Biochemistry, Biophysics, and Structural Biology Commons^™

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 …

A Genetic Analysis Of The Rare Endemic Astragalus Ripleyi Barneby, Juan Antonio Jaramillo-Chico

Master's Theses

Astragalus ripleyi Barneby is a rare endemic species found in the San Luis Valley of the southern portions of the Rocky Mountains in Colorado and New Mexico. Though not federally listed as endangered, the species is on the Bureau of Land Management’s Sensitive Species List, warranting protection and continued management. This study aims to provide information about the genetic health of the species to inform conservation efforts and provide updated management recommendations. A genetic health analysis was conducted investigating the levels of diversity present in the species, how genetic diversity is structured across the known range of the species and …

Prenatal Acoustic Programming Of The Developing Hypothalamus: A Multi-Omic Analysis Of Heat Call Exposure In Zebra Finch Embryos, Prakrit Subba

All Dissertations

Climate change is intensifying thermal stress on wildlife globally, yet the developmental mechanisms by which embryos use prenatal cues to adjust to predicted environments remain unclear. In Australian zebra finches (Taeniopygia guttata), incubating parents produce distinctive heat call vocalizations at high ambient temperatures, and embryos exposed to these calls during late incubation develop altered growth trajectories, thermoregulatory capacity, and reproductive outcomes, suggesting a form of anticipatory developmental programming triggered by sound alone. To investigate the molecular basis of this response, I initially hypothesized that prenatal heat call exposure would act primarily through hypothalamic neuroendocrine reprogramming, given the central …

From Geometry To Recognition: A Quantitative Framework For Tcr-Pmhc Structural Analysis In The Age Of Predicted Structures, Kun Hee Kim

Dissertations and Theses (Open Access)

Recognition of antigen by a T cell begins with a single physical event, the engagement of the T cell receptor (TCR) with a peptide-major histocompatibility complex (pMHC), and this interaction is encoded in the geometry with which the receptor docks onto the composite pMHC surface. Whether that docking geometry is biologically organized, and whether the structures now produced at scale by prediction preserve recognition or only reproduce that organization, are the two questions this thesis addresses. Two gaps stand in the way. The first is a gap of measurement, because docking geometry has never been made quantitatively comparable across many …

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, …

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 …

Structure-Based Discovery Of Malate Dehydrogenase Inhibitors With Efficacy Against C. Parvum Oocysts, Ankita Bharatbhai Kheni

Biochemistry and Molecular Biology

Cryptosporidium parvum, the etiological agent of Cryptosporidiosis (diarrheal illness) represents a significant global health burden, particularly affecting immunodeficient and pediatric populations. Since the parasite has a highly reduced mitochondrion and relies on glycolysis, enzymes such as C. parvum malate dehydrogenase (CpMDH), which are believed to be indispensable for parasite viability due to their pivotal roles in NAD⁺ regeneration and redox balance, remain largely unexplored as therapeutic targets. The present study employed a multifaceted experimental and computational strategy to evaluate the inhibitory activity of two lead-like and drug-like small molecules, referred to as compound 1.8 and compound 1.5, against the cofactor …

Unc-45b As A Potential Chaperone For The Transcription Factor, Gata-4, Kaylah Owings

Electronic Theses and Dissertations

The cardiac myosin–specific chaperone UNC-45B has been shown to physically interact with the cardiac myosin transcription factor GATA-4. Specifically, this interaction occurs within the chaperoning region of UNC-45B, known as the UCS domain. However, the precise nature of this interaction has not yet been fully elucidated. The present study was conducted to confirm earlier findings and to evaluate whether UNC-45B functions as a chaperone for GATA-4 using bioinformatic approaches. Analysis of the interaction using AlphaFold 3 modeling verified not only that binding occurs at the UCS (chaperoning) domain of UNC-45B, but also that the interaction is associated with an increase …

Bioinformatic Resolution Of Candidate Stress-Response Homologs In Cryptosporidium Parvum: P53-Family Vs Sestrin Identity, Freeman Tobechukwu Ezeala Mr.

Biochemistry and Molecular Biology

Cryptosporidium parvum is an apicomplexan protozoan of major public-health importance, but accurate genome annotation in this organism remains difficult because of its compact genome, deep protein divergence, and the presence of compositionally biased or low-complexity regions that can mislead similarity-based analysis.

In this thesis, I examined one such annotation problem involving a conserved Cryptosporidium stress-response candidate protein, CPATCC_0028580_t1 (833 aa). The central question was whether this protein is better interpreted as a member of the p53 family, based on similarity to p53-like DNA-binding domains (PF00870), or as a member of the Sestrin family associated with the PA26 domain.

I explored …

Ai×Life 2026: Advances In Computational Biology Across Scales For Life & Health Sciences, Suma Mohan S., Devika N. T., Pranavathiyani G.

Conference Proceedings

Book of Abstracts of the International Conference, AIxLife 2026: Advances in Computational Biology Across Scales for Life & Health Sciences, held on 17–18 April 2026, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, INDIA 

About the Conference

Conventional computational biology laid the foundation for biological data analysis through statistical models, algorithms, and curated databases, enabling insights into genes, proteins, and pathways. Today, the integration of artificial intelligence, spanning machine learning, deep learning, and large language models (LLMs) is driving a transformative shift across biological scales, from atomic and molecular interactions to pathways, cellular systems, organisms, and populations.

AI-powered approaches …

Design And Optimization Of Peptide Inhibitors Targeting Kinesin: Molecular Modeling Studies And Virtual Screening For Therapeutic Candidate Development, Maraf Mbah Bake

Open Access Theses & Dissertations

Kinesins are ATP-driven molecular motors essential for intracellular transport and mitotic spindle assembly, and their mechanochemical behavior has been extensively characterized through computational tools. The first project reviews decades of advances in molecular dynamic simulations, including all-atom and coarse-grained molecular dynamics, Markov state models, Brownian dynamics, and free-energy approaches, which have collectively deepened our understanding of conformational transitions, microtubule-binding interfaces, and ligand interactions, especially for the mitotic motor Eg5. The second review examines the rapid emergence of quantum computing as a transformative technology for drug discovery, highlighting key historical milestones, recent progress in hybrid quantum-classical algorithms, quantum-enhanced docking, and quantum …

Cleft Palate And The Coordination Of Wnt Signaling And Pax9 In Murine Palatogenesis, Landon Wyatt

Honors Theses

Cleft palate is a common craniofacial birth defect that arises when the molecular and morphogenetic events guiding secondary palate formation lose coordination during a narrow developmental window. In mice, successful palatogenesis requires the paired palatal shelves to grow vertically, elevate above the tongue, and fuse at the midline; disruption of any of these steps can result in clefting. Two important regulators of this process are canonical Wnt signaling and the transcription factor Pax9, both of which contribute to normal palatal mesenchymal growth and patterning during early development. This paper first examines whether altered Dkk1/Wnt signaling contributes to the Pax9-null palate …

Intermediates Or Intermedius? An Examination Of Lotic Sternotherus In Baldwin And Mobile Counties, Al, Peyton A. Wilson

Theses

The Southeastern United States is a biodiversity hotspot, and turtles are no exception to the rule. This is particularly true for the genus Sternotherus. Alabama is the only state home to all six species of Sternotherus, including the recently described Intermediate Musk Turtle (Sternotherus intermedius). It was thought that the Perdido River was the western boundary of Sternotherus intermedius; however, surveys in recent years produced questionable individuals in several small watersheds feeding into the Mobile-Tensaw Delta, bringing the species true range into question, as well as the question of if this species has hybridized with its congener, …

Characterization And Advancement Of Molluscan Venom Gland Cell Model Systems, James V. Parziale

Dissertations, Theses, and Capstone Projects

Venomous mollusks, including cone snails and coleoid cephalopods, produce rich repertoires of bioactive peptides with profound effects on cellular physiology, yet there are few tractable experimental systems that exist to study their development, maintenance, and venom secretion. Although therapeutics such as the cone snail peptide Ziconotide demonstrate the biomedical potential of molluscan venoms, progress in understanding how venom glands form, function, and evolve has been hindered by the lack of reliable husbandry and the complete absence of in vitro cell models. Modern comparative genomics has revealed widespread convergent evolution across venomous lineages, but molluscan datasets remain underrepresented, limiting insights into …

Computational And Functional Characterization Of Terebrid Venom Peptides, Favour T. Achimba

Dissertations, Theses, and Capstone Projects

Venom peptides represent a natural repertoire of bioactive compounds that are potent modulators of ion channels. Teretoxins, venom peptides from terebrid snails, remain underexplored despite their structural and functional diversity. This thesis is the first to comprehensively explore the structure and function of teretoxins using a comparative computational sequence and structure model followed by experimental assays. The majority of the functional focus has been on identifying the ion channel molecular targets of uncharacterized teretoxins. Teretoxins, like other venom peptides, are hypothesized to manipulate the cellular function of a diversity of ion channels. Dysregulation of ion channels leads to several …

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 …

Analysis Of Alternative Oxidase In Non-Angiosperm Plants, Anissa M. Francis

Theses and Dissertations (Comprehensive)

Alternative oxidase (AOX) is a mitochondrial terminal oxidase that provides an alternative pathway for electron transport, allowing plants to maintain respiratory flexibility under environmental stress conditions. While AOX has been extensively studied in angiosperms (flowering plants), little is known about its distribution and conservation in non-angiosperms. Based on gaps identified in the literature, this thesis investigated the distribution of AOX across non-angiosperm plant lineages. Although AOX is present in many green algae and is therefore considered to be an ancient protein that originated before the existence of non-angiosperm plants, it remains unclear whether the protein is uniformly distributed across these …

Design And Advancement Of Analytical Frameworks For In Vivo Single-Photon Calcium Imaging To Characterize Temporal- And Treatment-Dependent Neural Adaptations To Opioid Exposure And Withdrawal In The Medial Prefrontal Cortex, Alexia R. Alsum Dr.

Theses and Dissertations--Pharmacy

Despite the availability of several approved medications for opioid use disorder (OUD), it remains a significant public health concern characterized by persistent neurobiological adaptations that drive relapse and impede successful recovery. The medial prefrontal cortex (mPFC), a region critical for executive control and decision-making, undergoes pronounced functional changes during chronic opioid exposure and withdrawal, yet the cellular mechanisms underlying these adaptations remain poorly understood. This dissertation aims to investigate longitudinal alterations in mPFC neural activity across opioid exposure and withdrawal using in vivo single-photon calcium imaging and newly developed computational frameworks.

Following standard preprocessing to extract and normalize calcium traces, …

Systematics Of Disk-Winged Bats (Thyroptera), Courtney L. Klumpp

Capstone Showcase

This thesis investigates the evolutionary relationships among disk-winged bats in the genus Thyroptera, a small group of Neotropical bats known for the adhesive suction disks on their wings and feet that allow them to roost inside tightly rolled leaves. The distinctive morphology and behavior of these bats have not been extensively documented, and their phylogenetic relationships remain only partially resolved. The goal of this research is to better understand how these species are related to one another and to determine whether the five recognized species of Thyroptera form a single monophyletic group. To address this question, morphological and genetic …

From Theory To Ecosystems: Exploring Biodiversity And Ecosystem-Function In Pitcher Plant (Darlingtonia Californica) Microbial Communities, Gavin Sutter

Cal Poly Humboldt theses and projects

The relationship between biodiversity and ecosystem-function (BEF) has been a central focus of ecological research for the last three decades, yet the role of space in shaping BEF relationships remains relatively unknown. Research has shown that community diversity and composition can strongly influence productivity, nutrient cycling, and decomposition, but much of this work treats communities as spatially isolated, leaving open how dispersal and other spatial processes shape BEF at broader scales. To begin addressing this gap, I used microbial communities inhabiting Darlingtonia californica pitcher plant leaves to evaluate how spatial organization and successional change shape biodiversity and ecosystem-functioning. I quantified …

Computational Methods For Rna 3d Structure Classification And Structural Motif Discovery, Nabila Shahnaz Khan

Graduate Studies Theses and Dissertations 2026

Non-coding RNAs perform diverse and essential cellular functions, and the study of RNA structures is expanding rapidly. The growing volume of RNA 3D structures highlights the need for efficient computational methods to identify recurring structural motifs, which are often conserved and critical to RNA function. However, the complexity and redundancy of RNA structures in existing databases pose significant challenges for motif discovery and structural analysis. To address these challenges, this dissertation presents three complementary computational approaches. First, a non-redundant RNA structural dataset, RNA-NRD, was developed to systematically reduce redundancy in RNA structural data and provide a reliable foundation for downstream …

Gene Expression Of Anthocyanin Pigments In The California Native Plant Leptosiphon Parviflorus: Interactions Between Flower Color Morphology And Abiotic Stressors, Weston Gonor

Master's Theses

For plants to survive in harsh conditions imposed by abiotic stressors, they must develop mechanisms of adaptation. One of the common types of adaptation seen in plants is the production of anthocyanin pigments, which have been shown to protect plants from UV radiation, metabolic stress, and drought. In this study, we used the flower color polymorphic species Leptosiphon parviflorus to investigate the role of anthocyanin pigments in protecting plants from abiotic stress. To accomplish this, RNA samples were taken from flower, leaf and root tissue of different flower color morphs of Leptosiphon parviflorus (Polemoniaceae) grown in high magnesium and water …

Empowering Science With The World's First High Accuracy And High Throughput Functional Assay, Christopher Giacoletto

UNLV Theses, Dissertations, Professional Papers, and Capstones

Understanding the functional consequences of genetic mutations remains a central challenge in modern biology, with far-reaching implications for human health and disease. While early systematic methods like alanine scanning and phage display provided foundational insights into protein structure and function, the emergence of high-throughput approaches—such as Multiplexed Assays of Variant Effect (MAVEs)—and predictive tools powered by artificial intelligence have vastly expanded our ability to profile mutational landscapes. However, these methods are often constrained by trade-offs between accuracy, scalability, and biological relevance.This dissertation presents the development and application of the GigaAssay, the world’s first high-throughput functional assay capable of delivering both …

In Silico Prediction Of Cytotoxic T-Cell Epitopes From Helicobacter Pylori Virulence Factors Using An Immunoinformatics Approach, Demy Valerie Chacon, Kiana Alika Co, Daphne Noreen Enriquez, Aubrey Love Labarda, Reanne Eden Manongsong, Edward Kevin B. Bragais

Biology Faculty Publications

Background: Helicobacter pylori infects approximately half of the global population, leading to gastric and duodenal ulcers. Despite the availability of antibiotics, challenges such as patient reluctance, high treatment costs, and antibiotic resistance limit their effectiveness, making vaccination a promising alternative. This study used immunoinformatics to identify candidate epitopes for a multiepitope vaccine construct against H. pylori.

Material and methods: The protein variability server was utilized for conservation analysis. The epitopes were screened for antigenicity, allergenicity, toxicity, cross-reactivity, and population coverage. Selected epitopes were docked with their corresponding human leukocyte antigen (HLA) alleles, and thermodynamic quantities were determined. Five virulence …

Elucidating The Roles Of Eukaryotic Initiation Factors Involved In Dap5 Mediated Translation, Jacob Nk Quartey

Dissertations, Theses, and Capstone Projects

Translation initiation in eukaryotes is a highly regulated process essential for accurate protein synthesis. It is a dynamic process that involves a complex interplay between messenger RNAs (mRNAs), ribosomal subunits, and a host of initiation factors, ensuring precise start codon selection and the subsequent assembly of the translation machinery. This process has well been known to be mediated by the eukaryotic Initiation Factor (eIF4F), which consists of the cap binding protein eIF4E, the scaffolding protein eIF4GI, and the helicase factor eIF4A.The recognition and binding of eIF4E to the m⁷G cap structure of the mRNA is essential for the …

Generation Of A Transgenic Vector For The Purpose Of Transforming Charcoal Rot Resistance Into Soybeans (Glycine Max), John M. Bear Jr

Electronic Theses & Dissertations

Charcoal rot, caused by Macrophomina phaseolina, is among the most devastating fungal pathogens affecting G. max, particularly in drought-susceptible regions such as the midwestern United States. Traditional agricultural practices have included crop rotation and irrigation, which have proved ineffective or economically unfeasible. Charcoal rot infects over 500 other species of plants and can overwinter as dormant sclerotia which can germinate once soybeans are re-planted and infect young plants. As a result, transgenic solutions have offered a promising alternative for the development of disease-resistant soybeans. This thesis documents the construction of a transgenic vector to express BOZO, a …

Monitoring Cellular Glycolysis Pathway Kinetics In The Extracellular Medium Using Label-Free, Raman Spectroscopy, Nitin Patil, Zohreh Mirveis, Hugh J. Byrne

Articles

This study explored the potential of Raman spectroscopy to holistically monitor the glycolysis pathway kinetics as a function of time through the extracellular medium. Initially, the collinearity of individual metabolites of interest- glucose and lactic acid as a function of their concentration was tested followed by the sensitivity analysis of the approach by elucidating the limits of detection (0.85 mM and 2.8 mM) and quantification (2.5 mM and 9.5 mM) for glucose and lactic acid respectively in the biological range. In the process several datamining approaches were also explored. Finally, the A549 cell culture was used for kinetic spectral acquisition …

Intraspecific Genetic Variation In Green Salamanders (Aneides Aeneus) At Bays Mountain Park, Brianna Drake

Electronic Theses and Dissertations

Accurate taxonomy is crucial for conserving vulnerable cryptic species like the green salamander (Aneides aeneus) in the Southern Appalachian Mountains. Prior studies identified three distinct lineages within the A. aeneus complex: Northern Appalachians, Southern Appalachians, and Blue-Ridge Escarpment. One previously collected sample indicated green salamanders in northeast Tennessee fit within the Northern lineage. The present study uses molecular data of A. aeneus at Bays Mountain Park (BMP) in Kingsport, Tennessee, to determine where the BMP population fits within these lineages. It was hypothesized that individuals from BMP belong in the northern lineage. Tail tips were collected from thirty-four …

Molecular Interaction Of Purple Rice Ferulic Acid And Skin Aging-Related Enzymes, Ernanin Dyah Wijayanti, Fatchiyah Fatchiyah, Anna Safitri, Dian Siswanto

Makara Journal of Science

Purple rice is rich in ferulic acid, a phenolic acid abundant in rice. Ferulic acid (FA) has long been recognized for its anti-oxidant properties, which are linked to its skin anti-aging activity owing to its ability to scavenge free radicals and pro-tect cells from damage. Skin anti-aging activity could be assessed by inhibiting skin aging enzymes. However, there was limited information on the mechanism of FA inhibition of these enzymes. This study focused on the molecular interac-tion between purple rice FA and collagenase or tyrosinase, both with and without their substrates. The interaction be-tween FA (CID 445858), collagenase (2Y6I), tyrosinase …

Bloom: Behavioral Learning And Outcome Observation In Microbes, Sean Sarwar Haque, Luke Compton Wharton, Ming Lin, Razvan Voicu

Symposium of Student Scholars

Understanding how pathogens respond to physical changes in their environment is crucial for developing effective treatments and preventative measures. Current research often relies on static models or experimental data that either fail to capture the dynamic interactions within cellular environments or are not generalizable to other types of pathogens. This project aims to address this gap by creating a comprehensive cell simulation that models pathogens and their response to chemical, physical, and physiological changes. The proposed solution is a simulation that integrates biological data and computational modeling to replicate the behavior of pathogens in real time as they are affected …