Biochemistry Commons^™

Development Of A High-Throughput System For Screening Of Anti-Prion Molecules, Katherine Do

Dissertations and Theses (Open Access)

The misfolded prion protein causes and transmits disease in both humans and animals. As other infectious agents, prions display strain variation, which can generate different pathological outcomes in affected individuals. Unfortunately, there are no known therapies for these diseases, which at present are invariably fatal. In this work, the Protein Misfolding Cyclic Amplification technology (PMCA, an in vitro test that replicates minimum quantities of infectious prions) has been modified to screen for small molecules inhibiting prion protein misfolding in a strain-specific manner. In order to approach a high-throughput PMCA system, technical aspects in PMCA has been optimized for application of …

The Synthesis, Purification, And Characterization Of The P3 Peptoid, Myles Joyce

Chemical Engineering Undergraduate Honors Theses

The relatively young field of nano-systems has vast applications over various different fields. Peptoids (peptide analogues) and their uses are consistently investigated components of these nano-studies. A particularly interesting group of peptoids are able to self-assemble into secondary structures under the right conditions. The P3 peptoid is able to form microspheres if properly synthesized and purified. Microspheres are frequently studied due to their low surface area to volume ratios. This unique aspect of microspheres makes them an excellent candidate for drug delivery systems; however, these systems must also be robust so that the desired compound can be encapsulated within the …

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 …

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 …

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 …

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 …

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 …

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

Petersheim Academic Exposition

No abstract provided.

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

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 …

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 …

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 …

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.

Effects Of Electrical Stimulation On Glioma Cells In Vitro With Implications For Treating Chronic Pain: Development Of A Model System, David C. Platt

Theses and Dissertations

Glial cells comprise over 70% of the central nervous system cells and exhibit diverse functions including regulation of synaptic transmission, neuron protection/repair, maintenance of neuronal metabolism, and are implicated in the development of persistent neuropathic pain. In addition, a perturbation in the concentration of intracellular reactive oxygen species (ROS) and reactive nitrogen species (RNS) has likewise been associated with the development of a chronic pain state. This perturbation in ROS/RNS creates an environment of oxidative stress. However, the mechanism by which the pain signal transmission is modulated, and the roles ROS play in the perpetuation of the pain state are …

Developing Tale Proteins As A Biosensor For Detecting Pathogen Specific Double-Stranded Dna, Kathrine Gaiko

Mahurin Honors College Capstone Experience/Thesis Projects

Transcription activator-like effector (TALE) proteins are important for DNA binding. They bind to specific nucleotide sequences by the use of two residues in each repeat allowing them to target specific DNA sequences. Their modular structure makes TALEs advantageous over other DNA binding proteins such as zinc finger proteins. Zinc finger proteins (ZFP) use a finger like projection to bind 3-4 subsequence base pairs while TALE proteins use two amino acid residues in each repeat to bind one nucleotide. ZFP can use SEER-Lac system for colorimetric detection, while TALE proteins can use fluorescence labeling with Alexa for detection of binding to …

Characterization Of Psychromonas Aquimarina, A New Model Organism For Climate Change, Carrie Carpenter

Experiential Learning Projects

The current increase of average global temperature puts 25 to 35 percent of plant and animal species at an increased risk of extinction (Climate Change, 2018). Changing any environmental factor, such as increasing growth temperature, can significantly impact any organisms’ ability to survive. Because of the diversity of organisms on the planet, it is not feasible to study how each individually might adapt, but rather it is more efficient to study select organisms. This research focuses on a psychrophilic bacterium, Psychromonas aquimarina, which can survive in colder regions where most bacteria would not. This bacterium was chosen because climate change …

Characterization Of Iron-Sulfur Cluster Proteins From Methanococcus Maripaludis, Melody Salmanian

Honors Capstones

No abstract provided.