Biochemistry, Biophysics, and Structural Biology Commons^™

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 …

Anemarrhena Asphodeloides Bunge And Its Constituent Timosaponin‐Aiii Induce Cell Cycle Arrest And Apoptosis In Pancreatic Cancer Cells, Catherine B. Marelia, Arielle Sharp, Tiffany A. Shemwell, Y. C. Zhang, Brant R. Burkhardt

Molecular Biosciences Faculty Publications

Pancreatic cancer is one of the most recalcitrant and lethal of all cancers. We examined the effects of Anemarrhena asphodeloides (AA) and timosaponin‐AIII (TAIII), a steroidal saponin present in AA, on pancreatic cancer cell proliferation and aimed to elucidate their potential apoptotic mechanisms of action. Viability assays and cell cycle analysis revealed that both AA and TAIII significantly inhibited pancreatic cancer cell proliferation and cell cycle progression compared to treatment with gemcitabine, the standard chemotherapeutic agent for advanced pancreatic cancer. We identified a dose‐dependent increase in caspase‐dependent apoptosis and activation of pro‐apoptotic PI3K/Akt pathway proteins, with a subsequent downregulation of …

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 …

Preparation And Characterization Of Functionalized Heparin-Loaded Poly-Ɛ-Caprolactone Fibrous Mats To Prevent Infection With Human Papillomaviruses, Daniela Gonzalez, Jorge Ragusa, Peter C. Angeletti, Gustavo F. Larsen

Department of Chemical and Biomolecular Engineering: Faculty Publications

In this study, heparin-loaded poly-ε-caprolactone (PCL) fibrous mats were prepared and characterized based on their physical, cytotoxic, thermal, and biological properties. The main objective of the work described here was to test the hypothesis that incorporation of heparin into a PCL carrier could serve as bio-compatible material capable of inhibiting Human Papillomavirus (HPV) infection. The idea of firmly anchoring heparin to capture soluble virus, vs. a slow heparin release to inhibit a virus in solution was tested. Thus, one material was produced via conventional heparin matrix encapsulation and electrohydrodynamic fiber processing in one step. A second type of material was …

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 …

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 …

Zika Modulates Arthropod Histone Methylation In Mosquito Cells, Telvin Lee Harrell

Biological Sciences Theses & Dissertations

Epigenetics is the heritable series of covalent modifications that affect chromatin structure, gene expression, and protein function. Methylation is one such epigenetic modification that involves the addition of chemical modifying entities, such as methyl groups, on nucleic acids or proteins. Recent studies have reported that Zika virus (ZIKV) modulates methylation of human and viral RNA important for its replication in vertebrate cells. However, little is known whether ZIKV exerts methylation in arthropod vectors. In this study, I show that ZIKV modulates S-adenosyl methionine (SAMe) synthase, an enzyme involved in the production of SAMe, and histone methylation for its survival in …

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 …

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 …

Exploring The Role Of Rna Polymerase Iii Complex Assembly On Ribosomal Dna Silencing In Saccharomyces Cerevisiae, Kyle Thomas Kern

LSU Doctoral Dissertations

The yeast rDNA region is host to a number of transcriptional regulatory elements, which work in conjunction to generate essential RNA subunits of ribosomes, as well as protecting the region from DNA damage. The role of RNA polymerase III complex binding at the 5S gene on rDNA silencing in the NTS2 region was investigated, both by use of a TY1:MET15 reporter insert and a MET15 gene integration at an endogenous SphI site. It was discovered that Pol III complexes do have an effect on reporter expression in the NTS2 region, though the specific effect was different based on the method …

Study Of The Visual Adaptation Mechanism In Marine Species With The Change Of Habitation Depth., Demid Osipov, Daniil Moshnikov

The International Student Science Fair 2018

The goal of our work was to determine the principal mechanisms that provide the difference in visual perception of two marine species that live on different depths: T. Pacificus and O. Vulgaris. In nature, visual perception of species that live deeper is shifted towards the blue region. This is related to the fact that red, orange and yellow light is absorbed more strongly by water than the blue light. On the other hand, the visual perception spectrum of an animal is determined by the absorption spectrum of the "light sensor" located in rods and cones of its eye retina. These …

Snf1 Cooperates With The Cwi Mapk Pathway To Mediate The Degradation Of Med13 Following Oxidative Stress, Stephen D Willis, David C Stieg, Kai Li Ong, Ravina Shah, Alexandra K. Strich, Julianne H Grose, Katrina F Cooper

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Eukaryotic cells, when faced with unfavorable environmental conditions, mount either pro-survival or pro-death programs. The conserved cyclin C-Cdk8 kinase plays a key role in this decision. Both are members of the Cdk8 kinase module that, along with Med12 and Med13, associate with the core Mediator complex of RNA polymerase II. In Saccharomyces cerevisiae, oxidative stress triggers Med13 destruction, which releases cyclin C into the cytoplasm to promote mitochondrial fission and programmed cell death. The SCFGrr1 ubiquitin ligase mediates Med13 degradation dependent on the cell wall integrity pathway, MAPK Slt2. Here we show that the AMP kinase Snf1 activates a second …

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 …

Identification And Folding Of Mirna Through Machine Learning, Xavier Pellow

The International Student Science Fair 2018

As of writing, there is currently no efficient way to accurately identify miRNA or predict the structure of miRNA without the usage of a lab. The purpose of this work is to provide a framework which allows for efficient identification of mature miRNA and folding of pre-miRNA using a feedforward neural network (FFNN) and probabilistic context-free grammar (PCFG) parsing, respectively. After training, the FFNN developed an accuracy of 98%. Out of all control cases using high confidence miRNA, the PCFG used returned folded structures that matched the canonical structures to an accuracy of 81%. The results of this work indicates …

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 …