Biochemistry, Biophysics, and Structural Biology Commons^™

Semiconductors In Space: Data Analysis Of Microgravity's Impact On Crystal Formation, Keegan Jo Jackson

Undergraduate Honors Thesis Collection

Comprehensive data analysis on crystal growth in microgravity is a requisite to inform understanding of prior work. Our research constructed and analyzed a database containing data gathered from research focusing on semiconductors grown in microgravity. Data curation spanned multiple decades, countries, and semiconductor materials. All relevant reported information was recorded in the database, notably data regarding the metrics used to determine the impact space had on crystal growth: size, structure, uniformity, and performance. After data cleaning and data processing, the database was organized and readied for analysis. Data analysis was performed using RStudio and SciKit-learn. RStudio was employed for data …

Linking The Past And The Future: Understanding How Pollutants Cause Corrosion During An Oddy Test, Kylie Blair Blake

Undergraduate Honors Thesis Collection

Artifacts and artwork continue to tell a story long after a time or culture has disappeared. Preventive art conservation science involves careful and responsible management of the objects entrusted in the care of the museum staff to ensure environmental and display conditions do not cause damage so future generations can observe and learn about past cultures. An accelerated metal corrosion test, the Oddy test, has been used to help determine the suitability of display and storage materials. The Oddy test is subjective, so newer methods are being developed involving the use of gas chromatography and mass spectrometry to identify specific …

A New Transition Metal Borate, Co6(B24O39(Oh)6(H2O) 6·2.21h2O, Synthesized Via A Mild Hydrothermal Synthesis, Alevtina Maksimova, Patrick Belt, Nilah Whitfield, Mark D. Smith, Gopabandhu Panigrahi, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

A new transition metal borate hydrate, Co₆B₂₄O₃₉(OH)₆(H₂O)₆·2.21H₂O, was synthesized via a mild hydrothermal method using boric acid as the melt. The compound crystallizes in the trigonal space group P 3‾ with lattice parameters a = b = 13.17840(10) Å, c = 12.3287(2) Å, and a unit cell volume of 1854.27(4) ų (Z = 2). This borate hydrate crystallizes in a new structure type comprised of layers containing [BO3] trigonal planar units and [BO4] tetrahedra that are linked by CoO6 and Co(OH)2(H2O)4 octahedra via corner-sharing. The …

Innovation Scholars Program, Lauren Voll, Olivia Latour, Owen Montreuil, Kaennae Mortimer

Celebrating Scholarship and Creativity Day (2018-)

The innovations scholar program spans roughly five months and included two trips to Mayo Clinic Rochester. The team of four undergraduate students and an MBA student worked with Mayo Clinic ventures to assess the viability of a few patents. The project included a 40-page comprehensive paper as well as a 30-minute presentation. The specific details are protected under an NDA agreement however our key takeaways are shared on the poster.

Neuro-Immune Regulation Of Feeding Behavior And Alcohol Intoxication In Caenorhabditis Elegans, Kamya Kiranbhai Shah

Theses, Dissertations and Culminating Projects

Alcohol use disorder (AUD) and obesity are major public health concerns, contributing to more than 28 million deaths annually. Despite extensive research, the mechanisms underlying excessive alcohol and food consumption remain incompletely understood. Emerging evidence suggests that neuro-immune crosstalk plays a pivotal role in feeding and alcohol-induced behaviors, with inflammation as a key pathological hallmark. Toll-like receptors (TLRs), traditionally recognized for their role in innate immunity, have recently been implicated in modulating neural responses to ethanol. However, the mechanisms of how TLR signaling influences feeding and alcohol-related behaviors remain largely unknown. To address this gap, we leveraged Caenorhabditis elegans (C. …

Exploring The Role Of Lysine Acetylation During Biofilm Formation In Bacillus Subtilis, Jennifer Nguyen, Briana Ericka Reid, Valerie Carabetta

Rowan-Virtua Research Day

Biofilms are structured communities of bacterial cells encased in a self-produced extracellular matrix, composed of polysaccharides, extracellular DNA, and proteins. Bacteria in a biofilm pose significant challenges in healthcare due to their resistance to disinfectants and tolerance to antibiotics. In some species, histone-like proteins were found to be important structural components of the biofilm. Nε-Lysine acetylation is a widespread post-translational modification (PTM) in bacteria, which can alter a protein’s function. The histone-like protein HBsu in Bacillus subtilis is acetylated at seven sites in vivo. We hypothesized that the acetylation state of HBsu may alter biofilm structure or the genetic programming, …

Exploring Intracellular Signaling Responses To Ks18, A Potent Mcl-1 Inhibitor, In Multiple Myeloma, Emily Nelson, Omar S Al-Odat, Dhruti A. Brahmbhatt, Tulin Budak-Alpdogan, Subash Jonnalagadda, Manoj Kumar Pandey

Rowan-Virtua Research Day

Multiple myeloma (MM), a cancer of plasma B cells, is a hematological malignancy in which patients inevitably relapse and develop drug resistance. Mcl-1, a member of the anti-apoptotic subgroup of Bcl-2 family proteins, plays a critical role in the progression of multiple myeloma and contributes significantly to drug resistance. Elevated Mcl-1 expression is observed in approximately 52% of MM patients at diagnosis, increasing to 81% at relapse. Given its driving role in disease progression and therapy resistance, Mcl-1 inhibition has emerged as a promising therapeutic target, prompting ongoing research into the development and clinical evaluation of Mcl-1 inhibitors, particularly for …

Antiproliferative Effects Of Salvia On Breast Cancers., Allison C. Portaro

College of Arts & Sciences Senior Theses

Breast cancer is the most common cancer diagnosed in female adults, with 2.3 million new cases worldwide in 2020. Plants have been used in traditional medicine and are a potential source of pharmaceuticals. One example is the large Lamiaceae (mint) family. The Salvia genus, commonly known as the sages, is the largest genus in Lamiaceae with almost 900 known species. Salvia lyrata (lyre-leaved sage) has a history of Native American medicinal use to treat cancers and other ailments resulting in this plant being referred to as ‘cancer weed.’ Extracts were produced from the leaves of S. lyrata, S. lyrata …

Leveraging Natural Variation In Yeast To Understand Susceptibility Differences In Parkinson’S Disease, Julio Andres Molina Pineda

Graduate Theses and Dissertations

Parkinson’s Disease (PD) is a neurodegenerative disorder that causes countless suffering around the world. Both forms, familial and sporadic, have been associated with the misfolding and cytotoxicity of α-synuclein, an otherwise non-pathogenic protein suspected to have various roles in the normal maintenance of the central nervous system. Model organisms have emerged as great vessels to uncover the cellular and molecular mechanisms that shape α-syn biology, and great strides have been made to understand it. Yet, it is still unclear why some individuals are affected by α-syn toxicity, while others not so much. Since it’s extremely complicated to study and probe …

Examining The Molecular Mechanisms Of Glucagon-Like Peptide-1 Receptor Agonists In Cancer Cell Biology, Oliver G. Sabet

Honors Scholar Theses

Glucagon-like peptide-1 receptor agonists (GLP-1RAs) are synthetic analogs of glucagon-like peptide-1 (GLP-1) used to treat obesity and diabetes by reducing blood glucose levels and appetite. While early rodent studies suggested a link between GLP-1RAs and thyroid cancer pathogenesis, evidence in humans remains inconclusive, with randomized controlled trials not supporting that link. Due to the rapid, widespread use of these drugs, concerns have expanded to other obesity-associated cancers, with conflicting findings on their role in cancer progression. With this contradictory evidence in a novel intersection of obesity medicine and oncology, this literature review aims to summarize current understandings between GLP-1-RAs and …

The Role Of Myosin L In The Survival Of Toxoplasma Gondii And The Importance Of Mlc1 For In Vitro And In Vivo Myosin F Motility, Victoria K. Yi

Honors Scholar Theses

My thesis discusses the work that I have conducted on two myosins in Toxoplasma gondii, which is an obligate intracellular parasite that has chronically infected around 10% of the American population. It causes toxoplasmosis and severe health consequences for individuals with compromised immune systems or when infections occur in utero. However, immunocompetent individuals are asymptomatic or present with subclinical symptoms. In the Heaslip lab, I investigated two myosins in the parasite: Myosin L and Myosin F. MyoL is an uncharacterized motor that localizes at the apical end of the parasite. It was shown to be important for parasite …

Effects Of Cholesterol Concentration On Liposome And Proteoliposome Behavior, Ehsaneh Khodadadi

Graduate Theses and Dissertations

Cholesterol is crucial in modulating the behavior and characteristics of biological membranes, liposomes, and proteoliposomes, for instance in drug delivery applications. Cholesterol regulates membrane stability by influencing lipid density, phase separation, and protein-membrane interactions. In planar bilayers, cholesterol enhances membrane thickness, reduces permeability, and promotes lipid ordering, adding rigidity and fluidity. Cholesterol also modulates membrane curvature in curved bilayers and vesicles, stabilizing low-curvature regions. In this work, all-atom molecular dynamics (MD) simulations were employed to examine how varying cholesterol concentrations influence the structure and dynamics of membranes, focusing on planar and curved geometries. Bilayers with cholesterol molar ratios of 0%, …

Direct Synthesis Of Cerium Oxide Nanoparticles In Reducing Sugars: Enhanced Ce3+ Surface Density For Biological Application, Balaashwin Babu, Elayaraja Kolanthai, Craig J. Neal, Samarah V. Harb, Udit Kumar, Yifei Fu, Sudipta Seal

Rowan-Virtua Research Day

Cerium oxide nanoparticles (CNPs) are recognized for their ability to scavenge reactive oxygen species (ROS), making them promising candidates for mitigating oxidative damage in biomedical applications. However, many conventional synthesis methods limit the formation of Ce³⁺ states, which are critical for this antioxidant function. Building upon previous findings that glucose can promote Ce³⁺ formation, this study investigates the broader impact of both reducing (glucose, fructose, galactose) and non-reducing (dextran, sucrose, cyclodextrin) natural sugars on CNP synthesis. CNPs were synthesized in the presence of these sugars, and the surface densities of Ce³⁺ were measured. Results showed that reducing sugars significantly increased …

Implications Of Type Iv Pilus Retraction For Dna Uptake By Acinetobacter Baumannii, Yafan Yu

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Horizontal gene transfer (HGT) via natural competence allows bacteria to incorporate extracellular DNA (eDNA) into their genomes, facilitating genetic diversity and adaptation. In Acinetobacter species, natural competence depends on DNA binding and uptake mediated by type IV pili (T4P). T4P are dynamic extracellular filaments composed primarily of the major pilin subunit PilA, along with a few minor subunits. T4P drive a range of cellular functions including twitching motility, biofilm formation, and DNA uptake, with some functions dependent on pilus retraction and others not. However, how Acinetobacter T4P bind DNA and how T4P/eDNA interactions impact biofilm formation remain unclear. Here, I …

Screening For Chloroplast Inner Envelope-Thylakoid Membrane Contact Site Proteins, Evan W. Labrant

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Most life on Earth is dependent upon the capture of solar energy and subsequent fixation of carbon. In members of the Archaeplastida lineage these biological processes take place in semi-autonomous organelles called chloroplasts. Chloroplasts are bounded by a double membrane envelope and contain the photosynthetic membrane system, thylakoid membranes, where light capture takes place. While a great deal is known about how thylakoid lipids are synthesized and protein complexes therein are properly maintained, very little is known regarding the processes by which lipids are transported to thylakoids which lack de novo glycerolipid synthesis. We have worked to identify candidate proteins …

Treating The Black Fever: Evaluating Combination Chemotherapy For Leishmania Donovani, Robert Frank Mickatavage

Biochemistry and Molecular Biology

Visceral leishmaniasis (VL) is a neglected tropical disease (NTD) endemic to Africa, Asia, and the Americas, caused by the parasite L. donovani and spread by the Phlebotomine sandfly. If left untreated, VL is almost always fatal, bearing a mortality rate of over 95%. Many individuals within endemic regions are often too poor to afford treatment, and the financial burden of current treatments may only exacerbate their poverty. Antimonials and more modern treatments display varying effectiveness, but are nonetheless toxic to the host, commonly inducing hepatotoxicity, nephrotoxicity, and renal failure. The development of more effective and safer treatments is crucial, particularly …

Sodium And Potassium In Health And Cellular Function, Jordyn Branz

Honors Program: Senior Projects (Public)

Sodium (Na⁺) and potassium (K⁺) are essential electrolytes that regulate numerous physiological processes. These include cell function, nerve transmission, and muscle contraction. The Na+/K+-ATPase plays a critical role in maintaining the balance of these ions by actively transporting three sodium ions out of the cell and two potassium ions into the cell against their concentration gradients. This process is vital for maintaining the resting membrane potential and supporting the function of excitable cells. The Na+/K+-ATPase consists of two main subunits, with the alpha-subunit being primarily responsible for ion transport activity. Isoforms alpha1, alpha2, and alpha3 are tissue-specific and contribute to …

Hypoxia Induced Ribosomal Rna Fragmentation Mediated By Rnase L, Vanessa Kristina Pizutelli, Dimitri G Pestov

Rowan-Virtua Research Day

Ischemic injury contributes to a range of global pathologies. Ischemia/Reperfusion Injury (IRI) is a paradoxical phenomenon that involves an initial restriction of blood flow followed by a sudden restoration of perfusion. This type of injury takes place in conditions such as myocardial infarction, acute kidney disease, and ischemic stroke and often leads to cellular death. Additionally, IRI exacerbates post-surgical outcomes and plays a role in graft dysfunction and transplant rejection. Despite efforts to develop therapies targeting known IRI pathways, clinical trials have largely been unsuccessful, underscoring the need for alternative mechanisms and biomarkers associated with IRI-induced apoptosis. Reactive oxygen species …

Understanding The Properties Of Repair Protein P26 For Dry-State Preservation Of Biological Materials., Hannah Skaggs

College of Arts & Sciences Senior Theses

The preservation of complex biological materials in the frozen state has been well established and plays a critical role in the advancement of clinical applications and the pharmaceutical industry. Cryopreservation of complex biological materials has several clinical applications, including vaccine preservation, bone marrow transplants, cell therapeutics, and increasing the shelf life of red blood cells (RBCs) for transfusion. However, many challenges are present, including the use of toxic protective agents and the financial burden of maintaining extremely low temperatures between 193.15 and – 77.6 K (Parihar, Kumar et al. 2023). Lyophilization, or freeze-drying, presents an opportunity to mitigate such challenges. …

Towards The Design Of A Super Fgf1-Fgf10 Chimera, Megan Brown, Suresh Thallapuranam

Biological Sciences Undergraduate Honors Theses

The Fibroblast Growth Factor family consists of 23 different fibroblast growth factors (FGFs) that are each involved in various cellular processes, including cell proliferation and tissue repair. Fibroblast growth factor receptors (FGFR) are different tyrosine kinase receptors. There are four FGFRs in the human body, each binding to different combinations of FGFs. Fibroblast growth factor 1 (FGF1) is the only FGF that can bind with all four types of fibroblast growth factor receptors. Therefore, it is the most powerful mitogen. However, FGF1 has low thermodynamic stability under the physiological conditions. Prior work in the Kumar lab has constructed several points …

The Expression Of Intestinal Tight Junction Proteins Induced By 1,25-Dihydroxyvitamin D3-Glycosides Supplementation To Reduce Bacterial Chondronecrosis With Osteomyelitis Lameness In Broilers, Kennedy M. Hicks

Biological Sciences Undergraduate Honors Theses

Bacterial Chondronecrosis with Osteomyelitis (BCO) is a leading cause of lameness in broiler chickens, impacting animal welfare and commercial poultry production. Supplementation using organic trace minerals, vitamin D, probiotics, and prebiotics has been studied to mitigate BCO lameness incidences in broiler chickens. Our previous study demonstrated that feeding Panbonis®-G-1,25(OH)₂D₃ from Solanum glaucophyllum, containing 1 µg/kg G-1,25(OH)₂D₃, to broilers for the first 28 days of their production cycle reduced BCO lameness by approximately 50%. In this study, we investigated the impact of 1,25-dihydroxy vitamin D₃ supplementation on the expression of tight junction …

Bpa Adsorption On Microplastics In Different Chemical Conditions, Addison Zehren

University Honors Program Senior Projects

Microplastics (plastic particles < 5 mm in size) are increasingly seen as a health and environmental issue, both for their direct effects when ingested by living organisms and for their ability to adsorb and concentrate other pollutants. Current water treatment processes do not adequately remove microplastics from municipal water supplies, so a thorough understanding of how microplastics affect water quality is needed. The objective of this study is to evaluate the effects of certain water quality parameters on the ability of polystyrene microplastics (PS MPs) to adsorb Bisphenol A (BPA). BPA is an endocrine disruptor (chemically like estrogen) used in plastics which can be released into the environment and act as a water pollutant. Water quality chemical parameters investigated were chloride, nitrate, phosphate, and copper ions. Concentrations of each solute were selected based upon Environmental Protection Agency (EPA) guidelines and previous results obtained from testing Chicago River water samples. A constant amount of PS MPs and BPA were added to each sample and the mixtures were shaken for 5 days to allow time for the BPA to adsorb. The samples were then filtered and the amount of BPA left in the water was determined by measuring its UV absorbance on a UV-vis spectrophotometer. BPA concentrations decreased in the water indicating that it had been adsorbed onto the microplastic surface, with the highest adsorption present with copper, which reduced BPA concentrations from 6.7 mg/L to 3.9 mg/L. Statistical analyses showed differences between copper, phosphate, nitrate, and chloride (df = 9, p = 0.002). Future work can apply these results to investigate the implications of pollutant transportation in urban waterways like the Chicago River.

The Regulatory Role Of Collagen Α1(Xi) Amino-Terminal Domain Isoforms In Collagen Fibrillogenesis, Abu Sayeed Chowdhury

Boise State University Theses and Dissertations

Collagen α1(XI) is a minor fibrillar collagen involved in the critical regulation of collagen fibrils, such as nucleation, assembly, and regulation of fibril diameter. The amino-terminal domain consists of an amino-propeptide (Npp) domain and a variable region, which is the result of alternative splicing from exon 6A, 6B, 7, and 9. The spliced variants involving Npp, with the combinations of exon 6A, 6B, 7, and 9 gives rise to different isoforms with very distinctive chemical nature. The Npp of collagen α1(XI) chain is retained on the surface of the collagen fibril for an extended period of time and may play …

Bang!: Real-Time Measurements And Transcriptomics Of Metabolic Reprogramming In Activated Macrophages At Fever Temperature, Kenneth Howard Taylor

Graduate Theses and Dissertations

We investigated the real-time metabolic rates of activated macrophage cell lines derived from mouse, chicken and rainbow trout. Each species showed a different kinetic signature with metabolic rates accelerating under fever conditions specific to each organism. Upon activation mouse macrophages increased their rate of glycolysis early and then a later reprogramming phase occurred with a dramatic decrease in oxidative phosphorylation (OXPHOS) accompanied by a reciprocal second increase in glycolytic rates. Chicken macrophages showed an initial increase in both glycolytic and OXPHOS rates. The late drop OXPHOS rates also occurred in chicken however there was no reprogramming that occurred as glycolytic …

3d Printing Protein-Rrna Mutations In The Ribosome, Abigail Wilson

Senior Honors Projects

Sometimes conveying research can be difficult through two-dimension models. In my project, I aimed to highlight the significance of three-dimensional visualization in science, thereby enhancing the understanding of complex biomedical concepts. Through my work in Dr. Steven Gregory’s lab, I have been studying the ribosome – the macromolecular machine that utilizes messenger RNA and transfer RNA to link together amino acids thereby synthesizing proteins. Proteins are critical for most processes that occur within every cell. I specifically focus on the interactions between ribosomal proteins and ribosomal RNA (rRNA) at the peptidyl transferase center – the active site where amino acids …

Understanding The Role Of Sabp2-Interacting Proteins Sip432: A Premnaspirodiene Oxygenase Enzyme In Stress Signaling, Cristiana F. Martinez

Undergraduate Honors Theses

This study focuses on the characterization of a SABP2-interacting protein (SIP)-432. SIP432 is a putative premnaspirodiene oxygenase-like P450 enzyme. Premnaspirodiene is a 15-carbon compound that can be converted into antimicrobial compounds by a hydroxylation reaction. The interaction of SIP432 with SABP2, a critical component of salicylic acid-mediated plant immunity, implies a role for SIP432 in plant stress signaling. This study uses the T-DNA knockout mutant of Arabidopsis thaliana SIP432 (homolog of NtSIP432) to help understand its role in abiotic and biotic stress responses. Plants were subjected to abiotic and biotic stress to understand their role in stress response pathways. Gene …

Fc Gamma Receptors Facilitate Antigenic Modulation Of Lilrb4 And Function As Predictive Biomarkers In Acute Monocytic Leukemia, Joshua Morse

Dissertations and Theses (Open Access)

Acute monocytic leukemia (monocytic AML) is a subtype of AML marked by a proliferation of abnormal monoblasts. This subtype represents approximately 10% of AML cases. The prognosis of monocytic AML is poor, with a 5-year survival of ~30%. Most patients are diagnosed at an age when they are unlikely to survive first-line non-targeted cytotoxic chemotherapy as a bridge to hematopoietic stem cell transplant (HSCT). Even patients who achieve remission commonly relapse. This population of patients would greatly benefit from precision-targeted therapies but currently there are none approved for monocytic AML.

Leukocyte immunoglobulin-like receptor B4 (LILRB4) is an immune checkpoint expressed …

Expanding Inducible Epithelial Resistance Against Pneumonia: Novel Virus, Novel Receptor, Michael Longmire

Dissertations and Theses (Open Access)

Pneumonia is the leading infectious cause of death worldwide and presents a continuing risk among immunocompromised patients. Our work has been focused for many years on the phenomenon of inducible epithelial resistance, where activation of the innate immune response in the airway epithelium is necessary and sufficient to produce a pathogen-killing but self-protective environment to prevent severe disease. Inducible resistance is pathogen-agnostic and has been demonstrated against an array of respiratory infections. We achieve this using a combination of pattern recognition receptor agonists – Pam2CSK4 and ODN M362 being the current formulation – which produce synergistic levels of pathogen reduction …

Effect Of Glycation On The Binding Interactions Of Serum Albumin And Silver Nanoparticles, Megan Kirk

Celebrating Scholarship and Creativity Day (2018-)

Nanoparticles are particles ranging from 1-100 nanometers in size. Most nanoparticles, upon contact with biological matrices, are immediately coated with proteins, forming the protein corona, which can alter the structure and function of proteins. Despite the tremendous advancement of nanotechnology over the last decade, the interactions of nanoparticles with proteins are not well characterized. This project investigates the effect of glycation on the binding interactions of HSA, the most abundant protein in human blood, with silver nanoparticles using various spectroscopic techniques. This is important because in diabetic patients, HSA is exposed to high concentrations of glucose over extended periods of …

Identification Of Cadmium As A Structural And Functional Modulator Of Psd-95 Regulating Nmdars At Postsynaptic Membranes, Claudia Garza

Theses and Dissertations

Postsynaptic density-95 (PSD-95) is an essential scaffolding protein in excitatory neurons. PSD-95’s N-terminal palmitoylation region elicits synaptic plasticity by targeting, anchoring, and trafficking glutamate receptors, such as N-methyl-d-aspartate receptors (NMDAR), to the postsynaptic membrane. The molecular interactions of PSD-95 and its dysregulation in excitatory synapses are currently being explored as primary causes of neurodegenerative diseases and disorders, such as Alzheimer’s disease, Schizophrenia, and Parkinson’s disease. Recent studies demonstrate an overaccumulation of zinc at two cysteines (C3 and C5) and two histidines (H24 and H28) of PSD-95 blocks palmitoylation, causing a loss of NMDAR at the postsynaptic membrane. In addition, exposure …