Biochemistry, Biophysics, and Structural Biology Commons^™

Cellular Localization Of Rad51d Mutant Proteins And The Application Of Art To Increase Scientific Literacy In America, Claire L. Chabot

Senior Theses

Ovarian cancers are the leading cause of death from cancer of the female reproductive system. Approximately 50% of ovarian cancers have defects in the homologous recombination (HR) DNA repair pathway that is required for the repair of DNA double-stranded breaks. The status of HR genes, such as BRCA1, BRCA2, and the RAD51 family, contributes to ovarian cancer development as well as treatment decisions regarding chemotherapy, radiation, and immunotherapy. The overarching goal of this project is to identify new insights into HR that can integrate with Precision Medicine Initiatives and align with the goals of the Cancer Moonshot 2020 Program. I …

It’S Not Easy Being Green: A Study Of The Chemical Phenology Of The Eastern Hemlock Throughout A Growing Season, Nick Houseman, Evan Preisser

Senior Honors Projects

Phenology is the study of seasonally timed developmental events that are driven by environmental cues. Phenolic compounds and terpenoids are the two main classes of secondary metabolites present in conifer needles, and speaking generally, they correlate with needle age. Understanding the phenology of secondary metabolites is important, since variation in these compounds can affect a tree’s resistance to pest and pathogen attack. Terpenoids function in a wide array of ecological processes vital to conifer survival, including regulating forest dynamics through allelopathic inhibition of seed germination, altering rates of soil nutrient cycling and nitrification, and conferring resistance to pathogenic fungi and …

Delineation Of Events In Centripetal Migration During Drosophila Oogenesis, Travis Tait Parsons

UNLV Theses, Dissertations, Professional Papers, and Capstones

All multicellular organisms initially start out as a single cell. This cell must use the genetic information encoded in its DNA to multiply in number and build itself into a complex multicellular organism. How this process occurs is the focus of developmental biology, a field that seeks to understand how a combination of genetic information and environmental conditions shape a cell from its beginnings as a zygote all the way to maturity. A fundamental part of this process is the ability of cells to work together in order to build complex tissues and organs. Cells achieve this coordination by using …

Targeting Sec61Α By Ipomoeassin F Leads To Highly Cytotoxic Effect, Zhijian Hu

Graduate Theses and Dissertations

Ipomoeassin F is a flagship congener of a resin glycoside family that inhibits growth of many tumor cell lines with only single-digital nanomolar IC50 values. However, biological and pharmacological mechanisms of ipomoeassin F have been undefined. To facilitate exploration of the biological and pharmacological properties, we performed sophisticate SAR (Structure–activity relationship) studies of ipomoeassin F to understand its pharmacophore and structure properties so that we can design favorable probes for further biological investigation. By applying appropriate deviates that possess fluorescent groups and similar bio-activity, the target protein was found to be localized in endoplasmic reticulum (ER). Through biotin affinity pull …

Multiple Local Σ-Aromaticity Of Nonagermanide Clusters, Nikolay V. Tkachenko, Alexander I. Boldyrev

Chemistry and Biochemistry Faculty Publications

Nonagermanide clusters are widely used in inorganic synthesis and are actively studied by experimentalists and theoreticians. However, chemical bonding of such versatile species is still not completely understood. In our work we deciphered a bonding pattern for various experimentally obtained nonagermanide species. We localized the electron density via the AdNDP algorithm for the model structures ([Ge₉]⁴⁻, [Ge₉{P(NH₂)₂}₃]⁻, Cu[Ge₉{P(NH₂)₂}₃] and Cu(NHC)[Ge₉{P(NH₂)₂}₃]) and obtained a simple and chemically intuitive bonding pattern which …

Generalizing Metallocene Mechanochemistry To Ruthenocene Mechanophores, Ye Sha, Yudi Zhang, Enhua Xu, C Wayne Mcalister, Tianyu Zhu, Stephen L. Craig, Chuanbing Tang

Faculty Publications

Recent reports have shown that ferrocene displays an unexpected combination of force-free stability and mechanochemical activity, as it acts as the preferred site of chain scission along the backbone of highly extended polymer chains. This observation raises the tantalizing question as to whether similar mechanochemical activity might be present in other metallocenes, and, if so, what features of metallocenes dictate their relative ability to act as mechanophores. In this work, we elucidate polymerization methodologies towards main-chain ruthenocene-based polymers and explore the mechanochemistry of ruthenocene. We find that ruthenocene, in analogy to ferrocene, acts as a highly selective site of main …

Potential Interactions Between Glucocorticoid Receptors And L-Type Cav1.3 Ion Channels Expressed In Chinese Hamster Ovary (Cho) Cells, Mallory Soska

Undergraduate Distinction Papers

L-type calcium channels couple membrane depolarization to muscle contraction and aid in signal conduction between cells. Cav1.3 calcium channel isoform is expressed in neurons and endocrine cells. Nervous and endocrine tissues also express both Glucocorticoid (GR) and Mineralocorticoid receptors (MR) that are responsible for binding serum cortisol to induce immediate and long term changes within the cell. While neurons co-express both GRs and MRs, GR activation occurs in response to high concentrations of cortisol. There is a direct correlation between GR activation and the amplitude of calcium currents (Champeau, 2007). To determine potential interactions between the GR and the calcium …

Characterization Of The Perilipin 5 C-Terminus, Tim D. Clinton

Undergraduate Honors Thesis Projects

The crystallization of protein with subsequent X-Ray crystallography analysis is a powerful technique for uncovering a protein’s structure. This methodology is cutting edge and innovations are being made daily on how to best use the fundamentals of this technique for clearer characterizations. The protein Perilipin 5 could benefit from this technique as properties involving the structure of the molecule are still largely unknown. Knowing the structural aspects of perilipin 5 is important as several research efforts indicate that is a key factor in the regulation of lipolysis, or the breakdown of fats within a biological system. In the life sciences, …

The Effects Of Ultraviolet Light Exposure On The Activity Of Catalase In The Coelomocytes Of Sea Urchins Lytechinus Variegatus And Arbacia Punctulata, Kandis Arlinghaus

Undergraduate Theses

Many sea urchins play important ecological roles in their environments, and it is important to study the impacts of environmental stressors on their physiology. Ultraviolet radiation (UVR) exposure has significant negative impacts on marine organisms including an increase in reactive oxygen species (ROS). Oxidative damage by ROS at the cellular level can cause lipid peroxidation, DNA fragmentation, and even cell death that may result in inflammation or disease. To prevent this cellular damage, organisms generate enzymes, such as catalase, that breakdown ROS into harmless substances. Elevated catalase activities under UVB, a range of UVR from 280–315 nm, exposure have been …

Pbrm1 Regulates Stress Response In Epithelial Cells, Elizabeth G. Porter, Alisha Dhiman, Basudev Chowdhury, Benjamin C. Carter, Hang Lin, Jane C. Stewart, Majid Kazemian, Michael K. Wendt, Emily C. Dykhuizen

Department of Biochemistry Faculty Publications

Polybromo1 (PBRM1) is a chromatin remodeler subunit highly mutated in cancer, particularly clear cell renal carcinoma. PBRM1 is a member of the SWI/SNF subcomplex, PBAF (PBRM1-Brg1/Brm-associated factors), and is characterized by six tandem bromodomains. Here we establish a role for PBRM1 in epithelial cell maintenance through the expression of genes involved in cell adhesion, metabolism, stress response, and apoptosis. In support of a general role for PBRM1 in stress response and apoptosis, we observe that loss of PBRM1 results in an increase in reactive oxygen species generation and a decrease in cellular viability under stress conditions. We find that loss …

Interactions Of (My) 6 (M = Zn, Cd; Y = O, S, Se) Quantum Dots With N-Bases, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

(MY)₆ clusters, with M = Zn and Cd and Y = O, S, Se, form double-layer drum-like structures containing M–Y covalent bonds. The positive regions near the M atoms attract the N atom of both NH₃ and NMe₃ so as to form a noncovalent M···N bond. This bond is quite strong, with interaction energies exceeding 35 kcal/mol. The bond strength diminishes with reduced electronegativity of the Y atom (O > S > Se) and is stronger for M = Zn than for Cd. Trimethylation of the base enhances the bond strength. The interaction is dominated by the electrostatic component …

Yield Stress Analysis With Dv-Iii Rheometer, Leah Margaret Cook

Honors Theses

The purpose of this thesis is to understand the behavior of everyday substances (toothpaste, lotions, ect.) and chemicals through the analysis of yield stress. By measuring the flow properties of these products, one can determine the stability, uses, and other properties of a substance. Yield stress is experienced everyday from squeezing a tube of toothpaste, to stirring a batch of cake batter, or canning products in a factory. Yield stress along with viscosity helps us predict the behavior of chemicals, cosmetics, and food that we handle daily. Yield stress, torque, and strain values were measured with a DV-III Rheometer and …

Gamete Nuclear Migration In Animals And Plants, Umma Fatema, Mohammad F. Ali, Zheng Hu, Anthony J. Clark, Tomokazu Kawashima

Plant and Soil Sciences Faculty Publications

The migration of male and female gamete nuclei to each other in the fertilized egg is a prerequisite for the blending of genetic materials and the initiation of the next generation. Interestingly, many differences have been found in the mechanism of gamete nuclear movement among animals and plants. Female to male gamete nuclear movement in animals and brown algae relies on microtubules. By contrast, in flowering plants, the male gamete nucleus is carried to the female gamete nucleus by the filamentous actin cytoskeleton. As techniques have developed from light, electron, fluorescence, immunofluorescence, and confocal microscopy to live-cell time-lapse imaging using …

Department Of Chemistry And Biochemistry 24th Departmental Symposium In Conjunction With The Petersheim Academic Exposition, Seton Hall University

Petersheim Academic Exposition

No abstract provided.

Semisynthetic Aurones Inhibit Tubulin Polymerization At The Colchicine-Binding Site And Repress Pc-3 Tumor Xenografts In Nude Mice And Myc-Induced T-All In Zebrafish, Yanqi Xie, Liliia M. Kril, Tianxin Yu, Wen Zhang, Mykhaylo S. Frasinyuk, Svitlana P. Bondarenko, Kostyantyn M. Kondratyuk, Elizabeth Hausman, Zachary M. Martin, Przemyslaw P. Wyrebek, Xifu Liu, Agripina G. Deaciuc, Linda P. Dwoskin, Jing Chen, Haining Zhu, Chang-Guo Zhan, Vitaliy M. Sviripa, Jessica S. Blackburn, David S. Watt, Chunming Liu

Molecular and Cellular Biochemistry Faculty Publications

Structure-activity relationships (SAR) in the aurone pharmacophore identified heterocyclic variants of the (Z)-2-benzylidene-6-hydroxybenzofuran-3(2H)-one scaffold that possessed low nanomolar in vitro potency in cell proliferation assays using various cancer cell lines, in vivo potency in prostate cancer PC-3 xenograft and zebrafish models, selectivity for the colchicine-binding site on tubulin, and absence of appreciable toxicity. Among the leading, biologically active analogs were (Z)-2-((2-((1-ethyl-5-methoxy-1H-indol-3-yl)methylene)-3-oxo-2,3-dihydrobenzofuran-6-yl)oxy)acetonitrile (5a) and (Z)-6-((2,6-dichlorobenzyl)oxy)-2-(pyridin-4-ylmethylene)benzofuran-3(2H)-one (5b) that inhibited in vitro PC-3 prostate cancer cell proliferation with IC₅₀ values below 100 nM. A xenograft study in nude mice using …

The Nifz Accessory Protein Has An Equivalent Function In Maturation Of Both Nitrogenase Mofe Protein P-Clusters, Emilio Jimenez-Vicente, Zhi-Yong Yang, Julia S. Martin Del Campo, Valarie L. Cash, Lance C. Seefeldt, Dennis R. Dean

Chemistry and Biochemistry Faculty Publications

The Mo-dependent nitrogenase comprises two interacting components called the Fe protein and the MoFe protein. The MoFe protein is an α₂β₂ heterotetramer that harbors two types of complex metalloclusters, both of which are necessary for N₂reduction. One type is a 7Fe-9S-Mo-C-homocitrate species designated FeMo-cofactor, which provides the N₂-binding catalytic site, and the other is an 8Fe-7S species designated the P-cluster, involved in mediating intercomponent electron transfer to FeMo-cofactor. The MoFe protein's catalytic partner, Fe protein, is also required for both FeMo-cofactor formation and the conversion of an immature form of P-clusters to the …

Peroxisomal Protein Defects Disrupt Coordinated Peroxisomal Processes And Affect Early Seedling Development Through Accumulating Toxic Catabolic Intermediates, Ying Li

Dissertations

Many peroxisomal proteins act in β-oxidation processes on a range of substrates. It is unclear how these proteins are coordinated to determine the flux of peroxisomal processes and meet the requirements for plant growth and development. Using mutant analysis and metabolic profiling, I examined proteins predicted to act in fatty acid and indole-butyric-acid (IBA) β-oxidation. ECH2 confers enoyl-CoA hydratase activity for the auxiliary β-oxidation of fatty acids with an even cis-unsaturated bond. ECH2 was suggested to function in IBA β-oxidation, as ech2 seedlings have altered IBA response. ech2 seedlings have reduced root length and cotyledon area. ech2 seedlings accumulate 3-hydroxyoctenoate …

The Transesterification Of Hickory Nuts Into Biodiesel Fuel, Hannah Trauger, Madilynn Dewell, Jahida A. Mendoza

Undergraduate Research Conference

• Biodiesel fuels can be produced from a fat and an alcohol via transesterification

• Hickory nuts have a high fat content (~60 % by weight)

• Can nuts from shagbark hickory (Carya ovata) be used to produce a biodiesel fuel using existing acidcatalyzed transesterification methods?

Longitudinal Study Of Lanana Creek, Bayler Barnes, Jackson T. Ortiz, Trace Washburn

Undergraduate Research Conference

A longitudinal study was done to collect data on the various conditions of LananaCreek in Nacogdoches, Texas over a seven week span from September 14 to November 2, 2018. The part of the creek studies is a 3.5 mile stretch from East Austin Street to Hoya Soccer Complex, mostly located on the campus of Stephen F. Austin State University. There were 6 different testing sites selected along this expanse. Collection of samples was performed by the General Chemistry I Honors class as part of the laboratory experience. Once collected, the samples were transported back to the lab for testing. The …

Extraction And Quantification Of Hydrolyzable Tannins In Acorns From Different Species Of Oak Trees (Quercus Spp.), Sarah Browning, Marshall E. Woodruff

Undergraduate Research Conference

Do white-tailed deer (Odocoileus virginianus) prefer to eat certain types of acorns based on tannin content?

Hydrolyzable tannins consist of gallate groups connected via ester linkages to a carbohydrate (D-glucose)

The Prussian Blue method was used to determine hydrolyzable tannin content

Transcriptional Regulation Factors Of The Human Mitochondrial Aspartate/Glutamate Carrier Gene, Isoform 2 (Slc25a13): Usf1 As Basal Factor And Foxa2 As Activator In Liver Cells, Paolo Convertini, Simona Todisco, Francesco De Santis, Ilaria Pappalardo, Dominga Iacobazzi, Maria Antonietta Castiglione Morelli, Yvonne N. Fondufe-Mittendorf, Giuseppe Martelli, Ferdinando Palmieri, Vittoria Infantino

Molecular and Cellular Biochemistry Faculty Publications

Mitochondrial carriers catalyse the translocation of numerous metabolites across the inner mitochondrial membrane, playing a key role in different cell functions. For this reason, mitochondrial carrier gene expression needs tight regulation. The human SLC25A13 gene, encoding for the mitochondrial aspartate/glutamate carrier isoform 2 (AGC2), catalyses the electrogenic exchange of aspartate for glutamate plus a proton, thus taking part in many metabolic processes including the malate-aspartate shuttle. By the luciferase (LUC) activity of promoter deletion constructs we identified the putative promoter region, comprising the proximal promoter (−442 bp/−19 bp), as well as an enhancer region (−968 bp/−768 bp). Furthermore, with different …

The Presence Of Photoreceptor Sensilla In The Posterior Sucker Of Medicinal Leeches Inferred Through Functional Visual Response., Claire Spivey

Honors Theses

Medicinal leeches gather visual input from both its eyecups and photoreceptors across its body surface; each of its 21 midbody segments possesses 14 photoreceptive sensilla. It has been previously established that the posterior sucker is composed of seven body segments that are fused during embryogenesis. Similarly, four body segments fuse to create the anterior brain. There are five bilateral pairs of eyes located on the dorsal surface of the leech’s head and seven bilateral pairs of sensilla distributed over the surface of each midbody segment (Kretz et al., 1975). If no sensilla were lost during the fusion of the seven …

A Polyphasic Approach In Understanding Green Algal Ecology, Blia Lor

Biology Theses

Pithophora and Cladophora are two representative genera of the order Cladophorales as filamentous Chlorophyta. These two genera are major contributors to the total algal biomass of littoral communities in freshwater and shallow marine water and have been reported as nuisance algae as they proliferate fast with the influx of nutrients. However, the wide geographical distribution and the overlap of plastic morphological characteristics between the two genera have complicated taxonomic identification at species level and phylogenetic studies. In the present study, a population of a monospecific, filamentous algal community was collected in Jewell, Georgia from the Ogeechee River. The monospecific, filamentous …

Mechanisms Of Oriented Cell Division And Their Roles In Tissue Development, Evan Blake Dewey

Biology ETDs

Properly executed cell division is crucial to development, maintenance, and longevity of multicellular organisms. Defects in both symmetric and asymmetric divisions can lead to improper developmental patterning, as well as genomic instability, disruption of tissue homeostasis, and cancer. Our research focuses on how regulators orchestrate proper cell divisions. Mushroom Body Defect (Mud) is one such regulator, and here we describe how Mud is regulated via the Hippo signaling pathway kinase Warts (Wts), showing Wts phosphorylates Mud to enhance interaction with the polarity protein Partner of Inscuteable, promoting spindle orientation activity. We next focus on another regulator, Shortstop (Shot), describing a …

Extracellular Vesicles As Biological Shuttles For Targeted Therapies., Stefania Raimondo, Gianluca Giavaresi, Aurelio Lorico, Riccardo Alessandro

College of Osteopathic Medicine (TUN) Publications and Research

The development of effective nanosystems for drug delivery represents a key challenge for the improvement of most current anticancer therapies. Recent progress in the understanding of structure and function of extracellular vesicles (EVs)-specialized membrane-bound nanocarriers for intercellular communication-suggests that they might also serve as optimal delivery systems of therapeutics. In addition to carrying proteins, lipids, DNA and different forms of RNAs, EVs can be engineered to deliver specific bioactive molecules to target cells. Exploitation of their molecular composition and physical properties, together with improvement in bio-techniques to modify their content are critical issues to target them to specific cells/tissues/organs. Here, …

Use Of Site-Directed Mutagenesis To Probe The Cystine Binding Site Within System Xc-, Kevin Catalfano

18th Annual Celebration of Undergraduate Research and Creative Activity (2019)

The Chase lab studies System xc-, which is a heterodimeric transporter that functions as a Na+-independent antiporter exchanging extracellular cystine for intracellular glutamate. The transporter functions as an obligate heterodimer and is comprised of two proteins, xCT, which functions specifically in amino acid exchange, and 4F2HC, which appears to play a role in transporter stability. System xc- belongs to the SLC7 family of transporters, which is further subdivided into the cationic amino acid transporters (CAT) and the L-type amino acid transporters (LAT), the latter of which is the subfamily which includes System xc-. In recent years, there have been advances …

Incorporation Of Egfr And Ron Receptors Into Nanodiscs, Cristina Flores-Cadengo

Biomedical Engineering ETDs

Understanding the structure-function relationship of membrane receptors is essential to comprehend the crosstalk between key signaling pathways. Aberrant trans-activation between receptors can lead to tumorigenesis. Two of these receptors known to be involved in cancer development are receptor tyrosine kinases (RTKs), RON (Recepteur d'Origine Nantais) and EGFR (Epidermal Growth Factor Receptor). There has been evidence of heterodimerization and crosstalk between these two receptors based on co-immunoprecipitation, however the structural requirements behind these interactions remain unknown. Structural studies could provide insights into these RTKs’ modes of dimerization and structure-function relationship. However, structural studies of full-length membrane proteins are often difficult due …

Design And Synthesis Of A Novel Lsoxazoline As A Potential Pam-Agonist, Josselyn Roosenberg

Honors Theses

Progression of Alzheimer's disease is associated with a loss of Ml receptor activation in the brain. However, a lack of clinical success following attempts to activate the Ml receptor at the orthosteric site has contributed to a transition towards the allosteric pocket of the receptor. Here, positive allosteric modulators (PAMs) interact to potentiate the acetylcholine response. Recent research proposes that optimization of PAM activity at the expense of intrinsic agonism may posit a means to limit adverse side effects. Therefore, this project proposes a design and synthesis of a novel isoxazoline as a potent PAM agent with weak intrinsic agonism.

Analysis Of Dl-Amino Acid Ratios In Eggshells Using Reverse Phase-High Pressure Liquid Chromatography, Gergana Milkova

Honors Theses

HPLC methodology was developed to determine the concentrations and ratios of D to L amino acids in emu and ostrich eggshells treated with heat at different temperatures . We aimed to determine an internal standard and how ratios were affected under different conditions. An HPLC method was determined that gave consistent retention times and satisfactory enantioseparation . Calibration curves for each amino acid were developed from single and multi-amino acid containing dilution series producing a model that most closely replicates the eggshell-extracted amino acids.

You Are What You Eat At Any Age: Carbon And Nitrogen Analysis Of Mummies From An Ancient Egyptian Necropolis, Stephen Funk, R. Paul Evans

Library/Life Sciences Undergraduate Poster Competition 2019

The BYU Egypt Project at Fag el-Gamus necropolis and adjacent Seila Pyramid has studied over 700 mummies excavated over the past 30 years. The necropolis includes an open area with densely located vertical burial shafts and a hill with horizontal burial shafts. The chronological and dietary history of the mummies was assessed using stable isotopy and 14C analysis of accessible biological samples.