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Discovery And Characterisation Of A Novel Toxin From Dendroaspis Angusticeps, Named Tx7335, That Activates The Potassium Channel Kcsa, Ivan O. Rivera-Torres, Tony B. Jin, Martine Cadene, Brian T. Chait, Sébastien F. Poget

Publications and Research

Due to their central role in essential physiological processes, potassium channels are common targets for animal toxins. These toxins in turn are of great value as tools for studying channel function and as lead compounds for drug development. Here, we used a direct toxin pull-down assay with immobilised KcsA potassium channel to isolate a novel KcsA-binding toxin (called Tx7335) from eastern green mamba snake (Dendroaspis angusticeps) venom. Sequencing of the toxin by Edman degradation and mass spectrometry revealed a 63 amino acid residue peptide with 4 disulphide bonds that belongs to the three-finger toxin family, but with a unique modification …

The Effect Of Nitrate On The Release Of Glucose Into The Hemolymph Of Crayfish, Procambarus Clarkii, Alec R. Flores, Lee Kats, David Green, Gary Bucciarelli

Seaver College Research And Scholarly Achievement Symposium

Pollutants can change the behaviors of invertebrate stream animals. The level of one common pollutant, nitrate (NO3), has been rising in many local rivers and streams throughout the United States due to increases in anthropogenic sources. Nitrate, heavily regulated for its toxic effects to human health, namely the aiding in the development of cancer, also dangerously affects aquatic species by converting oxygen-carrying pigments to forms that are incapable of carrying oxygen. To understand the stress effects of ambient nitrate exposure on P. clarkii, we collected hemolymph samples from red swamp crayfish (Procambarus clarkii) over a 48-hour period after exposure to …

Section Abstracts: Chemistry

Virginia Journal of Science

Abstracts of the Chemistry Section for the 94th Annual Virginia Academy of Science Meeting, May 18-20, 2016, at University of Mary Washington, Fredericksburg, VA.

The Anode Challenge For Lithium-Ion Batteries: A Mechanochemically Synthesized Sn-Fe-C Composite Anode Surpasses Graphitic Carbon, Zhixin Dong, Ruibo Zhang, Dongsheng Ji, Natasha A. Chernova, Khim Karki, Shawn Sallis, Louis Piper, Stanley M. Whittingham

Chemistry Faculty Scholarship

Carbon-based anodes are the key limiting factor in increasing the volumetric capacity of lithium-ion batteries. Tin-based composites are one alternative approach. Nanosized Sn-Fe-C anode materials are mechanochemically synthesized by reducing SnO with Ti in the presence of carbon. The optimum synthesis conditions are found to be 1:0.25:10 for initial ratio of SnO, Ti, and graphite with a total grinding time of 8 h. This optimized composite shows excellent extended cycling at the C/10 rate, delivering a first charge capacity as high as 740 mAh g(-1) and 60% of which still remained after 170 cycles. The calculated volumetric capacity significantly exceeds …

Analysis Of Scientific Argumentation In Two Physical Chemistry Classrooms Using The Pogil Approach, Alena C. Moon

Open Access Dissertations

The benefits of facilitating argumentation in science education have been well reported (Jimenez-Aleixandre & Erduran, 2007). Engaging in argumentation has shown to model authentic scientific inquiry as well as promote development of content knowledge. However, less emphasis has been placed on facilitating argumentation in upper level undergraduate courses, though it is important for evaluating undergraduate curricula to characterize upper level students’ scientific reasoning. This work considers two implementations of the POGIL physical chemistry curriculum and evaluates the classroom argumentation. The researchers aimed to consider the content of the arguments and dialectical features characteristic of socially constructed arguments (Nielson, 2013). To …

The Coastal Monitor: Vol. 1, No. 2, John Tanacredi Ph.D.

The Coastal Monitor

At a recent event a colleague asked me, “So what do you do at CERCOM?” My immediate response was the “M” word fundamentally! After 45 years involved in environmental sciences, monitoring remains the most important and critical aspect of not only any field station in support of the academics conducted, but the seminal responsibility to be able, as a scientist, to reveal trends in the massive volume of data collected through routine monitoring exercises. It is extremely rare for a single data point, or even a single season of data, no matter how accurate the individual data point is, to …

Analysis Of Linoleic Acid Peroxidation Products By Gc/Ms, Joy Nyaanga

Celebration of Scholarship 2012-2017

This project utilized gas chromatography – mass spectrometry (GC-MS) to analyze the lipid peroxidation products of linoleic acid, an essential ω-6 fatty acid, and its reaction with oxygen. Optimum reaction conditions were identified by testing various combinations of variables: buffer, pH, oxidant, and time. With treatment of optimum conditions, several products were identified including, 2,4-decadienal, 4-hydroxy-2-nonenal (HNE), and 4-oxo-2-nonenal (ONE). The mechanisms behind the formation of these products have been proposed by several researchers. It was identified that varying oxidant concentration, pH, or time greatly impacted the obtained concentrations of final oxidation products. Additionally, beta-carotene and Vitamin E were tested …

Proposed Mechanism Of Alzheimer’S Disease: The Role Of Oxidative Stress A Review Of Scientific Literature, Alicia Monahan

Senior Honors Projects

Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder that has become the sixth leading cause of death in the United States. The most notable neuropathological hallmarks of AD are the accelerated accumulation of β-amyloid deposits around neurons and the accumulation of neurofibrillary tangles (NFT) within neurons. These abnormalities block proteasome function, inhibit mitochondrial function, alter biometal levels, stimulate inflammatory processes, disrupt synaptic communication, and ultimately result in cell death. Mitochondrial dysfunction has been cited as an underlying cause of AD pathologies, specifically by enhancing the production and accumulation of β-amyloid. Once the β-amyloid oligomers form, they disrupt the Ca^{2+ …}

Advances In Solid Phase Microextraction For The Analysis Of Volatile Compounds In Explosives, Tire Treatments, And Entomological Specimens, William D. Kranz

Open Access Dissertations

Solid phase microextraction is a powerful and versatile technique, well-suited to the analysis of numerous samples of forensic interest. The exceptional sensitivity of the SPME platform, combined with its adaptability to traditional GC-MS systems and its ability to extract samples with minimal work-up, make it appropriate to applications in forensic laboratories.

In a series of research projects, solid phase microextraction was employed for the analysis of explosives, commercial tire treatments, and entomological specimens. In the first project, the volatile organic compounds emanating from two brands of pseudo-explosive training aids for use in detector dog imprinting were determined by SPME-GC-MS, and …

Development Of A Kinetic Model For The Transesterification Of Glycerol Fatty Acid Triesters Using 1H (1d And 2d) Nmr, Leonard W. Sprague

Honors Program Theses and Projects

Fossil fuels dating back to the first coal mine dug from the Earth have been vital to society’s advances, but have come at a significant cost. Rise in pollutants such as CO2 and particulate matter due to combustion byproducts of these fuels (coal, oil, gasoline, diesel) continue to negatively impact the environment, harming various ecosystems by disrupting precarious balances. Attempts have been made to “clean” fossil fuels, but only to temporary degrees of success. Alternative energy sources such as solar, wind, or hydroelectric are increasing in viability, but are often a difficult transition for fossil fuel reliant individuals. Biodiesel (Fatty …

Synthesis And Characterization Of Organic-Inorganic Hybrid Materials For Thermoelectric Devices, Paige M. Huzyak

Masters Theses & Specialist Projects

The development of organic-inorganic hybrid materials is of great interest in thermoelectrics for its potential to combine the desirable characteristics of both classes of materials. Thermoelectric materials must combine low thermal conductivity with high electrical conductivity, but in most materials, thermal and electrical conductivity are closely related and positively correlated. By combining the low thermal conductivity, flexibility, facile processing, and low cost of organic components with the high electrical conductivity and stability of inorganic components, materials with beneficial thermoelectric properties may be realized.

Here, we describe the synthesis and characterization of anthracene-containing organic-inorganic hybrid materials for thermoelectric purposes. Specifically, POSS-ANT …

Binding Of Oxaliplatin And Its Analogs With Dna Nucleotides At Variable Ph And Concentration Levels, Rippa Sehgal

Masters Theses & Specialist Projects

Oxaliplatin is one of the three FDA-approved platinum anticancer drugs and considered a third generation drug, discovered after the first generation drug cisplatin and second generation drug carboplatin. It is known to react with proteins and DNA nucleotides in the body. Reaction with DNA occurs primarily at guanosine residues and secondarily at adenine residues for oxaliplatin and other platinum drugs. We have previously studied oxaliplatin and an analog with additional steric hindrance in the amine ligand and found that the analog had different reactivity with methionine. Now, we have prepared oxaliplatin and its three analogs Pt(Me2dach)(ox), Pt(en)(ox) and Pt(Me4en)(ox) and …

Polyglutamine Aggregates Impair Lipid Membrane Integrity And Enhance Lipid Membrane Rigidity, Chian Sing Ho, Nawal K. Khadka, Fengyu She, Jianfeng Cai, Jianjun Pan

Physics Faculty Publications

Lipid membranes are suggested as the primary target of amyloid aggregates. We study aggregates formed by a polyglutamine (polyQ) peptide, and their disruptive effect on lipid membranes. Using solution atomic force microscopy (AFM), we observe polyQ oligomers coexisting with short fibrils, which have a twisted morphology that likely corresponds to two intertwined oligomer strings. Fourier transform infrared spectroscopy reveals that the content of β-sheet enriched aggregates increases with incubation time. Using fluorescence microscopy, we find that exposure to polyQ aggregates results in deflated morphology of giant unilamellar vesicles. PolyQ aggregates induced membrane disruption is further substantiated by time-dependent calcein leakage …

Investigation Of The Interactions Between Pt(Ii) And Pd(Ii) Derivatives Of 5,10,15,20-Tetrakis (N-Methyl-4-Pyridyl) Porphyrin And G-Quadruplex Dna, Navin C. Sabharwal , '14, O. Mendoza, John Michael Nicoludis , '12, Thomas Ruan , '16, J.-L. Mergny, Liliya A. Yatsunyk

Chemistry & Biochemistry Faculty Works

G-quadruplexes are non-canonical DNA structures formed by guanine-rich DNA sequences that are implicated in cancer and aging. Understanding how small molecule ligands interact with quadruplexes is essential both to the development of novel anticancer therapeutics and to the design of new quadruplex-selective probes needed for elucidation of quadruplex biological functions. In this work, UV–visible, fluorescence, and circular dichroism spectroscopies, fluorescence resonance energy transfer (FRET) melting assays, and resonance light scattering were used to investigate how the Pt(II) and Pd(II) derivatives of the well-studied 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) interact with quadruplexes formed by the human telomeric DNA, Tel22, and by the G-rich sequences …

Mutlifunctional Platforms For Gene And Drug Delivery For Cancer Therapy, Jeffery J. Ambrose Jr.

Doctoral Dissertations

The National Cancer Institute and the American Cancer Society estimate that 1.6 million new cancer incidences and over half a million cancer related deaths occur annually [1][2]. Cancer the second most common cause of death in the United States [1], [2]. Although the causes of cancer can vary depending on cell type, all or almost all instances of cancer arise from a mutation or from an abnormal activation of the cellular genes that control cell growth and mitosis [3].

Treatment of a given cancer type depends on the subtype, stage and progression of the cancer. Varieties of cancer therapy include …

Folate-Peg-Histidine For Use In Detection, Capture, And Analysis Of Fr+ Cells, Sean Dwyer

All Capstone Projects

Folate receptor alpha is a membrane-bound protein displaying high affinity for folic acid. This receptor serves as a receptor-mediated transport system of folic acid into cancer and cells associated with inflammation (e.g., macrophages). Folate is a basic component of cell metabolism in both the synthesis of DNA and proteins, which is hypothesized to be necessary for maintaining adequate processes during increased metabolic demand. Interestingly, most normal cells in the body have little or no high affinity folate receptor alpha. Based on these attributes, folate based drug delivery, imaging systems, and diagnostic systems are in several stages of development worldwide. To …

Feasibility Study Of Waste Isolation And Characterization By Instrumental Methods, Janith A. Wiehe-Wazio

All Capstone Projects

The original focus of this project was to develop an in house procedure for the recovery of commonly used science laboratory solvents consisting of Acetone, Ethyl (Ethanol) Alcohol, Hexane, Methanol and Hydrochloric Acid from everyday laboratory waste. However, the projects scope shifted a little further back to basics when it was discovered that Laboratory Waste Safety and Accounting practices were insufficient. It was assumed that identification of waste products was being recorded accurately. It became apparent with the very first waste bottle analysis that chemicals recorded on the standardized waste log sheets were not always what was in the waste …

Mechanistic Binding Insights For 1-Deoxy-D-Xylulose-5-Phosphatesynthase, The Enzyme Catalyzing The First Reaction Of Isoprenoid Biosynthesis In The Malaria-Causing Protists, Plasmodium Falciparum And Plasmodium Vivax, Matthew R. Battistini, Christopher Shoji, Sumit Handa, Leonid Breydo, David J. Merkler

Chemistry Faculty Publications

We have successfully truncated and recombinantly-expressed 1-deoxy-D-xylulose-5-phosphate synthase (DXS) from both Plasmodium vivax and Plasmodium falciparum. We elucidated the order of substrate binding for both of these ThDP-dependent enzymes using steady-state kinetic analyses, dead-end inhibition, and intrinsic tryptophan fluorescence titrations. Both enzymes adhere to a random sequential mechanism with respect to binding of both substrates: pyruvate and D-glyceraldehyde-3-phosphate. These findings are in contrast to other ThDP-dependent enzymes, which exhibit classical ordered and/or ping-pong kinetic mechanisms. A better understanding of the kinetic mechanism for these two Plasmodial enzymes could aid in the development of novel DXS-specific inhibitors that might prove useful …

Purification And Preparation Of Intrinsically Disordered Proteins For Nmr Spectroscopy, Kyle Chamberlain

Open Access Theses

NMR spectroscopy has recently become a promising field for protein characterization and dynamic studies. As the technology and pulse sequences improve for tracking proteins, a greater demand for developing effective purification protocols to produce NMR grade protein samples have arisen. This thesis explores two proteins: histone H4 tail and Mucin 1; Two very different proteins that require different methods of expression and purification to achieve a high enough yield for NMR analysis. H4 is a water soluble protein that weighs ~2.7 kDa, and has no extinction coefficient. Since the protein is too small for many methods of expression and purification, …

Targeted Metabolomics On The Shikimate And Aromatic Amino Acid Biosynthetic Pathways, Robert E. Wheeler

Open Access Theses

The shikimate and aromatic amino acid biosynthesis pathways are some of the most studied biosynthetic pathways in nature due to their fundamental importance. Interest in this field stems from synthesis of the essential amino acids, tryptophan, tyrosine and phenylalanine. The pathways also are important as generating the precursors of thousands of secondary metabolites and lignin. Inhibiting the pathway has led to discovery of herbicides, pesticides as well as tuberculosis drugs. However there is currently a lack of a comprehensive targeted method for detecting and quantifying the majority of the intermediates in these pathways. Often multiple extraction and detection methods are …

Direct Drug Screening And Lipid Profiling Using Ambient Mass Spectrometry, Yuan Su

Open Access Dissertations

Mass spectrometry (MS) stands in an outstanding position in analysis of biological specimens owing to its abundant structural information, high accuracy, incomparable sensitivity, high speed, and the large variety of its applications. The ion source, an instrumental part for converting the analyte into ions, has played an important role in analyzing biological specimens by MS. However, the performance of conventional spray-based ionization methods always suffers from chemical interferences derived from complex biological matrices. A series of sample extraction, purification, and separation steps is required before the ionization, so as to ensure excellent performance of MS analysis. In order to simplify …

Application Of Electrospray Ionization Mass Spectrometry For Ionic Liquids And Their Biodegradation Products, Sepideh Rahbarirad

Masters Theses

Ionic liquids (ILs) are organic salts with unique physico-chemical properties and are used as green alternatives to volatile organic solvents. ESI-MS is a sensitive technique to detect these stable, permanent ions. My research focused on (1) Identification of biodegradation products of ionic liquids and (2) Multiplexed tandem MS by modulation of ionization efficiency.

Studies, have demonstrated that ILs are toxic to the environment, which makes their biodegradability an important consideration. In this work, metabolites generated during the biodegradation of 1-butyl-3-methylimidazolium chloride (BMIM), a degradation resistant and commonly used ionic liquid, are identified using high performance liquid chromatography-mass spectrometry (LC-MS).

Multiplexed …

A New Ligation System For Protein Conjugation, Alicia J. Curti, Patrick H. Dussault

UCARE: Research Products

Click chemistry describes crosslinking reactions in which pairs of functional groups selectively “click” together to form linkages. The idea of our project is to explore the use of cyclobutene-containing fatty acids as a new class of “click” reagents as a tool for protein modification.

There is great interest in performing click reactions under biologically relevant conditions, in the presence of cells, and even within cells. The best known click reaction, the cycloaddition of alkynes and azides, is highly specific, can be conducted in the presence of buffers and proteins, and forms stable cycloadducts. However, use in biological systems is limited …

Effect Of The Spiroiminodihydantoin Lesion On Nucleosome Stability And Positioning, Erika Norabuena, Sara Barnes Williams, Margaret A. Klureza, Liana J. Goehring, Brian Gruessner, Mala L. Radhakrishnan, Elizabeth R. Jamieson, Megan E. Núñez

Chemistry: Faculty Publications

DNA is constantly under attack by oxidants, generating a variety of potentially mutagenic covalently modified species, including oxidized guanine base products. One such product is spiroiminodihydantoin (Sp), a chiral, propeller-shaped lesion that strongly destabilizes the DNA helix in its vicinity. Despite its unusual shape and thermodynamic effect on double-stranded DNA structure, DNA duplexes containing the Sp lesion form stable nucleosomes upon being incubated with histone octamers. Indeed, among six different combinations of lesion location and stereochemistry, only two duplexes display a diminished ability to form nucleosomes, and these only by ∼25%; the other four are statistically indistinguishable from the control. …

Development Of New Ligand Scaffolds For The Preparation Of Heterobimetallic Complexes, Alexander Richard Treleven

Master's Theses (2009 -)

There is currently much interest in the development of methods to harness sustainable, CO2 neutral, non-fossil fuel based energy sources due to diminishing worldwide supply of fossil fuels and concerns over historically high levels of CO2 in the atmosphere, which may have a devastating impact on the world’s climate. One such avenue is through the conversion of atmospheric CO2 into useful, high-energy density, organic fuel sources. Photosynthesis is the biological process by which plants convert sunlight, water, and CO2 into the reduced organic materials that we extract from the earth and burn (completing the cycle back to CO2) to release …

Synthetic And Mechanistic Studies Of Ruthenium Catalyzed C-C And C-O Bond Activation Reactions, Junghwa Kim

Dissertations (1934 -)

Etherification of alcohols is one of the most fundamental transformations in organic synthesis. Williamson ether synthesis is the most well-known synthetic method of unsymmetrical ether synthesis which is still being used in both industrial and academic laboratories. We have developed a novel catalytic etherification reaction using two different alcohols by using a well-defined cationic ruthenium catalyst. The reaction scope as well as the mechanistic study of the reaction are described.Hydroacylation is considered to be a powerful synthetic transformation for producing functionalized ketones from relatively simple olefin substrates. Despite remarkable progress in intra and intermolecular hydroacylations, the substrate scope of the …

Photochemical Electrocyclic Ring Closure And Elimination Reactions Of N-(Oxothioxanthenyl)Naphthothiophene Carboxamides, Himali Devika Jayasekara

Dissertations (1934 -)

Photochemical cleavage reactions have found a widespread used in biological applications that require the photorelease of biologically active molecules such as proteins, peptides, neurotransmitters, and nucleotide phosphates. This research focuses on the design of photoremovable protecting groups which can be utilized to release these biomolecules by photolysis. These biomolecules are attached to the photoremovable protecting group at the sites of functional groups that are present within these substrates. Such functional groups are carboxylates, phosphates, thiolates, or phenolates, which upon exposure to light, are released as anions of varying basicities. The photochemical reaction involved is an electrocyclic ring closure between aromatic …

Novel Numerical Models Of Electrostatic Interactions And Their Application To S-Nitrosothiol Simulations, Maxim Vadimovich Ivanov

Dissertations (1934 -)

Atom-centered point charge model of the molecular electrostatics remains a major workhorse in the atomistic biomolecular simulations. However, this approximation fails to reproduce anisotropic features of the molecular electrostatic potential (MEP), and the existing methods of the charge derivation are often associated with the numerical instabilities. This work provides an in-depth analysis of these limitations and offers a novel approach to describe electrostatic interactions that paves the way toward efficient next-generation force fields. By analyzing the charge fitting problem from first principles, as an example of the mathematical inverse problem, we show that the numerical instabilities of the charge-fitting problem …

Synthesis And Characterization Of Biologically Relevant Fe(Ii) Complexes Containing Redox-Active (Hydro)Quinone Ligands, Amanda Elizabeth Baum

Dissertations (1934 -)

Redox-active p-(hydro)quinones work in concert with transition-metal centers to facilitate electron transfers in numerous biological contexts. While p-(hydro)quinones are known to interact with both heme and nonheme iron cofactors, the nonheme systems are particularly relevant to photosynthetic and bioremediation processes. In photosynthesis, two p-quinones facilitate an electron transfer away from the photoexcited P680 cofactor via a non-heme Fe(II) center. Based on EPR results, this interaction results in formation of transient Fe(II)/p-semiquinone (pSQ) species. In addition, a superoxo-iron(II)-pSQ species has been proposed as an intermediate of the oxidative cleavage mechanism of hydroquinone dioxygenases (HQDOs), which play a central role in the …

Ruthenium-Catalyzed Amination Of Secondary Alcohols Using Borrowing Hydrogen Methodology, Kostiantyn O. Marichev, James M. Takacs

Department of Chemistry: Faculty Publications

A new ruthenium complex catalyzes the amination of primary and secondary alcohols and the regioselective mono- and sequential diamination of diols via the borrowing hydrogen pathway. Several variations on new intra- and intermolecular cyclizations of aminoalcohols, diols and diamines lead to heterocyclic ring systems.