Biochemistry, Biophysics, and Structural Biology Commons^™

Endogenous Light In The Brain: Investigating Sources, Propagation, And State-Dependent Emission, Emre Cicek

Theses and Dissertations (Comprehensive)

Ultraweak photon emission (UPE), and by extension light, has long been thought to be a modality of communication in nature. Prior studies have already identified that UPE can depend on cell type and can be used to discern between malignant and benign cells. However, besides theoretical models, not much effort has been made to identify possible biological structures that would allow for light to be used as a method of communication in the human body. According to the framework set by Shannon’s Information Theory, for communication to be possible at minimum a transmitter, a transmission channel, and a receiver are …

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 …

Establishing A Neural Crest Cell Culture To Investigate Rna Localization, Victoria Vang

Electronic Theses, Projects, and Dissertations

Neural crest cells (NCCs) are a transient, highly migratory embryonic stem cell population unique to vertebrates. During development, they give rise to diverse tissues, including craniofacial cartilage, peripheral neurons, glia, melanocytes, and components of the cardiac outflow tract. As NCCs migrate through complex environments, precise spatial and temporal regulation of gene expression is needed to coordinate migration and developmental fate. Defects in NCC development and migration can result in a broad class of disorders known as neurocristopathies (NCPs), including craniofacial abnormalities, Hirschsprung’s disease, and neuroblastoma. Despite the importance of NCC migration during development, many of the molecular mechanisms regulating this …

Development Of A Protein Mass Spectrometric Assay For The Characterization Of Colorectal Cancer Exosomes, Frank J. Reed Iv

Science University Research Symposium (SURS)

Exosomes (sEV) carry proteins involved in intracellular communication and colorectal cancer (CRC) biology, but their morphologic overlap with non-vesicular extracellular particles (NVEPs), and other extracellular vesicles (EVs), including exomeres and supermeres, complicates proteomic characterization. This aim of this study is to develop mass spectrometric assays that evaluate sEV enrichment, purity, and distinguish sEV CRC-associated protein cargo from EV and NVEP CRC-associated protein cargo to better classify the role of sEVs in CRC biology.

Our lab previously analyzed conditioned media from DiFi, cystic clone (CC), and spikey clone (SC) CRC cell lines purified using dialysis, concentration, and electrophoresis enrichment (DCE) by …

Impacts Of Acetaminophen Treatment On Hl-60 Cell Viability, Differentiation, And Apoptosis, Emma Crenshaw, Shannon Finney, Todd Mount, Gabriela M. Ramirez, Harshita Negi, Charles Andrew Schumpert

Caroliniana Undergraduate Research Journal

Acetaminophen is a widely used analgesic and antipyretic, but its effects on cancer cell behavior remain unclear. This study examined the effects of low concentrations of acetaminophen on HL-60 leukemia cells, focusing on cell viability, apoptosis, and differentiation. HL-60 cells were treated with 33 nM and 66 nM acetaminophen for 1-hour and 24-hour periods. Cell viability and density were assessed using a Trypan Blue Viability Assay, apoptosis was measured using a Caspase-Glo 3/7 Assay, and morphological changes were analyzed by May-Grünwald Giemsa Staining. Results showed decreased cell viability and density with increased apoptosis in a dose-dependent manner, with the stronger …

Seasonal Changes In Estuary-Dependent Fish Community Of Rotationally Managed Impoundments In Merritt Island, Indian River Lagoon, Florida, Usa, John Duvall, Seth Sims

Sustainability Conference

Florida’s Indian River Lagoon (IRL) is one of the most biodiverse estuaries in the world, providing habitat for over 600 known fish species. In the 1950s, much of the IRL’s intertidal wetlands were diked and flooded to prevent mosquito reproduction. Beginning in the 1980s, rotational impoundment management (RIM) was implemented, allowing for seasonal flooding of impoundments during mosquito breeding season, creating a temporary barrier for fish migration. To understand the role of RIM on community assembly, this study (1) collects, identifies, and measures fish in impounded and control locations, (2) processes environmental DNA (eDNA) from impounded and control sites using …

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, …

Roles Of Brca1 Sumoylation In Dna Damage Repair, Chromosome Segregation And Genome Instability, Samantha C. Wild

Biology Theses

Global inhibition of SUMOylation increases chromosomal instability and nuclear abnormalities, including chromatin bridges, micronuclei, nuclear buds, and binuclei. However, the underlying mechanisms remain unclear. In this study, we hypothesized that SUMOylation of BRCA1 is pivotal for DNA double-strand break (DSB) repair and genome stability. My immunofluorescence microscopy revealed an increase in co-localization of BRCA1 and SUMO-2/3 at DSB foci in COS-7 cells after hydroxyurea treatment, suggesting that SUMOylation may play an important role in BRCA1 recruitment to DNA double-strand breaks. Using multiple bioinformatic tools, including UniProt, AlphaFold-2, PDB Viewer, GPS-SUMO 2.0, and DeepSUMO, I found that the BRCA1 RING and …

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 …

De Novo Molecular Design With Agentic Ai: Integrating Tree Search And Iterative Refinement, Yukhe Lavinia, Dony Ang, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Agentic AI frameworks that couple language model generation with iterative tool feedback offer a promising paradigm for automating complex molecular design tasks, yet systematic comparisons of agentic design patterns, such as exploration-focused, refinement-focused, and hybrid, remain scarce. Here, we evaluate three such strategies applied to structure-based de novo molecular design. Language Agent Tree Search (LATS) frames generation as Monte Carlo Tree Search-guided exploration of chemical space. A Reflexion-inspired Self-Improvement (SI) loop critiques and revises candidates using cheminformatics filters and docking feedback. A Hybrid strategy uses LATS to generate diverse, high-quality seeds, which are then refined with SI. We benchmark these …

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 …

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 …

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 The Dhcr7/Nadsyn1 Rs4944946 Variant And Breast Cancer Susceptibility: A Case-Control Study In An Indonesian Cohort, Dian Tri Wahyudi, Rafika Indah Paramita, Sonar Soni Panigoro

Indonesian Journal of Medical Chemistry and Bioinformatics

Background: The rs4944946 variant, located in the 5’UTR of the DHCR7 gene and upstream of NADSYN1, is biologically implicated in vitamin D and cholesterol metabolism pathways closely linked to cancer pathogenesis. This study aimed to experimentally validate the association between the rs4944946 polymorphism and breast cancer susceptibility in an independent cohort of Indonesian women. Method: A case-control study was conducted involving 36 breast cancer patients and 39 healthy adult females. Genotyping of the rs4944946 variant was performed using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). The genetic association was evaluated across codominant, dominant, and recessive models. Luminal B was the …

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 …

Bambara Groundnut (Vigna Subterranea L.) Supplementation Ameliorates The Histological Structure Of Skeletal Muscle In Protein-Deficient Mice, Raquellynda Fadilla Syafanisa, Rimonta Febby Gunanegara, Sunarti Sunarti, Siti Aeniah, Ardaning Nuriliani

Makara Journal of Science

Protein deficiency may cause histological alterations and pathological effects in skeletal muscle, leading to reduced mus-cle size and functional degeneration. Bambara groundnuts contain essential amino acids that have the potential to meet the body’s protein requirements. Therefore, this study aimed to investigate the effect of bambara groundnut supplemen-tation on skeletal muscle in protein-deficient mice. Twenty-five female mice were divided into five groups (control, pro-tein deficiency, and protein deficiency with 100, 200, and 300 g of bambara groundnut supplementation/kg of feed). The treatment was administered for 2 months. At the end of the experiment, the left gastrocnemius muscles of the mice …

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 …

Three-Dimensional Chromatin Architecture Is Rapidly Restored After Dna Replication, Tyler K. Fenstermaker, Svetlana Petruk, Alexander Mazo

Department of Biochemistry and Molecular Biology Faculty Papers

Studies of post-replicative chromatin exclusively focus on the kinetics of protein binding after DNA replication to understand maintenance of transcriptional programs. Here we investigated both chromatin-bound factors and the three-dimensional architecture of the post-replicative genome in human cells. We found that transcription factors and chromatin looping proteins rapidly associate with nascent DNA. We discovered that the architectural factors, CTCF and YY1, bind to their target sequences immediately following DNA replication, and that chromatin loops from 39 to 425 kb re-form within 10 min of DNA replication. This suggests that the 3D structure of chromatin is at most briefly disrupted by …

Ddrr Acts As A Dna Damage-Induced Cell Division Inhibitor In Acinetobacter Baumannii, Christian P. Lowe, Deborah Cook, Lily Hoard, Mckinnley Martin, Janelle M. Hare

Acinetobacter baumannii DNA Damage Database

An article titled, "DdrR acts as a DNA damage-induced cell division inhibitor in Acinetobacter baumannii" published in the Journal of Bacteriology on September 9, 2026.