Biochemistry, Biophysics, and Structural Biology Commons^™

Gamma-Aapeptides As A New Class Of Peptidomimetics: Synthesis, Structures, And Functions, Haifan Wu

USF Tampa Graduate Theses and Dissertations

Peptidomimetics are synthetic oligomers that resemble the activities of peptides. Their advantages over peptides include high stability towards proteolysis and enormous chemical diversity. Over the past two decades, there have been extensive efforts to develop peptide mimics, such as beta-peptides, peptoids, D-peptides, etc. The research on peptidomimetics have led to many important applications in both medicinal and material science. In order to explore new functions, the discovery of peptidomimetics with novel frameworks is essential. We reported the synthesis and evaluation of a new class of peptidomimetics, termed as gamma-AApeptides. Previous studies of gamma-AApeptides have revealed that gamma-AApeptides are highly resistant …

Functional Expression And Characterization Of A Truncated Candida Antarctica Lipase B In Yeast, Samantha Robinson

Theses and Dissertations

Candida antarctica lipase B is an enzyme capable of hydrolyzing ester bonds in a lipid-water interface with potential to become a useful biocatalyst for production of biodiesel fuel. Enzymatically catalyzing the transesterification of triacylglycerides to produce fatty acid alkyl esters (biodiesel) is an environmentally cleaner alternative to the current process which utilizes chemical reagents as catalysts. Optimization and development of strains to express highly active, stable, large quantities of these biocatalysts is essential for inexpensive production of biodiesel. Additionally, lipase enzymes can be immobilized onto a resin, eliminating the need to recover the catalyst from the product and allowing multiple …

Long-Term Impacts Of Disturbance On Nitrogen-Cycling Bacteria In A New England Salt Marsh, Anne E. Bernhard, Courtney Dwyer, Adrian Idrizi, Geoffrey Bender, Rachel Zwick

Biology Faculty Publications

Recent studies on the impacts of disturbance on microbial communities indicate communities show differential responses to disturbance, yet our understanding of how different microbial communities may respond to and recover from disturbance is still rudimentary. We investigated impacts of tidal restriction followed by tidal restoration on abundance and diversity of denitrifying bacteria, ammonia-oxidizing bacteria (AOB), and ammonia-oxidizing archaea (AOA) in New England salt marshes by analyzing nirS and bacterial and archaeal amoA genes, respectively. TRFLP analysis of nirS and betaproteobacterial amoA genes revealed significant differences between restored and undisturbed marshes, with the greatest differences detected in …

A Quick Guide For Building A Successful Bioinformatics Community., Aidan Budd, Manuel Corpas, Michelle D Brazas, Jonathan C Fuller, Jeremy Goecks, Nicola J Mulder, Magali Michaut, B F Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg

Computational Biology Institute

"Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding …

Intramolecular S···O Chalcogen Bond As Stabilizing Factor In Geometry Of Substituted Phenyl-Sf3 Molecules, Vincent De Paul Nziko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Density functional methods are used to examine the geometries and energetics of molecules containing a phenyl ring joined to the trigonal bipyramidal SF3 framework. The phenyl ring has a strong preference for an equatorial position. This preference remains when one or two ether -CH2OCH3 groups are added to the phenyl ring, ortho to SF3, wherein an apical structure lies nearly 30 kcal/mol higher in energy. Whether equatorial or apical, the molecule is stabilized by a S···O chalcogen bond, sometimes augmented by CH···F or CH···O H-bonds. The strength of the intramolecular S···O bond is estimated to lie in the range between …

Characterization Of Ranbpm Molecular Determinants That Control Its Subcellular Localization, Louisa M Salemi, Sandra O Loureiro, Caroline Schild-Poulter

Biochemistry Publications

RanBPM/RanBP9 is a ubiquitous, nucleocytoplasmic protein that is part of an evolutionary conserved E3 ubiquitin ligase complex whose function and targets in mammals are still unknown. RanBPM itself has been implicated in various cellular processes that involve both nuclear and cytoplasmic functions. However, to date, little is known about how RanBPM subcellular localization is regulated. We have conducted a systematic analysis of RanBPM regions that control its subcellular localization using RanBPM shRNA cells to examine ectopic RanBPM mutant subcellular localization without interference from the endogenously expressed protein. We show that several domains and motifs regulate RanBPM nuclear and cytoplasmic localization. …

The Artificial Divide Between Biomedical Sciences And Clinical Medicine In Undergraduate Medical Education, Abdul Rehman, Noor Ul-Ain Baloch, Muhammad Awais

Department of Biological & Biomedical Sciences

No abstract provided.

Proline Metabolism Increases Katg Expression And Oxidative Stress Resistance In Escherichia Coli, Lu Zhang, James R. Alfano, Donald F. Becker

Department of Biochemistry: Faculty Publications

The oxidation of L-proline to glutamate in Gram-negative bacteria is catalyzed by the proline utilization A (PutA) flavoenzyme, which contains proline dehydrogenase (PRODH) and _1-pyrroline-5-carboxylate (P5C) dehydrogenase domains in a single polypeptide. Previous studies have suggested that aside from providing energy, proline metabolism influences oxidative stress resistance in different organisms. To explore this potential role and the mechanism, we characterized the oxidative stress resistance of wild-type and putA mutant strains of Escherichia coli. Initial stress assays revealed that the putA mutant strain was significantly more sensitive to oxidative stress than the parental wild-type strain. Expression of PutA in the …

Functional Characterization Of The Plant 15-Cis-Zeta-Carotene Isomerase Z-Iso, Jesus Alonso Beltran Zambrano

Dissertations, Theses, and Capstone Projects

Vitamin A deficiency is a widespread health issue in the tropics. To solve this issue, efforts are underway to increase provitamin A carotenoids such as β-carotene in staple crops which can be achieved by breeding, metabolic engineering or a combination of both approaches. However, rational strategies to improve carotenoid content in crops require sufficient knowledge of pathway regulation. Therefore, to better understand how plants synthesize provitamin A and to guide metabolic engineering strategies in crops such as maize, the functional characterization of the new ζ-carotene isomerase (Z-ISO) is of significant importance.

Z-ISO was recently discovered in maize and Arabidopsis (Chen …

De Novo Design And Engineering Of Functional Metal And Porphyrin-Binding Protein Domains, Bernard Howard Everson

Dissertations, Theses, and Capstone Projects

In this work, I describe an approach to the rational, iterative design and characterization of two functional cofactor-binding protein domains. First, a hybrid computational/experimental method was developed with the aim of algorithmically generating a suite of porphyrin-binding protein sequences with minimal mutual sequence information. This method was explored by generating libraries of sequences, which were then expressed and evaluated for function. One successful sequence is shown to bind a variety of porphyrin-like cofactors, and exhibits light- activated electron transfer in mixed hemin:chlorin e6 and hemin:Zn(II)-protoporphyrin IX complexes. These results imply that many sophisticated functions such as cofactor binding and electron …

Conformational Heterogeneity And Exchange Within The Junction Of The Human U2-U6 Snrna Complex Measured By 19f Nmr Spectroscopy, Caijie Zhao

Dissertations, Theses, and Capstone Projects

Pre-mRNA splicing, the process by which non-coding sequences are removed and coding sequences are ligated, plays an important role in the maturation of precursor messenger RNA molecules prior to their translation into proteins. In eukaryotes, splicing is catalyzed by the spliceosome, a large and dynamic nuclear macromolecular "machine" that comprises five small nuclear (sn)RNA molecules and more than one hundred proteins. Among the RNA components, the complex formed between the U2 and U6 snRNA molecules is implicated in catalytic activity. In this dissertation, I have used ¹⁹F NMR techniques to characterize the conformation ("fold") and dynamics of a protein-free …

Using Multiconformation Continuum Electrostatics Model For Pka And Proton Transfer Pathway Calculations In Protein, Xuyu Zhu

Dissertations, Theses, and Capstone Projects

Residue protonation state changes and proton transfer reactions in protein are basic and ubiquitous reactions in biological chemistry. The Multiconformation Continuum Electrostatics (MCCE) program is applied here to calculate the pKa of residues in the specially engineered protein staphylococcal nuclease (SNase) and further modified to investigate the unidirectional proton transfer mechanism in the proton pump protein bacteriorhodopsin. The pKa$_s$ are obtained by Monte Carlo sampling of coupled side chain protonations and positions as a function of pH in MCCE. The pKa$_s$ of 96 acids and bases introduced into buried sites in the SNase protein were calculated and the results compared …

Synthesis Of Bioinspired Carbohydrate Amphiphiles That Promote And Inhibit Biofilms, Eric L. Dane, Alicia E. Ballok, George A. O'Toole, Mark W. Grinstaff

Dartmouth Scholarship

The synthesis and characterization of a new class of bioinspired carbohydrate amphiphiles that modulate Pseudomonas aeruginosa biofilm formation are reported. The carbohydrate head is an enantiopure poly-amido-saccharide (PAS) prepared by a controlled anionic polymerization of β-lactam monomers derived from either glucose or galactose. The supramolecular assemblies formed by PAS amphiphiles are investigated in solution using fluorescence assays and dynamic light scattering. Dried samples are investigated using X-ray, infrared spectroscopy, and transmission electron microscopy. Additionally, the amphiphiles are evaluated for their ability to modulate biofilm formation by the Gram-negative bacterium Pseudomonas aeruginosa. Remarkably, from a library of eight amphiphiles, we identify …

Protein Motions Control Activity In Biologically Important Phosphatases, Ryan Hirschi, Gwen Moise

Research on Capitol Hill

No abstract provided.

Altered Cd161bright Cd8+ Mucosal Associated Invariant T (Mait)-Like Cell Dynamics And Increased Differentiation States Among Juvenile Type 1 Diabetics., Robert Z. Harms, Kristina M. Lorenzo, Kevin P. Corley, Monina S. Cabrera, Nora Sarvetnick

Journal Articles: Regenerative Medicine

Type 1A diabetes (T1D) is believed to be caused by immune-mediated destruction of β-cells, but the immunological basis for T1D remains controversial. Microbial diversity promotes the maturation and activation of certain immune subsets, including CD161bright CD8+ mucosal associated invariant T (MAIT) cells, and alterations in gut mucosal responses have been reported in type 1 diabetics (T1Ds). We analyzed T cell populations in peripheral blood leukocytes from juvenile T1Ds and healthy controls. We found that proportion and absolute number of MAIT cells were similar between T1Ds and controls. Furthermore, while MAIT cell proportions increased with age among healthy controls, this trend …

A Hierarchical Cascade Of Second Messengers Regulates Pseudomonas Aeruginosa Surface Behaviors, Yun Luo, Kun Zhao, Amy E. Baker, Sherry L. Kuchma, Kimberly A. Coggan, Matthew C. Wolfgang, Gerard C.L. Wong, George A. O’Toole

Dartmouth Scholarship

Biofilms are surface-attached multicellular communities. Using single-cell tracking microscopy, we showed that apilY1 mutant of Pseudomonas aeruginosa is defective in early biofilm formation. We leveraged the observation that PilY1 pro- tein levels increase on a surface to perform a genetic screen to identify mutants altered in surface-grown expression of this pro- tein. Based on our genetic studies, we found that soon after initiating surface growth, cyclic AMP (cAMP) levels increase, depen- dent on PilJ, a chemoreceptor-like protein of the Pil-Chp complex, and the type IV pilus (TFP). cAMP and its receptor protein Vfr, together with the FimS-AlgR two-component system (TCS), …

Characterization Of Biomass Burning Emissions From Cooking Fires, Peat, Crop Residue, And Other Fuels With High-Resolution Proton-Transfer-Reaction Time-Of-Flight Mass Spectrometry, C. Stockwell, P. Veres, J. Williams

Chemistry and Biochemistry Faculty Publications

We deployed a high-resolution proton-transferreaction time-of-flight mass spectrometer (PTR-TOF-MS) to measure biomass-burning emissions from peat, crop residue, cooking fires, and many other fire types during the fourth Fire Lab at Missoula Experiment (FLAME-4) laboratory campaign. A combination of gas standard calibrations and composition sensitive, mass-dependent calibration curves was applied to quantify gas-phase non-methane organic compounds (NMOCs) observed in the complex mixture of fire emissions. We used several approaches to assign the best identities to most major “exact masses”, including many high molecular mass species. Using these methods, approximately 80–96% of the total NMOC mass detected by the PTR-TOFMS and Fourier …

Structural Mechanism Of Laforin Function In Glycogen Dephosphorylation And Lafora Disease, Madushi Raththagala, M. Kathryn Brewer, Matthew W. Parker, Amanda R. Sherwood, Brian K. Wong, Simon Hsu, Travis M. Bridges, Bradley C. Paasch, Lance M. Hellman, Satrio Husodo, David A. Meekins, Adam O. Taylor, Benjamin D. Turner, Kyle D. Auger, Vikas V. Dukhande, Srinivas Chakravarthy, Pascual Sanz, Virgil L. Woods Jr., Sheng Li, Craig Vander Kooi, Matthew S. Gentry

Molecular and Cellular Biochemistry Faculty Publications

Glycogen is the major mammalian glucose storage cache and is critical for energy homeostasis. Glycogen synthesis in neurons must be tightly controlled due to neuronal sensitivity to perturbations in glycogen metabolism. Lafora disease (LD) is a fatal, congenital, neurodegenerative epilepsy. Mutations in the gene encoding the glycogen phosphatase laforin result in hyperphosphorylated glycogen that forms water-insoluble inclusions called Lafora bodies (LBs). LBs induce neuronal apoptosis and are the causative agent of LD. The mechanism of glycogen dephosphorylation by laforin and dysfunction in LD is unknown. We report the crystal structure of laforin bound to phosphoglucan product, revealing its unique integrated …

Observations And Analysis Of Organic Aerosol Evolution In Some Prescribed Fire Smoke Plumes, A. A. May, T. Lee, G. R. Mcmeeking, Sheryl Kashi Akagi, A. P. Sullivan, S. P. Urbanski, Robert Yokelson, S. M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Open biomass burning is a significant source of primary air pollutants such as particulate matter and non-methane organic gases. However, the physical and chemical atmospheric processing of these emissions during transport is poorly understood. Atmospheric 5 transformations of biomass burning emissions have been investigated in environmental chambers, but there have been limited opportunities to investigate these transformations in the atmosphere. In this study, we deployed a suite of real-time instrumentation on a Twin Otter aircraft to sample smoke from prescribed fires in South Carolina, conducting measurements at both the source and downwind to character10 ize smoke evolution with atmospheric aging. …

Accidental Poison: Analysis Of 1,4-Butanediol In A Popular Children's Arts And Crafts Toy, Christopher R. Dockery, John H. Shugart, Jonathan D. Parker, William J. Lawson

Faculty Articles

A popular children's arts and crafts toy made international headlines when it was discovered that 1,4-butanediol had been substituted into some of its formulations. The chemical 1,4-butanediol rapidly converts to the date-rape drug g-hydroxybutyric acid (GHB) upon ingestion and resulted in the accidental poisoning of some children. In this experiment, students extract 1,4-butanediol from commercially available toy beads (or prepared simulations) using their knowledge of pharmaceutical chemistry, solubility, etc. Using case studies available in the literature, students develop a quantitative analysis experiment for 1,4-butanediol extracted from the toy beads and, through approximation, relate the extractable amount of 1,4-butanediol to dose-response …

Ploidy Variation In Multinucleate Cells Changes Under Stress, Cori A. Anderson, Samantha Roberts, Huaiying Zhang, Courtney M. Kelly, Alexxy Kendall, Changhwan Lee, John Gerstenberger, Aaron B. Koenig, Ruth Kabeche, Amy S. Gladfelter

Dartmouth Scholarship

Ploidy variation is found in contexts as diverse as solid tumors, drug resistance in fungal infection, and normal development. Altering chromosome or genome copy number supports adaptation to fluctuating environments but is also associated with fitness defects attributed to protein imbalances. Both aneuploidy and polyploidy can arise from multinucleate states after failed cytokinesis or cell fusion. The consequences of ploidy variation in syncytia are difficult to predict because protein imbalances are theoretically buffered by a common cytoplasm. We examined ploidy in a naturally multinucleate fungus, Ashbya gossypii. Using integrated lac operator arrays, we found that chromosome number varies substantially …

Identification And Characterization Of N-Acyltransferase Enzymes That Are Involved In The Biosynthesis Of Fatty Acid Amides, Daniel Robert Dempsey

USF Tampa Graduate Theses and Dissertations

Fatty acid amides are an emerging family of bioactive lipids that consists of N-acylethanolamines, N-acylarylalkylamides, N-acylglycines, N-acyl amino acids, N-monoacylpolyamides, and primary fatty acid amides. Short chain fatty acid amides are products of inactivated biogenic amines such as dopamine, histamine, octopamine, and serotonin, whereas long chain fatty acid amides have been implicated in a number of physiological process such as the perception and inhibition of chronic pain through binding to their specific receptors. The most famous; therefore, the most studied long chain fatty acid amide is anandamide or also known as N-arachidonylethanolamine. The biosynthesis …

Membrane Topology Of A Broad-Spectrum Resistance Factor Responsible For Lipid Modification In Enterococcus Faecium., Jesse Harrison

Electronic Theses and Dissertations

Aminoacylphosphatidylglycerol synthases (aaPGSs) are integral membrane proteins that use aminoacyl-tRNAs as substrates to catalyze the addition of amino acids to phosphatidylglycerol (PG) in the cytoplasmic membranes of bacteria. Addition of amino acids to PG decreases the net negative charge of the membrane, conferring resistance to various classes of antibacterial agents (i.e., cationic antimicrobial peptides, beta-lactams, glycopeptides, and lipopeptides) and protecting the cell against osmotic stress and acidic conditions. aaPGS homologs are found in a variety of clinically relevant microorganisms, including Enterococcus faecium, which is increasingly found to be the etiologic agent of antibiotic-resistant nosocomial infections. Although the broad distribution of …

Trail-Based High Throughput Screening Reveals A Link Between Trail-Mediated Apoptosis And Glutathione Reductase, A Key Component Of Oxidative Stress Response., Dmitri Rozanov, Anton Cheltsov, Eduard Sergienko, Stefan Vasile, Vladislav Golubkov, Alexander E Aleshin, Trevor Levin, Elie Traer, Byron Hann, Julia Freimuth, Nikita Alexeev, Max A Alekseyev, Sergey P Budko, Hans Peter Bächinger, Paul Spellman

Computational Biology Institute

A high throughput screen for compounds that induce TRAIL-mediated apoptosis identified ML100 as an active chemical probe, which potentiated TRAIL activity in prostate carcinoma PPC-1 and melanoma MDA-MB-435 cells. Follow-up in silico modeling and profiling in cell-based assays allowed us to identify NSC130362, pharmacophore analog of ML100 that induced 65-95% cytotoxicity in cancer cells and did not affect the viability of human primary hepatocytes. In agreement with the activation of the apoptotic pathway, both ML100 and NSC130362 synergistically with TRAIL induced caspase-3/7 activity in MDA-MB-435 cells. Subsequent affinity chromatography and inhibition studies convincingly demonstrated that glutathione reductase (GSR), a key …

Investigation Of Sex Differences In The Expression Of Rora And Its Transcriptional Targets In The Brain As A Potential Contributor To The Sex Bias In Autism, Valerie Wailin Hu, Tewarit Sarachana, Rachel M. Sherrard, Kristen M. Kocher

Biochemistry and Molecular Medicine Faculty Publications

Background

Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by significant impairment in reciprocal social interactions and communication coupled with stereotyped, repetitive behaviors and restricted interests. Although genomic and functional studies are beginning to reveal some of the genetic complexity and underlying pathobiology of ASD, the consistently reported male bias of ASD remains an enigma. We have recently proposed that retinoic acid-related orphan receptor alpha (RORA), which is reduced in the brain and lymphoblastoid cell lines of multiple cohorts of individuals with ASD and oppositely regulated by male and female hormones, might contribute to the sex bias …

Bioxpress: An Integrated Rna-Seq-Derived Gene Expression Database For Pan-Cancer Analysis., Quan Wan, Hayley Dingerdissen, Yu Fan, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Cheng Yan, Haichen Zhang, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

BioXpress is a gene expression and cancer association database in which the expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas, International Cancer Genome Consortium, Expression Atlas and publications. The BioXpress database includes expression data from 64 cancer types, 6361 patients and 17 469 genes with 9513 of the genes displaying differential expression between tumor and normal samples. In addition to data directly retrieved from RNA-seq data repositories, manual biocuration of publications supplements the available cancer association annotations in the database. All cancer types are mapped to Disease Ontology terms to facilitate a uniform …

Enabling Real-Time Ultrasound Imaging Of Soft Tissue Mechanical Properties By Simplification Of The Shear Wave Motion Equation, Aaron J. Engel, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Ultrasound based shear wave elastography (SWE) is a technique used for non-invasive characterization and imaging of soft tissue mechanical properties. Robust estimation of shear wave propagation speed is essential for imaging of soft tissue mechanical properties. In this study we propose to estimate shear wave speed by inversion of the firstorder wave equation following directional filtering. This approach relies on estimation of first-order derivatives which allows for accurate estimations using smaller smoothing filters than when estimating second-order derivatives. The performance was compared to three current methods used to estimate shear wave propagation speed: direct inversion of the wave equation (DIWE), …

2015 Oklahoma Research Day Full Program, Northeastern State University

Oklahoma Research Day Abstracts

This document contains all abstracts from the 2015 Oklahoma Research Day held at Northeastern State University.

An Investigation Of The Effect Of Mn2+ On The Fth1 Ire-Irp Complex, Eric Thomas Mendenhall

Theses, Dissertations and Capstones

Iron is a widely distributed metal found in almost every physiological system in nature, thus being an essential part of life. Iron homeostasis in the human body must be tightly regulated as iron is both beneficial and harmful to different cellular processes. Ferritin is a protein that has a prominent role in maintaining iron homeostasis via iron sequestration. Additionally, this protein itself is regulated by the Iron Responsive Element (IRE) and its interaction with an apoaconitase protein or the Iron Regulatory Protein (IRP). The binding of the IRP to this IRE, located on the 5’ untranslated stem loop region of …

Epigenetic Role Of Ptip In Mouse Spermatogenesis, Chengjing Liu

Theses, Dissertations and Capstones

In mammals, spermatogenesis is a biological process inside the testis to produce spermatozoa from spermatogonia. This process is governed by both genetic and epigenetic mechanisms and thus is a powerful system for epigenetic research. Methylation of histone 3 lysine 4 (H3K4) is an epigenetic mark, which has been found to be dynamically modulated in mouse male germ cells during spermatogenesis. Pax2 Transactivation domain Interaction Protein (PTIP) has been recently identified as part of a H3K4 methyltransferase complex. In this study, I hypothesize that PTIP is an essential epigenetic regulator in mouse spermatogenesis. To test this hypothesis, I first established a …