Biochemistry, Biophysics, and Structural Biology Commons^™

Uv Damage Mapping Reveals Different Impacts Of Xpd Mutations On Global Genomic And Transcription-Coupled Dna Repair, Allyson Hoag

Biomedical Sciences ETDs

Nucleotide Excision Repair (NER) is a fundamental cellular process that removes bulky and helical distorting lesions from the genome through the separate responses of its two subpathways – global genomic (GG-NER) and transcription coupled (TC-NER) DNA repair. The pathways converge with the recruitment of the TFIIH complex, a key step that is mediated by the translocase and helicase activities of  its XPD subunit. Germline mutations in XPD result in the clinical disorders, Xeroderma Pigmentosum (XP) and XP combined with Cockayne Syndrome (XP/CS). The goal of this thesis was to understand if XPD XP and XP/CS mutations differentially impact GG-NER and …

Ionophore-Based Plga Nanosensor For Selective Ion Detection And Imaging, Zhiyu Tang

Electronic Theses and Dissertations

Accurate detection of electrolyte ions is essential for biological research, disease diagnosis, and the investigation of cellular function. In this study, we developed ionophore-based PLGA nanosensors for the optical detection of biologically important ions. The nanosensors were prepared by encapsulating ionophores, chromoionophore III, and ion exchangers within PLGA nanoparticles. The resulting nanosensors showed uniform morphology, good colloidal stability, and concentration-dependent optical responses toward Na⁺, K⁺, and Ca²⁺ over the range of 10⁻⁶ to 10⁻¹ M. Reversible fluorescence responses under repeated ion concentration changes confirmed the stability and robustness of the sensors. The nanosensors also demonstrated reliable analytical performance for K⁺ …

Effects Of Variable Light On Sexual Competition In Kelp Species, Jaycee Lanza

Master's Theses

As foundation species, kelps significantly influence the structure and composition of their surrounding habitat by modifying environmental conditions, including light levels, currents, nutrient availability, sedimentation, and seawater chemistry. Light, in particular, is a critical resource that varies greatly within kelp forests, affecting kelp reproductive processes such as gametogenesis, fertilization, and recruitment, which are vital to population persistence. Biological factors, such as density-dependent competition for resources and sexual competition with other kelps, can also affect such processes. To understand how environmental variables influence kelp populations, it is crucial to recognize their combined effects. This study investigated the impacts of light levels …

Selenoprotein P And Selenium As Potential Diagnostic Biomarkers For Breast Cancer Patients, Farah A. Rashid, Rawaa A. Ali, Hanaa A. Ali

Karbala International Journal of Modern Science

Breast cancer incidence increases in last decade. Oxidative stress increases during cancer development causes consuming of antioxidants. Selenium and its transporting protein, selenoprotein P have an important role in redox homeostasis. This study aims to investigate whether or not selenium and selenoprotein P could be diagnostic biomarkers for breast cancer patients. This study was included 30 individuals in control group who is age- and BMI-matched with 60 breast cancer patients. Selenium was measured by colorimetric assay kit and selenoprotein P was determined by Sandwich ELISA kits. The results indicate significant decrease (p < 0.0001) of serum selenium and selenoprotein P in breast cancer patients compared to control. A positive significant correlation (r = 0.6214, p < 0.0001) was found between selenium and selenoprotein P in breast cancer patients. Selenium has an excellent diagnostic accuracy with area under curve 0.9831, sensitivity 95% and specificity 100% at cut-off less than 3.54 mmol/L. Furthermore, selenoprotein P has also an excellent area under curve 0.9958 with sensitivity 96.77% and specificity 100% at cut-off less than 4.15 ng/ml. These exploratory findings appear that selenium and selenoprotein P could be potential diagnostic biomarkers for breast cancer patients. Further investigations in large-multicenter populations are needed to confirm results.

Summer Research Internships In Agricultural Biotechnology For Off-Campus Undergraduate Students, Aaron J. Thomas

Funded Research Records

No abstract provided.

Mechanistic Determination Of Host Environmental Impacts On Shigella Virulence, Nicholas E. Dickenson

Funded Research Records

No abstract provided.

Out Of This World: An Exoplanetary Workshop, Monica Storss, Bart Kuipers

ELO (un)supervised 2026

The workshop investigates how scientific constraints can productively defamiliarize human experience and create new frameworks for creativity and expression. Participants will produce original work while considering broader questions about environment, perception, and cultural formation in speculative contexts, and how the arts, sciences, and technology inform each other in relational multiplicities. This generative workshop explores how astronomical data from confirmed exoplanets can generate new poetic forms and linguistic constraints. Participants will examine how exoplanetary conditions can shape language, metaphor, and narrative structure. We'll develop from writing exercises that respond to non-terrestrial physical parameters: alternative light spectra, gravitational variations, and atmospheric compositions. …

Fish Tissue Digestion And Microplastic Polymer Identification Protocol Using Open-Source Ftir Database, Shawn L. Kissinger, Vick-Ariel Privert, Jason Bystriansky, Kyle A. Grice

DePaul Discoveries

Microplastic (MP) contamination in aquatic ecosystems poses significant concerns for environmental and public health, as seafood represents a critical food source worldwide. Despite increasing evidence of MP presence in marine organisms, efficient and accessible detection methods remain essential for characterizing contamination patterns and informing regulatory frameworks. This study extracted MPs from brain, gill, intestine, liver, and muscle tissues of gilt-head bream (Sparus aurata) and European sea bass (Dicentrarchus labrax), two commercially important species from the Gulf of Cádiz, Spain, using a NaOH–HNO₃ chemical digestion protocol. Isolated particles were characterized by Fourier Transform Infrared (FTIR) spectroscopy, with …

Decoding The Allosteric Grammar Of Protein Kinases: A Dual-Stream Framework Integrating Protein Language Models And Energy Landscape Frustration Analysis, Will Gatlin, Max Ludwick, Lucas Turano, Brandon Foley, Kamila Riedlova, Vít Škrhák, Marian Novotný, David Hoksza, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The spatial and energetic encoding of allosteric regulatory sites remains a major challenge in structural biology, frequently representing a “blind spot” for sequence-based artificial intelligence (AI) models. We present a protein language model (PLM)-guided approach complemented by the energy landscape frustration analysis as a dual-stream framework to investigate the relationship between AI prediction of binding sites and biophysical organization of regulatory pockets across the human kinome. By probing a fine-tuned residue-level PLM classifier across 453 kinase structures, a clear performance gap is discovered between highly predictable orthosteric pockets (Types I, I.5, and II) and poorly resolved distal allosteric sites (Type …

Upar-Guided Dendrimer Gel Nanoparticles Reprogram Inflammation To Stabilize Atherosclerotic Plaques, Hsin Yin Chuang, Huari Kou, Yue-Wern Huang, Hu Yang

Biological Sciences Faculty Research & Creative Works

Atherosclerosis is characterized by lipid deposition, chronic inflammation, and apoptosis within the arterial wall, leading to plaque progression and instability. Current lipid-lowering therapies fail to fully address residual cardiovascular risk driven by local inflammation and cell death. Here, we report the development of uPA-functionalized, rapamycin-encapsulated dendrimer nanoparticles (G5PM-uPA/RA) that preferentially accumulate in urokinase plasminogen activator receptor (uPAR)-enriched atherosclerotic plaque, including macrophage- and apoptosis-rich lesion microenvironments. G5PM-uPA/RA was constructed by cross-linking reaction-enabled flash nanoprecipitation in a custom-made multi-inlet vortex mixer, followed by thiol-maleimide conjugation of uPA for uPAR-guided targeting. The nanoparticles demonstrated uniform morphology, favorable stability, and efficient rapamycin loading. In …

Biophysical Insights Into A Cryptic Ligand Site In The Hydrophobic Core Of Human Pcna, Alexis N. Dispensa, Sharon N, Greenwood, Jason Yang, Daniel E. Logatto, James Fusco, E. Railey White, Roderic G. Eckenhoff, Zhiwei Liu, Brian P. Weiser

Department of Anesthesiology Faculty Papers

Proteins contain small pockets that form due to imperfections in residue packing or the rotational and conformational movement of amino acids. In this work, we used the fluorescent probe 1-aminoanthracene (AMA) to detect a small ligand pocket in the hydrophobic core of human proliferating cell nuclear antigen (PCNA), which is a critical protein for DNA replication and repair. Fluorescence measurements of AMA reported that the core of PCNA had a dielectric constant (ε) of 4, which was very apolar and similar to cyclohexane (ε = 2). Protein mutagenesis, photoaffinity labeling, and molecular dynamics simulations localized the binding site for AMA …

Investigation Into Molecular Bases Of Pregnancy-Associated Malaria, Nicole Pozo

Biochemistry and Molecular Biology

Plasmodium falciparum causes the most severe and deadly form of malaria and remains a major global health problem, especially in sub-Saharan Africa (Milner, 2018). The parasite infects and multiplies inside red blood cells, leading to fever, anemia, organ damage, and death if untreated (Milner, 2018; Song et al., 2022). It is especially dangerous because it avoids the immune system by changing surface proteins called Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), which are encoded by more than 60 var genes. By switching between these genes, the parasite hides from immune detection and creates repeated waves of infection (Deitsch & Dzikowski, …

Personalizable Metabolic Models To Enable Immune Characterization And Drug Discovery, Joshua Loecker

Department of Biochemistry: Dissertations, Theses, and Student Research

Cellular metabolism is reshaped by disease and physiological state, and genome-scale metabolic networks (GSMNs) offer a systematic way to interrogate this biology and identify therapeutic targets. Building a GSMN from expression data, however, requires a sequence of stages including read processing, normalization and gene-activity classification, multi-omic integration, model reconstruction, simulation, and biological interpretation. These are typically handled by disconnected tools spanning multiple programming languages, file formats, and databases. The resulting reliance on heterogeneous interfaces and manual steps threatens reproducibility. This work develops an ecosystem of computational tools that carry an analysis from raw sequencing reads to mechanistic biological interpretation. First, …

Recent Advances In Phosphatidylinositol Phosphate Kinases (Pipks) And Their Inhibitors, Mengxia Sun, Jian Hu, Xuefei Huang

BAU Journal - Science and Technology

Phosphatidylinositol phosphate kinases (PIPKs) are an important class of enzymes in humans, which produce lipid signaling molecules playing central roles in pathogenesis of diseases such as cancer, neurodegenerative diseases, and viral infection. Consequently, they are attracting increasing attention as drug targets for disease treatment. This review summarizes the functions of the PIPK family enzymes and highlights recent efforts on designing novel inhibitors against PIPKs. These advances are extensively discussed to stimulate interest in this field and promote further development of highly potent and selective inhibitors for innovative therapeutic applications.

Comparative Screening Of Cytotoxic Potential Of Berberis Aristata And Senna Alexandrina Extracts, Rida Noor Akhtar, Javaria Zahoor, Rizwan Ullah Khan, Aziz Ullah, Naila Malkani

Journal of Bioresource Management

Medicinal plants provide a safe and efficient source of drugs for cancer treatment. Berberis aristata and Senna alexandrina are traditionally used to treat several ailments because they contain compounds with antimicrobial, antitoxic, anti-inflammatory, and other properties. The objective of the study was to prepare crude ethanolic extracts of B. aristata and S. alexandrina and to determine their cytotoxic potential against cancer cells. Ethanolic extracts were prepared for both plants. Hepatocellular carcinoma cells (HepG2) were used for all assays. The cytotoxicity of extracts was determined by 3‑(4,5‑Dimethylthiazol‑2‑yl)‑2,5‑diphenyltetrazolium bromide (MTT) assay using various concentrations of extracts. The obtained sub-lethal concentrations were used …

In Vitro Anticancer Evaluation Of Tamoxifen And Paclitaxel-Loaded Chitosan Nanoparticles Against Breast And Lung Cancer With In Silico Docking, Arshia Amaan, Farah Mehak, Amer Jamil, Fatma Hussain

Journal of Bioresource Management

Breast and lung cancer are the primary cause of death worldwide, underlining the need for an improved therapeutic strategy. In the current study, tamoxifen (TAM) and paclitaxel (PTX) loaded chitosan nanoparticles (NPs) were produced for the evaluation of sustained drug delivery and enhanced anticancer potential of nanocarriers over conventional chemotherapy against breast and lung cancers, respectively. Nanoparticles were produced by the ionic gelation method and characterized by UV-visible spectroscopy, Dynamic Light Scattering and Fourier Transform Infrared Microscopy (FTIR), verifying the nanoscale morphology, stability and successful encapsulation. A drug release profile study (in vitro) (78 %, 60-75 %) and …

Investigating Quinclorac Binding To Human Serum Albumin Using Spectroscopy And Molecular Docking, Le Nguyen, L. Hicks, L. Jodoin, S. Carby, D. S. Sanford, D. Benavides, A. Mishra, R. Yadav

Journal of the Arkansas Academy of Science

Human serum albumin (HSA) is the most abundant plasma protein and serves as a major transporter and reservoir for a wide range of endogenous ligands, including fatty acids, heme, bilirubin, prostaglandins, and metal ions, as well as numerous exogenous compounds, such as pharmaceuticals. HSA is a 66 kDa monomeric, multidomain protein containing two principal ligand-binding sites, Sudlow sites I and II. Sudlow site I contains Trp214, the sole tryptophan residue in HSA, whose intrinsic fluorescence provides a sensitive probe for studying ligand–protein interactions.

In this study, the interaction between HSA and the persistent organochlorine herbicide quinclorac (QNC) was investigated using …

In Silico And Toxicological Evaluation Of Crescentia Cujete Aqueous Extract: Potential Anticancer Activity Against Breast Cancer, Rahma Diyan Martha, Fatimah Fatimah, Syahputra Wibowo, Bantari Wisynu Kusuma Wardhani, Josephine Elizabeth Siregar, Elisabeth Farah Novita Coutrier, Alfia Fitrianita, Andri Pramesyanti Pramono, Ita Margaretha Nainggolan, Yudhi Nugraha, Danar Danar, Naufal Abiyyu, Lalu Unsunnidhal, Aswin Rafif Khairullah, Arif Nur Muhammad Ansori, Hesty Parbuntari, Wimbuh Tri Widodo

Makara Journal of Science

Majapahit plant (Crescentia cujete), commonly found in Indonesia, has not been extensively explored for its medicinal properties. Given that many cancer treatments are derived from plants, this study aimed to examine the effects of plants on cancer chemical composition of the C. cujete fruit pulp extract, identify its primary compounds, and assess its potential as an antioxidant, anticancer agent, particularly for breast cancer. An insilico approach was used to evaluate the toxicity and interactions, of the compounds with cancer biomarker proteins, in addition to an in vivo Brine Shrimp Lethality Test (BSLT) for BSLT, toxicity screening using six …

Rna G-Quadruplexes Function As A Tunable Switch Of Fus Phase Separation, Jenny L. Carey, Miyuki Hayashi, Emily A. Welebob, Laura R. Ganser, Huan Wang, Kerry Buckhaults, Jacquelyn A. Depierro, Zheng Shi, James Shorter, Sua Myong, Aaron R. Haeusler, Lin Guo

Department of Biochemistry and Molecular Biology Faculty Papers

Fused in sarcoma (FUS) undergoes liquid-liquid phase separation (LLPS) to support essential cellular functions, but aberrant phase transitions promote toxic aggregation in neurodegenerative disease. Short RNA oligonucleotides can reverse this behavior, yet the structural determinants that govern RNA activity remain poorly defined. Here, we identify RNA G-quadruplexes (rG4s) as tunable structural motifs that potently modulate FUS LLPS. rG4 activity depends on its concentration and is modulated by rG4 length and stability: increasing repeat number switches rG4s from inhibitor to nucleator of FUS assembly, whereas chemical modifications that stabilize rG4 enhance inhibitory function and render these activities resilient to ionic perturbation. …

Advancing Paradigm Of Quantitative Synthetic Biology And Strengthening Mission-Oriented Basic Research, Chenli Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Synthetic biology is an important frontier in the life sciences, yet its further development remains constrained by limited capacity for rational design. Quantitative synthetic biology, which iteratively integrates quantitative modeling with the construction and analysis of synthetic systems, offers a promising paradigm for addressing this challenge. In this perspective, the study discusses the background and motivations underlying the emergence of this field and summarizes recent developments and exploratory efforts. Considering the unique characteristics of quantitative synthetic biology, it is suggested that progress in the field may benefit from strategically organized collaborative research that balances mission-oriented goals with investigator-driven exploration. On …