Biochemistry Commons^™

Blue Light Induces A Neuroprotective Open Access Gene Expression Program In Drosophila Photoreceptors, Hana Hall, Jingqun Ma, Sudhanshu Shekhar, Walter D. Leon-Salas, Vikki M. Weake

Department of Biochemistry Faculty Publications

Background: Light exposure induces oxidative stress, which contributes to ocular diseases of aging. Blue light provides a model for light‑induced oxidative stress, lipid peroxidation and retinal degeneration in Drosophila melanogaster. In contrast to mature adults, which undergo retinal degeneration when exposed to prolonged blue light, newly‑eclosed fies are resistant to blue light‑induced retinal degeneration. Here, we sought to characterize the gene expression programs induced by blue light in fies of diferent ages to identify neuroprotective pathways utilized by photoreceptors to cope with light‑induced oxidative stress.

Results: To identify gene expression changes induced by blue light exposure, we profled the nuclear …

Conjugation Of Nanomaterials And Nematic Liquid Crystals For Futuristic Applications And Biosensors, Thomas George, Amit Choudhary, Guoqiang Li

Chemistry & Biochemistry Faculty Works

The established role of nematic liquid crystals (NLCs) in the recent rapid development of displays has motivated researchers to modulate the electro-optical properties of LCs. Furthermore, adding nanomaterials into NLCs has led to enhancements of the properties of NLCs, like reduced threshold of the operating voltage, variation in pretilt angle, reduced switching time, etc. These enhanced properties, due to interfacial dynamics, are enabling wider applications of NLCs and nanomaterials. The recent literature of nanomaterial-doped NLCs is rich with various kinds of nanomaterials in a variety of NLCs. The light has been focused on the most widely used and studied gold …

Proper Splicing Contributes To Visual Function In The Aging Drosophila Eye, Rachel Stegeman, Hana Hall, Spencer E. Escobedo, Henry C. Chang, Vikki M. Weake

Department of Biochemistry Faculty Publications

Changes in splicing patterns are a characteristic of the aging transcriptome; however, it is unclear whether these age‐related changes in splicing facilitate the progressive functional decline that defines aging. In Drosophila, visual behavior declines with age and correlates with altered gene expression in photoreceptors, including downregulation of genes encoding splicing factors. Here, we characterized the significance of these age‐regulated splicing‐associated genes in both splicing and visual function. To do this, we identified differential splicing events in either the entire eye or photoreceptors of young and old flies. Intriguingly, aging photoreceptors show differential splicing of a large number of visual function …

Cross Photoreaction Of Glyoxylic And Pyruvic Acids In Model Aqueous Aerosol, Sha-Sha Xia, Alexis J. Eugene, Marcelo I. Guzman

Chemistry Faculty Publications

Aerosols of variable composition, size, and shape are associated with public health concerns as well as with light-particle interactions that play a role in the energy balance of the atmosphere. Photochemical reactions of 2-oxocarboxylic acids in the aqueous phase are now known to contribute to the total secondary organic aerosol (SOA) budget. This work explores the cross reaction of glyoxylic acid (GA) and pyruvic acid (PA) in water, the two most abundant 2-oxocarboxylic acids in the atmosphere, under solar irradiation and dark thermal aging steps. During irradiation, PA and GA are excited and initiate proton-coupled electron transfer or hydrogen abstraction …

Structural Insights From Hiv-Antibody Co-Evolution And Related Immunization Studies, Jeffrey O. Zhou , '19, Therese Ton , '19, Julia W. Morriss , '19, Diep Nguyen , '19, Daniela Fera

Chemistry & Biochemistry Faculty Works

Human immunodeficiency virus type 1 (HIV-1) is a rapidly evolving pathogen and causes the acquired immunodeficiency syndrome (AIDS) in humans. There are ~30-35 million people infected with HIV around the world, and ~25 million have died since the first reported cases in 1981. Additionally, each year 2-3 million people become newly infected and more than one million die of AIDS. An HIV-1 vaccine would help halt an AIDS pandemic, and efforts to develop a vaccine have focused on targeting the HIV-1 envelope, Env, found on the surface of the virus. A number of chronically infected individuals have been shown to …

Transcriptomics Of Learning, Pablo Iturralde

Theses

Learning is a basic and important component of behavior yet we have very little empirical information about the interaction between mechanisms of learning and evolution. In our work, we are testing hypotheses about the neurogenetic mechanisms through which animal learning abilities evolve. We are able to test this directly by using experimentally evolved populations of flies, which differ in learning ability. These populations were previously evolved within the lab by creating worlds with different patterns of change following theoretically predicted effects on which enhanced learning will evolve. How has evolution acted to modulate genes and gene expression in the brain …

High-And Low-Temperature Pyrolysis Profiles Describe Volatile Organic Compound Emissions From Western Us Wildfire Fuels, Kanako Sekimoto, Abigail R. Koss, Jessica B. Gilman, Vanessa Selimovic, Matthew M. Coggon, Kyle J. Zarzana, Bin Yuan, Brian M. Lerner, Steven S. Brown, Carsten Warneke, Robert J. Yokelson, James M. Roberts, Joost De Gouw

Chemistry and Biochemistry Faculty Publications

Biomass burning is a large source of volatile organic compounds (VOCs) and many other trace species to the atmosphere, which can act as precursors to secondary pollutants such as ozone and fine particles. Measurements performed with a proton-transfer-reaction time-of-flight mass spectrometer during the FIREX 2016 laboratory intensive were analyzed with positive matrix factorization (PMF), in order to understand the instantaneous variability in VOC emissions from biomass burning, and to simplify the description of these types of emissions. Despite the complexity and variability of emissions, we found that a solution including just two emission profiles, which are mass spectral representations of …

A Series Of 4- And 5-Coordinate Ni(Ii) Complexes: Synthesis, Characterization, Spectroscopic, And Dft Studies, Jack Ghannam, Talal Al Assil, Trey C. Pankratz, Richard L. Lord, Matthias Zeller, Wei-Tsung Lee

Chemistry: Faculty Publications and Other Works

A series of four- and five-coordinate Ni(II) complexes Cz^tBu(Pyr^iPr)₂NiX (1–3 and 1·THF–3·THF), where X = Cl, Br, and I, were synthesized and fully characterized by NMR and UV–vis spectroscopy, X-ray crystallography, cyclic voltammetry, and density functional theory calculations. The solid-state structures of 1–3 reveal rare examples of seesaw Ni(II) complexes. In solution, 1–3 bind reversibly to a THF molecule to form five-coordinate adducts. The electronic transitions in the visible region (630–680 nm), attributed to LMCT bands, for 1 → 3 exhibit a …

Interrogation Of Protein Function With Peptidomimetics, Olapeju Bolarinwa

USF Tampa Graduate Theses and Dissertations

Proteins can be described as the “machineries” responsible for almost all tasks in the levels of organizational complexity in multi-cellular organisms namely: the cells, tissues, organs and systems. Any disorder in the function of a protein at any of these levels could result in disease, and a study of protein function is critical to understanding the pathological features of the disease at the molecular level. A quick glance at these abundantly present proteins reveals two striking features: large diversity of biological function, and the variations in structural complexity, which varies from simple random coils, to turns and helices, and on …

Hydrogen Sulfide Gas Detection Via Multivariate Optical Computing, Bin Dai, Christopher Michael Jones, Megan Pearl, Mickey Pelletier, Michael L. Myrick

Faculty Publications

Hydrogen-sulfide gas is a toxic, colorless gas with a pungent odor that occurs naturally as a decomposition by-product. It is critical to monitor the concentration of hydrogen sulfide. Multivariate optical computing (MOC) is a method that can monitor analytes while minimizing responses to interferences. MOC is a technique by which an analogue calculation is performed entirely in the optical domain, which simplifies instrument design, prevents the drift of a calibration, and increases the strength and durability of spectroscopic instrumentation against physical perturbation when used for chemical detection and identification. This paper discusses the detection of hydrogen-sulfide gas in the ultraviolet …

Dynamics And Interactions Of Membrane Proteins, Azamat Galiakhmetov

Dissertations (1934 -)

Membrane proteins are members of the class of proteins that perform their functions while being associated with a lipid bilayer. In the cell, they serve as transporters, receptors, anchors and enzymes. The domain organisation of these proteins suggests importance of lipid membrane and protein-lipid interactions for protein function. The requirement of a membrane mimic and the level of its resemblance to a native one for protein investigation makes the studies of membrane proteins a challenging project. My research work is focusing on the biophysical and biochemical studies of membrane proteins. This dissertation outlines two separate projects, each with their own …

Strategies For The Modulation Of Protease Activated Receptors (Pars), Disha M. Gandhi

Dissertations (1934 -)

Protease-activated receptors (PARs) are class A G protein-coupled receptors (GPCRs) with 4 subtypes (PAR 1 – 4) and with a unique mode of action. PARs are cleaved by extracellular proteases at the N-terminus, creating a new tethered ligand that activates the receptor and transduces biological signals into the cell. PARs have been implicated in various productive and pathological signals, including those related to thrombosis, inflammation, reperfusion injury, and cancer cell metastasis. Despite the fact that PARs are attractive as drug targets, their intramolecular mode of activation makes it challenging to modulate them with drugs in a selective manner, and only …

Characterizing The Recognition Motif And Novel Substrates Of Carm1, Sitaram Gayatri

Dissertations and Theses (Open Access)

A limited pool of proteins attains vast functional repertoire due to posttranslational modifications (PTMs). Arginine methylation is a common posttranslational modification, which is catalyzed by a family of nine protein arginine methyltransferases or PRMTs. These enzymes deposit one or two methyl groups to the nitrogen atoms of arginine side-chains. Elucidating the substrate specificity of each PRMT will promote a better understanding of which signaling networks these enzymes contribute to. Although many PRMT substrates have been identified, and their methylation sites mapped, the optimal target motif for each of the nine PRMTs has not been systematically addressed. Here we describe the …

Characterizing The Activity Of Antimicrobial Peptides Against The Pathogenic Bacterium Clostridium Difficile In An Anaerobic Environment, Adenrele Mojeed Oludiran

Chemistry & Biochemistry Theses & Dissertations

Clostridium difficile is an anaerobic Gram-positive pathogen with high treatment costs and mortality and very high antibiotic tolerance. Antimicrobial host-defense peptides (HDPs) produced naturally by animal immune systems are promising candidates to develop novel therapies for bacterial infection because they cause oxidative stress that damages multiple targets in bacterial cells, so it is difficult for bacteria to evolve resistance to these attacks.

Piscidins, fish-derived HDPs that can also form complexes with copper (Cu) to enhance their activities, are very active against multiple bacterial species in an aerobic environment. We examined their activity against C. difficile and other species in an …

Advances In Amino Acid Analysis For Marine Related Matrices And Its Application To Coastal Shelf Settings In The Canadian Arctic, Rachel M. Mcmahon

OES Theses and Dissertations

Amino acids comprise up to 50% of organic matter in cellular material and are a major fraction of oceanic organic carbon. Amino acids are also considered highly labile during organic matter recycling, making them useful proxies for organic carbon cycling. Nevertheless, analysis of individual amino acids has been burdened by lengthy derivatization and complex analysis since the 1950s. In this thesis, I describe the modification of advanced analytical techniques, developed in the biomedical field, for analysis of marine matrices which allow the determination of at least 40 amino acids without the need for lengthy sample preparation and derivatization, twice the …

Lipid Transport Required To Make Lipids Of Photosynthetic Membranes, Evan Labrant, Allison C. Barnes, Rebecca Roston

Department of Biochemistry: Faculty Publications

Photosynthetic membranes provide much of the usable energy for life on earth. To produce photosynthetic membrane lipids, multiple transport steps are required, including fatty acid export from the chloroplast stroma to the endoplasmic reticulum, and lipid transport from the endoplasmic reticulum to the chloroplast envelope membranes. Transport of hydrophobic molecules through aqueous space is energetically unfavorable and must be catalyzed by dedicated enzymes, frequently on specialized membrane structures. Here, we review photosynthetic membrane lipid transport to the chloroplast in the context of photosynthetic membrane lipid synthesis. We independently consider the identity of transported lipids, the proteinaceous transport components, and membrane …

Glucosamine From Hydrolysis Of 3d Printing Chitosan For Osteoarthritis Treatment, Ruj Dansriboon, Laphon Premcharoen

The International Student Science Fair 2018

This project aims to introduce a new way for osteoarthritis treatment which is expected to increase in the future. Glucosamine is the main subject for a treatment, which can be derived by hydrolyzing chitosan. This project also includes extraction of chitosan from shrimp waste to make a worthy use of food waste from industry. In this project, 3D printer is applied to print chitosan gel since 3D printing is adjustable to form various shapes of the gel.

The research process begins with the extraction of chitosan from shrimp shells. For the next step, the percent of deacetylation of chitosan was …

Utilization Of Papaya’S Sap (Carica Papaya L.) And Water Lettuce (Pistia Stratiotes) To Reduce Protein Amount On Liquid Tofu Waste, Muhammad Dzulfikar Farkhan, Naila Aliyahandra Anzani, Nabila Fikria Santoso

The International Student Science Fair 2018

ABSTRACT

Liquid waste from tofu production is one of the causes of environmental pollution. This condition happens because liquid tofu waste contain protein. Protein is metabolized by bacteria formed ammonia which emits foul odor. On this research, the protein amount in liquid tofu waste is reduced by the application of papaya’s sap and water lettuce. This research is divided into several steps. First, collecting the liquid tofu waste. second, tapping the papaya’s sap. Third, poured the papaya’s sap into the tofu waste. the next step is keep the mixture between tofu waste and papaya’s sap rest for 6, 18, and …

Aβ42 Protofibrils Interact With, And Are Trafficked Through, Microglial-Derived Microvesicles, Lisa Gouwens, Mudar Ismail, Victoria Rogers, Nathan Zeller, Evan Garrad, Fatima Amtashar, Nyasha Makoni, David Osborn, Michael Nichols

Chemistry & Biochemistry Faculty Works

Microvesicles (MVs) and exosomes comprise a class of cell-secreted particles termed extracellular vesicles (EVs). These cargo-holding vesicles mediate cell-to-cell communication and have recently been implicated in neurodegenerative diseases such as Alzheimer’s disease (AD). The two types of EVs are distinguished by the mechanism of cell release and their size, with the smaller exosomes and the larger MVs ranging from 30 to 100 nm and 100 nm to 1 μm in diameter, respectively. MV numbers are increased in AD and appear to interact with amyloid-β peptide (Aβ), the primary protein component of the neuritic plaques in the AD brain. Because microglial …

N-Glycosylation In The Protease Domain Of Trypsin-Like Serine Proteases Mediates Calnexin-Assisted Protein Folding, Hao Wang, Shuo Li, Juejin Wang, Shenghan Chen, Xue-Long Sun, Qingyu Wu

Chemistry Faculty Publications

Trypsin-like serine proteases are essential in physiological processes. Studies have shown that N-glycans are important for serine protease expression and secretion, but the underlying mechanisms are poorly understood. Here, we report a common mechanism of N-glycosylation in the protease domains of corin, enteropeptidase and prothrombin in calnexin-mediated glycoprotein folding and extracellular expression. This mechanism, which is independent of calreticulin and operates in a domain-autonomous manner, involves two steps: direct calnexin binding to target proteins and subsequent calnexin binding to monoglucosylated N-glycans. Elimination of N-glycosylation sites in the protease domains of corin, enteropeptidase and prothrombin inhibits corin and enteropeptidase cell surface …