Digital Commons Network^™

Determining The Function Of Type Iv-B Crispr-Cas Systems, Eric Jenkins, Brendon Guinn

Student Research Symposium

CRISPR-Cas systems are a diverse group of prokaryotic adaptive immune systems that defend against Mobile Genetic Elements (MGEs) such as bacteriophages and plasmids. CRISPR-associated (Cas) proteins bind to guide RNAs (crRNAs) transcribed from a DNA repeat array (CRISPR array) containing spacers complementary to MGEs. Upon infection by a MGE, the Cas protein-crRNA complex binds to the target sequence in the invaders genome and cleaves the nucleic acid.

Detection Of Co2 Locally Generated By Formate Dehydrogenase Using Carbonate Ion-Selective Micropipette Electrodes, Seol Baek, Salvador Gutierrez-Portocarrero, Rokas Gerulskis, Shelley D. Minteer, Sean R. German, Henry S. White

Chemistry Faculty Research & Creative Works

Many technologies involve immobilizing catalysts such as enzymes on surfaces, and the catalytic activities or functional efficiencies of these surface-bound catalysts can vary depending on orientations, localized binding sites, active sites, and intrinsic molecular nature. Accurate and rapid quantification of reaction products from surface-immobilized catalysts is crucial for understanding the selectivity, mechanisms, and reaction dynamics of catalytic systems and for revealing heterogeneous catalytic activities and reaction sites for applications such as biosensors and energy conversion/generation systems. Here, we demonstrate the feasibility of localized enzymatic activity measurements using microscale carbon dioxide (CO₂)-sensitive ion-selective electrode (ISE) pipettes (0.5-2.5 μm tip …

Living With Alzheimer’S: A Guide To How To Lower The Risk Of Memory Loss & Care For Those With Alzheimer’S, Mona Muzammil, Washain Muzammil

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Despite the frequent characterization of Alzheimer's disease as a “loss of self,"" this enlightening book demonstrates unequivocally that a person's unique self persists throughout the course of the disease. The important message in Caring for People with Alzheimer’s is how much can be done in care settings to support a person's sense of identity and thereby enrich the lives of people experiencing the many losses associated with dementia. Drawing from a diverse body of research, this book brings together the recommendations of the best thinkers and practitioners in multiple disciplines to illustrate the meaning of self and the importance of …

Highly Regenerable Magnetic Sulfonated Chitosan Crosslinked With Glutaraldehyde Composite Beads (Iron Sand/Naso3-Chi-G) For Aqueous Mercury Removal, Fathurrahmi Fathurrahmi, Rahmi Rahmi, Lelifajri Lelifajri, Anggun Sixthia Wulan Ayu, Muhammad Iqhrammullah

Karbala International Journal of Modern Science

We developed a novel adsorbent from sulfonated, glutaraldehyde-crosslinked chitosan embedded with magnetic iron sand. The adsorbent was synthesized through a two-step process: (1) sulfonation with N(SO₃Na)₃ to introduce sulfonate groups, and (2) crosslinking with glutaraldehyde to enhance structural stability. The optimal formulation, containing 43.5% iron sand and crosslinked with 0.17 M glutaraldehyde, exhibited the highest Hg²⁺ adsorption capacity (30.74 mg/g) at pH 3. The adsorbents were characterized using Scanning Electron Microscopy (SEM), Fourier transform infra-red spectroscopic (FT-IR), and X-ray diffraction (XRD) techniques. Adsorption equilibrium was achieved within 60 minutes, and isotherm modeling showed that the process followed the Freundlich model …

Antioxidant Activity Of Pamam Dendrimer Stabilized Ascorbic Acid, Gabriella Srikureja

Honors Theses

Ascorbic acid (vitamin C) is an essential micronutrient for human health. It acts as an enzymatic cofactor in anabolic biochemical pathways such as the synthesis of collagen, dopamine, and norepinephrine. Unfortunately, this versatility comes at the cost of a high degradation rate both in and outside of the food matrix. Previous research exploring stabilizing aqueous ascorbic acid through Poly(amidoamine) (PAMAM) dendrimers found success in reducing the rate of degradation.

To confirm the antioxidant activity of ascorbic acid in its stabilized dendrimer complex, 2,2-Diphenyl-1-picrylhydrazyl (DPPH) assays examined via Cary 5000 UV-Vis-NIR spectrophotometer found that performing the DPPH assay under aqueous conditions …

Transition Metal Nanocomposites: Nonenzymatic Biosensor For Neurochemical Detection, Amitav Sen, Ace Cannon, Manashi Nath

Miners Solving for Tomorrow Research Conference

No abstract provided.

Maldi-Mass Spectrometry Imaging To Investigate Distribution Of Per- And Polyfluoroalkyl Substances In Exposed Poplar Tissues, Tonglin Zhou, Varuni Abhayarayne, Joseph Akor, Honglan Shi, Paul Ki-Souk Nam, Joel Gerard Burken, John Yang

Miners Solving for Tomorrow Research Conference

No abstract provided.

The Effect Of Nanomorphology As Quantified Via The K‑Index On The Drug Delivery Properties Of Isocyanate-Derived Aerogels, Stephen Y. Owusu, A. B. M. Shaheen Ud Doulah, Vaibhav A. Edlabadkar, Kamden J. George, Chariklia Sotiriou-Leventis

Miners Solving for Tomorrow Research Conference

No abstract provided.

Exploring Rotational Energy Transfer Of Intermolecular Collisions In Complex Systems: A Mqct Approach, Carolin Anna Joy

Dissertations (1934 -)

The accurate modeling of molecular spectra in astrophysical environments requires detailed understanding of collisional energy transfer processes, which remains a significant challenge due to the computational complexity of quantum mechanical calculations for larger molecules, heavier projectiles, and higher collision energies. This dissertation addresses this challenge through the development and application of Mixed Quantum/Classical Theory (MQCT), a hybrid approach that combines quantum mechanical treatment of internal molecular motion with classical description of translational degrees of freedom. The methodology was first validated through detailed study of rotational energy transfer in the ND3 + D2 system, demonstrating excellent agreement with full quantum results …

Application Of Analytical Methodologies To The Analysis Of Food Flavoring Agents: Part Ii, James Daniel, Kexin Li, Anaaya Monroe, Melissa C. Rhoten

Spring Showcase for Research and Creative Inquiry

No abstract provided.

Chalmers Library Research Award Winner 1 2025, Tasnim Islam Orco

Chalmers Library Research Award

No abstract provided.

Expanding The Lexa Bacterial Two-Hybrid System For Human Protein-Protein Interaction Screening: Application To Tumor Suppressor Par-4, Rebecca M. Richardson

Chemistry & Biochemistry Theses & Dissertations

Protein-protein interactions (PPI) are fundamental to cellular function, influencing processes such as signaling, structural organization, and disease progression. Disruptions in PPIs are implicated in cancer and neurodegenerative diseases, highlighting their importance as therapeutic targets. However, traditional methods for studying human PPIs, such as yeast two-hybrid and co-immunoprecipitation mass spectrometry, are costly and technically demanding. This dissertation explores the LexA-based bacterial two-hybrid (LexA-B2H) system as a cost effective and accessible alternative for investigating human PPIs.

This study focuses on the interaction between glucose-regulated protein 78 (GRP78) and cleaved prostate apoptosis response-4 (cl-Par-4), a tumor suppressor protein involved in apoptosis and neurodegenerative …

Kinetic Control And Trapping In The Supramolecular Polymerization Of M-Terphenyl Bis-Urea Macrocycles, Sophya V. Garashchuk, Gamage Isuri P. Wijesekera, Isabella G. Rushton, Vaibhavi A. Samant, Fahidat A. Gbadamosi, Dr. Md Faizul Islam, Sophya V. Garashchuk, Prof. Dr. Linda S. Shimizu

Faculty Publications

Herein, we examine pathway complexity in the supramolecular polymerization of a novel m-terphenyl bis-urea macrocycle. Designed to induce kinetically metastable states, the macrocycle‘s concentration-dependent aggregation was studied via 1H NMR and IR spectroscopy in THF and CHCl₃. Temperature-dependent UV-Vis spectroscopy in water/THF revealed a cooperative nucleation-growth mechanism, indicated by a shift in λmax to longer wavelengths upon cooling. Morphological studies using DLS, AFM, and SEM demonstrated fibrous aggregate formation. Thermal hysteresis observed in assembly-disassembly cycles indicated kinetically trapped species, with cooling governed by kinetic control and heating by thermodynamic processes. Deviations in ΔH values during cooling, compared to van′t …

Click-Based Synthesis Of Hemibastadin Derivatives And Their Applications As Antimicrobial And Biofilm Inhibiting Agents, James B. Daniel Iii

Longwood Senior Thesis Proposal

Antimicrobial agents are one of the most important tools used in the medical industry. With the ever growing numbers of antibiotic resistant bacteria, new strategies have been developed to combat them, one of which being biofilm inhibiting agents. A class of molecules called hemibastadins, first discovered from sea sponges, have been of recent interest in the field. Building from previous work done in this lab on hemibastadins, a hemibastadin derivative containing a triazole in place of the oxime has been identified as a potential antibiofilm agent. This work will target a derivative that will more closely mimic the hemibastadins found …

College Of Natural Sciences Newsletter, Spring 2025, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message from Dr. Sen Subramanian
Page 2 Student Spotlights
Page 3 Kaushik honored, Three-Minute Thesis, & Ice Cores revealed
Page 4 Alumni Spotlight
Page 5 Day of Scholars
Page 6 Cyanide research, Record Research Expenditures, Adhikari awarded Miller Research Award
Page 8 Hanson Receives NSF Grant
Page 9 Snow Lab Research Team
Page 10 Faculty Awards
Page 11 Drone Day
Page 13 Khalaf Awarded Presidential Award

Next-Generation Biomedical Implants And Stimuli Responsive Soft Optical Arrays Via Surface Functionalized Elastomeric Materials, John M. Kapitan

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The demands of emerging technologies, such as soft robotics, stretchable electronics, and next generation biomedical implants, has led to the development of diverse polymeric and hybrid organic/inorganic materials specifically tuned to meet these challenges. These materials typically have low Young’s moduli and are inert with high chemical stability. However, this has led to materials that are static in nature, lacking any meaningful way of responding to changes in their environment and adapting to these changes. This has driven a shift towards the design, manufacturing, and characterization of various stimuli responsive surfaces, relying on precise control of surface chemical coatings and …

Synthetic And Mechanistic Investigations Of Ruthenium Catalyzed Coupling Reactions Via C−C And C−N Bond Activation, Aldiyar Shakenov

Dissertations (1934 -)

Transition-metal catalyzed C-N and C-C bond activation reactions are synthetically valuable reactions for selective and atom-economical synthesis of complex organic molecules. Catalytic reactions that involve activation of unreactive bonds are important for the stereoselective synthesis of molecular scaffolds from readily available substrates derived from bio-mass feedstock. Despite these advances, designing a broadly applicable catalytic method faces challenges of selectivity and harsh reaction conditions. A five coordinate Ru-H complex was found to be an effective catalyst for promoting the multicomponent deaminative coupling reaction of anilines, aldehydes and tertiary amines to selectively afford 2,3-disubstituted quinoline products. The scope of the reaction was …

Utilizing Drainage Induced Pfas Enrichment In Cascade Generated Foam For Efficient Removal At Wastewater Treatment Plants, Ethan Samuel Coffin

Dissertations

Observed trends in municipal solid waste landfills reveal a distinct disparity between per- and polyfluorinated alkyl substances (PFAS) composition entering in waste, mostly as diPAP and FTOH, and leaching out as FTCA and PFCA. These patterns are elucidated by compiling PFAS compositions in paper, textiles, and carpet, with known precursor transformations that generate FTCA and PFCA in leachate. Landfill leachate is commonly discharged to wastewater treatment plants (WWTP), which are ineffective at degrading PFAS and only serve as key conduits and discharge points for PFAS to the environment. Foam fractionation has been identified as a promising technology for concentrating and …

Reply To Bratchenko And Bratchenko, “Overestimation Of The Classification Model For Raman Spectroscopy Data Of Biological Samples”, Xin Ru Wen, Jia-Wei Tang, Liang Wang

Research outputs 2022 to 2026

No abstract provided.

Optimizing Transcription Efficiency Through Mutations In The T7 Rna Polymerase, Claire N. Novak

Honors Program: Senior Projects (Public)

The production of RNA is vital for many commercial and research purposes, with one of the more notable reasons being vaccine production. The RNA polymerase, derived from T7 bacteriophage, is commonly used for RNA production due to its ability to produce full-length RNA transcripts. However, researchers have faced limitations in optimizing this polymerase. For example, the polymerase generates heterogeneous RNA products that require additional purification steps during RNA production. Here, we selected three amino acid point substitutions based on a recent publication from Moderna that showed increased RNA purity compared to the wild type T7 RNA polymerase sequence. We created …

Brain-Targeted Reactive Oxygen Species In Hypertension: Unveiling Subcellular Dynamics, Immune Cross-Talk, And Novel Therapeutic Pathways, Renjun Wang, Min Wang, Dongshu Du, Zhiying Shan, Lanrong Bi, Qing-Hui Chen

Michigan Tech Publications

Hypertension (HTN) is a complex disease with significant global health implications, driven by neural and oxidative mechanisms. Reactive oxygen species (ROS), once considered mere metabolic byproducts, are now recognized as one of the key contributors to dysfunction of the autonomic nerve system, which involves the onset and progression of HTN. This review highlights the dynamic roles of ROS in neuronal signaling, subcellular compartmentalization, and brain-immune interactions, focusing on their impacts on synaptic remodeling, neuroinflammation, and epigenetic modifications within key autonomic regions such as the paraventricular nucleus and rostral ventrolateral medulla. We discuss novel ROS sources, including microglia-derived and endoplasmic reticulum …

Recent Advances In Non-Enzymatic Electrochemical Sensors For Theophylline Detection, Gustria Ernis, Yulia M T A Putri, Muhammad Iqbal Syauqi, Prastika Krisma Jiwanti, Yeni Wahyuni Hartati, Takeshi Kondo, Qonita Kurnia Anjani, Jarnuzi Gunlazuardi

Journal of Electrochemistry

Detection of target analytes at low concentrations is significant in various fields, including pharmaceuticals, healthcare, and environmental protection. Theophylline (TP), a natural alkaloid used as a bronchodilator to treat respiratory disorders such as asthma, bronchitis, and emphysema, has a narrow therapeutic window with a safe plasma concentration ranging from 55.5–111.0 μmol·L^–1 in adults. Accurate monitoring of TP levels is essential because too low or too high can cause serious side effects. In this regard, non-enzymatic electrochemical sensors offer a practical solution with rapidity, portability, and high sensitivity. This article aims to provide a comprehensive review of the recent developments …

College Of Natural Sciences 2024 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 2 Dean's Message
Page 3 Department Highlights
Page 4 One Day for State
Page 5 New Students in Wecota
Page 6-8 Faculty Excellence
Page 9 SDSU Physics Students Recognized
Page 9 Prairie Doc Watch Party
Page 10-11 Student Excellence
Page 11 Connections Abroad
Page 12-13 CNS’s Research Centers
Page 14 Connections Abroad
Page 14 Dean Wolf-Hall Retired
Page 15 Outreach Program
Page 15 Events and Traditions
Page 16 Student Spotlight
Page 17 Alumni Spotlight
Page 18-19 SDSU Alum at Paris Paralympics
Page 20 Work Anniversaries & Programs

The Mechanistic Target Of Rapamycin Mediates Clostridium Perfringens-Induced Chicken Necrotic Enteritis Attenuated By Secondary Bile Acid Deoxycholic Acid, Mohit Bansal, Tahrir Alenezi, Ying Fu, Janashrit Shrestha, Ayidh Almansour, Hong Wang, Anamika Gupta, Rohana Liyanage, Xiaolun Sun

Poultry Science Faculty Publications and Presentations

Clostridium perfringens is a prevalent gut bacterial pathogen in humans and animals. This study investigated the role of the mechanistic targets of rapamycin (mTOR) and deoxycholic acid (DCA) on C. perfringens intestinal infection. Chickens were sequentially infected with Eimeria maxima and received the mTOR inhibitor rapamycin and DCA. C. perfringens-induced necrotic enteritis (NE) was evaluated using body weight gain (BWG), histopathology, bile acids, pathogen colonization, cell infiltration and death, and gene expression. The significant difference of p < 0.05 was analyzed by one-way ANOVA and multiple comparisons. Notably, rapamycin strongly reduced the subclinical and clinical NE histopathologies. DCA and DCA combined with rapamycin alleviated clinical NE and BWG loss. Rapamycin, DCA, and DCA + rapamycin attenuated bile acid reduction in NE birds, and they also reduced immune cell infiltration into the intestinal lamina propria as well as immune cell migration in vitro. At molecular levels, DCA and DCA + rapamycin reduced proinflammatory IFN gamma, MMP9, IL23, and IL17 gene expression. Rapamycin, DCA, and DCA + rapamycin reduced NE-induced intestinal cell apoptosis. Together, these results suggest that mTOR signaling mediates C. perfringens-induced ileitis, and combining mTOR inhibition and DCA improves the intervention efficacy against NE ileitis and BWG loss.

Per- And Polyfluoroalkyl Substance (Pfas) Degradation In Water And Soil Using Cold Atmospheric Plasma (Cap): A Review, Victor Somtochukwu Mbanugo, Boluwatife Stephen Ojo, Ta Chun Lin, Yue-Wern Huang, Marek Locmelis, Daoru Han

Biological Sciences Faculty Research & Creative Works

Per- and polyfluoroalkyl substances (PFASs) are persistent organic chemicals found in numerous industrial applications and everyday products. The excessive amounts of PFASs in water and soil, together with their link to severe health issues, have prompted substantial public concerns, making their removal from the environment a necessity. Existing degradation techniques are frequently lacking due to their low efficiency, cost-effectiveness, and potential for secondary contamination. Cold Atmospheric Plasma (CAP) technology has emerged as a promising alternative, utilizing energized reactive species to break down PFASs under ambient conditions. Therefore, this review examines the efficacy and effectiveness of CAP in degrading PFASs by …

Drug Targets Illumination: An Evidence-Based Data Analytics & Informatics Approach To Hypothesis Generation Through Clinical Trials And Genomic Variants, Jeremiah I. Abok

Chemistry and Chemical Biology ETDs

DRUG TARGETS ILLUMINATION: AN EVIDENCE-BASED DATA ANALYTICS & INFORMATICS APPROACH TO HYPOTHESIS GENERATION THROUGH CLINICAL TRIALS AND GENOMIC VARIANTS

Target Illumination Clinical Trial Analytics with Cheminformatics (TICTAC) introduces a scalable data integration pipeline that aggregates multivariate clinical trial evidence to systematically rank disease–target associations. By harmonizing metadata from AACT and employing confidence-scoring techniques, TICTAC facilitates hypothesis-driven target selection for drug discovery, enabling a data-driven approach to therapeutic development. In parallel, a bioinformatics-driven analysis of gnomAD exome mutations in the ZPR1 gene highlights the broader role of genetic variants in disease association. By employing variant effect predictors, protein stability modeling, and …

Development, Optimization, And Validation Of A High-Sensitivity Capillary Zone Electrophoresis System For Bioanalytical Applications, Aaron I. Mena

Electronic Theses and Dissertations

Capillary zone electrophoresis (CZE) is a powerful analytical technique widely used for biomolecular separation due to its high resolution, efficiency, and sensitivity. This report presents the development and validation of a novel CZE system designed to improve modularity, reproducibility, and operational efficiency. The system integrates a laser-induced fluorescence (LIF) detection method with a 488 nm laser, enhanced fluid control through a negative pressure system, and a user-friendly GUI for automated operation and data acquisition. Performance verification included pressure stability tests, fluorescence accuracy assessments, and electrophoretic reproducibility studies. Comparative analysis with a previous CZE iteration confirmed improved baseline stability, peak resolution, …

Synthetic Protein Mimetic Based Therapies For Neurodegeneration, Nicholas H. Stillman

Electronic Theses and Dissertations

Protein-protein interactions (PPIs) are crucial for the regulation of a majority of, if not every fundamental cellular process. Despite their role in regular biological processes, dysregulated and/or aberrant protein-protein interactions (aPPIs) are often related to the onset of disease including cancer, viral infection, and amyloid diseases. aPPIs have historically been deemed ‘undruggable’ due to their large surface area and lack of a binding cavity; however, today, more than 40 disease-related aPPIs have been targeted with small molecules and several of those have reached clinical trials.

A class of synthetic protein mimetics called oligopyridylamides (OPs) has been shown to inhibit disease-related …

An Alternative To Biliverdin, Mesobiliverdin Ixα And Mesobiliverdin-Enriched Microalgae: A Review On The Production And Applications Of Mesobiliverdin-Related Products, Naveena Poudyal, Jon Y. Takemoto, Yuan-Yu Lin, Cheng-Wei T. Chang

Chemistry and Biochemistry Student Research

Despite attracting interest for decades due to its anti-inflammatory and antioxidant capabilities, the use of biliverdin IXα (BV) in medicine and agriculture is hampered by uncertain purity and limited availability. A significant amount of effort has been devoted to the production and application of BV, but with limited success. Mesobiliverdin IXα (MBV), a natural BV analog derived from microalgae, offers a path to overcome the limitations of BV. MBV production is scalable, and it can be obtained at high purity. MBV and BV share important structural features (e.g., bridging propionate groups) and both are substrates of biliverdin reductase A (BVRA), …

Phase Separation Clustering Of Poly Ubiquitin Cargos On Ternary Mixture Lipid Membranes By Synthetically Cross-Linked Ubiquitin Binder Peptides, Soojung Kim, Kamsy K. Okafor, Rina Tabuchi, Cedric Briones, Il Hyung Lee

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Ubiquitylation is involved in various physiological processes, such as signaling and vesicle trafficking, whereas ubiquitin (UB) is considered an important clinical target. The polymeric addition of UB enables cargo molecules to be recognized specifically by multivalent binding interactions with UB-binding proteins, which results in various downstream processes. Recently, protein condensate formation by ubiquitylated proteins has been reported in many independent UB processes, suggesting its potential role in governing the spatial organization of ubiquitylated cargo proteins. We created modular polymeric UB binding motifs and polymeric UB cargos by synthetic bioconjugation and protein purification. Giant unilamellar vesicles with lipid raft composition were …