Biochemistry, Biophysics, and Structural Biology Commons^™

Transesterification And Recovery Of Intracellular Lipids Using A Single Step Reactive Extraction, Daniel R. Nelson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A single-step, extractive reaction for extraction of lipids such as biodiesel components, omega-3 fatty acids, or other triglycerides from microbial cells was examined. Conventional methods for lipid extraction use toxic solvents, and require multiple steps and long processing times. When the goal is to produce fatty acid methyl esters or FAMEs, the extracted lipids are subjected to a separate transesterification reaction with simple alcohols in the presence of an acid or base catalyst. A simplified, single-step reactive extraction method can be applied that combines the sequential extraction followed by transesterification using acidified alcohols - a process known as in situ …

A Synthetic Biological Engineering Approach To Secretion- Based Recovery Of Polyhydroxyalkanoates And Other Cellular Products, Elisabeth Linton

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The costs associated with cellular product recovery commonly account for as much as 80% of the total production expense. As a specific example, significant recovery costs limit commercial use of polyhydroxyalkanoates (PHA), which comprise a class of microbially-accumulated polyesters. PHAs are biodegradable compounds that are of interest as a sustainable alternative to petrochemically-derived plastics. Secretion-based recovery of PHAs was studied to decrease PHA production costs. Type I and II secretory pathways are commonly used for the translocation of recombinant proteins out of the cytoplasm of E. coli. Proteins were targeted for translocation using four signal peptides (HlyA, TorA, GeneIII, …

Role Of Protein Kinase C Isotypes In 1,25-Dihydroxyvitamin D3 Mediated Signal Transduction Through The 1,25d3 Membrane Associated, Rapid Response Steroid Binding Receptors In Chick Intestinal Cells, Sakara Tunsophon

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

It is now accepted that 1,25(OH)2D3 mediates its rapid actions on the control of phosphate and calcium homeostasis through its membrane receptor termed the 1,25D3-MARRS (membrane associated rapid response steroid binding) protein. I determined the various PKC isotypes involved in the rapid regulation of phosphate uptake and calcium extrusion in chick intestinal cells. 1,25(OH)2D3-mediated phosphate uptake was stimulated within 1 min after addition of the hormone. Western blot analyses on isolated intestinal cells treated with steroid hormone resulted in dose-dependent increases in PKC alpha and PKC beta in postnuclear centrifugation fractions, but not in the low speed centrifugation fractions. The …

Development Of Novel Methods And Their Utilization In The Analysis Of The Effect Of The N-Terminus Of Human Protein Arginine Methyltransferase 1 Variant 1 On Enzymatic Activity, Protein-Protein Interactions, And Substrate Specificity, Brenda Bienka Suh-Lailam

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein arginine methyltransferases (PRMTs) are enzymes that catalyze the methylation of protein arginine residues, resulting in the formation of monomethylarginine, and/or asymmetric or symmetric dimethylarginines. Although understanding of the PRMTs has grown rapidly over the last few years, several challenges still remain in the PRMT field. Here, we describe the development of two techniques that will be very useful in investigating PRMT regulation, small molecule inhibition, oligomerization, protein-protein interaction, and substrate specificity, which will ultimately lead to the advancement of the PRMT field. Studies have shown that having an N-terminal tag can influence enzyme activity and substrate specificity. The first …

Molecular Analysis Of B3galtl In A Patient With Peters' Plus Syndrome, Taiyabah Naeem

Undergraduate University Honors Capstones

Chromosomal rearrangement such as microdeletions or microduplications, which can alter the dosage of one or more genes, are commonly seen in patients with multiple congenital anomalies (MCA). Alternatively, the discovery of a microdeletion may sometimes uncover an autosomal recessive disorder if the gene on the non-deleted allele carries a mutation. This study reports molecular analysis of a patient with MCAs, including an enlarged head, developmental delay, clouding of the corneas, and short stature. Peters Plus Syndrome (PPS) is characterized as an autosomal recessive disorder. Phenotypical symptoms include various eye abnormalities and structural organ defects. The B3GGALTL has been found to …

Tied Together: A Molecular Role For Tie1 In Angiopoietin Tie2 Signaling, Tom Cm Seegar

Theses and Dissertations

The primary function of the vascular system is the maintenance of oxygen homeostasis for all metazoan tissue. Angiogenesis, the remodeling and maintenance of new blood vessels from an existing vessel, is primarily controlled through the endothelial specific receptor tyrosine kinase Tie2, and the orphan receptor tyrosine kinase, Tie1. Although these receptors share highly conserved, genetic and biochemical analysis has shown these receptors have distinct and essential roles in angiogenesis. Tie2 activation typically results in vessel stability and quiescences and has further been shown to interact with all four sub-types of the angiopoietin signaling factors, Ang1-4. Conversely, Tie1 is involved in …

The Rho Family Gtpase: Determining Gef Specificity Through Recombinant Expression, Farrah Steinke

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Protein Evolution Via Amino Acid And Codon Elimination, Lise Goltermann, Marie Sofie Yoo Larsen, Ranat Banerjee, Andreas C. Joerger, Michael Ibba, Thomas Bentin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background
Global residue-specific amino acid mutagenesis can provide important biological insight and generate proteins with altered properties, but at the risk of protein misfolding. Further, targeted libraries are usually restricted to a handful of amino acids because there is an exponential correlation between the number of residues randomized and the size of the resulting ensemble. Using GFP as the model protein, we present a strategy, termed protein evolution via amino acid and codon elimination, through which simplified, native-like polypeptides encoded by a reduced genetic code were obtained via screening of reduced-size ensembles.

Methodology/Principal Findings
The strategy involves combining a sequential …

Oxidation Of Methane By A Biological Dicopper Centre, Ramakrishnan Balasubramanian, Stephen M. Smith, Swati Rawat, Liliya A. Yatsunyk, Timothy L. Stemmler, Amy C. Rosenzweig

Biochemistry and Molecular Biology Faculty Publications

Vast world reserves of methane gas are underutilized as a feedstock for the production of liquid fuels and chemicals owing to the lack of economical and sustainable strategies for the selective oxidation of methane to methanol1. Current processes to activate the strong C–H bond (104 kcal mol−1) in methane require high temperatures, are costly and inefficient, and produce waste2. In nature, methanotrophic bacteria perform this reaction under ambient conditions using metalloenzymes called methane monooxygenases (MMOs). MMOs thus provide the optimal model for an efficient, environmentally sound catalyst3. There are two types of MMO. Soluble MMO (sMMO),expressed by several strains of …

Partitioning Of Minimotifs Based On Function With Improved Prediction Accuracy, Sanguthevar Rajasekaran, Tian Mi, Jerlin Camilus Merlin, Aaron Oommen, Patrick R. Gradie, Martin R. Schiller

Life Sciences Faculty Research

Background

Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions.

Methodology/Principal Findings

Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have …

Neuroprotection With Anesthetics In Two Models Of Cerebral Ischemia, Rafael Eduardo Chaparro Buitrago

USF Tampa Graduate Theses and Dissertations

Neuroprotection with anesthetics has been studied for many decades; important advances in this field have modified the way Anesthesiologists treat patients in the operating room. Animal models have played an important role in the study of ischemia in the operating room. Recent studies have demonstrated that the effect of anesthetics seems to be different in different animal models. We decided to evaluate anesthetics in a well-known model of cerebral ischemia and also in hypotensive models designed by us. We used a model of cerebral ischemia (MCAO) to test anesthetics neuroprotective effect in a two-week period. Then, we used a model …

How The Sequence Of A Gene Can Tune Its Translation, Kurt Fredrick, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Sixty-one codons specify 20 amino acids, offering cells many options for encoding a polypeptide sequence. Two new studies (Cannarrozzi et al., 2010, Tuller et al., 2010) now foster the idea that patterns of codon usage can control ribosome speed, fine-tuning translation to increase the efficiency of protein synthesis.

T10c12 Conjugated Linoleic Acid Causes Delipidation In 3t3-L1 Adipocytes And Mice, Shan Jiang

Department of Animal Science: Dissertations, Theses, and Student Research

T10c12 conjugated linoleic acid (t10c12 CLA) causes the reduction of triglyceride contents in adipocytes. T10c12 CLA’s delipidation effect is associated with decreased nutrient uptake, adipogenesis, lipogenesis, and increased energy expenditure, lipolysis, fatty acid oxidation in adipocytes. However, the molecular mechanisms of CLA’s delipidation effects are still unknown. AMP-activated protein kinase (AMPK), a central regulator of cellular energy levels, is activated by an increase in the cellular AMP:ATP ratio or various cellular stresses. We demonstrated that t10c12 CLA activated AMPK in 3T3-L1 adipocytes, leading to inhibition of anabolic biosynthesis and increase of energy expenditure. Strong activation of AMPK can induce an …

Ribosomal Rna Mutations That Inhibit The Activity Of Transfer-Messenger Rna Of Stalled Ribosomes, Jacob N. Crandall

Theses and Dissertations

In eubacteria, stalled ribosomes are rescued by a conserved quality-control mechanism involving transfer-messenger RNA (tmRNA) and its protein partner SmpB. Mimicking a tRNA, tmRNA enters stalled ribosomes, adds Ala to the nascent polypeptide, and serves as a template to encode a short peptide that tags the nascent protein for destruction. To further characterize the tagging process, we developed two genetic selections that link tmRNA activity to cell death. These negative selections can be used to identify inhibitors of tagging or to identify mutations in key residues essential for ribosome rescue. Little is known about which ribosomal elements are specifically required …

Dynamics On Multiple Timescales In The Rna-Directed Rna Polymerase From The Cystovirus Φ6, Zhen Ren, Hsin Wang, Ranajeet Ghose

Publications and Research

The de novoinitiating RNA-directed RNA polymerase (RdRP), P2, forms the central machinery in the infection cycle of the bacteriophage ϕ6 by performing the dual tasks of replication and transcription of the double-stranded RNA genome in the host cell. By measurement and quantitative analysis of multiple-quantum spin-relaxation data for the δ1 positions of Ile residues that are distributed over the 3D-fold of P2, we find that the enzyme is dynamic both on the fast (ps–ns) and slow (µs–ms) timescales. The characteristics of several motional modes including those that coincide with the catalytic timescale (500–800/s) are altered in the presence of …

Aspergillus Fumigatus Stimulates The Nlrp3 Inflammasome Through A Pathway Requiring Ros Production And The Syk Tyrosine Kinase, Najwane Saïd-Sadier, Eduardo V. Padilla, Gordon Langsley, David M. Ojcius

All Dugoni School of Dentistry Faculty Articles

Invasive aspergillosis (IA) is a life-threatening disease that occurs in immunodepressed patients when infected with Aspergillus fumigatus. This fungus is the second most-common causative agent of fungal disease after Candida albicans. Nevertheless, much remains to be learned about the mechanisms by which A. fulmigatus activates the innate immune system. We investigated the inflammatory response to conidia and hyphae of A. fumigatus and specifically, their capacity to trigger activation of an inflammasome. Our results show that in contrast to conidia, hyphal fragments induce NLRP3 inflammasome assembly, caspase-1 activation and IL-1β release from a human monocyte cell line. The ability of Aspergillus …

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 88th Annual Meeting for the Virginia Academy of Science, May 20-21, 2010, James Madison University, Harrisonburg, VA.

Section Abstracts: Structural Biology, Biochemistry, And Biophysics

Virginia Journal of Science

Abstracts of the Structural Biology, Biochemistry, and Biophysics Section for the 88th Annual Meeting of the Virginia Academy of Science, May 20-21, 2015. James Madison University, Harrisonburg, Virginia.

An Entrepreneurial Approach To Librarianship, Flora Shrode, Jennifer Duncan, Wendy Holliday

Library Faculty & Staff Publications

Librarians from Utah State University explain recent efforts to encourage subject librarians to take a more holistic view of their roles. We are shifting from a traditional emphasis primarily on collection development and refocusing on natural connections between collections, instruction, liaison, and reference service. The poster provides background about Utah State University’s situation and explains our approach to analyzing local needs and culture to inform development of a new organizational structure. We describe our vision of subject librarianship, the process by which we assessed librarians’ ideas and goals for performing as subject librarians, and the actions we are taking to …

Increasing Lipoxygenase Solubility Through Fusion Of Highly Acidic Peptides, Rachel Fabacher

Honors Capstones

No abstract provided.