offers the …

Machine Learning Model And Molecular Docking For Screening Medicinal Plants As Hiv-1 Reverse Transcriptase Inhibitors, Muthia Rahayu Iresha, Firdayani Firdayani, Agam Wira Sani, Nihayatul Karimah, Shelvi Listiana, Irfansyah Yudhi Tanasa, Arief Sartono, Ayu Masyita

Karbala International Journal of Modern Science

The human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) plays a significant role in viral replication and is one of the targets for anti-HIV. However, a mutation in viral strains rapidly developed the resistance of the com-pounds to the protein, reducing the effectiveness of the inhibitors. This work seeks to utilize machine learning-based quantitative structure-activity relationship (QSAR) analysis in combination with molecular docking simulations to forecast the presence of active compounds derived from medicinal plants. Specifically, the objective is to identify com-pounds that have the potential to operate as inhibitors of HIV-1 reverse transcriptase (RT), encompassing both wild-type and …

Historical Analysis Of Urban Dust Generated By The Great Salt Lake Playa, Callum Flowerday, Jaron C. Hansen, Rebekah Stanley, Kaitlyn Brewster

ScholarsArchive Data

Historical PM10 filters, provided by the Utah Division of Air Quality, were analyzed for elemental composition of various metals. This was done using ICP-MS.

Also included, EPA PM10 historical data and bathymetry data provided by the Utah USGS.

An Observational Framework For Constructing Ozone Isopleths From Long-Term Monitoring Data: Demonstration In Salt Lake City, Utah, Callum Flowerday, Isaac Sudweeks, Brad Adams, Jaron C. Hansen

ScholarsArchive Data

EPA quality assured data, collected by the Utah Division of Air Quality, was used for this analysis.

Unimer Suppression Enables Supersaturated Homopolymer Swollen Micelles With Long-Term Stability After Glassy Entrapment, Eric R. Williams, Christian X. Ruff, Morgan Stefik

Faculty Publications

Micelle sizes are critical for a range of applications where the simple ability to adjust and lock in specific stable sizes has remained largely elusive. While micelle swelling agents are well-known, their dynamic re-equilibration in solution implies limited stability. Here, a non-equilibrium processing sequence is studied where supersaturated homopolymer swelling is combined with glassy-core (“persistent”) micelles. This path-dependent process was found to sensitively depend on unimer concentration as revealed by DLS, SAXS, and TEM analysis. Here, lower-selectivity solvent combinations led to the formation of unimer-homopolymer aggregates and eventual precipitation, reminiscent of anomalous micellization. In contrast, higher-selectivity solvents enabled supersaturated homopolymer …

Unimer Suppression Enables Supersaturated Homopolymer Swollen Micelles With Long-Term Stability After Glassy Entrapment, Eric R. Williams, Christian X. Ruff, Morgan Stefik

Faculty Publications

Micelle sizes are critical for a range of applications where the simple ability to adjust and lock in specific stable sizes has remained largely elusive. While micelle swelling agents are well-known, their dynamic re-equilibration in solution implies limited stability. Here, a non-equilibrium processing sequence is studied where supersaturated homopolymer swelling is combined with glassy-core (“persistent”) micelles. This path-dependent process was found to sensitively depend on unimer concentration as revealed by DLS, SAXS, and TEM analysis. Here, lower-selectivity solvent combinations led to the formation of unimer-homopolymer aggregates and eventual precipitation, reminiscent of anomalous micellization. In contrast, higher-selectivity solvents enabled supersaturated homopolymer …

Multi-Agent System For Portfolio Profit Optimization For Future Stock Trading, Usha Devi, Mohan R

Karbala International Journal of Modern Science

Stock trading highly contributes to the economic growth of the country. The stock trading objective is to earn profits with buy/sell/hold decisions on the set of stocks in the portfolio. The portfolio optimization problem is finding the decision sequence that leads to higher profit and lower risk. Portfolio optimization is challenging due to complex price history patterns and an uncertain environment. Incorrect decisions in stock trading lead to massive losses. The proposed Multi-Agent System for Portfolio Profit Optimization (MASPPO) aims to optimize trading profit and reduce risk with accurate predictions. The proposed model integrates the Fuzzy c-means with the Deep …

Use Of Dft Calculations As A Tool For Designing New Solvatochromic Probes For Biological Applications, Cynthia M. Dupureur

Educator Preparation & Leadership Faculty Works

The intramolecular charge transfer behavior of push–pull dyes is the origin of their sensitivity to environment. Such compounds are of interest as probes for bioimaging and as biosensors to monitor cellular dynamics and molecular interactions. Those that are solvatochromic are of particular interest in studies of lipid dynamics and heterogeneity. The development of new solvatochromic probes has been driven largely by the need to tune desirable properties such as solubility, emission wavelength, or the targeting of a particular cellular structure. DFT calculations are often used to characterize these dyes. However, if a correlation between computed (dipole moment) and experimentally measured …

An Itpa Enzyme With Improved Substrate Selectivity, Nicholas E. Burgis, Kandise Vanwormer, Devin Robbins, Jonathan Smith

Chemistry and Biochemistry Faculty Publications

Recent clinical data have identified infant patients with lethal ITPA deficiencies. ITPA is known to modulate ITP concentrations in cells and has a critical function in neural development which is not understood. Polymorphism of the ITPA gene affects outcomes for both ribavirin and thiopurine based therapies and nearly one third of the human population is thought to harbor ITPA polymorphism. In a previous site-directed mutagenesis alanine screen of the ITPA substrate selectivity pocket, we identified the ITPA mutant, E22A, as a gain-of function mutant with enhanced ITP hydrolysis activity. Here we report a rational enzyme engineering experiment to investigate the …

College Of Natural Sciences 2023 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message
Page 3 Department Highlights
Page 4 One Day for State
Page 5 Noble Prize Winner Speaks on Campus
Page 6-7 Faculty Excellence
Page 8-9 Student Excellence
Page 10 Outreach Program
Page 10 Events and Traditions
Page 11 Connections Abroad
Page 12 Student Spotlight
Page 13 Alumni Spotlight
Page 14 First Ever Drone Day
Page 15 Grand Opening of POET Bioproducts Center
Page 16 Work Anniversaries

Rational Design Of Peptide-Based Materials Informed By Multiscale Molecular Dynamics Simulations, Dhwanit Rahul Dave

Dissertations, Theses, and Capstone Projects

The challenge of establishing a sustainable and circular economy for materials in medicine and technology necessitates bioinspired design. Nature's intricate machinery, forged through evolution, relies on a finite set of biomolecular building blocks with through-bond and through-space interactions. Repurposing these molecular building blocks requires a seamless integration of computational modeling, design, and experimental validation. The tools and concepts developed in this thesis pioneer new directions in peptide-materials design, grounded in fundamental principles of physical chemistry. We present a synergistic approach that integrates experimental designs and computational methods, specifically molecular dynamics simulations, to gain in-depth molecular insights crucial for advancing the …

Biomolecular Crystals As Functional Materials, Fahmeed Khan Sheehan

Dissertations, Theses, and Capstone Projects

The field of supramolecular chemistry has undergone significant evolution over the last few decades, progressing from fundamental studies of self-assembling systems to the rational design of functional materials with exceptional properties. Among these materials, short peptides have emerged as a chemically simple yet highly versatile class of biomimetic compounds. Initially, short peptides were used as model systems to understand larger protein interactions. As the field progressed, short peptides were found to have exceptional functionality, and are now explored as functional nanomaterials for diverse applications. In many cases, short peptide materials have displayed properties not found in biology, in some cases …

Heavy Metals Analysis And Physicochemical Characterization Of Groundwater At A Battery Recycling Site In South-Western Nigeria, Adeniyi T. Adeleke, Rasaki K. Odunaike, Shamsideen K. Alausa, Idris O. Olayiwola, Adetoro T. Talabi, Qasim A. Adeniji, Adejumobi C. Adeniyi

Tanzania Journal of Science

Indiscriminate dumping of battery waste is a huge issue that endangers human health and the environment. This study aimed at analysing the health impacts of exposure to pollution from spent battery recycling in Ogun State, which houses a diverse range of battery recycling industries. At this study site, forty water samples were studied over the Wet and Dry seasons to assess the impact of battery recycling waste on groundwater. Except for the TSS, the physiochemical parameters of the groundwater vary with season and are within the permissible limits. The electrical conductivity (EC), turbidity, Phosphorus, Biochemical oxygen demand (BOD), Dissolve oxygen …

Synthesis Of Template-Free Flower-Like Zno Nanorods Using A Simple Chemical Bath Technique, Benard S. Mwankemwa

Tanzania Journal of Science

Flower-like ZnO nanorods were successfully synthesised using a template-free, low-temperature chemical bath deposition method. The effects of growth time on the structural, morphological, and vibrational properties of flower-like zinc oxide were investigated. X-ray diffraction (XRD) and scanning electron microscopy (SEM) indicated that the crystallite size and density of flower-like ZnO nanorods increased with increasing growth time. Raman spectroscopy confirmed the existence of specific Raman modes that correspond to the wurtzite structure of ZnO. In addition, Raman measurements revealed that increased growth time increases the Raman modes intensity of the flower-like ZnO nanorods. Moreover, the measurements of the Au/ZnO nanorods/FTO Schottky …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

Genome-Wide Profiling Of Novel Conserved Zea Mays Micrornas Along With Their Key Biological, Molecular And Cellular Targets And Validation Using An Rt-Pcr Platform, Abdul Baqi, Sami Ullah, Muhammad Ayub, Muhammad Zafar Saleem, Ghulam Mustafa Khan, Asad Ullah

Karbala International Journal of Modern Science

MicroRNAs (miRNAs), which are typically non-coding RNAs that start off as endogenous molecules and regulate post-transcriptional levels of gene expression by mRNA degradation or translational repression. They are 18–26 nucleotides long, evolutionarily conserved and essential for predicting novel miRNAs in a variety of plants. Maize (Zea mays) is a significant food and forage crop in the globe today. In the present study, many maize miRNAs have been found to be associated with both plant development and responses to stress. In this study, 66 unique conserved maize miRNAs from 65 different miRNA families were predicted using several genomics-based methods …

The Role Of Cu (0-0.03) And Zn (0.02) Substitution On The Structural, Optical And Magnetic Properties Of Mgo Nanoparticles, S. Naseem Shah, Atif Dawar, Yasmeen Bibi, Abid Ali, M. Asif Siddiqui

Karbala International Journal of Modern Science

The co-precipitation method was employed to prepared Cu (0-0.03) and Zn (0.02) dual doped MgO nanoparticles. The secondary phases of CuO and Cu₂O were observed along with the cubical phase of MgO. The doping induced effect was noticed for the crystallite size variations (14.39-19.89 nm). The morphological transformation from spherical to rice-like shape were observed. The estimated values of optical bandgap (4.66-4.45 eV) were well correlated with the crystallite size and dopant concentrations. The ferromagnetic ordering was observed at room temperature and the enchantment in the coercivity (142.27 Oe) with Zn (0.02) doping was noticed. Such type of …