Molecular Biology Commons^™

The Identification Of Small Molecule Inhibitors To Candida Albicans Phosphatidylserine Synthase, Yue Zhou

Doctoral Dissertations

Candida albicans phosphatidylserine (PS) synthase, encoded by the CHO1 gene, has been identified as a potential drug target for new antifungals against systemic candidiasis due to its importance in virulence, absence in the host and conservation among fungal pathogens. This dissertation is focused on the identification of inhibitors for this membrane enzyme. Cho1 has two substrates: cytidyldiphosphate-diacylglycerol (CDP-DAG) and serine. Previous studies identified a conserved CDP-alcohol phosphotransferase (CAPT) binding motif present within Cho1, and here we revealed that mutations in all but one conserved amino acid within the CAPT motif resulted in decreased Cho1. For serine, we have predicted a …

Characterization Of Arabidopsis Eukaryotic Translation Initiation Factor 2Α (Eif2Α) Mutants, Mark Edens

Masters Theses

Plants are stationary organisms that are charged with overcoming a multitude of biotic and abiotic stresses. The eukaryotic translation initiation factor 2 (eIF2) is responsible for charging the P-site of the forming 80S ribosome with the initiator methionyl-tRNA. Thus, eIF2 is a protein of utmost consequence in the growth and development of organisms. The eIF2 protein is also a mediator of global translational regulation in the eukaryotic integrated stress response (ISR), where the α-subunit is phosphorylated by protein kinases, such as the kinase GCN2. Here, five eIF2α allele mutants in Arabidopsis were found to be deleterious to plant growth, development, …

A Novel Transmembrane Ligand Inhibits T Cell Receptor Activation, Yujie Ye

Doctoral Dissertations

T lymphocytes (T cells) play essential roles in the adaptive immune system. Each mature T cell expresses one type of functional T cell receptor (TCR). The TCR recognizes antigens bound to the major histocompatibility complex (MHC) in antigen presenting cells. The resulting stimulation signal crosses the transmembrane domain of TCR and initiates downstream signaling cascades. The human immune system relies on TCRs to recognize a variety of pathogens. Normally, TCR can distinguish the self-antigens from pathogenic antigens. However, dysfunction or aberrant expression of TCRs causes different inflammatory and autoimmune diseases, which afflict millions of people annually (Chapter I). Current treatments …

Mechanisms By Which Xenorhabdus Nematophila Interacts With Hosts Using Integrated -Omics Approaches, Nicholas C. Mucci

Doctoral Dissertations

Nearly all organisms exist in proximity to microbes. These microbes perform most of the essential metabolic processes necessary for homeostasis, forming the nearly hidden support system of Earth. Microbial symbiosis, which is defined as the long-term physical association between host and microbes, relies on communication between the microbial community and their host organism. These interactions among higher order organisms (such as animals, plants, and fungi) and their bacteria links metabolic processes between interkingdom consortia. Many questions on microbial behavior within a host remain poorly understood, such as the colonization efficiency among different microbial species, or how environmental context changes their …

Nodulin 26 Like Intrinsic Proteins: Structurally Similar Membrane Channels With Diverse Functions In Plant Hypoxia Stress, Metalloid Nutrition & Toxicity, Zachary Beamer

Doctoral Dissertations

Plant nodulin 26 intrinsic proteins are categorized into three groups (NIP I, II, and III) based on pore architecture. NIP II and III participate in metalloid nutrition, whilst the function of a third (NIP I) is less understood. Here we investigate the physiological function of one NIP I protein (Arabidopsis thaliana NIP2;1) as a lactic acid channel, and also explore the structural basis for metalloid and water permeability of NIP I and NIP II proteins in general. In addition, a strategy was developed for the purification and crystallization of soybean nodulin 26 as a step towards structure determination of a …

Unraveling The Molecular Foundations Behind The Diverged Behaviors Of Mouse Insulin 1 And Insulin 2, Connecting Diabetes Risk With Glucocorticoid Treatment And Chronic Migraine Through The Analysis Of Islet Chemistry, And Capturing Key Posttranslational Modifications All Through The Application Of A Novel Lc-Ims-Ms Workflow, Connor Christopher Long

Select or Award-Winning Individual Scholarship

We display the capabilities of our established liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) workflow in the investigations of islet chemistry at the sub-single-islet level. We begin by characterizing the structural differences of Ins1 and Ins2 to present novel insights as to why their behaviors diverge. We then examine the effects of the stress hormone corticosterone, the rodent equivalent of human cortisol that is often used as a therapeutic, on pancreatic peptide hormone secretion. We also uncover the molecular connection behind the inverse relationship between type 2 diabetes (T2D) risk and chronic migraine via the neuropeptides CGRP and PACAP. Lastly, we …

Investigating The Role Of Dullard And Tmem-188 In Lipid Droplet Biogenesis In Mammalian Cells, Mia Kaitlin Buono

Chancellor’s Honors Program Projects

No abstract provided.

Mutations In The N-Terminus Of The Mod(Mdg4) Btb Domain Reveal An Unexpected Role Of Mod(Mdg4) In Chromosome Segregation In Female Meiosis, Gwyneth D E Walker, Bruce D. Mckee

Chancellor’s Honors Program Projects

No abstract provided.

Calmodulin Like 38 Is Required For Autophagy Of Hypoxia-Induced Cytoplasmic Rna Granules In Arabidopsis Thaliana, Sterling Field

Doctoral Dissertations

In response to the energy crisis resulting from submergence stress and hypoxia, the model plant Arabidopsis thaliana limits non-essential mRNA translation, and accumulates cytosolic stress granules. Stress granules are phase-separated mRNA-protein particles that partition transcripts for various fates: storage, degradation, or return to translation after stress alleviation. Another response by the plant cell to low oxygen stress is the induction of the turnover pathway autophagy. Stress granule regulation by autophagy occurs by a ‘granulophagy’ pathway in yeast and mammalian systems through which parts or whole stress granules are degraded. Whether this occurs in plants has not been investigated.

A connection …

Erecta Family Genes Regulate The Shoot Apical Meristem And Organ Formation, Daniel A. Degennaro

Doctoral Dissertations

Plants are sessile and must adjust their organ growth to their environments. A reservoir of stem cells in the shoot apical meristem (SAM) supplies cells for differentiation into organs. The SAM must balance organ production with stem cell maintenance. The ERECTA family (ERfs) encodes the leucine-rich repeat receptor-like kinases ERECTA (ER), ERECTA-LIKE 1 (ERL1), and ERL2. ERf signaling regulates organ initiation and stem cell maintenance. Results presented in this work include the following:

1) WUSCHEL (WUS) and CLAVATA3 (CLV3) make up a negative feedback loop to maintain SAM size. WUS and CLV3 expression localization is critical for …

Microbial Community Dynamics Of A Microcystis Bloom, Helena Pound

Doctoral Dissertations

Harmful algal bloom events are notoriously associated with massive economic and environmental consequences, causing wildlife and human health risks. As these blooms increase in occurrence, duration, and severity around the world, it is essential to understand conditions leading to bloom formation and why they persist. Abiotic factors such as nutrients are commonly considered in bloom dynamics, but biotic interactions with co-occurring microbial species and viruses must also be taken into account. Harmful algal blooms dominated by the cyanobacterial genus Microcystis occur in bodies of water around the world and provide an ideal system in which to study top-down controls on …

A Novel Approach For Characterizing The Ultra-Micro Size-Fraction Community, Abdullah Ahmed Salim, Priscilla Nicole Pineda, Isabella Alamilla, Andrew Dean Putt

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

A Novel Approach for Characterizing the Ultra-Micro Size-Fraction Community

Students: Abdullah Salim, Priscilla Pineda, Isabella Alamilla

Mentors/Supervisors: Andrew Putt, Terry C. Hazen

ABSTRACT

The ultra-micro size-fraction (UMSF) are bacteria that can pass through the 0.2 µm pore membrane filters employed in environmental surveys. Despite being ubiquitous and having high metabolic activity, UMSF remain elusive and largely uncultured. Investigations of UMSF are skewed by difficulties in culturing and a lack of techniques for measuring UMSF biogeochemical signatures. This study measures surface stream UMSF community diversity, and community response to the addition of the synthetic pharmaceutical and cosmetic carbon product cyclodextrin which …

60. Epfl Genes And Their Role In Flower Development In Arabidopsis Thaliana, Rachael Deboe

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Flowers are composed of four floral organ types: sepals, petals, stamens, and a pistil. In Arabidopsis thaliana, the ERECTA family leucine rich repeat receptor like kinases (LRR-RLKs) have been shown to regulate plant morphology. Epidermal Patterning Factor-Like (EPFL) genes encode for small secretory proteins that are ligands for ERECTA Family (ERf) receptors. It is suspected that EPFL’s act as a signal to coordinate proper lateral organ number, patterning, and spacing. ERf mutants have significant defects in flower development, including difficulty forming anther lobes and pistils, yet little is known about how individual EPFL ligands contribute to ERf signaling. In order …

The Histone Variant H2av Regulates Stress Responses And Tissue Development Through Interactions With Chromatin Insulator Proteins In Drosophila Melanogaster, James Ryan Simmons

Doctoral Dissertations

The ability of a cell to sense and respond to various forms of stress is essential to maintain integrity of the genome. Numerous pathways have been implicated in cellular responses to environmental and genotoxic stresses, often involving proteins and complexes that bind DNA directly to orchestrate changes in transcription and genome organization. Chromatin insulators describe a class of protein complex that bind specific sequences in the genome and work through two classically described functions: to restrict communication between enhancers and promoters through physical separation into different genomic domains and to prevent the spread of heterochromatin into euchromatic regions of the …

Modulation Of Protein Dynamics By Ligand Binding And Solvent Composition, Richard J. Lindsay

Doctoral Dissertations

Many proteins undergo conformational switching in order to perform their cellular functions. A multitude of factors may shift the energy landscape and alter protein dynamics with varying effects on the conformations they explore. We apply atomistic molecular dynamics simulations to a variety of biomolecular systems in order to investigate how factors such as pressure, the chemical environment, and ligand binding at distant binding pockets affect the structure and dynamics of these protein systems. Further, we examine how such changes should be characterized. We first investigate how pressure and solvent modulate ligand access to the active site of a bacterial lipase …

Engineering Modularity Of Ester Biosynthesis Across Biological Scales, Hyeongmin Seo

Doctoral Dissertations

Metabolic engineering and synthetic biology enable controlled manipulation of whole-cell biocatalysts to produce valuable chemicals from renewable feedstocks in a rapid and efficient manner, helping reduce our reliance on the conventional petroleum-based chemical synthesis. However, strain engineering process is costly and time-consuming that developing economically competitive bioprocess at industrial scale is still challenging. To accelerate the strain engineering process, modular cell engineering has been proposed as an innovative approach that harnesses modularity of metabolism for designing microbial cell factories. It is important to understand biological modularity and to develop design principles for effective implementation of modular cell engineering. In this …

The Effect Of Nuclear Perturbations On The 3d Organization Of The Genome, Rosela Golloshi

Doctoral Dissertations

Cells in our body experience constant mechanical forces that influence biological functions such as growth and development. The nucleus has been implicated as a key mechanosensor and can directly influence chromatin organization and epigenetic alterations leading to gene expression changes. However, the mechanism by which such mechanical forces lead to genomic alterations and expression of mechanosensitive genes is not fully understood. The work presented in this dissertation investigates the effect of mechanical and epigenetic perturbations on the 3D genome organization. To investigate this 3D genome folding, we use Chromosome Conformation Capture followed by high throughput sequencing (Hi-C) (Chapter-1) which identifies …

Iojap: Morphological And Physiological Phenotype Characterization In Arabidopsis, Thomas Jay Payne

Doctoral Dissertations

IOJAP protein is found in all organisms that contain a ribosome of bacterial origin. The majority of studies suggest that IOJAP plays a role in translation, although this has yet to be thoroughly investigated in plants. Using Arabidopsis thaliana, an extensive phenotype characterization of iojap mutants was performed. Many processes of plant growth were slightly impaired at optimal temperature (22˚C) but became severely hindered at low temperature (12˚C and 4˚C). These cold temperature defects manifested in an overall reduction of plant growth as well as variegation, chlorosis, leaf hyponasty, as well as reduced maximum quantum yield (F_v/F …

Root Phosphomonoesterase As A Vital Component Of Increasing Phosphorus Availability In Tropical Forests, Kristine Grace Manno Cabugao

Doctoral Dissertations

Tropical forests, relative to other terrestrial ecosystems, exchange the largest amount of carbon with the atmosphere and also constitute a significant carbon sink. However, nutrient limitation, particularly of phosphorus (P), could limit growth of tropical forests and their function with the global carbon cycle. Thus, understanding root mechanisms to acquire P is necessary to representing the P cycle and corresponding interactions with plant growth. A large portion of total soil P in tropical forests occurs in organic forms, only accessible through root and microbial production of phosphatase enzymes. These phosphatase enzymes mineralize organic P into orthophosphate, the form of P …

Needles In A Haystack Of Protein Diversity: Interrogation Of Complex Biological Samples Through Specialized Strategies In Bottom-Up Proteomics Uncover Peptides Of Interest For Diverse Applications, Manuel I. Villalobos Solis

Doctoral Dissertations

Peptide identification is at the core of bottom-up proteomics measurements. However, even with state-of the-art mass spectrometric instrumentation, peptide level information is still lost or missing in these types of experiments. Reasons behind missing peptide identifications in bottom-up proteomics include variable peptide ionization efficiencies, ion suppression effects, as well as the occurrence of chimeric spectra that can lower the efficacy of database search strategies. Peptides derived from naturally abundant proteins in a biological system also have better chances of being identified in comparison to the ones produced from less abundant proteins, at least in regular discovery-based proteomics experiments. This dissertation …

Molecular Characterization Of A Gene Encoding Insulin-Like Peptide 5 (Ilp5) In Drosophila Virilis, Nikolas R. Likourentzos, Jae H. Park

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

The study of the insulin-like peptides of Drosophila can provide insight of their similarities to mammalian insulin and their potential usage in treating human insulin-related diseases. In this study, we isolated and characterized cDNA encoding insulin-like peptide (ILP) 5 in D. virilis by using RNA purification, reverse transcription, and RACE protocols. Subsequently, various bioinformatic softwares were employed to predict peptide structure. The ILP5 gene (587 base pairs) codes for 121 amino acids that make up prepro-ILP5. After maturation, functional ILP5 is a peptide of two 25 amino acid chains, A- and B-chain, connected by two disulfide bonds. Sequencing genomic DNA …

The Current Neuroscientific Understanding Of Alzheimer's Disease, Rachel A. Brandes

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

Alzheimer’s disease is a degenerative neurological illness characterized by the deterioration of brain regions implicated in memory and cognitive function. While researchers have yet to find a cure or effective treatment, they have gained a better understanding of its pathology and development. Through years of neuroscience research, scientists have discovered much of what happens in the brain during Alzheimer’s disease onset and how this causes its symptoms; many hypotheses regarding this aspect of the illness involve temporal lobe atrophy, neurofibrillary tangles, and amyloid plaques. Although Alzheimer’s disease affects millions of people every day, it seems that most are unaware of …

Crosstalk Between Rho-Family Gtpases At The Division Site During Cytokinesis, Emma Nicole Koory

Chancellor’s Honors Program Projects

No abstract provided.

Characterization Of Tmx Transmembrane Protein In Bacillus Subtilis And Its Effects On Antibiotic Resistance, Membrane Permeability, And Membrane Fluidity, Henna Zaver

Chancellor’s Honors Program Projects

No abstract provided.

Cell Separation Delay And Membrane Trafficking Defects In Cdc42 Gap Mutants, Haylee Young

Chancellor’s Honors Program Projects

No abstract provided.

Cell Separation Delay And Membrane Trafficking Defects In Cdc42 Gap Mutants, Haylee Grace Young

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Cytokinesis is the final step in cell division, where a cell separates into two daughter cells. Cytokinesis involves many steps that must be organized in a spatiotemporal manner. In many eukaryotes, it involves the assembly and constriction of an actomyosin ring. The fission yeast Schizosaccharomyces pombe serves as a good model system to study cytokinesis because they divide via actomyosin-dependent-cytokinesis.

The Rho-family of small GTPases are molecules involved in the regulation of cell growth and division. The GTPase Cdc42 helps promote timely onset of ring constriction and septum formation in fission yeast. Studies with many other organisms show that Cdc42 …

Investigation For Novel Anti-Apoptotic Factors In The Neurons Of Drosophila Melanogaster, Haylie Rachel Lam

Chancellor’s Honors Program Projects

No abstract provided.

Constitutive Expression Of Thioglucoside Glucohydrolase 1 (Tgg1) Decreases Intercellular Trafficking In Arabidopsis Thaliana, Alessandro Francesco Sarno

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Plasmodesmata (PD) are pores that traverse plant cell walls, providing a route for intercellular trafficking of essential metabolites, nutrients, and signaling molecules between adjacent plant cells, thereby aiding communication. The increased size exclusion limit 2 (ise2) mutant of Arabidopsis thaliana has an increased abundance of branched PD, as well as a greater flux of intercellular trafficking. A search for proteins that interact with ISE2 identified THIOGLUCOSIDE GLUCOHYDROLASE 2 (a myrosinase). A. thaliana also encodes a second, closely-related myrosinase, TGG1. Myrosinases are enzymes that catalyze the hydrolysis of glucosinolates, a type of secondary metabolite that are amino acid derivatives. The breakdown …

Tea Induction Of Cyp6a8 Promoter In Drosophila Melanogaster, Fiona Retzer

Chancellor’s Honors Program Projects

No abstract provided.

Characterizing Tmx And Chemotactic Receptor Arrays Through Bacterial Two-Hybrid And Beta-Galactosidase Assays, Adam Keith Hubler

Faculty Publications and Other Works -- Biochemistry, Cellular and Molecular Biology

No abstract provided.