Physical Sciences and Mathematics Commons^™

Towards A New Role Of Mitochondrial Hydrogen Peroxide In Synaptic Function, Cliyahnelle Z. Alexander

Student Theses and Dissertations

Aerobic metabolism is known to generate damaging ROS, particularly hydrogen peroxide. Reactive oxygen species (ROS) are highly reactive molecules containing oxygen that have the potential to cause damage to cells and tissues in the body. ROS are highly reactive atoms or molecules that rapidly interact with other molecules within a cell. Intracellular accumulation can result in oxidative damage, dysfunction, and cell death. Due to the limitations of H₂O₂ (hydrogen peroxide) detectors, other impacts of ROS exposure may have been missed. HyPer7, a genetically encoded sensor, measures hydrogen peroxide emissions precisely and sensitively, even at sublethal levels, during …

Time Scale Separation In Life-Long Ovarian Follicles Population Dynamics Model, Romain Yvinec, Frédérique Clément, Guillaume Ballif

Biology and Medicine Through Mathematics Conference

No abstract provided.

Identifiability For Pde Models Of Fluorescence Microscopy Experiments, Veronica Ciocanel

Biology and Medicine Through Mathematics Conference

No abstract provided.

Statistical Mobility Of Aggregated Microswimmers, Yonatan Ashenafi

Biology and Medicine Through Mathematics Conference

No abstract provided.

College Of Natural Sciences Newsletter, Spring 2024, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message
Page 2 New Faculty and New Club on Campus
Page 3 2024 URSCAD Awards
Page 4 Day of Scholars 2024
Page 5 SDSU's First Representation at the Association for Anatomy's 2024
Annual Conference
Page 6-7 2024 Honor's College Convocation
Page 8 Other Student Activities
Page 9 Faculty Awards
Page 10-11 Other News
Page 12 2024 Drone Day and American Association of Geographers Convention - Hawaii
Page 13 55th Annual Geography Convention
Page 14 2024 Stethoscope Ceremony
Page 15 Open PRAIRIE Data

The Mental Health And Developmental Effects Of Bisphenol-A, Maryann Rettig

Scholars Day Conference

My directed study focuses on the mental health and developmental effects of bisphenol-A (BPA) on individuals in close contact with the chemical product. BPA is an organic chemical produced in large quantities that is used in the production of many polycarbonate plastics, feminine hygiene products, and epoxy resins that coat some metal food cans. Because of it being everywhere, BPA often leaches dermally and orally into the human body. The physical effects of BPA have been known and observed for years. However, its mental health effects specifically are not as commonly known. Therefore, in my directed study I would be …

Hgs-3 The Influence Of A Tandem Cycling Program In The Community On Physical And Functional Health, Therapeutic Bonds, And Quality Of Life For Individuals And Care Partners Coping With Parkinson’S Disease, Leila Djerdjour, Jennifer L. Trilk

SC Upstate Research Symposium

Purpose Statement: Several studies have shown that aerobic exercise can have a positive impact on alleviating symptoms experienced by individuals with Parkinson's disease (PD). Despite this evidence, the potential benefits of exercise for both PD patients and their care partners (PD dyad) remain unexplored. This research project investigates the effectiveness, therapeutic collaborations, and physical outcomes of a virtual reality (VR) tandem cycling program specifically designed for PD dyads.

Methods: Following approval from the Prisma Health Institutional Review Board, individuals with PD were identified and screened by clinical neurologists. The pre-testing measures for PD dyads (N=9) included emotional and cognitive status …

Killing Cancer: Manipulating Hydrophobic Vanadium Complexes To Improve Anti-Cancer Activity, Levi Ausherman, Debbie C. Crans, Peter A. Lay, Maggi Braasch-Turi

SACAD: John Heinrichs Scholarly and Creative Activity Days

Hydrophobic vanadium complexes have recently shown improved anti-cancer activities compared to cisplatin. The hydrophobicity and anti-proliferative activity of [VO(Hshed)(dtb)] ([Hshed= N-(salicylideneaminato)-N’-(2-hydroxyethyl)-1,2-ethanediamine and dtb= 3,5-di(tert-butyl)catechol)]) have inspired the development of a library of hydrophobic vanadium complexes. Increasing the steric bulk of the catechol ligand has been shown to have a direct impact on hydrophobicity and anti-proliferative activities. Currently at Fort Hays State University, the Braasch-Turi group is synthesizing VO(HSHED)(dtb) to build up material to support the chemical analysis and biological assay performed by our collaborators at Colorado State University and the University of Sydney, Australia, respectively. In the future, we plan …

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 …

Deep Learning Can Be Used To Classify And Segment Plant Cell Types In Xylem Tissue, Reem Al Dabagh, Benjamin Shin, Sean Wu, Fabien Scalzo, Helen Holmlund, Jessica Lee, Chris Ghim, Samuel Fitzgerald, Marinna Grijalva

Seaver College Research And Scholarly Achievement Symposium

Studies of plant anatomical traits are essential for understanding plant physiological adaptations to stressful environments. For example, shrubs in the chaparral ecosystem of southern California have adapted various xylem anatomical traits that help them survive drought and freezing. Previous studies have shown that xylem conduits with a narrow diameter allows certain chaparral shrub species to survive temperatures as low as -12 C. Other studies have shown that increased cell wall thickness of fibers surrounding xylem vessels improves resistance to water stress-induced embolism formation. Historically, these studies on xylem anatomical traits have relied on hand measurements of cells in light micrographs, …

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

Evidence Of Direct Interaction Between Cisplatin And The Caspase-Cleaved Prostate Apoptosis Response-4 Tumor Suppressor, Krishna K. Raut, Samjhana Pandey, Gyanendra Kharel, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Prostate apoptosis response-4 (Par-4) tumor suppressor protein has gained attention as a potential therapeutic target owing to its unique ability to selectively induce apoptosis in cancer cells, sensitize them to chemotherapy and radiotherapy, and mitigate drug resistance. It has recently been reported that Par-4 interacts synergistically with cisplatin, a widely used anticancer drug. However, the mechanistic details underlying this relationship remain elusive. In this investigation, we employed an array of biophysical techniques, including circular dichroism spectroscopy, dynamic light scattering, and UV–vis absorption spectroscopy, to characterize the interaction between the active caspase-cleaved Par-4 (cl-Par-4) fragment and cisplatin. Additionally, elemental analysis was …

Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

Microstructure-Based Modeling Of Primary Cilia Mechanics, Nima Mostafazadeh, Andrew Resnick, Y.-N. Young, Zhangli Peng

Physics Faculty Publications

A primary cilium, made of nine microtubule doublets enclosed in a cilium membrane, is a mechanosensing organelle that bends under an external mechanical load and sends an intracellular signal through transmembrane proteins activated by cilium bending. The nine microtubule doublets are the main load-bearing structural component, while the transmembrane proteins on the cilium membrane are the main sensing component. No distinction was made between these two components in all existing models, where the stress calculated from the structural component (nine microtubule doublets) was used to explain the sensing location, which may be totally misleading. For the first time, we developed …

Machine Learning As A Tool For Early Detection: A Focus On Late-Stage Colorectal Cancer Across Socioeconomic Spectrums, Hadiza Galadima, Rexford Anson-Dwamena, Ashley Johnson, Ghalib Bello, Georges Adunlin, James Blando

Community & Environmental Health Faculty Publications

Purpose: To assess the efficacy of various machine learning (ML) algorithms in predicting late-stage colorectal cancer (CRC) diagnoses against the backdrop of socio-economic and regional healthcare disparities. Methods: An innovative theoretical framework was developed to integrate individual- and census tract-level social determinants of health (SDOH) with sociodemographic factors. A comparative analysis of the ML models was conducted using key performance metrics such as AUC-ROC to evaluate their predictive accuracy. Spatio-temporal analysis was used to identify disparities in late-stage CRC diagnosis probabilities. Results: Gradient boosting emerged as the superior model, with the top predictors for late-stage CRC diagnosis being anatomic site, …

Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam

SMU Data Science Review

Abstract. This research used deep learning for image analysis by isolating and characterizing distinct DNA replication patterns in human cells. By leveraging high-resolution microscopy images of multiple cells stained with 5-Ethynyl-2′-deoxyuridine (EdU), a replication marker, this analysis utilized Convolutional Neural Networks (CNNs) to perform image segmentation and to provide robust and reliable classification results. First multiple cells in a field of focus were identified using a pretrained CNN called Cellpose. After identifying the location of each cell in the image a python script was created to crop out each cell into individual .tif files. After careful annotation, a CNN was …

The Staying Power Of Asbestos Hazards: A Critical Environmental Justice Case Analysis, Emily Qian

Sociology Between the Gaps: Forgotten and Neglected Topics

No abstract provided.

Intracellular Transport And Filament Organization In Neurons, Maria-Veronica Ciocanel

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

College Of Natural Sciences Newsletter, September - October 2023, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message
Page 2 New Faculty an Staff for the Fall 2023 Semester
Page 3 Awards
Page 4 Student Ambassadors in CNS
Page 5 Meet our Jacks
Page 6-8 Events
Page 9-11 Media Coverage of CNS
Page 12-13 Spring 2023 Dean's List
Page 14 Open PRAIRIE Data

Structural Insights Into The Cl-Par-4 Protein: Ionic Requirements, Conformational Transitions, And Interaction With Cisplatin, Krishna Kumar Raut

Chemistry & Biochemistry Theses & Dissertations

Cancer continues to be the leading global cause of death, with challenges in early diagnosis, drug resistance, non-specific drug targeting, and cancer recurrence and metastasis posing formidable obstacles in cancer therapy. In this context, Prostate Apoptosis Response-4 (Par-4), a pro-apoptotic tumor suppressor protein, emerged as a promising therapeutic target due to its ability to selectively induce apoptosis in cancer cells, thereby minimizing the drug-associated adverse effects. However, a comprehensive understanding of the structural features of Par-4, specifically the caspase-cleaved fragment (cl-Par-4), is crucial for therapeutic advancements.

This dissertation investigated the effects of various ions, both monovalent and divalent, on the …

A Quantitative Visualization Tool For The Assessment Of Mammographic Risky Dense Tissue Types, Margaret R. Mccarthy

Electronic Theses and Dissertations

Breast cancer is the second most occurring cancer type and is ranked fifth in terms of mortality. X-ray mammography is the most common methodology of breast imaging and can show radiographic signs of cancer, such as masses and calcifcations. From these mammograms, radiologists can also assess breast density, which is a known cancer risk factor. However, since not all dense tissue is cancer-prone, we hypothesize that dense tissue can be segregated into healthy vs. risky subtypes. We propose that risky dense tissue is associated with tissue microenvironment disorganization, which can be quantified via a computational characterization of the whole breast …

Modeling Biphasic, Non-Sigmoidal Dose-Response Relationships: Comparison Of Brain- Cousens And Cedergreen Models For A Biochemical Dataset, Venkat D. Abbaraju, Tamaraty L. Robinson, Brian P. Weiser

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

Biphasic, non-sigmoidal dose-response relationships are frequently observed in biochemistry and pharmacology, but they are not always analyzed with appropriate statistical methods. Here, we examine curve fitting methods for “hormetic” dose-response relationships where low and high doses of an effector produce opposite responses. We provide the full dataset used for modeling, and we provide the code for analyzing the dataset in SAS using two established mathematical models of hormesis, the Brain-Cousens model and the Cedergreen model. We show how to obtain and interpret curve parameters such as the ED50 that arise from modeling, and we discuss how curve parameters might change …

Studying The Stability Of Collagen/Heparin Coatings To Be Used In Cell Therapy Applications, Gavin Mussino

Biological Sciences Undergraduate Honors Theses

This honors thesis aims to investigate the reusability and performance of cell coatings for cell therapy applications. Cell therapy, which involves the use of human cells to repair or replace damaged tissues, holds immense potential for medical advancements. However, ensuring the survival and functionality of transplanted cells remains a significant challenge. We focused on studying the effectiveness of coatings applied to cells for improved cell growth and viability. The research project involved the preparation of the coatings using a layer-by-layer method and the subsequent seeding of cells. The coated cells were then subjected to a series of experiments to assess …

Atomistic Assessment Of Drug-Phospholipid Interactions Consequent To Cancer Treatment: A Study Of Anthracycline Cardiotoxicity, Yara Elsayed Ahmed

Theses and Dissertations

Despite being one of the most effective chemotherapeutic agents developed to date, Anthracyclines are notorious for their cardiotoxicity. Their clinical use is frequently limited both in dosage and in prescription due to the severe cardiac damage they cause. The mechanism of anthracycline-induced cardiotoxicity is not yet fully understood. However, it is hypothesized that interactions with the myocardial membrane play an important role in imparting cardiotoxicity. In this study, we use molecular dynamics simulations and density functional theory calculations to study the anthracycline drug molecules and the interactions that they have with the myocardial membrane. We construct a myocardial membrane model …

Chemoattractant Distribution In Complex Geometry Impacts The Trajectory Of Clustered Cell Migration, Naghmeh Akhavan

Biology and Medicine Through Mathematics Conference

No abstract provided.

College Of Natural Sciences Newsletter, March - May 2023, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 4, Issue 2

Page 1 Dean's Message
Page 2-7 Awards and Recognition
Page 8 March 3rd Corothers Seminar
Page 9 54th Geography Convention
Page 10 Spring 2023 Day of Scholars
Page 11 2023 URSCAD Snaps
Page 12-14 Media Coverage of CNS
Page 15 Open PRAIRIE Data

Rattus Norvegicus As A Biological Detector Of Clandestine Remains And The Use Of Ultrasonic Vocalizations As A Locating Mechanism, Gabrielle M. Johnston

Master's Theses

In investigations, locating missing persons and clandestine remains are imperative. One way that first responder and police agencies can search for the remains is by using cadaver dogs as biological detectors. Cadaver dogs are typically used due to their olfactory sensitivity and ability to detect low concentrations of volatile organic compounds produced by biological remains. Cadaver dogs are typically chosen for their stamina, agility, and olfactory sensitivity. However, what is not taken into account often is the size of the animal and the expense of maintaining and training the animal. Cadaver dogs are typically large breeds that cannot fit in …

Trace Dna Detection Using Diamond Dye: A Recovery Technique To Yield More Dna, Leah Davis

Master's Theses

This study aspires to find a new screening approach to trace DNA recovery techniques to yield a higher quantity of trace DNA from larger items of evidence. It takes the path of visualizing trace DNA on items of evidence with potential DNA so analysts can swab a more localized area rather than attempting to recover trace DNA through the general swabbing technique currently used for trace DNA recovery. The first and second parts consisted of observing trace DNA interaction with Diamond Dye on porous and non-porous surfaces.

The third part involved applying the Diamond Dye solution by spraying it onto …

College Of Natural Sciences Newsletter, February 2023, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 4, Issue 1

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3-4 Nobel Recipient Visits Campus
Page 4 Adopting the Pantry
Page 5 Growing a Recruitment Mindset
Page 6 February Outreach Events
Page 7 Media Coverage of CNS
Page 8 Open PRAIRIE Data
Page 9 54th Geography Convention, and Tom Loveland EROS Geography Scholarship
Page 10 Photos of Dr. Carolyn Bertozzi's Visit

Intellectual Disability Related To De Novo Germline Loss Of The Distal End Of The P-Arm Of Chromosome 17: A Case Report, Eden Pope, Matthew Huertas, Amar Paul, Braden Cunningham, Matthew Jennings, Ryan Perry, Stephanie Chavez, John A. Kriak, Kyle B. Bills, David W. Sant

Annual Research Symposium

Hypothesis/Purpose: In this report we present a case of a 20-year-old female with congenital intellectual disability, stunted growth, and hypothyroidism. Competitive genetic hybridization (CHG) revealed a loss of 17p13.3, and the deletion was not present in either parent. This deletion has not previously been characterized, but mutations on the p-arm of chromosome 17 are responsible for Miller-Dieker Syndrome and Isolated Lissencephaly Sequence, both of which share symptoms in common with the patient.

Methods: Peripheral mononuclear cells (PBMCs) were used for karyotyping and competitive genetic hybridization (CHG). Bioinformatic analysis was carried out using the Genome Data Viewer (ncbi.nlm.nih.gov/genome/gdv).

Results: Karyotype was …