Biochemistry, Biophysics, and Structural Biology Commons^™

The Effects Of Intercalating Molecules On The Polymer Properties Of Dna, Joseph Tibbs

Honors Program Theses

This project used Atomic Force Microscopy (AFM) imaging to examine the effects of different intercalation conditions upon the elastic properties of intrinsically straight DNA molecules. Three intercalating molecules (chloroquine, ethidium bromide, and acridine) were used to demonstrate the dependence of persistence length and mean polymer extension on the intercalator type. It was found that all three intercalators significantly increased persistence length, and that this effect was most pronounced for ethidium bromide. In addition, an analysis of the normal bending modes of the static molecules corroborated these results. The only intercalator which resulted in significant extension of the DNA polymers was …

Reversible Inhibition Of Mycobacterial Dnab Protein Splicing By Zinc, Gabrielle Hardison

Honors College Theses

Inteins are emerging as post-translational regulatory elements, undergoing conditional protein splicing in response to a variety of environmental cues. Inteins are seamlessly removed by self-splicing from exteins, or flanking portions of the host protein, which they interrupt. DnaB of Mycobacterium smegmatis, a helicase essential for replication, harbors two inteins known as DnaBi1 and DnaBi2, each with discrete structural characteristics and insertion positions. DnaBi1 was used here to design a reporter system which links splicing with resistance to the antibiotic kanamycin. We built a construct that strictly requires catalytically active DnaBi1 for survival in the presence of kanamycin and used …

Alpha-Gal Syndrome: Molecular Characterization Of Amblyomma Americanum Α-D-Galactosidase In Α-Gal Metabolism And Onset Of Red Meat Allergy, Ahmed A. Mohamed

Honors Theses

Tick-borne red meat allergy is an IgE-mediated delayed hypersensitivity reaction, increasingly widespread in tick endemic areas in the United States of America, and worldwide. Bites from the lone-star tick (Amblyomma americanum) are believed to be involved as the source of the sensitization of humans to the oligosaccharide galactose-⍺-1,3-galactose (α-gal), which is found in most mammal-derived food products, including gelatin, broths, and red meat. The purpose of this study is to functionally characterize the lone-star tick α-D-galactosidase (AGS) enzyme and assess its role in α-gal metabolism. This enzyme cleaves terminal α-galactose moieties from glycoproteins and glycolipids. Hence, I hypothesized …

Cloning And Expression Of Human Synaptosome Associated Protein 29 In E. Coli, Logan M. Ryals

Honors Theses

Acting as the chief mediators of vesicular fusion, soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) play a role in many intracellular trafficking events by moving opposing membranes into close proximity. One such event takes place in the process of autophagy. A key SNARE involved in autophagy is Synaptosome Associated Protein 29 (SNAP-29), which acts on the autophagosome membrane to promote autophagosome and lysosome fusion. Kaposi’s Sarcoma Herpesvirus (KSHV) proteins ORF33 and ORF38 were demonstrated to interact with SNAP-29. The exact mechanism of this interaction is yet to be elucidated but it is hypothesized that these interactions allow KSHV to modulate …

A Putative Cystathionine Beta-Synthase Homolog Of Mycolicibacterium Smegmatis Is Involved In De Novo Cysteine Biosynthesis, Saroj Kumar Mahato

Graduate Theses and Dissertations

Mycobacteria include serious pathogens of humans and animals. Mycolicibacterium smegmatis is a non-pathogenic model that is widely used to study core mycobacterial metabolism. This thesis explores mycobacterial pathways of cysteine biosynthesis by generating and study of genetic mutants of M. smegmatis. Published in vitro biochemical studies had revealed three independent routes to cysteine synthesis in mycobacteria involving separate homologs of cysteine synthase, namely CysK1, CysK2, and CysM. However, in vivo data were lacking. The M. smegmatis genome encodes only a CysM homolog and lacks orthologs for CysK1 or CysK2. The gene that codes for CysM is a part of an …

Characterization Of Avidin And Case9 Single Protein Molecules By A Solid-State Nanopore Device, Haopeng Li

Graduate Theses and Dissertations

The shape and charge of a protein play significant roles in protein dynamics in the biological system of humans and animals. Characterizing and quantifying the shape and charge of a protein at the single-molecule level remains a challenge. Solid-state nanopores made of silicon nitride (SiNx) have emerged as novel platforms for biosensing such as diagnostics for single-molecule detection and DNA sequencing. SSN detection is based on measuring the variations in ionic conductance as charged biomolecules translocate through nanometer-sized channels driven by an external voltage applied across the membrane. In this paper, we observe the translocation of asymmetric cylindrical structure CRISPR-Cas9 …

A Comparative Taxonomic And Diversity Study Of Litter-Associated Fungi In Northwest Arkansas Forests, Rajaa Abdulrazzaq Abbas Al Aanbagi

Graduate Theses and Dissertations

Fungi are taxonomically the most species-rich group of organisms on the earth, ecologically occupy distinctive niches and interact with diverse other organisms throughout their biogeographic distributions and functionally play key roles through their various lifestyles. Plant litter, in particular, is a keystone component in ecosystems and provides heterogeneous microhabitats for the often overlooked litter-decomposing fungi and other organisms on the floor of temperate deciduous forests. Litter fungi involve indirect interactions with the plant, soil and whole food web network. However, the community structure and functions of litter-associated fungi as well as patterns of species richness distributed across various litter microhabitats …

Cloning, Protein Expression, And Characterization Of Interleukin 1 Alpha, Musaab Habeeb Ali Al Ameer

Graduate Theses and Dissertations

Recombinant DNA technology and the ability to produce recombinant proteins have significantly changed the world of pharmaceutical market. Recombinant DNA technology using E. coli cells has successfully produced many therapeutic proteins. In this study, the designed tag Ark-RUBY-tag facilitates rapid, and reproducible purification of recombinant proteins expressed as inclusion bodies in E. coli cells. Purification of Ark-RUBY-fused recombinant protein(s) can be obtained by using imidazole fractions. Target protein can be easily removed from the Ark-RUBY-tag by enzymatic cleavage. Ark-RUBY-fused recombinant proteins can be quantitatively detected using polyclonal antibodies. Ark-RUBY-tag can be used to purify small peptides. By using Ark-RUBY-tag, purified …

Investigating The Interactions Between Individual Calmodulin And Hiv-1 Protein Domains, Riley K. Kendall, Jerry Larue

Student Scholar Symposium Abstracts and Posters

The World Health Organization found that 37.9 million people were living with HIV by the end of 2018. HIV is a virus that weakens the immune system through viral replication and the destruction of CD4⁺ T-cells, which are white blood cells that detect infection and make antibodies. A cure for HIV has not yet been discovered. HIV-1 contains a Gag polyprotein which regulates the stages of viral replication. Previous studies suggest that the myristoyl group of a matrix protein peptide found on the Gag polyprotein, MA, forms a complex with a calcium-binding, multifunctional regulatory protein called Calmodulin (CaM). CaM …

The Toxic Effect Of Mobile Phone Radiation On Rabbit Organs, Shudong Zhu, Yan Zhu, Hao Li, Doudou Zhang, Dianzheng Zhang

PCOM Scholarly Works

Whether electromagnetic radiation (EMR) emitted from mobile phones is hazardous to human health is largely unknown. We investigated the effects of mobile phone radiation on critical organs in a rabbit model by exposing the animals to mobile phone radiation with sub-thermal specific absorption rate (SAR) of 1.0 and 0.7 W/kg for the head and the body, respectively, for 16 weeks (6 h/day, 6 days/week). There is no apparent change at the organ level. However, H&E staining showed that radiation-exposure significantly increased inflammatory cell infiltration in the liver and the lungs with a lesser degree of myocardial cell cytoplasmic vacuolation. In …

Discrimination Of Monozygotic Twins Using Dna Methylation Levels Of One Cpg Site At Chromosome 3, Dino O. Robinson

Student Theses

Conventional STR typing, commonly used in forensics for human identification, poses a problem in criminal cases and paternity disputes involving monozygotic (MZ) twins because they share identical DNA sequences. To date, no routine method is available in forensics to differentiate between individuals of MZ pairs. Recently, epigenetic methods measuring differential DNA methylation patterns have been applied to MZ twin differentiation. In this study, we investigated the potential to identify MZ twins using a previously identified DNA methylation site in chromosome 3, cg18562578, in a sample of 129 MZ and 37 dizygotic (DZ) twin pairs. We used bisulfite converted saliva DNA …

Toxicity Analysis Of 2’-Deoxyguanosine-N2-6-Aminopyrene And 2’-Deoxyguanosine-N2-8-Aminopyrene In Escherichia Coli, Emily Janeiro

Honors Scholar Theses

Cancer is a disease that stems from genomic errors that are not corrected properly by cellular repair mechanisms. Errors are more likely to form when organisms are subjected to DNA damage by mutagenic compounds. 1-Nitropyrene, a nitrated polycyclic aromatic hydrocarbon (nitro-PAH), has been shown to be a potent mutagen that causes cancer. Nitro-PAHs can arise from diesel exhaust products in the environment. Out of all nitro-PAHs, 1-nitropyrene is found in largest quantities in the environment. This poses a great need to study its effects biochemically in order to address its toxicity in DNA. Other nitropyrene derivatives, including 1,6-dinitropyrene and 1,8-dinitropyrene, …

Computational Molecular Docking Models And Design Of Diarylpentanoids For The Androgen Receptor, Jarett Guillow

Computational and Data Sciences (MS) Theses

The androgen receptor (AR) is a member of the nuclear receptor protein family that, upon binding to its natural ligand dihydrotestosterone (DHT) in the cytoplasm, translocates to the nucleus and exerts nuclear transcription factor activity to drive gene expression related to normal prostate development. AR signaling becomes overactive during the development and progression of prostate cancer through different mechanisms, including over-expression and mutation of the AR. Therefore, the AR is a prominent molecular target in the clinical management of prostate cancer. However, all therapeutic modalities targeting the AR, including androgen ablation therapy and AR block suffer from transient efficacy and …

Examining Various Aspects Of Zika Virus Dissemination In Aedes Aegypti, Ileana C. Lozano

Theses and Dissertations

South Texas is one of the few locations where Zika virus has been locally transmitted in the U.S. It has a climate which is distinct to other areas with autochthonous transmission, with extremely hot, dry summers and moderate winter temperatures. Studying mosquito transmission of Zika in a range of temperatures conditions replicating where virus transmission is occurring is essential in order to have a better understanding of transmission patterns. These factors were examined by infecting mosquitoes and monitoring the dissemination status through real-time PCR analysis.

To further characterize dissemination of Zika virus within south Texas mosquitoes a time series immunohistochemical …

Toxoplasma Gondii Requires Its Plant-Like Heme Biosynthesis Pathway For Infection, Amy Bergmann, Kathleen Floyd, Melanie Key, Carly Dameron, Kerrick C. Rees, L. Brock Thornton, Daniel C. Whitehead, Iqbal Hamza, Zhicheng Dou

Publications

Heme, an iron-containing organic ring, is essential for virtually all living organisms by serving as a prosthetic group in proteins that function in diverse cellular activities ranging from diatomic gas transport and sensing, to mitochondrial respiration, to detoxification. Cellular heme levels in microbial pathogens can be a composite of endogenous de novo synthesis or exogenous uptake of heme or heme synthesis intermediates. Intracellular pathogenic microbes switch routes for heme supply when heme availability fluctuates in their replicative environment throughout infection. Here, we show that Toxoplasma gondii, an obligate intracellular human pathogen, encodes a functional heme biosynthesis pathway. A chloroplast-derived …

Understanding The Implications Of Anandamide, An Endocannabinoid In An Early Land Plant, Physcomitrella Patens, Md Imdadul Haq

Electronic Theses and Dissertations

Endocannabinoid signaling is well studied in mammals and known to be involved in numerous pathological and physiological processes. Fatty acid amide hydrolase (FAAH) terminates endocannabinoid signaling in mammals. In Physcomitrella patens, we identified nine orthologs of FAAH (PpFAAH1 to PpFAAH9) with the characteristic catalytic triad and amidase signature sequence. Kinetics of PpFAAH1 showed specificity towards anandamide (AEA) at 37°C and pH 8.0. Further biophysical and bioinformatic analyses revealed that, structurally, PpFAAH1 to PpFAAH4 were closely associated to the plant FAAH whereas PpFAAH6 to PpFAAH9 were more closely associated to the animal FAAH. A substrate entry gate or ‘dynamic paddle’ …

Identification Of A Malaysian Tiger Milk Mushroom Specimen And Characterisation Of Its Mycelial (1,3)-Β-D-Glucan, Ahmad Usuldin Siti Rokhiyah

Student Works (2020-2029)

The tiger milk mushroom (Lignosus rhinocerus) is an important medicinal mushroom and regarded as Malaysia national heritage. Its sclerotia (tuber) has been consumed by the indigenous community (Orang Asli) to treat illnesses such as asthma, fever, cough, cancer and other diseases. The mushroom is rare and difficult to find in nature and has frequently been confused with another mushroom of similar anatomy. Traditionally, the cultivation of the sclerotium takes a long time and propagation of its mycelial biomass and exopolysaccharides (EPS) in a stirred-tank bioreactor is an excellent alternative technique. The present study aimed to identify the wild-Malaysian tiger milk …

Antioxidating Effect Of Ampelocissus Sp. (Isi Nyaru) On Streptozotocin-Induced Diabetic Rats, Zamri Elly Zulaikha

Student Works (2020-2029)

The Ampelocissus sp. locally known as Isi Nyaru has been traditionally used by native Malaysian for medical purpose. The tuber was extracted with hexane, petroleum-ether, chloroform, methanol and water solvents. The seperation and detection of bioactive compounds were done using Thin Layer Chromatography (TLC) and Gas Chromatography Mass Spectrometry (GCMS) methods. The TLC results showed the presence of phenolic acids, flavonoids and terpenoids. While in GCMS has revealed the presence of hydrocarbon groups such as alkene, ester and ether, amino acid groups, dicarboxylic acid and cyclic aromatic compound. The total phenol content and total flavonoid content were highest in methanolic …

Literature Review: The Role Of Inflammatory Biomarkers In The Connections Between Sleep And Chronic Health Conditions, Madeline Walker

Honors Program Theses

Decades of research has shown that sleep plays a vital role in our health, and disruptions in sleep can have long term detrimental effects on our lives (Yoo, 2007). The recommended amount of sleep by the National Sleep Foundation (NSF) for adults is between 7-9 hours each night (NSF, 2020). It is common knowledge that too few hours of sleep are unhealthy, but scientists are only beginning to understand the mechanisms that explain the connections between sleep patterns and health outcomes (CDC, 2011). Additionally, recent research has shown that excess sleep can be just as detrimental, if not more, to …

A Review Of Human Immunodeficiency Virus, Sophie Silver

Senior Honors Theses

Human immunodeficiency virus, also referred to as HIV, is a devastating virus which has infected millions. Characterized as a retrovirus, HIV has an RNA genome, which is reverse transcribed into DNA upon entry into the host cell. HIV primarily affects CD4⁺ T cells and is diagnosed by the significant reduction of CD4⁺ T cells. While no cure has been discovered yet, antiretroviral therapy (ART) has been demonstrated as an effective treatment option. In the progression of HIV, additional HIV-associated diseases may arise, including HIV-associated psoriasis and sensory neuropathy. In addition to the use of ART, clinicians often prescribe …