Physical Sciences and Mathematics Commons^™

Protein Stability In Solution And In The Gas Phase., Yousef Haidar

Electronic Thesis and Dissertation Repository

Electrospray Ionization mass spectrometry (ESI-MS) is widely used for probing proteins, yet many aspects of this technique remain elusive. Using MS, ion mobility spectrometry (IMS), and circular dichroism (CD) spectroscopy, this thesis sheds light on the stability differences of proteins in the gas phase and solution. After a general introduction (Chapter 1), Chapter 2 scrutinizes some aspects of native ESI. Our data highlight the significance of cone voltage in maintaining a native-like fold and show the advantage of using NH₄Ac in protein experiments. Chapter 3 focuses on hydrogen/deuterium exchange (HDX)-MS. Several studies have reported that D₂O …

Methane Dynamics Of Kentucky Bottomland Hardwood Forested Systems, Marissa Miles, Jessica B. Moon, Skylar Ross, Jarred Asselta, Niklas Klauss, Rosie Carey, Kabi Raj Khatiwada, Bassil El Masri, Gary Stinchcomb, Benjamin R. K. Runkle

Kentucky Water Resources Annual Symposium

No abstract provided.

Floating Vegetation As A Driver Of Ch4 Emissions In Small Ponds Across Louisville, Ky, Mark Tierney, C. Jalink, J. H. Loughrin, S. W. Antle, Andrew S. Mehring

Kentucky Water Resources Annual Symposium

No abstract provided.

Measuring The Contribution Of Bald Cypress “Knees” To Greenhouse Gas Emissions During Climate Extremes, Skylar Ross, Jessica B. Moon, Niklas Klauss, Marissa Miles, Kabi Raj Khatiwada4, Bassil El Masri, Gary Stinchcomb, Benjamin R. K. Runkle

Kentucky Water Resources Annual Symposium

No abstract provided.

Characterizing Louisville Wetlands From Above And Below To Better Predict Wetland Carbon Sink-Source Status, Andrea E. Gaughan, Andrew S. Mehring, Mark Tierney, David Brown, Kassidy Haynes, Madison Cicha

Kentucky Water Resources Annual Symposium

No abstract provided.

Microplastics In Water, Their Effects On The Aquatic Ecosystem And Human Public Health, And The Proposed Solutions, Mohanad Abouserie

The Undergraduate Research Journal

We could be swallowing a credit card's weight in plastic every week. Microplastic water pollution is becoming a threat to both humans and aquatic creatures. In this research, microplastic water contamination is discussed, and divergent solutions are proposed. This paper attempts to investigate the causes and effects of such pollution and analyze the current solutions for this issue. The adopted research method is secondary research, where several studies are explored and analyzed. This study explains numerous causes for this issue like cosmetics, cleaning products, factories, and sewage. Consequently, this contamination can negatively impact the organs and metabolisms of the living …

The Structure Of A Lactobacillus Helveticus Chlorogenic Acid Esterase And The Dynamics Of Its Insertion Domain Provide Insights Into Substrate Binding, Kellie K. Omori, Charles T. Drucker, Tracie L. S. Okumura, Nathaniel B. Carl, Brianna T. Dinn, Destiny Ly, Kylie N. Sacapano, Allie Tajii, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Chlorogenic acid esterases (ChlEs) are a useful class of enzymes that hydrolyze chlorogenic acid (CGA) into caffeic and quinic acid. ChlEs can break down CGA in foods to improve their sensory properties and release caffeic acid in the digestive system to improve the absorption of bioactive compounds. This work presents the structure, molecular dynamics, and biochemical characterization of a ChlE from Lactobacillus helveticus (Lh). Molecular dynamics simulations suggest that substrate access to the active site of LhChlE is modulated by two hairpin loops above the active site. Docking simulations and mutational analysis suggest that two residues within …

Multiple Structural And Functional Annotations Based In-Silico Characterization Of Q9brx8 Protein, Eiman Zahid, Muhammad Farhan Sarwar

Karbala International Journal of Modern Science

Numerous proteins found in humans are poorly understood because there is a dearth of experimental evidence. Hypothetical proteins (HPs) or uncharacterized proteins are the terms used to describe these proteins. In this work, one of these proteins, Q9BRX8, is investigated using in-silico or bioinformatics tools to reveal its significant properties. In this regard, NCBI for the sequence retrieval, ProtParam tool for analysis of physiochemical properties, SOPMA for secondary structure prediction, SWISS-Model for homology modelling, STRING for protein-protein interaction and HDOCK for protein-protein docking analysis among other tools, were incorporated. The physiochemical characteristics indicated that Q9BRX8, which has an instability score …

Bridging The Cultural Gap, Trish Ramos

Journal of Multicultural Affairs

Multicultural education is about teaching people about each other without bias. Banks, C. (2016) states “Teachers need to understand their students’ community and home life (pg. 278).” As teachers it is our duty to ensure that every student that enters our classroom leaves with a sense of worth and knowing that each of them matter regardless of ethnicity, religion, gender or cultural.

Development Of Antiviral Peptidomimetics, Songyi Xue

USF Tampa Graduate Theses and Dissertations

Protein-protein interactions (PPIs) are essential for biological processes and are associated with a number of diseases, including cancer, infectious diseases, and neurodegenerative diseases. As a result, modulation of PPIs has been recognized as one of the most promising strategies to develop the novel drugs. Peptide modulators always exhibit higher specificity and affinities with targets than small compounds or monoclonal antibodies, but their broad medicinal effectiveness is constrained by their poor bioavailability and biostability. Peptidomimetics, which have been developed to mimic the structure as well as function of bioactive peptides and proteins, have shown excellent potential in protein surface mimicry and …

An Implementation Of The Method Of Moments On Chemical Systems With Constant And Time-Dependent Rates, Emmanuel O. Adara, Roger B. Sidje

Northeast Journal of Complex Systems (NEJCS)

Among numerical techniques used to facilitate the analysis of biochemical reactions, we can use the method of moments to directly approximate statistics such as the mean numbers of molecules. The method is computationally viable in time and memory, compared to solving the chemical master equation (CME) which is notoriously expensive. In this study, we apply the method of moments to a chemical system with a constant rate representing a vascular endothelial growth factor (VEGF) model, as well as another system with time-dependent propensities representing the susceptible, infected, and recovered (SIR) model with periodic contact rate. We assess the accuracy of …

In Vitro Antioxidant, Anti-Inflammatory, And Photoprotective Activities Of Aqueous Extract Of The Endemic Plant Hammada Scoparia L. From Algeria, Benine Chaima, Djahra Ali Boutlelis, Laiche Ammar Touhami, Tlili Hajer, Tliba Ali, Ben Arfa Abdelkarim, Najjaa Hanen

Karbala International Journal of Modern Science

This study aimed to analyze the chemical profile and evaluate the biological activities of the aqueous extract of H. Scoparia, an endemic plant found in Southeastern Algeria. The aqueous extract was subjected to phytochemical screening, RP-HPLC, and FT-IR analysis. The anti-inflammatory activity was examined using the protein denaturation method, and the photoprotective activity was evaluated using UV-Visible spectrophotometry. The antioxidant activity was assessed using ABTS, DPPH, and FRAP assays. The study found the presence of various secondary metabolites such as polyphenols, tannins, and saponins. This study suggests that H. Scoparia extract has the potential as a natural source of bio-actives …

Mineral Licks As A Potential Nidus For Parasite Transmission, William J. Severud, Todd M. Kautz, Jerrold L. Belant, Seth A. Moore

Natural Resource Management Faculty Publications

Discrete landscape features can concentrate animals in time and space, leading to non-random interspecific encounters. These encounters have implications for predator-prey interactions, habitat selection, intraspecific competition, and transmission of parasites and other pathogens. The lifecycle of the parasitic nematode Parelaphostrongylus tenuis requires an intermediate host of a terrestrial gastropod. Natural hosts of P. tenuis are whitetailed deer, and an aberrant host of conservation concern is moose, which are susceptible to high levels of mortality as a naive host to the parasite. Intermediate hosts become infected when P. tenuis larvae are shed in deer feces, then consumed or enter the gastropod …

Fire Effects On Soil Organic Matter In The Creek Fire, Gracie E. Doolin

Master of Science in Environmental Sciences and Management Projects

Wildfires have increased in frequency and severity over the past few decades due to the increased concertation of CO2 emissions from anthropogenic influence. Soil carbon (C) sequestration has been identified as a climate change mitigation strategy; however, the influx of large-scale wildfires has accelerated landscape processes such as erosion, reducing soil aggradation, and soil C and nitrogen (N) protection. This trend is highlighted by the Creek Fire that occurred in September 2020 and burned 379,895 acres in the Sierra National Forest. This research is designed to close the knowledge gap regarding the impact of burn severity on soil organic matter …

Antiviral Susceptibility Of Clade 2.3.4.4b Highly Pathogenic Avian Influenza A(H5n1) Viruses Isolated From Birds And Mammals In The United States, 2022, Ha T. Nguyen, Anton Chesnokov, Juan De La Cruz, Philippe Noriel Q. Pascua, Vasiliy P. Mishin, Yunho Jang, Joyce Jones, Han Di, Andrei A. Ivashchenko, Mary Lea Killian, Mia K. Torchetti, Kristina Lantz, David E. Wentworth, Charles T. Davis, Alexandre V. Ivachtchenko, Larisa V. Gubareva

United States Department of Agriculture Wildlife Services: Staff Publications

Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) A(H5N1) viruses that are responsible for devastating outbreaks in birds and mammals pose a potential threat to public health. Here, we evaluated their susceptibility to influenza antivirals. Of 1,015 sequences of HPAI A(H5N1) viruses collected in the United States during 2022, eight viruses (∼0.8%) had a molecular marker of drug resistance to an FDA-approved antiviral: three adamantane-resistant (M2-V27A), four oseltamivir-resistant (NA-H275Y), and one baloxavir-resistant (PA-I38T). Additionally, 31 viruses contained mutations that may reduce susceptibility to inhibitors of neuraminidase (NA) (n = 20) or cap-dependent endonuclease (CEN) (n = 11). A panel of 22 …

Monarch Science Observer, Volume 17, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Fall 2023, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

The Bactericidal Activity Of A Novel Aneurinibacillus Aneurinilyticus Isolate Effectively Controls Foodborne Pathogens Campylobacter Jejuni And Listeria Monocytogenes, Peter M. Rubinelli, Rohana Liyanage, Jackson Lay, Jennifer C. Acuff

Chemistry & Biochemistry Faculty Publications and Presentations

Human zoonotic infection with Campylobacter is a major cause of gastroenteritis in the United States and worldwide. Listeria monocytogenes causes a potentially fatal infection in humans and is often attributed to contaminated food. Genetic typing has demonstrated that Campylobacter infection is often associated with the consumption of contaminated poultry products, with Campylobacter often colonizing the poultry gastrointestinal tract, while listeriosis is commonly associated with the consumption of contaminated ready-to-eat (RTE) foods. In this study, a strain of endospore-forming bacterium (strain NH) that is bactericidal towards the human food pathogens Campylobacter jejuni and Listeria monocytogenes was identified and characterized. Transwell experiments …

Chloeia Rozbaczyloi, A New Species Of Polychaete (Archinominae: Amphinomidae) And First Record Of The Family For The Nazca Ridge, Southeastern Pacific Ocean, Juan I. Cañete, María S. Romero, Erin E. Easton, Ariadna Mecho, Javier Sellanes

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Highlights

• A new species of amphinomid polychaete, Chloeia rozbaczyloi sp. nov. is described.

• The new species inhabits poorly explored seamounts of the remote Nazca Ridge off Chile.

• This finding constitutes the first report of the genus Chloeia for Chilean waters.

• Genetic data for Chloeia rozbaczyloi sp. nov is provided.

• The new species is reported for seamounts lying within the recently created Nazca Desventuradas Marine Park.

Abstract

The amphinomid polychaete Chloeia rozbaczyloi sp. nov., collected from seamounts of the Nazca Ridge (NR), northwest of Desventuradas islands, southeastern Pacific Ocean, is described. The new species was observed on only two of seven …

Advances And Perspectives Of Using Stable Isotope Probing (Sip)-Based Technologies In Contaminant Biodegradation, Jinha Kim, Myung Hwangbo, Chih-Hsuan Shih, Kung-Hui Chu

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Highlights

• Advances of SIP-based techniques/applications are comprehensively reviewed.

• Varying stable isotopes types/numbers/ positions reinforce biodegradation studies.

• SIP identifies microbes capable of co-metabolic degradation of contaminants.

• Single-cell SIP.and qSIP are promising to overcome cross-feeding effects.

Abstract

Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the …

Advances And Perspectives Of Using Stable Isotope Probing (Sip)-Based Technologies In Contaminant Biodegradation, Jinha Kim, Myung Hwangbo, Chih-Hsuan Shih, Kung-Hui Chu

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and …

Optimization And Application Of Graph Neural Networks, Shuo Zhang

Dissertations, Theses, and Capstone Projects

Graph Neural Networks (GNNs) are widely recognized for their potential in learning from graph-structured data and solving complex problems. However, optimal performance and applicability of GNNs have been an open-ended challenge. This dissertation presents a series of substantial advances addressing this problem. First, we investigate attention-based GNNs, revealing a critical shortcoming: their ignorance of cardinality information that impacts their discriminative power. To rectify this, we propose Cardinality Preserved Attention (CPA) models that can be applied to any attention-based GNNs, which exhibit a marked improvement in performance. Next, we introduce the Directional Node Pair (DNP) descriptor and the Robust Molecular Graph …

Guar-Based Injectable Hydrogel For Drug Delivery And In Vitro Bone Cell Growth, Humandra Poudel, Ambar R. Rangumagar, Pooja Singh, Adeolu Oluremi, Nawab Ali, Fumiya Watanabe, Joseph Batta-Mpouma, Jin-Woo Kim, Ahona Ghosh, Anindya Ghosh

Chemistry & Biochemistry Faculty Publications and Presentations

Injectable hydrogels offer numerous advantages in various areas, which include tissue engineering and drug delivery because of their unique properties such as tunability, excellent carrier properties, and biocompatibility. These hydrogels can be administered with minimal invasiveness. In this study, we synthesized an injectable hydrogel by rehydrating lyophilized mixtures of guar adamantane (Guar-ADI) and poly-β-cyclodextrin (p-βCD) in a solution of phosphate-buffered saline (PBS) maintained at pH 7.4. The hydrogel was formed via host-guest interaction between modified guar (Guar-ADI), obtained by reacting guar gum with 1-adamantyl isocyanate (ADI) and p-βCD. Comprehensive characterization of all synthesized materials, including the hydrogel, was performed using …

Alkaline Pretreatment And Air Mixing For Improvement Of Methane Production From Anaerobic Co-Digestion Of Poultry Litter With Wheat Straw, Yuanhang Zhan, Jun Zhu, Yiting Xiao, Leland C. Schrader

Biological and Agricultural Engineering Faculty Publications and Presentations

Alkaline pretreatment (AL) and air mixing (air) both have the potential to improve anaerobic co-digestion (Co-AD) of poultry litter with wheat straw for methane production. In this study, the effects of the combination of AL (pH 12 for 12 h) and air mixing (12 mL·d⁻¹) on the Co-AD process were investigated. The substrate hydrolysis was enhanced by AL, with soluble chemical oxygen demand increased by 4.59 times and volatile fatty acids increased by 5.04 times. The cumulative methane yield in the group of Co-AD by AL integrated with air (Co-(AL + air)), being 287 mL·(g VS_added) …

Out-Of-Distribution Generalization Of Deep Learning To Illuminate Dark Protein Functional Space, Tian Cai

Dissertations, Theses, and Capstone Projects

Dark protein illumination is a fundamental challenge in drug discovery where majority human proteins are understudied, i.e. with only known protein sequence but no known small molecule binder. It's a major road block to enable drug discovery paradigm shift from single-targeted which looks to identify a single target and design drug to regulate the single target to multi-targeted in a Systems Pharmacology perspective. Diseases such as Alzheimer's and Opioid-Use-Disorder plaguing millions of patients call for effective multi-targeted approach involving dark proteins. Using limited protein data to predict dark protein property requires deep learning systems with OOD generalization capacity. Out-of-Distribution (OOD) …

Singlet Oxygen-Mediated Conformational Flexibility, Antioxidant, And Isomerization Studies In Chemistry And Biochemistry, Oliver Turque

Dissertations, Theses, and Capstone Projects

Three chapters are included in this dissertation, each of which describes non-oxidative reactions, with peroxy intermediates formed between singlet oxygen (¹O₂) and substrate. (1) Novel discoveries related to the intermediate formed by ¹O₂ and dimethyl disulfane are explored. (2) A new mechanism is proposed, wherein the dihedral angle CS–SC (θ) determines the pro- or antioxidant activity of an organic disulfide. (3) A review of ¹O₂'s ability to facilitate the geometric isomerization of alkenes and polyenes is presented in Chapter 3.

Chapter 1 investigates the role of singlet oxygen potentially …

Construction And Performance Optimization Of Bioconjugated Nanosensors For Early Detection Of Breast Cancer And Pro-Inflammatory Diseases, Pooja Gaikwad

Dissertations, Theses, and Capstone Projects

In recent years, nanosensors have emerged as a tool with strong potential in medical diagnostics. Single-walled carbon nanotube (SWCNT) based optical nanosensors have notably garnered interest due to the unique characteristics of their near-infrared fluorescence emission, including tissue transparency, photostability, and various chiralities with discrete absorption and fluorescence emission bands. Additionally, the optoelectronic properties of SWCNT are sensitive to the surrounding environment, which makes them suitable for in vitro and in vivo biosensing. Single-stranded (ss) DNA-wrapped SWCNTs have been reported as optical nanosensors for cancers and metabolic diseases. Breast cancer and cardiovascular diseases are the most common causes of death …

Lead Exposure Of Mainland Australia's Top Avian Predator, Jordan O. Hampton, Michael T. Lohr, Aaron J. Specht, Damien Nzabanita, Jasmin Hufschmid, Lee Berger, Kate Mcginnis, Jane Melville, Emma Bennett, James M. Pay

Research outputs 2022 to 2026

Lead (Pb) toxicity, through ingestion of lead ammunition in carcasses, is a threat to scavenging birds worldwide, but has received little attention in Australia. We analyzed lead exposure in the wedge-tailed eagle (Aquila audax), the largest raptor species found in mainland Australia and a facultative scavenger. Eagle carcasses were collected opportunistically throughout south-eastern mainland Australia between 1996 and 2022. Lead concentrations were measured in bone samples from 62 animals via portable X-ray fluorescence (XRF). Lead was detected (concentration > 1 ppm) in 84% (n = 52) of the bone samples. The mean lead concentration of birds in which lead was detected …

A Description Of The Grassland Communities Of The Wildcat Hills Region Of Northwestern Nebraska Including Scotts Bluff National Monument And Rare Plant Survey Of The Wildcat Hills Region Of Northwestern Nebraska, Volume I, Terri Hildebrand, Steven B. Rolfsmeier

Nebraska Game and Parks Commission: White Papers, Conference Presentations, and Manuscripts

This study resulted from a Cooperative Agreement between Nebraska Game and Parks Commission and the National Park Service (NPS), with funding provided by the Natural Resource Preservation Program of the NPS. Scotts Bluff National Monument was seeking to characterize the native grassland communities of the Wildcat Hills region in order to develop species composition models for prairie restoration of disturbed lands at the monument. Nebraska Game and Parks Commission needed similar information to refine community classification for the Wildcat Hills region, and to update rare plant species inventories. This report includes a description of the grassland communities and a rare …

A Description Of The Grassland Communities Of The Wildcat Hills Region Of Northwestern Nebraska Including Scotts Bluff National Monument And Rare Plant Survey Of The Wildcat Hills Region Of Northwestern Nebraska, Volume Ii, Terri Hildebrand, Steven B. Rolfsmeier

Nebraska Game and Parks Commission: White Papers, Conference Presentations, and Manuscripts

This study resulted from a Cooperative Agreement between Nebraska Game and Parks Commission and the National Park Service (NPS), with funding provided by the Natural Resource Preservation Program of the NPS. Scotts Bluff National Monument was seeking to characterize the native grassland communities of the Wildcat Hills region in order to develop species composition models for prairie restoration of disturbed lands at the monument. Nebraska Game and Parks Commission needed similar information to refine community classification for the Wildcat Hills region, and to update rare plant species inventories. This report includes a description of the grassland communities and a rare …

Vegetative Sampling Of The Wildcat Hills Region Of Northwestern Nebraska Including Scotts Bluff National Monument And Rare Plant Survey Of The Wildcat Hills Region Of Northwestern Nebraska, A Final Report To: Nebraska Game And Parks Commission, Terri Hildebrand, Steven B. Rolfsmeier

Nebraska Game and Parks Commission: White Papers, Conference Presentations, and Manuscripts

The Wildcat Hills region of northwestern Nebraska is a ridge extending westerly from Chimney Rock in Morrill county to west of Kiowa Creek in central Scotts Bluff county and southerly into the northernmost portions of Banner county (Fig. 1). Much of the expanse is fronted along its northern portion by the North Platte River and US Highway 26. Also included within the study area are the federal lands of Scotts Bluff National Monument and Chimney Rock National Historic Site. Two large portions of state lands, Wildcat Hills State Recreation Area and Buffalo Creek Wildlife Management Area, are located just easterly …