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Characterization Of Cytidylyltransferase Enzyme Activity Through High Performance Liquid Chromatography, James Brault

Theses and Dissertations

The cytidylyltransferases are a family of enzymes that utilize cytidine 5â?? triphosphate (CTP) to synthesize molecules that are precursors to membrane phospholipids. There are four well known enzymes: CTP: phosphoethanolamine cytidylyltransferase (ECT), CTP: glycerol-3-phosphate cytidylyltransferase (GCT), 2-C-methyl-D-erythritol-4-phosphate cytidylyltransferase synthetase (CMS), and CTP: phosphocholine cytidylyltransferase (CCT). Previously, a radioisotope tagging method was employed to study cytidylyltransferase catalysis. Using CCT as a model, a method utilizing high performance liquid chromatography (HPLC) was developed to replace the radioisotope scintillation technique. The development of this new HPLC method is cheaper, more efficient, and more accurate than the previously established method.

The targets of separation …

Bodipy-Based Fluorescent Probes For Sensing Protein Surface-Hydrophobicity, Nethaniah Dorh, Shilei Zhu, Kamal B. Dhungana, Ranjit Pati, Fen-Tair Luo, Haiying Liu, Ashutosh Tiwari

Department of Chemistry Publications

Mapping surface hydrophobic interactions in proteins is key to understanding molecular recognition, biological functions, and is central to many protein misfolding diseases. Herein, we report synthesis and application of new BODIPY-based hydrophobic sensors (HPsensors) that are stable and highly fluorescent for pH values ranging from 7.0 to 9.0. Surface hydrophobic measurements of proteins (BSA, apomyoglobin, and myoglobin) by these HPsensors display much stronger signal compared to 8-anilino-1-naphthalene sulfonic acid (ANS), a commonly used hydrophobic probe; HPsensors show a 10- to 60-fold increase in signal strength for the BSA protein with affinity in the nanomolar range. This suggests that these HPsensors …

Photooxidation Reactions Of Small-Chain Methyl Esters, Aerosol Photoelectron Spectroscopy, And The Photodissociation Of Ethylenediamine, Giel Muller

Master's Theses

Research conducted at the University of San Francisco is presented within this masters thesis, including the Cl-initiated photooxidation reactions of methyl propanoate, methyl butanoate, and methyl valerate (pentanoate), the aerosol photoelectron spectroscopy of isoprene and gamma-valerolactone, and the TPEPICO investigation of ethylenediamine. Experiments were conducted at the Lawrence Berkeley National Lab Advanced Light Source (ALS), the National Synchrotron Radiation Research Center in Hsinchu City (NSRRC), and the University of Stockton in California, respectively.

Microsolvation Of Anions By Molecules Forming Ch∙∙X- Hydrogen Bonds, Steve Scheiner, Binod Nepal

Chemistry and Biochemistry Faculty Publications

Various anions were surrounded by n molecules of CF₃H, which was used as a prototype CH donor solvent, and the structures and energies studied by M06-2X calculations with a 6-31+G∗∗ basis set. Anions considered included the halides F^-, Cl^-, Br^- and I^-, as well as those with multiple proton acceptor sites: CN^-, NO₃ ^-, HCOO^-, CH₃COO^-, HSO₄ ^-, H₂PO₄ ^-, and anions with higher charges SO₄ ^2-, HPO₄ ^2- and PO_{4 …}

Solid-State Nmr Study Of The Tertiary Structure Of The Peptidoglycan Of Enterococcus Faecalis And The Structures Of Phorbol Diacetate And Bryostatin Bound To Protein Kinase Cδ C1b Domain, Hao Yang

Arts & Sciences Graduate Student Theses and Dissertations

Solid-state NMR was used to study the structures of phorbol diacetate and bryostatin bound to protein kinase Cδ C1b domain in lipid bilayers. The interaction of protein kinase C (PKC) with native physiological ligands drives fundamental cellular signal transductions, and aberrant PKC signaling is associated with cancer, cardiovascular disease, neurological disorders, stroke, pain, etc. Bryostatin modulates PKC and exhibits remarkable potential in treating cancer, Alzheimer's disease, and HIV/AIDS. However, the structural information and dynamics of this modulation, which are crucial for better understanding of PKC-ligand interactions in the membrane microenvironment to drive the development of new drugs, remain elusive. REDOR …

Investigation Of 89zr-Siderophores As Molecular Imaging Agents For Positron Emission Tomography Imaging Of Bacterial Infections, Nora C. M. Goscinski

Arts & Sciences Graduate Student Theses and Dissertations

Siderophores are small molecules synthesized by bacteria to harvest Fe³⁺ from their environment. In infection scenarios, their production can increase infection virulence by increasing the ability of bacteria to obtain Fe³⁺ and therefore grow more rapidly. The selective uptake of siderophores in vivo in multi-bacteria environments indicates that this class of molecules has a potential use as selective imaging agents. In this work, DFO-NCS and a library of trihydroxamate siderophores were evaluated as vehicles to deliver ⁸⁹Zr selectively to bacteria for Positron Emission Tomography (PET) imaging of bacterial infections. Productive work with radiometals involves thorough knowledge of …

Approaching Aromatic Interactions With Small Molecule Model Systems: Assessing N-Heteroarene In ∏ -Stacking And Ch-∏ Interactions, Crystal Engineering Of Atropisomeric Rotors, And Developing Responsive Organic Charge-Transfer Complex, Ping Li

Theses and Dissertations

Non-covalent interactions involving aromatic species are important in many areas in chemistry, biochemistry, and materials sciences. During the past two decades, small molecule model systems have emerged as a powerful tool to advance our knowledge of the stability trends for aromatic interactions in the condensed phase. Among these, the Cshape N-arylimide molecular balances developed by our laboratory have proven to be one most successful and versatile model systems that can be readily adapted to investigate various types of aromatic interactions. These molecular balances are particularly apt at isolating and accurately measuring the targeted weak aromatic interaction energies for different geometries. …

Supramolecular Coordination Networks Of S- And F-Block Metals Featuring The 1,8-Naphthalimide Tecton, Andrew Paul Leitner

Theses and Dissertations

The reactions of (S)-2-(1,8-naphthalimido)propanoic acid (HLala), and (S)-2-(1,8- naphthalimido)-3-hydroxypropanoic acid (HLser), protonated forms of ligands that contain a carboxylate donor group, an enantiopure chiral center and a 1,8-naphthalimide π...π stacking supramolecular tecton and in the case of HLser an alcohol functional group, with the appropriate alkali metal hydroxide followed by a variety of crystallization methods leads to the formation of crystalline K(Lala)(MeOH) (1), K(Lala)(H2O) (2), Na(Lala)(H2O) (3), KLser (4), CsLser (5) and CsLala (6). Each of these new complexes has a solid state structure based on six-coordinate metals linked into homochiral helical rod SBU central cores. In addition to the …

Defining The Effects Of Gdf-2 On TgfB Signaling In Tumorigenic Epithelial Cells, Tirthankar Bandyopadhyay

Theses and Dissertations

Cancer cells can be viewed as such cells, which have disrupted/aberrant signaling pathways for maintaining cellular homoeostasis. Identifying such altered signaling mechanisms can help us target these pathways in a better way. GDF-2 (Growth and differentiation factor – 2) or BMP9 (Bone morphogenetic protein – 9), a multifunctional cytokine, is a member of the Bone Morphogenetic Protein subfamily, under TGFβ superfamily, with roles distinct from BMP2/4/7. While GDF-2 is known to be one of the most potent ectopic inducers of bone and cartilage formation, it rose to significance with the identification of its receptor ALK1 in endothelial cells. TGFβ’s role …

Optimization Of Shell Growth And Influence Of Surface Ligands For Colloidal Cdse/Cds Core/Shell Quantum Dots, Rui Tan

Theses and Dissertations

Progress in the colloidal synthesis of semiconductor quantum dots (QDs) has triggered a burst of research toward applications in QD based light emitting diodes, biological imaging as fluorescent tags, and advanced solar cell designs. In order to adjust and optimize the photo physical properties of QDs, QD heterostructures have been introduced and widely explored. This dissertation is focused on studies of growth of semiconductor colloidal CdSe/CdS core/shell quantum dots and the influences of neutral surface ligands to their photo-physical properties. Chapter 1 provides an introduction of the concept of semiconductor colloidal nanoparticles, core/shell heterostructures and the synthesis methods as well …

Optimized Spectral Processing Of Infrared Diffuse Reflection Spectra For The Detection Of Blood On Fabric, Stephanie Ann Dejong

Theses and Dissertations

The detection of bodily fluids such as blood on interfering backgrounds is important to the forensic community. Luminol, which participates in a chemiluminescent reaction with the heme groups of blood, is one of the most commonly used presumptive tests. Luminol has a few drawbacks, including the requirement of use in a dark environment and potential to degrade the amount of recoverable DNA in blood stains. A potential complementary method is infrared (IR) spectroscopy. These two methods are compared in this work. Infrared diffuse reflection (DR) spectroscopy works well to measure the IR spectrum of samples that are highly absorbing or …

Direct Phenotypic Screening In Mice: Identification Of Individual, Novel Antinociceptive Compounds From A Library Of 734 821 Pyrrolidine Bis-Piperazines, Richard A. Houghten, Michelle L. Ganno, Jay P. Mclaughlin, Colette T. Dooley, Shainnel O. Eans Torrey Pines Institute For Molecular Studies, Radleigh Santos, Travis Lavoi, Adel Nefzi, Greg Welmaker, Marc A. Giulianotti, Lawrence Toll

Mathematics Faculty Articles

The hypothesis in the current study is that the simultaneous direct in vivo testing of thousands to millions of systematically arranged mixture-based libraries will facilitate the identification of enhanced individual compounds. Individual compounds identified from such libraries may have increased specificity and decreased side effects early in the discovery phase. Testing began by screening ten diverse scaffolds as single mixtures (ranging from 17 340 to 4 879 681 compounds) for analgesia directly in the mouse tail withdrawal model. The “all X” mixture representing the library TPI-1954 was found to produce significant antinociception and lacked respiratory depression and hyperlocomotor effects using …

Substituent Effects On The Binding Of Halides By Neutral And Dicationic Bis-Triazolium Receptors, Binod Nepal, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The effects of substituent and overall charge upon the binding of a halide anion by a bis-triazolium receptor are studied by M06-2X DFT calculations, with the aug-cc-pVDZ basis set. Comparison is also made between a receptor that engages in H-bonds, with a halogen-bonding species. Fluoride is clearly most strongly bound, followed by Cl-, Br-, and I- in that order. The dicationic receptor engages in stronger complexes, but not by a very wide margin compared to its neutral counterpart. The binding is enhanced as the substituent on the two triazolium rings becomes progressively more electron-withdrawing. Halogen-substituted receptors, whether neutral or cationic, …

Method And Apparatus For Cancer Screening, Yinfa Ma, Stephen Gibbons

Chemistry Faculty Research & Creative Works

A method and apparatus for detection of pteridine levels in a biological sample using CE-LIF which is useful for early cancer screening involving fully oxidizing pteridine compounds in a sample such as a urine sample, subjecting to CE-LIF to assess compound concentration, and compare to expected levels in for healthy or cancer-bearing patients.

Uses Of Diaryliodonium Salts And Methods For Their Synthesis, Jordan M. Veness

Department of Chemistry: Dissertations, Theses, and Student Research

Diaryliodonium salts have been studied continuously since the first report of their synthesis in 1894. Diaryliodonium salts are I(III) derivatives that are air- and moisturestable. The reactivity of these compounds resembles the organometallic chemistry of heavy transition metal ions such as Pb(IV), Hg(II), Th(III), and Pd(II). A significant advantage of diaryliodonium salts is that they can carry undergo many of the aryl functionalization reactions of heavy metal organometallic complexes, yet they have little to no toxicity and they are relatively inexpensive to prepare. The DiMagno laboratory uses diaryliodonium salts as precursors in the final synthetic step of radiopharmaceuticals; given that …

Logistic Regression Models To Predict Solvent Accessible Residues Using Sequence- And Homology-Based Qualitative And Quantitative Descriptors Applied To A Domain-Complete X-Ray Structure Learning Set, Reecha Nepal, Joanna Spencer, Guneet Bhogal, Amulya Nedunuri, Thomas Poelman, Thejas Kamath, Edwin Chung, Katherine Kantardjieff, Andrea Gottlieb, Brooke Lustig

Faculty Publications, Chemistry

A working example of relative solvent accessibility (RSA) prediction for proteins is presented. Novel logistic regression models with various qualitative descriptors that include amino acid type and quantitative descriptors that include 20- and six-term sequence entropy have been built and validated. A domain-complete learning set of over 1300 proteins is used to fit initial models with various sequence homology descriptors as well as query residue qualitative descriptors. Homology descriptors are derived from BLASTp sequence alignments, whereas the RSA values are determined directly from the crystal structure. The logistic regression models are fitted using dichotomous responses indicating buried or accessible solvent, …

Controlled Hydrosilylations Of Carbonyl Compounds And Computational Investigations Of A Hydride Shuttle Mechanism For Alkene Hydrosilylation, Gabriela Trog

Chemistry & Biochemistry Theses - Archive

Chapter 1 describes tandem dual hydrosilylations of α,β-unsaturated enals. Hydrosilylations of both carbonyl compounds and alkenes have been utilized to create chiral alcohols. Tandem dual hydrosilylations (TDH) of α,β-unsaturated carbonyl compounds create five-membered oxasilacycles that can be further converted to 1,3- diols, which are a common structural motif in the polyketide natural product family. We present preliminary data and a substrate scope for the formation of these oxasilacycles en route to the 1,3-diol compounds. Chapter 2 describes hydrosilylations of esters that result in silyl acetals. The silyl acetals are chemical synthons of the corresponding aldehyde. This reaction can be coupled …

Evaluation Of Activated Carbon As A Commercial Drug Disposal Product Using Liquid Chromatography–Tandem Mass Spectrometry, Veronica B. Waybright

Chemistry & Biochemistry Theses - Archive

At present, pharmaceuticals, synthetic organic compounds, and endocrine disrupting compounds are ubiquitous in our environment. These have been introduced by consumers and manufacturers directly and indirectly for decades. There is plenty of published literature addressing the presence of these compounds, the development of newer and more sensitive techniques to detect them at low concentrations, as well as studies showing their effects in the environment and in human health. However, these studies are based on the measurement and detection of these compounds after the fact; and even though some have addressed the need to decrease these pollutants in the environment, procedures …

Determination Of Total And D-Amino Acid Content In Mice Brain Tissue By Achiral-Chiral Heart-Cutting Two-Dimensional Liquid Chromatography: Diagnostic And Clinical Relevance And A Comparison Between Non-Perfused And Perfused Tissue, Curran Parpia

Chemistry & Biochemistry Theses - Archive

A heart-cutting two dimensional liquid chromatographic method for the quantification of free amino acid enantiomers from mouse brain tissue is demonstrated. Evidence to support the occurrence of D-amino acids in significant concentrations in physiological samples has spurred studies toward the elucidation of their importance and function. In this work, the level and regional distribution of select amino acids were determined by achiral-chiral LC/LC. Additionally, the effect of tissue perfusion on these levels was investigated. The free amino acid extracts were analyzed as their 9-fluorenylmethyloxycarbonyl derivatives and separated in the reverse phase mode on superficially porous C18. In the second dimension, …

The Unique Electrochemical Reactivity Of Small Metal Nanoparticles., Rafael A. Masitas

Electronic Theses and Dissertations

This dissertation describes the factors controlling metal nanoparticle (NP) oxidation, using Au oxidation in Br- and Ag oxidation in acid as model systems. We found that the oxidation potential depends on size, surface charge, and electrode material. Size has a dramatic effect, shifting about 200 mV from > 200 nm diameter down to 4 nm diameter. The shift is more dramatic below 4 nm. 2.3 nm average diameter Au NPs oxidized in the 300-500 mV range and 1.5 nm average diameter Au NPs displayed several sharp peaks from 200 mV to as low as -200 mV. These smallest Au NPs show …

Development Of A Miniaturized Ambient Glow Discharge Ionization Source And Its Application In Elemental And Molecular Analysis, Xinyan Zhang

All Dissertations

Since the liquid sampling-atmospheric pressure glow discharge (LS-APGD) was first developed as an excitation source for atomic emission spectroscopy, it has been improved upon and demonstrated as an ionization source for elemental mass spectrometry, molecular mass spectrometry, and ambient desorption mass spectrometry. Multiple functions coming from one package allowed the LS-APGD to hold a unique position among all atmospheric pressure glow discharges. It also has the capabilities to work with different sample forms including liquids, bulk solids, and solution residues. The high salt/matrix tolerance reduces sample prep work and thus provides convenience for its potential use as a field-Based ionization …

Structure-Activity Relationships Of Ruthenium(Ii) Polypyridyl Complexes With Redox-Active Intercalating Ligands: Correlation Between Redox Activity, Dna Cleavage Capability And Cytotoxicity, Eugenia Soyo Narh

Chemistry & Biochemistry Theses - Archive

The investigation and development of transition metal complexes as cancer chemotherapeutics has gained a lot of interest in the past few decades and has become a promising area of research. Metal complexes of platinum and ruthenium in particular that have demonstrated success as anticancer drugs or are under exploration currently for clinical use are highlighted in Chapter 1. Chapter 2 describes studies undertaken to understand the neurotoxicity of ruthenium(II) polypyridyl complexes (RPCs), including toxicity in mice and inhibition of the enzyme acetylcholinesterase (AChE), as previous work by Dwyer demonstrated that RPCs could be acutely toxic in mice, presumably due to …

Synthesis Of Modified Ribose Spin-Label, Ke-Wei Chang

Chemistry & Biochemistry Theses - Archive

Transfer ribonucleic acids (tRNAs) from all organisms contain modified nucleosides, which are derived from four different nucleosides. Research has indicated that tRNA modifications affect translation and various metabolic pathways. Among these modifications, some of them need more than one enzyme to produce specific nucleosides. Researchers are interested in investigating the fundamental mechanisms and function of post-transcriptional modifying enzymes. A number of these enzymes are metal-dependent, such as MiaB and MiaE. MiaE enzyme (2-methylthio-N6-isopentenyl-adenosine(37)-tRNA monooxygenase) stereospecifically hydroxylates an adeonosine derivative at the 37th position of tRNA, ms2i6A37, to complete the hypermodification of 2-methylthio-N6-(4-hydroxyisopentenyl)-adenosine (ms2io6A37). Several studies showed that the ms2io6A37 modification …

Modification Of Cellular Dna By Synthetic Aziridinomitosenes, Chris M. Mallory, Ryan P. Carfi, Sangphil Moon, Kenneth A. Cornell, Don L. Warner

Chemistry and Biochemistry Faculty Publications and Presentations

Two synthetic aziridinomitosenes (AZMs), Me-AZM and H-AZM, structurally related to mitomycin C (MC) were evaluated for their anticancer activity against six cancer cell lines (HeLa, Jurkat, T47D, HepG2, HL-60, and HuT-78) and tested for their DNA-modifying abilities in Jurkat cells. Cytotoxicity assays showed that Me-AZM is up to 72-fold and 520-fold more potent than MC and H-AZM, respectively. Me-AZM also demonstrated increased DNA modification over MC and H-AZM in alkaline COMET and Hoechst fluorescence assays that measured crosslinks in cellular DNA. Me-AZM and H-AZM treatment of Jurkat cells was found to sponsor significant DNA-protein crosslinks using …

Analysis Of An Electrospun Nanofiber Device Applicable To Limb Salvage: Mass Loss, Morphological Changes, And Quantification Of Antibiotic Release, Caitlin Quinn

Honors Theses

The creation of an electrospun nanofiber embedded with two antibiotics that will be used to prevent infection while also stimulating bone regeneration will be explored. The nanofiber will contain an aminoglycoside and a glycopeptide, and it is sought to deliver a sustained release of antibiotics for up to 12 weeks. To determine release rate, nanofiber samples are immersed in 10.0 mL of MiliQ water (MQ), incubated at 37°C, assayed at specific time intervals, and then analyzed using ultra performance liquid chromatography in tandem with mass spectrometry. A hydrophilic interaction liquid chromatography (HILIC) method utilizing ultra-performance liquid chromatography (UPLC) in tandem …

Novel Methods For Identification Of Posttranslational Lipid Modified Proteins By Mass Spectrometry, Ruchika P. Bhawal

Chemistry & Biochemistry Dissertations - Archive

Study of posttranslational modifications (PTMs) is very important for developing potential new drugs for the treatment of several diseases. Posttranslational lipid modifications are major PTMs which help proteins to anchor to cell membranes and facilitate protein-protein interactions. There are several kinds of lipid modifications of proteins. The major lipid modifications are palmitoylation, myristoylation and prenylation. Prenylation are of two types - farnesylation and geranylgeranylation. These modifications are involved with several human cancers and genetic diseases. Hutchinson-Gilford progeria syndrome (HGPS), a disease which causes premature aging for children is the product of prenylation. Understanding the mechanism of prenylation and their substrates …

Capillary-Channeled Polymer Fibers As Stationary Phases For Protein Chromatography, Marissa Pierson

All Theses

Capillary-channeled polymer (C-CP) fibers have been studied in this laboratory as stationary phases for protein separations in high-performance liquid chromatography (HPLC). C-CP fibers are uniquely shaped so as to include eight continuous capillary-channels which interdigitate once packed into a column. The packed column resembles a monolithic structure of unobstructed flow through capillary channels which reduces backpressure and increases linear velocity, reducing separation time. Fibers are effectively nonporous with respect to macromolecules, resulting in fast mass transfer and high sample recovery. C-CP fibers made from polypropylene (PP) yield a fairly homogenous hydrophobic surface suitable for reversed phase (RP) chromatography. In a …

Unveiling The Crucial Intermediates In Androgen Production, Piotr J. Mak, Michael C. Gregory, Ilia G. Denisov, Stephen G. Sligar, James R. Kincaid

Chemistry Faculty Research and Publications

Significance: The human enzyme cytochrome P450 17A1 (CYP17A1) catalyzes the critical step in the biosynthesis of the male sex hormones, and, as such, it is a key target for the inhibition of testosterone production that is necessary for the progression of certain cancers. CYP17A1 catalyzes two distinct types of chemical transformations. The first is the hydroxylation of the steroid precursors pregnenolone and progesterone. The second is a different reaction involving carbon–carbon (C-C) bond cleavage, the mechanism of which has been actively debated in the literature. Using a combination of chemical and biophysical methods, we have been able to trap and …

Photochemistry Of A Series Of Weakly Coupled Dinuclear Ruthenium(Ii) Complexes, Latisha Michelle Puckett

Graduate Theses and Dissertations

An improved synthetic method was developed for symmetric ruthenium(II) polypyridine complexes with the form L2Ru(diphen)RuL2. The scope of the reaction was investigated in regards to the ligands, bridging ligands, and starting materials. Several ligands were successful in the synthesis, including 2,2’-bipyridine (bpy), 4,4’-dimethyl-2,2’-dipyridyl (dmb), 1,10-phenanthroline (phen), 4,7-diphenyl-1,10-phenanthroline (dpphen), and 3,4,7,8-tetramethyl-1,10-phenanthroline (tmphen). Ligands that did not react to form symmetric dimeric complexes were 2,2’-bipyrazine, bpz, and 2,2’-bipyrimidine, bpm.

Dpp, 2,3-bis(2-pyridyl)-pyrazine, effectively replaced diphen as the bridging ligand to produce (phen)2Ru(dpp)Ru(phen)24+. However, replacing the [Ru(CO)2Cl2]n with Ru(DMSO)4Cl2 did not prove successful. The newly developed synthesis was also applied to the synthesis of …

Influence Of Shelling Temperature And Time On The Optical And Structural Properties Of Cuins2/Zns Quantum Dots, Colette Robinson

Graduate Theses and Dissertations

CIS/ZnS core/shell QDs are an important class of nanomaterials for optoelectronic, photovoltaic and photoluminescence applications. They consist of lower toxicity materials than the prototypical II-VI Cd-based QDs and show long fluorescence lifetimes, which generates prospective in biological imaging applications. It is vital to develop reproducible synthetic methods for this new class of nanomaterials in order to maintain small sizes with high QYs. CIS core QDs have been shelled with ZnS at various temperatures from 90-210°C for reaction times ranging from 20-140 minutes to examine the role of thermodynamics and kinetics on the shell growth. Using HR-TEM and ICP-MS, it was …