Biochemistry, Biophysics, and Structural Biology Commons^™

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 …

The Neuroprotective Effect Of Cdc42 Inhibition In The G93a Mutant Hsod1 Mouse Model Of Als, Andrea Koly

Undergraduate Theses, Capstones, and Recitals

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease characterized by the selective loss of upper and lower motor neurons, leading to muscle weakness, neuromuscular junction (NMJ) degeneration, paralysis, and eventual death due to respiratory failure. Despite extensive research, effective disease-modifying therapies remain limited, underscoring the need to identify novel molecular targets involved in ALS pathogenesis. Dysregulation of Rho family GTPases has been implicated in neurodegeneration, with Rac and Rho exerting opposing effects on neuronal survival; however, the role of the closely related GTPase Cdc42 remains poorly understood in ALS. In this study, the therapeutic potential of inhibiting …

A Computational Micropatterning Approach To Study Caveolae And Protein Localization In Vascular Biology, Andrew B. Grespin

Electronic Theses and Dissertations

Caveolae are specialized, flask-shaped membrane invaginations highly expressed in endothelium and dysregulated in atherosclerosis. Caveolae play a central role in buffering membrane tension, yet the principles governing their spatial organization remain elusive. Thus, we sought to generate the most comprehensive and systematic analysis of blood vessel caveolar spatial organization. However, cell culturing, the backbone of human-focused biological research, does not standardly do well to model physiologically relevant cell behaviors such as migration or polarity-based tissue formation, particularly for punctate proteins and structures like caveolae. Micropatterns are cell-adhesive shapes that biophysically confine cell(s) to a user defined geometry which stereotype organelle …

Data From: Nek4 Suppresses Cell Proliferation In Bt20 Triple-Negative Breast Cancer Cells By Diminishing Expression Of Cell Cycle Genes, While Its Depletion Mitigates Proliferation In Other Cell Lines, Amanda Ashley

Chemistry & Biochemistry: Datasets

No abstract provided.

Centrosomal And Non-Centrosomal Microtubule Networks Coordinate To Drive Nuclear Dynamics In Developing Epithelium, Rashmi Budhathoki

Electronic Theses and Dissertations

The morphogenesis of developing tissues relies on extensive cellular rearrangements in shape, position, and identity. A key process in reshaping tissues is cell intercalation-driven elongation, where epithelial cells align and intercalate along a common axis. Typically, analyses focus on how peripheral cortical forces influence cell shape changes. Less attention is given to how inhomogeneities in internal structures, particularly the nucleus, impact cell shaping. Here, we examine how pulsed contractile and extension dynamics interact with the nucleus in elongating Drosophila embryos. Our data show that tightly packed nuclei in apical layers hinder tissue remodeling/oscillatory behaviors. We identify two mechanisms for resolving …

Analysis Of Synaptotagmin Isoforms In Lßt2 Gonadotrophs, Caitlin Vahl

Undergraduate Theses, Capstones, and Recitals

The anterior pituitary is comprised of five cell types which secrete regulatory hormones into the bloodstream. Specifically, gonadotrophs synthesize and release sex hormones follicle-stimulating hormone (FSH) and luteinizing hormone (LH) in response to gonadotropin-releasing hormone (GnRH). GnRH signals from the hypothalamus regulate the differential secretion of LH and FSH from the anterior pituitary. Exocytosis of FSH and LH from dense core vesicles (DCVs) occurs in response to an intracellular calcium signal, sensed by the synaptotagmins proteins. Various isoforms of synaptotagmins exist and each isoform has varying affinity for calcium, causing calcium-regulated exocytosis to be finely controlled. Because LH and FSH …

Phagolysosomes Break Down The Membrane Of A Non-Apoptotic Corpse Independent Of Macroautophagy, Shruti Kolli, Cassidy J. Kline, Kimya M. Rad, Ann M. Wehman

Biological Sciences: Faculty Scholarship

Cell corpses must be cleared in an efficient manner to maintain tissue homeostasis and regulate immune responses. Ubiquitin-like Atg8/LC3 family proteins promote the degradation of membranes and internal cargo during both macroautophagy and corpse clearance, raising the question how macroautophagy contributes to corpse clearance. Studying the clearance of non-apoptotic dying polar bodies in Caenorhabditis elegans embryos, we show that the LC3 ortholog LGG-2 is enriched inside the polar body phagolysosome independent of autophagosome formation. We demonstrate that ATG-16.1 and ATG-16.2, which promote membrane association of lipidated Atg8/LC3 proteins, redundantly promote polar body membrane breakdown in phagolysosomes independent of their role …

Unraveling The Role Of Hid-1: Insights Into Sgii Regulation, Breanna L. Sellers

Electronic Theses and Dissertations

The regulated secretory pathway is important for the secretion of hormones and neuropeptides from large dense core vesicles (LDCVs). Dysregulation of the biogenesis of LDCVs can result in metabolic and neurological diseases. Recent studies have suggested that the peripheral membrane protein HID-1 plays a role in the sorting and storage of granins which contribute to LDCV biogenesis. To further understand how HID-1 influences the regulation of granins, we investigated potential HID-1 interactors. We determined that while HID-1 is likely functioning in the same pathway as USP25, a deubiquitinating enzyme (DUB), the cause of reduced cellular SgII levels is likely not …

The Role Of Edc3 In Drosophila Melanogaster Neuronal Development, Keelan Zius

Electronic Theses and Dissertations

Enhancer of mRNA-decay 3 (Edc3) is a component of multiple decapping complexes that regulates the transcriptome by targeting a subset of transcripts for decapping for 5’-to-3’ messenger RNA (mRNA) decay. A missense mutation in the conserved Lsm domain of Edc3 has been reported in two siblings presenting with mild, non-syndromic intellectual disability (ID), however, the role of Edc3 is neuronal development has never been evaluated. Here, we use the Drosophila melanogaster model system to investigate the effects of Edc3 disruption on neuronal development. We found Edc3 reduction leads to significant hyperplasia at the larval neuromuscular junction (NMJ), providing the first …

Colocalization Of Odc And Amyloid Plaques In Patients With Alzheimer’S Disease And Down Syndrome, Julia S. Gielczynski

Undergraduate Theses, Capstones, and Recitals

Polyamines, and their rate-limiting enzyme ornithine decarboxylase (ODC), are crucial for many functions in the central nervous system but levels decrease with age. In neurodegenerative diseases, like Alzheimer’s Disease (AD), polyamine levels begin to increase again. Yet, there are still many unanswered questions surrounding polyamine’s possible role in AD, especially in those with Down Syndrome (DS), who also have an extra copy of the amyloid precursor protein (APP) and tend to get AD far earlier than the general population. We aim to investigate if there is colocalization between amyloid plaques and Ornithine Decarboxylase (ODC) in patients with AD and AD/DS, …

Morphological Remodeling Of The Endoplasmic Reticulum During Mitosis And Its Influence On The Integrity Of The Spindle Apparatus, Katie R. Rollins

Electronic Theses and Dissertations

The Endoplasmic Reticulum (ER) is the largest organelle in the cell by surface area and forms contacts with other organelles throughout the cell. In recent work, the ER has been implicated in numerous processes within the cell beyond its canonical roles of protein synthesis and calcium storage. The ER also undergoes a remarkable transition in morphology during cell division, with mitotic divisions requiring a massive remodeling of various membranous organelles such as the nuclear envelope and Golgi. However, whether changes in ER behaviors modulate mitotic events is less clear. The rapid cleavage divisions in the early Drosophila embryo are a …

Dna-Pkcs Rnaseq Data: Dna-Pkcs Wilde-Type Or Kinase-Dead Protein Regulate Basal And Etoposide-Induced Gene Expression Changes, Amanda Ashley

Chemistry & Biochemistry: Datasets

No abstract provided.

Identification Of The Functional Domain Of The Dense Core Vesicle Biogenesis Factor Hid-1, Blake H. Hummer, Theodore Carter, Breanna L. Sellers, Jenna D. Triplett, Cedric S. Asensio

Biological Sciences: Faculty Scholarship

Large dense core vesicles (LDCVs) mediate the regulated release of neuropeptides and peptide hormones. HID-1 is a trans-Golgi network (TGN) localized peripheral membrane protein contributing to LDCV formation. There is no information about HID-1 structure or domain architecture, and thus it remains unknown how HID-1 binds to the TGN and performs its function. We report that the N-terminus of HID-1 mediates membrane binding through a myristoyl group with a polybasic amino acid patch but lacks specificity for the TGN. In addition, we show that the C-terminus serves as the functional domain. Indeed, this isolated domain, when tethered to the TGN, …

Polar Body Membrane Breakdown Occurs Independent Of Macroautophagy In C. Elegans, Shruti Kolli

Electronic Theses and Dissertations

Failure to digest cell corpses can lead to lupus-like autoimmune disorders in mammals. To better understand if LC3-associated phagocytosis (LAP) drives cell corpse breakdown in phagolysosomes, we studied the clearance of the C. elegans polar body during embryonic development. ATG16L1 has separable roles in regulating LC3 recruitment during macroautophagy and LAP. We demonstrated that the ATG16L1 C. elegans orthologs, ATG-16.1 and ATG-16.2, function redundantly to promote polar body membrane breakdown. We also discovered that truncating the LAP-specific WD40 domain of ATG-16.2 unexpectedly disrupts autophagy. Furthermore, we confirmed that polar body membrane breakdown occurs independent of macroautophagy. We also showed that …

Polyphenolic Content And Radical Scavenging Activities Of The Peel, Pulp And Seed Of Avocado (Persea Americana Mill.) Grown In Tanzania, Ibrahim Juma, Jan-Eric Englund, Rodomiro Ortiz, Mulatu Geleta, Donatha D. Tibuhwa, Anders S. Carlsson, Agnes Nyomora, Moneim Fatih, Helena Persson Hovmalm

Tanzania Journal of Science

Avocado is a healthy fruit and the consumption is continuously growing worldwide. The fruit contains polyphenolic compounds with antioxidant effects. Globally, research has been devoted to exploring the fruit quality, especially compounds with antioxidant effects, from different avocado-growing sites. However, the fruit quality of the Tanzanian avocado has so far not been investigated. In this study, the contents of polyphenols in peel, pulp and seed of avocados sampled in south-western Tanzania are described. The levels of total polyphenolic and flavonoid contents were measured, and antioxidant activity was evaluated using a 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. The total polyphenolic content was highest in …

Small Gtpase Regulated Intracellular Protein Trafficking In Endothelium, Caitlin Francis

Electronic Theses and Dissertations

Intracellular protein trafficking is the movement of membrane-bound organelles to and from requisite locations within the cell. Small GTPases are a critical component to the spatiotemporal accuracy of intracellular trafficking pathways as they determine the specificity and direction of organelle transport. There exists over 150 small GTPases categorized into 5 sub-families and are employed across all cell types. Despite their universal expression and relevance to cellular function, small GTPases remain incompletely understood across tissue types. In various instances, the trafficking pathway of a particular Rab in one cell type may belong to a completely disparate pathway in another cell type. …

Uncovering Zn2+ And Ca2+ Homeostasis And Crosstalk In Primary Hippocampal Neurons, Chen Zhang

Electronic Theses and Dissertations

Zn²⁺ has been suggested to act as an intracellular signaling molecule due to its regulatory effects on numerous protein targets including enzymes, transcription factors, ion channels, neurotrophic factors, and postsynaptic scaffolding proteins. However, intracellular Zn²⁺ concentration is tightly maintained at steady levels under natural physiological conditions. Dynamic changes in intracellular Zn²⁺ concentration have only been detected in cells exposed to pathologic stimuli or upon receptor ligand binding. In the first project of my dissertation, for the first time, we revealed that developing neurons fire spontaneous and synchronous Zn²⁺ spikes at a specific time window (from 14 …

Developing Red Fluorescent Zn2+ Sensors And Characterizing Zn2+ Homeostasis In Mucolipidosis Type Iv Disease, Anna M. Dischler

Electronic Theses and Dissertations

Zinc (Zn²⁺) is a divalent, redox-inert metal that plays a vital role in many cellular processes either by acting as a catalytic cofactor or a labile signaling molecule in the cytoplasm. Cytosolic Zn²⁺ levels are tightly regulated to stay within a narrow window of concentrations, but fluctuations in Zn²⁺ signals have been detected in a variety of cells. We developed a genetically encoded, single red fluorescent protein (RFP) based Zn²⁺ sensor, RZnP1, that can be used alongside green-wavelength sensors for the simultaneous detection of different signaling molecules within the same cells or among different subcellular …

Determination Of Sugars, Amino Acids, Ph And Alcohol In Bamboo Beverage From Southern Highlands, Tanzania, Lilian D Kaale

Tanzania Journal of Science

The amounts of sugars and amino acids play significant roles in defining the fermentation process and quantifying the alcohol levels in beverages, while pH affects the biological stability, colour, oxidation rate, and protein stability of alcoholic beverages. This study investigated the sugar content, amino acids, alcohol levels, and pH of bamboo beverage from Tanzania's southern highlands. During storage, the sugars significantly decreased (p < 0.05), especially when kept at room temperature from 52.96 to 0.00 (source 1), 53.35 to 0.00 (source 2) and 53.57 to 0.00 (source 3) g/L for fructose, from 47.93 to 14.78 (source 1), 47.23 to 14.91 (source 2) and 47.61 to 14.77 (source 3) g/L for glucose, and from 0.40 to 0.00 (source 1), 0.36 to 0.00 (source 2) and 0.37 to 0.00 (source 3) g/L for sucrose after six days of storage. A total of 15 amino acids were determined from the bamboo beverage with tyrosine being the most prevalent (597.68 mg/L for source 1, 599.44 mg/L for source 2 and 597.83 mg/L for source 3), followed by valine (261.13 mg/L for source 1, 261.24 mg/L for source 2 and 262.54 mg/L for source 3), threonine (76.69 mg/L for source 1, 76.91 mg/L for source 2 and 77.13 mg/L for source 3), and serine (66.37 mg/L for source 1, 67.23 mg/L for source 2 and 66.68 mg/L for source 3). After six days of storage at room temperature, there was a significant decrease in pH from 4.04 to 3.63. Alcohol content ranged from 3.11 to 9.05% v/v at the room temperature storage. These results might facilitate the optimal use of bamboo beverages, which have been neglected due to lack of scientific information such as amino acid and sugar levels. Keywords:    Bamboo beverage, ulanzi, amino acids, sugars, alcohol content.

Anxiolytic Effects, Antioxidant And Anti-Inflammatory Activities Of The Methanol Extract Of Jatropha Tanjorensis Leaf, Anthony E. Aiwonegbe, Uwaila Omoruyi, Osahon K. Ogbeide, Blessing O. Imoukhuede, Benjamin O. Gabrielsson

Tanzania Journal of Science

The methanol leaf extract of Jatropha tanjorensis was analyzed for its bioactive components, in-vitro antioxidant, antidepressant, anxiolytic and anti-inflammatory activities using established methods. The phytochemicals detected were saponins, tannins, terpenoids, phenolic compounds, alkaloids, flavonoids and eugenols. The total phenolic content (TPC) was 36.48 mgGAE/g, while the total flavonoid content (TFC) was 145.92 mgQE/g of the extract. 1, 1-diphenyl-2-picrylhydrazyl radical scavenging activity gave an IC50 of 185.02 and 5.15 µg/mL for the extract and ascorbic acid (standard), respectively. The 50% lethal dose (LD50) was greater than 5000 mg/kg, while graded doses of 50, 100 and 200 mg/kg of the plant extract …

Foldamers Reveal And Validate Therapeutic Targets Associated With Toxic Α-Synuclein Self-Assembly, Jemil Ahmed, Tessa C. Fitch, Courtney M. Donnelly, Johnson A. Joseph, Tyler D. Ball, Mikaela M. Bassil, Ahyun Son, Chen Zhang, Aurélie Ledreux, Scott Horowitz, Yan Qin, Daniel Paredes, Sunil Kumar

Chemistry and Biochemistry: Faculty Scholarship

Parkinson’s disease (PD) is a progressive neurodegenerative disorder for which there is no successful prevention or intervention. The pathological hallmark for PD involves the self-assembly of functional Alpha-Synuclein (αS) into non-functional amyloid structures. One of the potential therapeutic interventions against PD is the effective inhibition of αS aggregation. However, the bottleneck towards achieving this goal is the identification of αS domains/sequences that are essential for aggregation. Using a protein mimetic approach, we have identified αS sequences-based targets that are essential for aggregation and will have significant therapeutic implications. An extensive array of in vitro, ex vivo, and in vivo assays …

The Role Of Ehd2 In Endothelial Cells, Rachael Judson

Electronic Theses and Dissertations

The role of EHD2 in terms of Cav1 interaction had not been previously characterized and was the main goal of this research. Cav1 has been shown to lead to the ubiquitination of Rac1. Because of this, the role of EHD2 in Rac1 regulation was investigated. An increase in long-term migration in endothelial cells was observed and suggested that EHD2 impacts the RhoA pathway instead of the Rac1 pathway. This lead to the hypothesis that EHD2 controls a part of the RhoA pathway. This hypothesis is supported by the loss of filamentous actin and an increase in serrated junctions in cells …

The Pathophysiological Mechanisms Of Alzheimer's Disease; Investigating Therapeutic Interventions For Disease Onset, Alexandra A. Sandberg

Electronic Theses and Dissertations

Alzheimer’s Disease is a multifarious disease that progressively affects more people as both the proportion of older adults in the population and life expectancy increase in both the United States and worldwide. This devastating disease is a result of rampant neuronal loss in the memory centers of the brain that robs the independence of those who are diagnosed and places a heavy burden on those who care for them. Traditionally speaking, research has focused on the hallmark pathology of amyloid plaques, targeting them to try and prevent disease onset. However, countless failures in clinical trials aimed at this said pathology …

Antioxidant Biomarkers And Nutraceutical Therapeutics In Neurodegeneration And Neurotrauma, Lilia A. Koza

Electronic Theses and Dissertations

Mild traumatic brain injury (mTBI), yielding a Glascow Coma Scale of 13-15, is the most commonly occurring severity of TBI. Pathology from mTBI consists of blood brain barrier disruption, neuroinflammation, oxidative stress, excitotoxicity, mitochondrial dysfunction, protein aggregation, axonal degeneration, and resulting neuronal death. These processes deplete the body’s endogenous antioxidant system. We report a retrospective analysis of antioxidant blood biomarkers in patients with a history of mTBI from a local sports medicine clinic, Resilience Code. We found persistent sex-specific antioxidant depletions in mTBI patients associated with worsened symptomology.

Certain populations, such as athletes, are at high risk for repetitive mTBI …

Organellar Zn2+ Homeostasis And The Role Of Trpml Channels In Neuronal Lysosome Physiology And Axonal Transport, Taylor Franklin Minckley

Electronic Theses and Dissertations

Zinc (Zn²⁺) is crucial for proper cellular function, and as such it is important to measure and track Zn²⁺ dynamics in living cells. Fluorescent sensors have been used to estimate Zn²⁺ content of subcellular compartments, but little is known about endolysosomal Zn2+ homeostasis. Similarly, although numerous sensors have been reported, it is unclear whether and how Zn²⁺ can be released from intracellular compartments into the cytosol due to a lack of probes that can detect physiological dynamics of cytosolic Zn²⁺. My dissertation started with comparing and characterizing different Zn²⁺ sensors including the …

Phosphatidylserine Externalization On Non-Apoptotic Cells And Lipid Scramblases In C. Elegans, Julia Frondoni

Electronic Theses and Dissertations

Cell corpse clearance is key for animals to avoid inflammation and autoimmune disease. To better understand the “eat me” signal of phosphatidylserine (PS) exposure for non-apoptotic corpse clearance, we attempted to disrupt the externalization of PS on C. elegans polar bodies. The second polar body undergoes a non-apoptotic form of cell death, loses membrane integrity, externalizes PS and is cleared by embryonic cells during early development. During apoptotic and necrotic cell death, PS asymmetry is disrupted by lipid scramblases, which translocate phospholipids between the leaflets of the lipid bilayer. We found neither apoptotic nor necrotic scramblases are required for PS …

Vps54 Regulates Lifespan And Locomotor Behavior In Adult Drosophila Melanogaster, Emily C. Wilkinson, Emily L. Starke, Scott A. Barbee

Biological Sciences: Faculty Scholarship

Vps54 is an integral subunit of the Golgi-associated retrograde protein (GARP) complex, which is involved in tethering endosome-derived vesicles to the trans-Golgi network (TGN). A destabilizing missense mutation in Vps54 causes the age-progressive motor neuron (MN) degeneration, muscle weakness, and muscle atrophy observed in the wobbler mouse, an established animal model for human MN disease. It is currently unclear how the disruption of Vps54, and thereby the GARP complex, leads to MN and muscle phenotypes. To develop a new tool to address this question, we have created an analogous model in Drosophila by generating novel loss-of-function alleles of the …

Nutritional Composition, Sensory Profile And Consumer Acceptability Of Wheat-Jackfruit Seed Composite Buns, Sarah S Ngwere, Richard J Mongi

Tanzania Journal of Science

Jackfruit seeds flour is very rich in nutrients and may be incorporated into wheat flour to develop nutrient dense baked products. Consumption of these products may improve the nutrition status of the people, hence fulfill sustainable development goal number two. In this study, nutritional composition, sensory profile, and consumer acceptability of wheat-jackfruit seeds composite buns (Mandazi) were investigated. Jackfruit seeds flour (JSF) was developed and incorporated into wheat flour (WF) at 10, 20, and 30% to produce composite flour used for bun preparation. Flours and buns were subjected to proximate, mineral, and sensory analyses with WF serving as a control …

Assessment Of The Quality And Quantity Of Organic Matter In The Rufiji Mangrove Surface Sediments Using Biochemical Composition, Daniel A Shilla

Tanzania Journal of Science

This study was carried out to investigate spatial changes in the quality and quantity of sedimentary organic matter in the Rufiji mangrove system, Tanzania. Sediment samples were collected from three sampling sites. Total organic matter in mangrove sediments ranged from 7.28 ± 2.02% to 10.58 ± 1.34%. Protein concentrations varied from 1,145.33 ± 20.33 μg/g to 2,747.50 ± 25.14 μg/g in the mangrove sediments. Total carbohydrates, lipids and biopolymeric carbon in mangrove sediments ranged between 1,110.50 ± 16.31 μg/g and 1,914.17 ± 27.79 μg/g, 1,436.50 ± 24.13 μg/g and 6,373.50 ± 25.79 μg/g, and 4,496 μg C/g and 10,231.50 μg …

Effects Of Drying, Packaging Conditions And Storage Time On Proximate Composition Of Chia Seeds (Salvia Hispanica), Ashura Katunzi-Kilewela, Leonard Rweyemamu, Oscar Kibazohi, Lilian Kaale

Tanzania Journal of Science

The effects of drying, packaging conditions and storage time on proximate composition of chia seeds were investigated. Chia seeds were dried at 63 °C for 30 min (low-temperature long time–LTLT) and at 75 °C for 30 s (high-temperature short time-HTST) using dry oven, air/vacuum-packed and stored for ten weeks. The effect of heat processing (drying) on chia seeds had significant difference (p < 0.05) in ash, fiber and fat contents while there was no significant difference (p > 0.05) in moisture and protein contents. Except for fiber content, there was no significant difference (p > 0.05) in moisture, ash, fat and protein of chia seeds dried at LTLT and HTST before storage. During storage time, there was …