Biochemistry, Biophysics, and Structural Biology Commons^™

Oral Streptococcus And Vitamin B12 Deficiency In E-Cigarette Users: A Microbial–Nutrient–Neurotransmitter Axis Linking To Mood Disturbances, Maryam Sabah Naser, Ali Jabbar Abd Al-Hussain Alkawaz, Ali Abbas Hashim Almusawi, Ali Jalil Obaid, Hasanain Ayed Mohammed Al-Khafaji, Reihaneh Sabbaghzadeh

Karbala International Journal of Modern Science

Background: With the rising popularity of e-cigarettes, questions have emerged regarding their broader influence on oral ecology, nutrient absorption, and psychological health. Disruptions in the oral microbiome may alter vitamin B12 dynamics. This, in turn, may indirectly influence serotonin biosynthesis and mood regulation.

Methods: An observational cross-sectional study involved 150 young adults segregated into groups of 50 each as vapers, smokers, or non-users. Streptococcus sanguinis and vitamin B12 metabolism-related variable statuses methylmalonic acid and holotranscobalamin were quantified in samples, along with inflammatory markers interleukin-6, kynurenine/tryptophan ratio, and serotonin. Statistical techniques, including ANOVA and the Kruskal-Walli’s test, correlation, and serial mediation …

Dapagliflozin Attenuates Cisplatin-Induced Nephrotoxicity In Rats Through Modulation Of Ros/Nf-Κb, Bcl2/Bax And Pink1/Parkin Signaling Pathways, Esraa K. Khallaf, Eman A. Ramadan, Mohey M. Elmazar, Marwa M. Safar

Pharmacy

Dapagliflozin (DPG), an anti-diabetic drug, has gained attention for its renal protective effects through multiple molecular pathways, yet its impact on mitophagy in cisplatin (CIS) nephrotoxicity remains unclear. This study aimed to examine the impact of DPG against CIS-induced nephrotoxicity in rats, targeting mainly PINK1/Parkin-mediated mitophagy and inflammatory/apoptotic pathways. Male Sprague Dawley rats received DPG (10 mg/kg; p.o) daily for 14 consecutive days and AKI was induced by a single injection of CIS (7 mg/kg; i.p) on day 10. Blood glucose, serum levels of creatinine and urea nitrogen, oxidative stress, inflammatory, apoptotic, mitophagy markers, and histological changes were assessed. DPG …

Chasing Disinfection Byproducts Through The Pipes: How 66 Dbps Change Over Time In Chlorinated Vs. Chloraminated Distribution Systems, Erik Niehaves, Patrick T. Justen, Ashley A. Perkins, Alexandria L.B. Forster, Caroline O. Granger, Susan D. Richardson

Faculty Publications

While disinfection byproducts (DBPs) are typically measured at drinking water treatment plants, levels can change dramatically within the distribution system before reaching the consumer. In this study, the spatio-temporal trends of 66 DBPs across 9 different classes were examined in two drinking water distribution systems with similar source waters, but different pretreatments and residual disinfectants. One system uses residual chlorine in the distribution system, and the other uses chloramine, allowing for examination of how DBP concentrations change over time in distribution systems with different residual disinfectants. Four routes were sampled for each system with six time points over three days …

Optimized Photoemission From Organic Molecules In 2d Layered Halide Perovskites, Muhammad S. Muhammad, Dilruba A. Popy, Hamza Shoukat, John M. Lane, Neeraj Rai, Vojtěch Vaněček, Zdeněk Remeš, Romana Kučerková, Vladimir Babin, Chenjia Mi, Yitong Dong, Mark D. Smith, Novruz G. Akhmedov, Daniel T. Glatzhofer, Bayram Saparov

Faculty Publications

In recent years, hybrid organic–inorganic metal halides have been at the forefront of materials research. Typically, the functional (e.g., optoelectronic) properties of hybrid halides are derived from the inorganic structural part, whereas the organic structural units can add extra advantages in terms of stability, rigidity, and processability. Here, we report the design, synthesis, and characterization of two new hybrid materials in which the outstanding photophysical properties originate from the organic structural part. The new compounds, (C₁₅H16N)₂CdCl₄ and((Br)C₁₅H₁₅N)₂CdCl₄, have 2D layered Ruddlesden–Popper-type perovskite structures. These hybrids are blue-white …

Defining Rna Oligonucleotides That Reverse Deleterious Phase Transitions Of Rna-Binding Proteins With Prion-Like Domains., Lin Guo, Jacob Mann, Jocelyn Mauna, Katie Copley, Hejia Wang, Jack Rubien, Cristian Bergmann, Jenny Carey, Jessica Merjane, Marilyn Ngo, Jiazhen Xu, Hana Odeh, Jiabei Lin, Bo Lim Lee, Laura Ganser, Emma Robinson, Kevin Kim, Anastasia Murthy, Tapas Paul, Bede Portz, Amanda Gleixner, Zamia Diaz, Ashleigh Smirnov, George Padilla, Ellen Lavorando, Carolann Espy, Yulei Shang, Eric Huang, Alessandra Chesi, Nicolas Fawzi, Sua Myong, Christopher Donnelly, James Shorter

Department of Biochemistry and Molecular Biology Faculty Papers

RNA-binding proteins (RBPs) with prion-like domains (PrLDs), such as FUS and TDP-43, condense into functional liquids, which can transform into pathological fibrils that underpin fatal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Here, we define short RNAs that prevent FUS fibrillization by promoting liquid phases and distinct short RNAs that prevent and reverse FUS condensation and fibrillization. These activities require interactions with multiple RNA-binding domains of FUS and are encoded by RNA sequence, length, and structure. We define a short RNA that dissolves cytoplasmic FUS aggregates, restores nuclear FUS, and mitigates FUS toxicity in optogenetic models and ALS …

Structural Characterization Of Peptide Nanoaggregates At Varying Concentrations And Their Impact On Cellular Responses, Malika Rozmetova

Theses and Dissertations

Peptide nano-assemblies can regulate cellular pathways in a structure-dependent manner. Here, we show that the enzyme-responsive peptide NapFFK(NBD)Yp forms distinct nanoscale assemblies at different concentrations, triggering differential ER stress and extracellular vesicle release in MDA-MB231 cells. These results highlight the importance of supramolecular organization in peptide–cell interactions.

Flux Crystal Growth Of Potassium Lanthanide Double Vanadates With Lanthanide-Dependent Coordination Number Variance, Hunter B. Tisdale, Hans Conrad Zur Loye

Faculty Publications

A series of potassium rare earth double vanadates is presented. Single crystals of double vanadates with stoichiometry K₃Ln(VO₄)₂ (Ln = La, Pr, Nd, and Sm) and crystallizing in the glaserite structure type were synthesized via a molten alkali chloride/fluoride flux reaction. Different structures were observed depending on the constituent rare earth: K₃La(VO₄)₂ crystallizes in an as-of-yet unreported modification of the typical glaserite structure in the space group P2₁/c, likely due to its larger ionic size that results in an increase in the lanthanide coordination number …

Protocol For Stable Isotope Tracing Of Primary Human Peripheral Blood Mononuclear Cells, Samantha N. Hart, Holden C. Williams, William B. Inabnet Iii, Joshua P. Steiner, Varun Jain, Philip A. Kern, Cecily R. Wood, Barbara S. Nikolajczyk, Lance A. Johnson

Molecular and Cellular Biochemistry Faculty Publications

Stable isotope tracing gives direct insight into the rate of metabolic reactions occurring in cells by analyzing the incorporation of labeled carbons into metabolic pathways. Here, we present a protocol for stable isotope tracing of primary human peripheral blood mononuclear cells (PBMCs). We describe the steps for culturing and exposing PBMCs to stable isotopes U¹³C glucose and U¹³C glutamine. We then detail procedures for derivatization, metabolite purification, and tracing analysis via single-quadrupole gas chromatography-mass spectrometry (GC-MS).

A Live Cell Biosensor Protocol For High-Resolution Screening Of Therapy-Resistant Cancer Cells, Viral D. Oza, Colin S. Williams, Jessica S. Blackburn

Molecular and Cellular Biochemistry Faculty Publications

The Genetically Encoded Death Indicator (GEDI) is a ratiometric, dual-fluorescence biosensor that enables real-time detection of cell death through calcium influx. Originally developed for use in neurodegeneration models, GEDI can be applied to cancer cells to quantify therapy-induced death at single-cell resolution. This protocol details how to generate GEDI-expressing cancer cell lines, empirically determine stress-induced GEDI thresholds using radiation or chemotherapeutic agents, and perform time-resolved imaging and image analysis to track cell fate. This workflow is optimized for high-throughput drug and radiation screening in heterogeneous populations and is especially useful for identifying chemo- and radio-resistant subclones. Key limitations include the …

31p Solution Nmr Investigation Of Abasic Dna, Clarissa R. Krimmel

Graduate Theses/Dissertations

Base excision repair (BER) mechanisms fix single base lesions in DNA, such as T:G mismatches. During the base excision repair mechanism, an abasic site (AP site) is formed as an intermediate. AP sites are unstable and highly mutagenic; they can stop DNA replication. This research investigates how the conformational properties of abasic sites in DNA affect the binding recognition of enzymes involved in DNA repair mechanisms, including BER. Three different abasic sequences are being analyzed for this research project. A second project looks at the effects of a naturally occurring purine derivative, hypoxanthine, on the DNA backbone. These hypoxanthine lesions …

A Phosphorylation Study Of Serine-8 And 26 In Two Fragments Of Amyloid Beta, A Peptide Involved In Alzheimer's Disease And Cancer, Colby J. Merrill

Senior Honors Theses and Projects

Both cancer and Alzheimer’s disease (AD) affect many people in the United States and impact the families of patients suffering from these challenging illnesses. Recently, it has been reported that these two diseases share several key pathophysiological features, and an inverse relationship exists between them. These diseases share several biochemical modulators, most notably the amyloid-beta protein, which affects tissues in both AD and cancer by misfolding and aggregating. Phosphorylation is believed to regulate the aggregation and toxicity of amyloid-beta by altering the protein's shape and charge, thereby changing its interactions with cells. Phosphorylation can also toggle some proteins on and …

Generating A Gfp Reporter Via Crispr To Visualize Ssa4 Export, Aara Khairollahi, Rebecca Adams

SPARK Symposium Presentations

In eukaryotic cells, the transport of mRNA from the nucleus to the cytoplasm is a very regulated process controlled by nuclear pore complexes (NPCs). During stress conditions, such as heat shock, most mRNA export is inhibited in Saccharomyces cerevisiae, yet the transcript for SSA4, a gene responsible for refolding denatured essential proteins, is exported. The mechanism behind this selective export remains unknown. To investigate this, we used CRISPR-Cas9 to generate a reporter strain in which the SSA4 open reading frame was replaced or inserted with green fluorescent protein (GFP). This reporter is designed to produce GFP only under conditions that …

Advancing Lipidomics Through Fluoroalcohol-Induced Multiphase Fractionation And Orthogonal Lc×Lc–Ms Detection, Md Al Amin

Chemistry & Biochemistry Dissertations

Comprehensive characterization of the lipidome remains a significant analytical challenge due to the immense structural diversity, wide dynamic range, and complex physicochemical continuum of lipid species. Conventional extraction methods, such as those by Bligh–Dyer and Folch, and one-dimensional liquid chromatography (1D-LC) often fail to resolve this complexity, leading to chromatographic overlap, severe ion suppression, and limited coverage of low-abundance or highly hydrophobic species. This dissertation addresses these bottlenecks by establishing a separation-driven analytical framework that integrates novel fluoroalcohol-induced multiphase systems (FAiTPS) with orthogonal multidimensional liquid chromatography–mass spectrometry (LC×LC–MS).

The core of this research is the development and physicochemical characterization of …

Crispr Transgenic Clytia Hemisphaerica As A Vector For Toxin Delivery In A Zebrafish Melanoma Model, Theodore G. Paz

Theses, Dissertations and Culminating Projects

The jellyfish Clytia hemisphaerica has the potential to be used in cancer therapies with the discovery of potential active toxin target regions to be modified for use. The program Venomix is a Uniprot-based database that was utilized in this experiment to generate likely flagged hit regions using Clytia hemisphaerica CDS files run against its database of terrestrial toxins (Furuno et al., 2003; Macrander et al., 2018). By themselves they are indeterminate as to whether they are active toxin region hits (Macrander et al., 2018). With further analysis such as toxin homology in closely related, annotated marine taxa and accounting for …

Interest, Self-Efficacy, And Belonging In Classroom Learning, K. Ann Renninger, Lux K. Barton , '21, Gia Bautista , '23, Mary Garcia-Barrios , '24, Iyinoluwa Ogunyinka , '24, Kathryn R. Riley

Educational Studies Faculty Works

Students’ interest, self-efficacy, and belonging are considered essential for classroom learning, as each has been shown to promote sustained engagement and school achievement. However, our review of the literature suggested that research on interest, self-efficacy, and belonging is largely siloed. To address practitioner questions about supporting classroom learning by working with the three variables, we added a mixed-method pilot study to the review process. Pilot participants were Black, middle-school-age youth living in a low-income community, who were enrolled in a five-week, inquiry-informed science workshop facilitated by a Black professor. Findings showed that during learning, interest, self-efficacy, and belonging were increasingly …

A Thymine Dimer Stalls A High-Fidelity Dna Polymerase By Providing No Template Information In The Same Manner As An Abasic Site, Amanda R. Walsh, Hye Rhee Kim, Lorena S. Beese, Eugene Y. Wu

Biology Faculty Publications

Cyclobutane pyrimidine dimers are photolesions that form when UV-B irradiation causes adjacent thymine or cytosine bases to covalently bond and can arrest DNA synthesis by replicative polymerases. To gain insight into the effects of cis-syn cyclobutane thymine dimers (T=T) on DNA replication in a model polymerase, we conducted solution and crystallographic studies of the Bacillus DNA polymerase I large fragment (BF) in complex with a T=T-containing template and an incoming dNTP. A thymine dimer lesion blocked nucleotide addition by BF in solution. The crystal structure of the BF-T=T-dATP complex indicated that the thymine dimer is too large to enter the …

Bpa: Effects Of The "Plastic Era", Bianca G. Pietrangeli

Student Work

Infographic review of sources of BPA and its impacts on human health with a focus on osteoporosis.

Toxic Torts Are In Your Blood: An Examination Of Pfas And Tort Liability, Aiden M. Holden

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Abstract

Per- and polyfluoroalkyl substances (PFAS), are a group of chemicals widely manufactured for industrial and commercial applications in the past decade due to their remarkable stability. Despite the “useful” nature of PFAS in various applications, they represent one of the most profound environmental and public health crises of the modern era. The chemical stability of PFAS has made them almost completely resistant to natural degradation, earning them the moniker “forever chemicals.” PFAS forever haunt our plant, contaminating the soil, water, and the blood of approximately 95% of the United States population. As the scale of corporate malfeasance by chemical …

Mxene-Enabled Wearable Biosensors: A Design Framework For Autonomous Biosensing, Jegan Rajendran, Gymama Slaughter

Center for Bioelectronics Publications

MXenes, a rapidly expanding family of two-dimensional transition metal carbides and nitrides, have emerged as leading materials for wearable bioelectronics due to their metallic conductivity, termination-rich surfaces, mechanical compliance, and tunable interlayer structures. However, wearable biosensor performance does not arise from conductivity alone, but from coupled interactions among surface termination chemistry, heterointerface engineering, hierarchical architecture, and device integration under dynamic physiological conditions. This review establishes a predictive structure-interface-device framework linking MXene chemistry to system-level performance across electrochemical, mechanical, gas, optical, and energy-storage modalities. We analyze how termination-controlled adsorption governs charge transfer and selectivity, how heterojunction formation modulates carrier density and …

Potential Environmental Triggers Of Goodpasture's Disease And The Role Of The Sulfimine Crosslink, Colton S. Miller, Andrea Florian, Elena Pokidysheva

SPARK Symposium Presentations

Goodpasture’s syndrome (GP) is an autoimmune disorder that primarily affects kidneys and lungs. The main issue for patients with Goodpasture's syndrome is the binding of autoantibodies to the glomerular basement membrane (GBM), which hinders the filtration of blood. A key characteristic of Goodpasture's syndrome is the presence of autoantibodies that target the NC1 domain of the α345 isoform of type IV collagen, a crucial component of the GBM that provides structural support and is critical for filtration function. Sulfilimine bonds crosslink the collagen IV NC1 hexamers, contributing to the stabilization of these structures. A recent clinical case of recurring Goodpasture's …