Biochemistry Commons^™

Sediment Redox-Driven Iron Flux And Phytoplankton Community Responses: Implications For Cyanobacterial Suppression And Functional Stability Across Boreal Lakes, Julia K. Kozak

Theses and Dissertations (Comprehensive)

Freshwater eutrophication contributes towards the development of cyanobacterial harmful algal blooms (cHABs), but nutrient availability alone does not fully explain variation in phytoplankton community composition or physiological performance. While phosphorus (P) availability has been known to regulate phytoplanktonic biomass, iron (Fe) is an important micronutrient supporting Fe-heavy processes within cyanobacteria (i.e., nitrogen fixation and photosynthetic electron transport). Sediment Fe availability in freshwater ecosystems is regulated by reduction oxidation (redox) conditions at the sediment-water interface (SWI), where nitrate (NO₃^-) has been found to maintain oxidizing conditions and prevent the reduction of Fe(III) to more readily bioavailable soluble Fe(II), …

Investigating The Ability Of Presequences To Influence Mitochondrial Protein Import, Youmian Yan

WUSM Theses and Dissertations – All Programs

Mitochondria are essential organelles housing over 1000 proteins, 99% of which are nuclear-encoded and synthesized in the cytosol. Most mitochondrial proteins are targeted by a positively charged sequence called the presequence, which lacks a common sequence motif and is poorly conserved across evolution. Accumulating evidence suggests that presequences encode meaningful information that influences mitochondrial protein uptake. For instance, multiple stress response models propose that stress sensing proteins contain “weak” presequences which allows them to monitor mitochondrial health. However, there is a lack of systematic examination about how presequences influence import kinetics and what constitutes presequence strength. These gaps in knowledge …

Release Of Bound Steroid From The Androgen And Estrogen Receptors Is Induced By Ddt And Its Analogs, Matthew D. Rosales, Tahyra Soto, Jacqueline I. Goodship, Ahyssa R. Cruz, Isaac A. Rodriguez, Ventura Cuba Flores, Amanda Chavez, Monica P. Solis, Esmeralda Lopez, Frank B. Dean, Evangelia Kotsikorou

School of Integrative Biological & Chemical Sciences Faculty Publications

The pesticide p,p'-DDT (DDT) and its analogs (p,p'-DDD, o,p'-DDD, and p,p'-DDE) inhibit the binding of dihydrotestosterone (DHT) to the androgen receptor (AR) and estradiol (E2) to the estrogen receptor (ERα) ligand-binding domains (LBDs), as previously reported. In this study, we introduce assays to measure the release of receptor-bound steroids. These compounds induced the release of DHT from the AR LBD and E2 from the ERα LBD. These findings suggest that DDT and its analogs may interact with a surface site on the LBD, thereby allosterically disrupting steroid binding. One potential site is binding function 3 (BF3). To explore this possibility, …

Analytical Biochemistry: A Practical Handbook For Undergraduates, Mark C. Hall

Purdue University Press Books

Methods for characterizing proteins are central to the early stages of drug development and are highly relevant to careers in the pharmaceutical and biotechnology industries. These skills are best learned through hands-on practice in academic laboratory settings. Analytical Biochemistry: A Practical Handbook for Undergraduates presents a laboratory course specifically designed to teach protein analytical techniques to postsecondary students in biochemistry and related fields. Readers are guided through a semester-long research project that mirrors how scientific work is conducted in both academic and industry environments. Instead of focusing on isolated weekly exercises, students work toward a single overarching goal and learn …

The Β2Αb Loop Determines Nad(P) Cofactor Specificity And Kinetics In Trypanosomal D-3-Hydroxybutyrate Dehydrogenases, Hideharu Hashimoto, Ian H. Mawn, William Escobar-Arrillaga, Linh Nguyen, Laura A. Madigan, Gina Antuono, Tatiana Rossy, Jorna Sojati, Anna Mienko, Erik W. Debler, Jennifer B. Palenchar

Department of Biochemistry and Molecular Biology Faculty Papers

Bacterial d-3-hydroxybutyrate dehydrogenases (HBDHs) catalyze the conversion between d-3-hydroxybutyrate and acetoacetate with NAD as the cofactor but not with NAD 2'-phosphate (NADP). However, HBDHs of the early-branched eukaryotic genus Trypanosoma utilize both NAD and NADP (T. brucei) or exclusively NADP (T. cruzi). Here we reveal that NADP specificity of T. cruzi HBDH arises from stabilization of the flexible β2αB loop by the 2'-phosphate interaction. Stabilization of this loop by a nearby C64Y mutation enables T. cruzi HBDH to use NAD in addition to NADP; thus, the Cys/Tyr residue is critical for determining cofactor specificity in trypanosomal HBDHs, suggesting that most …

Biosensor Development In East Africa: A Systematic Review Of Technologies, Applications, Challenges, And Future Directions, Ally Mahadhy

Tanzania Journal of Science

Biosensors integrate biological recognition elements with signal transduction systems to generate quantitative or semi-quantitative analytical information and have applications across healthcare, food safety, agriculture, environmental monitoring, and wildlife health. Despite substantial global advances, biosensor development in East Africa remains poorly characterized. This systematic review, conducted according to PRISMA 2020 guidelines, evaluated published evidence from 1995 to 2025 within a predefined East African Community geographical scope. Eligibility was based on IUPAC-aligned operational criteria requiring an integrated biological recognition element, transduction mechanism, and quantitative or semi-quantitative signal output. Three locally developed biosensors met the criteria: an electrochemical nano-biosensor for schistosomiasis diagnosis in …

Evaluation Of Polycyclic Aromatic Hydrocarbon Profiles In Fermented Artemisia Annua Leaf Extract, Mabitine Daniel Malo, Ohemu Adaofoyi Isaiah, Igaznda Terhemba James, Obamuwe Rebecca Joy, Ugber Erdoo Charity, Itodo Monday Christopher

Journal of Bioresource Management

This study evaluated the presence, profile and concentration of polycyclic aromatic hydrocarbons (PAHs) in the fermented leaf extract of Artemisia annua, a medicinal plant widely used for its antimalarial and skin-benefiting properties. Given the plant’s increased use in Nigerian traditional medicine, this research examines how fermentation a process known to enhance bioactive compound availability may influence PAH levels, which are of concern due to their carcinogenic, mutagenic, and teratogenic effects. The A. annua leaves were fermented using Saccharomyces cerevisiae cultures and subsequently analyzed using Gas Chromatography-Mass Spectrometry (GC-MS) to detect and quantify PAHs. The analysis identified 24 distinct PAH …

Development Of An Indirect Elisa Kit For Measurement Of Circulating Thyroid Peroxidase Levels In Patients With Hypothyroidism, Aulanni’Am Aulanni’Am, Devi Ramadani, Almas Dwi Khairana, Saidun Fiddaroini, Muhammad Fikri Nur, Andreas Budi Wijaya, Rulli Rosandi, Dyah Kinasih Wuragil, Wibi Riawan

Makara Journal of Science

Hypothyroidism, characterized by insufficient thyroid hormone production, affects approximately 5% of the population, especially women, thus increasing pregnancy-related risks. Conventional screening mainly measures thyroid-stimulating hormone (TSH) and free thyroxine (FT4). Detecting the presence of anti-thyroid peroxidase (anti-TPO) antibodies indi-cates autoimmune thyroid disease. This study developed an indirect enzyme-linked immunosorbent assay (ELISA) kit for detecting circulating TPO using polyclonal antibodies generated in rabbits. TPO was isolated from positive sera of pa-tients with hypothyroidism, purified by electroelution, and confirmed as a 52-kDa protein by Western blot. Rabbits immunized with this protein produced polyclonal antibodies with the highest titer (OD = 0.334) at …

Molecular And Structural Basis For Replication Initiation And Strand Separation By Human Mitochondrial Dna Polymerase Γ, Viktoriia Sokolova, Gina Buchel, S. Strock, Ashok R. Nayak, Dmitry Temiakov

Department of Biochemistry and Molecular Biology Faculty Papers

Defects in human mitochondrial DNA (mtDNA) replication can lead to somatic mutations associated with a range of devastating mitochondrial diseases. However, the molecular mechanisms governing the earliest steps of mtDNA replication and their fidelity remain poorly understood. Here, we found that DNA polymerase gamma (Polγ) forms stable complexes with RNA-DNA primer-template substrates, exhibiting greater stability and lower misincorporation than on DNA-primed substrates. Structural analysis revealed that Polγ interacts with the 2'-OH groups of ribose within the first four nucleotides of the primer, explaining the stability of complexes that utilize RNA primers. Although Polγ requires TWINKLE to extend RNA primers, its …

Waste Streams From Next Generation Molten Salt Reactors: The Challenge Of Creating An Insoluble Ceramic For Chloride Salt Waste, Alevtina A. Maksimova, Jake W. Amoroso, Matthew Page, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

Molten salt reactors (MSRs) design development is of interest to many research groups and companies. Waste management for MSRs is one of the most important issues that needs to be resolved due to its impact on environmental safety, primarily via the dissolution of radionuclides in water. Furthermore, the waste treatment strategy will have a significant influence on the operating cost of MSRs, which is why a reliable process for the immobilization, transportation, storage and disposal of MSR waste must be addressed. This work presents a new approach for the immobilization of chloride salts from molten salt reactors in stable oxyhalide …

Characterization Of Mettl3/14-Mediated M6a Modification In Human Transcriptome Using Nanopore Direct Rna Sequencing, Emily Kurtyan, Andrew J. Stein, Kelly J. Abdalla, Zhangerjiao Yuan, Miten Jain, Fadia Ibrahim

Department of Biochemistry and Molecular Biology Faculty Papers

Post-transcriptional RNA modifications modulate diverse aspects of RNA metabolism. N6-methyladenosine (m6A), one of the most abundant internal RNA modifications, is deposited by the core methyltransferase complex, METTL3 and METTL14. Oxford Nanopore Technologies (ONT) platform permits direct, single RNA molecule sequencing while preserving native modifications. However, without rigorous benchmarking, the accuracy and reproducibility of modification detection remain uncertain. Here, we leveraged ONT to comprehensively profile bona fide m6A modifications in cellular RNAs at single-nucleotide resolution by integrating two direct RNA sequencing chemistries (RNA002 and RNA004) with the m6Anet and Dorado modification-detection models. We independently depleted METTL3 and METTL14 in human cells …

Sec-Saxs And Sans Analyses Of The Talin•Vinculin Complex, Gilbert Reyes

Dissertations, Theses, and Capstone Projects

Focal adhesions (FA) are integrin-based cell-matrix adhesion sites composed of adaptor proteins that facilitate the generation of traction forces important for biological functions such as cell migration, embryo development, wound healing, tissue organization and stability, and immune responses. Mature FA are observed when both autoinhibited multi-domain scaffolding protein talin and membrane-cytoskeletal protein vinculin are activated and interact thus promoting the assembly and function of FA. While research has resolved truncated sections of autoinhibited talin and recruitment of vinculin due to mechanotransduction that exposes cryptic vinculin binding sites (VBS), little is known about the global modifications of full length talin in …

The Role Of External Factors In Shaping Carbohydrate Conformational Landscapes, Murat Yaman

Dissertations, Theses, and Capstone Projects

Carbohydrates (glycans) are among the most structurally diverse biomolecules and participate in a wide range of biological processes, including molecular recognition, cell adhesion, immune response, host-pathogen interactions, and cellular signaling. Their biological functions are governed by a complex interplay between sequence, stereochemistry, conformational flexibility, and environmental factors. However, the structural heterogeneity and dynamic nature of glycans present significant challenges for both experimental characterization and theoretical modeling. In particular, the relationships between glycan structure, conformational dynamics, and the resulting potential energy surfaces remain incomplete.

This dissertation investigates how external factors modulate the potential energy surfaces of carbohydrates through a combination of …

Riluzole As A Dual-Targeted Radiosensitizer For Osteosarcoma: Targeting Tumor Cells And Angiogenic Vasculature To Enhance Single High-Dose Radiotherapy Efficacy, Pooja P. Rao

Dissertations, Theses, and Capstone Projects

Osteosarcoma (OS), the most common primary bone malignancy of children and young adults, is intrinsically radioresistant, and outcomes for patients with unresectable or metastatic disease have not improved in over four decades. Single-dose radiation therapy (SDRT) is a potent modality against radioresistant, highly vascularized sarcomas, but its application in OS is constrained by dose-dependent normal tissue toxicity. Radiosensitizers achieving tumor control at lower doses therefore offer a direct route to widening the therapeutic window. Critically, OS radioresistance is not tumor-cell-autonomous. It emerges from two coordinated compartments: aberrant DNA repair and antioxidant capacity intrinsic to the tumor cell, and a radioprotective, …

Analysis Of Diterpenoid Alkaloids From American Aconitum Using Lc-Ms Metabolomic Methods, Yi Zhao

Dissertations, Theses, and Capstone Projects

Analysis of Diterpenoid Alkaloids from American Aconitum Using LC-MS Metabolomic Methods

by

Yi Zhao

Advisor: Edward J. Kennelly

Aconitum plants have been used as a traditional medicine in Asian countries for millennia to treat pain, rheumatism, syncope, fever, and other conditions. These therapeutic effects are mainly due to the bioactive diterpenoid alkaloids accumulated in the roots. Comparing with the large records and studies of Asian Aconitum and their medicinal use and the broad bioactive compounds, American Aconitum has been rarely investigated, not to mention how American Aconitum has been used medicinally. Based on previous phylogenetic and chemotaxonomic studies of Aconitum …

Synthesis, Utilization And Biological Evaluation Of Β-Hairpin Peptides As Inhibitors Of Immune Checkpoints, Sarah Naylon

Electronic Theses and Dissertations 2020 - Present

Peptide therapeutics have emerged as promising alternatives to monoclonal antibodies because of their smaller size, improved tissue penetration, and synthetic versatility. Yet their broader application is often limited by poor structural stability, rapid clearance, and reduced target residence times. This dissertation describes the design, synthesis, structural characterization, and biological evaluation of β-hairpin peptides as inhibitors of immune checkpoints and as peptide vaccine scaffolds while developing strategies to overcome these limitations. At first a series of antibody-derived β-hairpin peptides (mimics of complementary determining region heavy-chain 3: CDR-H3s) as covalent inhibitors of the PD-1/PD-L1 immune checkpoint were investigated. Electrophilic warheads were incorporated …

Instruction Guide, Mark C. Hall

Analytical Biochemistry: A Practical Handbook for Undergraduates

The instruction guide provides useful information for setting up and running the lab activities each week and assessing student preparation, performance, and comprehension.

Towards The Synthesis Of Dragonamide E And Analogs Thereof, Dante Glover

Chemistry Theses

Leishmaniasis is a disease caused by a parasite spread through the female sand fly. It is categorized as a Neglected Tropical Disease and can cause very severe symptoms, even death, if left untreated. Symptoms include skin lesions that can cause permanent scarring, and mucosal membrane infections that can cause facial deformities. More aggressive forms of leishmaniasis can lead to infections of internal organs like the liver and/or spleen and can lead to death. Drug resistance of these parasites has rendered treatment limited and the side effects of which can be harmful as well.

Scientists looking towards new treatments for tropical …

Crystal Structure Of New Polar Rare Earth Borates Na2.62Ln2.12(Bo3)3 (Ln = Pr, Nd, Sm) Containing Isolated Bo3 Groups, Alevtina A. Maksimova, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

Three new rare earth borates, Na2.62Ln2.12(BO3)3 (Ln = Pr, Nd, Sm), were synthesized via a high-temperature solution reaction using a BaCO3–H3BO3–NaF flux and structurally characterized by single-crystal X-ray diffraction analysis. The compounds crystallize in the orthorhombic space group Amm2 with lattice parameters a = 5.0985(10) Å, b = 11.180(2) Å, c = 7.1483(14) Å, and a unit cell volume of 407.48(14) ų (Z = 2) for Na2.62Pr2.12(BO3)3, a = 5.0983(10) Å, b = 11.181(2) Å, c = 7.1491(14) Å, and a unit cell volume of 407.51(14) ų (Z = 2) for Na2.62Nd2.12(BO3)3, and a = 5.08630(10) Å, b …

Single Crystal Growth Of The Orthoborate Nabalu(Bo3)2 And Optical Investigation Of Eu3+ And Tb3+ Doped Nabalu(Bo3)2, Alevtina A. Maksimova, Mark D. Smith, Lakshani W. Masachchi, Hans Conrad Zur Loye

Faculty Publications

Sodium barium lutetium borate NaBaLu(BO₃)₂ crystals were synthesized using a high-temperature solution method. The crystal structure of this layered orthoborate is described and corresponds to that of an extensive orthoborates family, NaBaR(BO₃)₂ (R = Sc, Y, Yb, Tb – Lu). NaBaLu(BO₃)₂ was doped by Eu³⁺ and Tb³⁺ to explore its performance as a host material and to investigate the luminescent properties of the Eu³⁺ and Tb³⁺ doped materials. The emission spectra of the NaBaLu(BO₃)₂:Ln (Ln = Eu, Tb) crystals are presented. The most …

Modulation Of Electrophysiology And Plaque Aggregation In Huntington’S Disease Patient-Derived Cells By Picosecond Pulsed Electric Fields, Mackenzie A. Tardif-Kunk

Biomedical Sciences Theses & Dissertations

Huntington’s Disease (HD) is a fatal, autosomal dominant neurodegenerative disorder characterized by progressive motor and cognitive decline. Unstable expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats in the huntingtin gene, often exceeding 35–40 repeats, results in an extended polyglutamine (PolyQ) tract in the translated protein. Abnormal folding of the mutant huntingtin (mHTT) protein leads to accumulation and aggregation within the cell, dysregulating various cellular processes through molecular sequestration. While several therapeutic strategies have been proposed, this disease remains incurable with treatments limited to symptom management.

Pulsed electric fields (PEF), primarily in the microsecond and nanosecond ranges, have been studied extensively for the …

Analysis Of The Atypical Temperature Dependence And Conformational Changes During Turnover Of A Lactobacillus Chlorogenic Acid Esterase, Nathaniel Carl, Yianni Tsigaris, Dan Ji, Nora K. Anpree, Kellie K. Omori, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Many bacterial chlorogenic acid esterases (ChlEs) exhibit atypical temperature behavior, featuring activities that barely change with temperature and activity maxima that fall below the thermal denaturation point. This work focuses on a ChlE from Lactobacillus helveticus (Lh–ChlE), which has a flat temperature dependence. First, it was determined that conformational changes during Lh–ChlE turnover are not rate-limiting and that the overall rate depends on the chemical step at all temperatures. Next, Lh–ChlE’s temperature dependence was investigated using a conformational equilibrium model that assumes the existence of a temperature-dependent equilibrium between an active and an inactive conformation and an activation heat capacity …

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 …

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

Funded Research Records

No abstract provided.

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 …

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 …