Digital Commons Network^™

Discrimination Of Automobile Carpet Fibers Using Multiple Analytical Techniques And The Subsequent Creation Of A Searchable Data, Derek Dorrien

Electronic Theses and Dissertations

Forensic fiber examination is an important part of trace evidence analysis. Fibers may be recovered from a crime scene that could link a particular suspect to the scene. Clothing fibers are most frequently encountered but automobile carpeting fibers may also be recovered. An understanding of the frequency of occurrence and the discrimination power of different analytical techniques is needed in order to better establish the evidentiary value of automobile carpet fiber evidence. Seventy-five automobile carpet fiber samples were analyzed using a series of techniques ranging from nondestructive to destructive. These techniques included polarized light microscopy, fluorescence microscopy, microspectrophotometry, Fourier-transform infrared …

Isotope Sourcing Of Prehistoric Willow And Tule Textiles Recovered From Western Great Basin Rock Shelters And Caves: Proof Of Concept, Larry V. Benson, E. M. Hattori, H. E. Taylor, S. R. Poulson, E. A. Jolie

United States Geological Survey: Staff Publications

Isotope and trace-metal analyses were used to determine the origin of plants used to manufacture prehistoric textiles (basketry and matting) from archaeological sites in the western Great Basin. Research focused on strontium (⁸⁷Sr/⁸⁶Sr) and oxygen (¹⁸O/¹⁶O) isotope ratios of willow (Salix sp.) and tule (Schoenoplectus sp.), the dominant raw materials in Great Basin textiles. The oxygen-isotope data indicated that the willow and tule used to produce the textiles were harvested from the banks of rivers or in marshes characterized by flowing water and not from lakes or sinks. The strontium-isotope …

Structural And Evolutionary Classification Of G/U Wobble Basepairs In The Ribosome, Neocles B. Leontis, Ali Mokdad, Maryna V. Krasovska, Jiří Sponer

Chemistry Faculty Publications

We present a comprehensive structural, evolutionary and molecular dynamics (MD) study of the G/U wobble basepairs in the ribosome based on high-resolution crystal structures, including the recent Escherichia coli structure. These basepairs are classified according to their tertiary interactions, and sequence conservation at their positions is determined. G/U basepairs participating in tertiary interactions are more conserved than those lacking any interactions. Specific interactions occurring in the G/U shallow groove pocket-like packing interactions (P-interactions) and some phosphate backbone interactions (phosphate-in-pocket interactions)-lead to higher G/U conservation than others. Two salient cases of unique phylogenetic compensation are discovered. First, a P-interaction is conserved …

Mechanism Of Shifts Of Potentials Of Hemosorbents Based On Activated Carbons Caused By Adsorption Of Organic Toxicants, Mark Goldin, Yury Goldfarb, Mikhail M. Goldin

Faculty Publications and Presentations

No abstract provided.

Direct Detection Of Double-Stranded Dna: Molecular Methods And Applications For Dna Diagnostics, Indraneel Ghosh, Cliff I. Stains, Aik T. Ooi, David J. Segal

Cliff Stains Publications

Methodologies to detect DNA sequences with high sensitivity and specificity have tremendous potential as molecular diagnostic agents. Most current methods exploit the ability of single-stranded DNA (ssDNA) to base pair with high specificity to a complementary molecule. However, recent advances in robust techniques for recognition of DNA in the major and minor groove have made possible the direct detection of double-stranded DNA (dsDNA), without the need for denaturation, renaturation, or hybridization. This review will describe the progress in adapting polyamides, triplex DNA, and engineered zinc finger DNA-binding proteins as dsDNA diagnostic systems. In particular, the sequence-enabled reassembly (SEER) method, involving …

Sequence-Enabled Reassembly (Seer) Peptides For The Detection Of Dna Sequences, Aik T. Ooi, Cliff I. Stains, Jason R. Porter, Indraneel Ghosh, David J. Segal

Cliff Stains Publications

By combining custom zinc finger (ZF) DNA-binding technology [1,2] with protein fragment complementation [3], we have developed a technology, designated SEER (Sequence-Enabled Reassembly), that has the potential to “see” or detect genetic information within a living cell (Figure 1). These agents consist of two inactive parts of signal-generating peptides that have the ability to recognize specific DNA sequences. The two parts bind near each other in the presence of a user-defined DNA target site and generate a fluorescent signal. Two prototype SEER systems have been constructed, based on the reassembly of green fluorescent protein (SEERGFP) [4] and the enzyme β-lactamase …

Solvent Targeting, Avoidance And Recovery Trials (Start), Kealan Allen

Theses

Solvent is the largest-volume raw material used at Janssen Pharmaceutical (Ire) Ltd. Over 2.2 million m³ were used in 2004. The top 13 solvents make up 99% of this amount. There are two main uses for solvent on site, processing and cleaning. Processing uses 55% of the total solvent used on site, cleaning uses the remainder.

Waste solvent forms the majority of the hazardous waste produced at Janssen. Three treatment options exist at present for this waste: incineration, recovery for reuse and energy recovery. All of the hazardous waste produced on site must be exported for these treatment options, …

Solution And Solid State Interactions Between Ionic Π-Systems, Jing Chen

University of Kentucky Doctoral Dissertations

Although attractive interactions between π systems (π-π interaction) have been known for many years, understanding of its origin is still incomplete. Quantitative measuring of π-stacking is challenging due to the weak nature of the π-π interaction. This dissertation aims at elucidating a quantitative conformational analysis by NMR ring current anisotropy of an organic compound capable of intramolecular π-stacking in solution and studying charge effects on the stacking of π-systems. This dissertation offers four contributions to the area. (1) A general approach to four-state, conformational analysis based on the magnetic anisotropy of molecules undergoing fast dynamic exchange is described. (2) Study …

Performance Efficacy Using A Comparison Of Commerical And In-House Y-Str Multiplex Systems For Operational Use, Kathleen Mayntz-Press

Electronic Theses and Dissertations

It is routine for the forensic scientist to obtain a genetic profile of an individual from DNA recovered from a biological stain deposited at a crime scene. In contrast, only a limited number of laboratories in the United States have the capability of performing Y-STR analysis in casework. In order to aid in facilitating the transfer of Y-STR technology to the crime laboratory community for operational use, a comparison between commercial products from three main vendors (Applied Biosystems AmpFLSTR Yfiler PCR Amplification Kit, Promega PowerPlex - Y System, Reliagene Y-PLEX 12) and two in-house Y-STR multiplexes (MPI and MPB) commenced. …

Synthesis Of An Aza-Cope Rearrangement - Mannich Cyclization Precursor From L-Proline, Patricia T. Sinawe

Senior Honors Theses and Projects

No abstract provided.

Lipid Metabolism In A549 And 9hte Cells Quantitation Of Lipid Peroxidation, Elizabeth Quintus

Senior Honors Theses and Projects

No abstract provided.

Tunneling Through Weak Interactions:  Comparison Of Through-Space-, H-Bond-, And Through-Bond-Mediated Tunneling, Westin Kurlancheek '03, Robert J. Cave

All HMC Faculty Publications and Research

Results from ab initio electronic structure theory calculations on model systems allow for the detailed comparison of tunneling through covalently bonded contacts, hydrogen bonds, and van der Waals contacts. Considerable geometrical sensitivity as well as an exponential distance dependence of the tunneling is observed for tunneling through various nonbonded contacts. However, the fundamental result from the present study is that at most a modest difference is observed between tunneling mediated by H-bonds and tunneling mediated by van der Waals contacts at typical distances for each type of interaction. These results are considered in relation to the pathways model of Beratan …

Fluorescent Analysis Of Translesion Dna Synthesis By Using A Novel, Non-Natural Nucleotide Analogue, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The replication of damaged DNA is a promutagenic process that can lead to disease development. This report evaluates the dynamics of nucleotide incorporation opposite an abasic site, a commonly formed DNA lesion, by using two fluorescent nucleotide analogues, 2-aminopurine deoxyribose triphosphate (2-APTP) and 5-phenylindole deoxyribose triphosphate (5-PhITP). In both cases, the kinetics of incorporation were compared by using a 32 P-radiolabel extension assay versus a fluorescence-quenching assay. Although 2-APTP is efficiently incorporated opposite a templating nucleobase (thymine), the kinetics for incorporation opposite an abasic site are significantly slower. The lower catalytic efficiency hinders its use as a probe to study …

Recent Developments Inthe Mechanistic Enzymology Of The Atp-Dependent Lon Protease From Escherichia Coli: Highlights From Kinetic Studies, Irene Lee, Anthony J. Berdis, Carolyn K. Suzuki

Chemistry Faculty Publications

Lon protease, also known as protease La, is one of the simplest ATP-dependent proteases that plays vital roles in maintaining cellular functions by selectively eliminating misfolded, damaged and certain short-lived regulatory proteins. Although Lon is a homo-oligomer, each subunit of Lon contains both an ATPase and a protease active site. This relatively simple architecture compared to other hetero-oligomeric ATP-dependent proteases such as the proteasome makes Lon a useful paradigm for studying the mechanism of ATP-dependent proteolysis. In this article, we survey some recent developments in the mechanistic characterization of Lon with an emphasis on the utilization of pre-steady-state enzyme kinetic …

The Adaptation Of The Fibrinolytic Enzyme Apcfib On Human Blood Stains, Gabriela Sanchez

Whittier Scholars Program

Current research is aimed at testing a purified solution of a fibrinolytic enzyme. Apcfib, which comes from the venom of Agkistrodon piscivorus conanti (Florida cottonmouth Snake) to dissolve blood stains on two different makes of fabric (80% cotton/ 20% polyester and 100% polyester) and test the enzyme’s ability to dissolve blood stains when combined with a protease, in this case thermolysin, Treatment of blood stains on 100% polyester was more effective overall than on the 80% cotton/100% polyester fabric. 2.0x10^ -4 ��mol/min of Apcfib activity added to a 200��L of blood stain was the minimum needed in order to significantly …

Self-Assembly And Its Inhibition In Bolaform Amphiphilic Dendrimers, Jirun Sun

LSU Doctoral Dissertations

Self-assembly is scientifically interesting, technologically important, and sometimes life-threatening. A striking example: Alzheimer’s disease is caused by the self-assembly of the â-amyloid fragment of amyloid precursor protein. Such natural amphiphiles normally are very expensive and complicated to isolate. Synthetic mimics that are much cheaper and easier to prepare can facilitate the development of efficient characterization methods, even as they suggest new materials science applications. Two-directional arborols are synthetic bolaform amphiphilic dendrimers. They dissolve in hot water and form reversible gels at room temperature. Bundles of fibrils, which are made by self-assembly of arborols, are found in the gels. The properties …

Synthesis Of 2-Oxo-16-(3', 4'-Methylenedioxyphenyl)-Trans-15-Hexadecene, Adelajda Zorba

Honors Theses

This work presents the progress made towards synthesizing 2-oxo-16-(3', 4'methylenedioxyphenyl)-trans-15-hexadecene, an antimycobacterial compound that was originally isolated from the leaves of Piper Sanctum. The hydrocarbon chain of the molecule was synthesized first by opening a 15-pentadecanolactone ring by means of HI, and performing an E2 elimination reaction on the molecule followed by an organolithium reaction with CH3Li. Hexadec-15-en-2-one that was afforded this way was later reacted with 5-bromobenzo[d][1,3]dioxole following the appropriate Heck reaction protocol that allows for the formation of a palladium catalyzed carbon-carbon bond.

The modes of action of 2-oxo-16-(3', 4'-methylenedioxyphenyl)-trans-15hexadecene are comparable to the ones of rifampicin, a …

Characterization Of The Wheat Grain Pkaba1-Interacting Protein Tawd40, Natalie Wayne

Honors Theses

Abscisic acid (ABA)-mediated gene expression is a critical component of plant responses to this important hormone, which affects plant growth, development, and responses to environmental stresses. Plant responses to ABA are mediated by a number of factors including PKABA 1> an ABA-induced protein kinase involved in ABA-suppressed gene expression in cereal grains, and TaWD40, which has previously been shown to physically interact with PKABA1. A full-length 1.9 kb TaWD40 cDNA, CK210682, was sequenced as part of this project. Based on the deduced protein sequence, it is thought that TaWD40 may belong to the family of E3 ubiquitin ligases, possibly targeting …

Spectroscopic Investigation Of Metal-Substitution Of Cytochrome C, Deepthi Kandi

Masters Theses

We study, by absorbance spectroscopy, the incorporation of various metal ions (Cu²+ and Zn2*) into metal-free porphyrin cytochrome c (H₂cyt) as well as the various conformational forms of metal-substituted cytochromes. The H2cyt and desired metalsubstituted cytochromes have significantly different absorption spectra, providing a simple means of monitoring the incorporation of Cu²* or Zn2* into the empty porphyrin prosthetic group. The rates of metal-ion incorporation were studied under protein denaturating conditions using chemical denaturants, like urea and guanidine hydrochloride (GuHCI), and temperature that partially and completely unfold H2cyt, facilitating the incorporation of a metal ion. Moreover, the structural stability of copper …

The Study Of Carbon Acylation Of Highly Delocalized Enolates Using Catalytic Dmap On 3-Phenyl Benzofuranone Derivatives, Xiguang Zhao

Masters Theses

Benzofuranones along with their derivatives compose a diverse array of natural products and drugs, and show a wide variety of biological effects. Several synthetic methods have been published that describe the preparation of 2-(3H)-benzofuranones having mono alkyl or aryl substituents attached to the fused furanone ring with moderate to high yields. To date, reports describing the preparation of disubstituted 2-(3H)-benzofuranones, especially with one acyl group, are rare. Early approaches are limited by low yields, economical expenditure and environmental risk.

Direct acylation of benzofuranones consistently provides O-acylated isomers rather than C-acylated isomers, which are desired products in the great majority of …

Formation Of Yttrium(Iii) Complexes With Salicylic Acid Derivatives In Aqueous Solution, Rahmi̇ye Aydin, Ulvi̇ye Özer

Turkish Journal of Chemistry

Complexes of yttrium(III) formed with 5-sulphosalicylic acid, 5-SSA (H_3L), and 5-nitrosalicylic acid, 5-NSA (H_2L), were investigated in 0.1 mol.dm^{-3} sodium perchlorate ionic medium at 25.0 \pm 0.1 °C potentiometrically for various molar ratios of Y(III) to these salicylic acid, SA (H_2L), derivatives. Y(III) forms YL and YL_2^{3-} type complexes with 5-SSA that have rather high stabilities (log \beta _1 = 7.91 \pm 0.01 and log \beta _2 = 14.56 \pm 0.06). In the Y(III):5-NSA system, YL^+ and YL_2^- type complexes appear with high stabilities (log \beta _1 = 7.39 \pm 0.02 and log \beta _2 = 13.50 \pm 0.07). Y(III):5-SSA …

Organotin (Iv) Derivatives Of 1-Ethyl-1,4-Dihydro-7-Methyl-4-Oxo- 1,8-Naphthyridine-3-Carboxylic Acid (Nalidixic Acid): Synthesis, Structural Elucidation And Biological Activities, Sajjad Ahmed, Moazzam Hussain Bhatti, Saqib Ali, Fiaz Ahmed

Turkish Journal of Chemistry

Organotin carboxylates of the general formulae R_2SnL_2 and R_3SnL, where R = CH_3, n-C_4H_9, C_6H_5, CH_2C_6H_5 and L = 1-ethyl-1,4-dihydro-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid (nalidixic acid), have been prepared. These compounds were characterized by FT-IR, mass and multinuclear NMR (^1H, ^{13}C and ^{119}Sn) spectroscopy. The geometry around the tin atom is compared both in solution and in solid state. These compounds were also screened for their antifungal and antibacterial activities.

Metal Complexes Of Schiff Bases: Preparation, Characterization, And Biological Activity, Gehad Genidy Mohamed, Mohamed Mohamed Omar, Ahmed Mohamed Hindy

Turkish Journal of Chemistry

Metal complexes of Schiff bases derived from 2-furancarboxaldehyde and o-phenylenediamine (L^1), and 2-thiophenecarboxaldehyde and 2-aminothiophenol (HL^2) are reported and characterized based on elemental analyses, IR ^1H NMR, solid reflectance, magnetic moment, molar conductance, and thermal analysis (TGA). The ligand dissociation, as well as the metal-ligand stability constants were calculated, pH-metrically, at 25 °C and ionic strength \mu = 0.1 (1 M NaCl). The complexes are found to have the formulae [M(L^1)(H_2O)_2](Cl)_n \cdot yH_2O (where M = Fe(III), Ni(II), Cu(II); n = 2-3, y = 2-4); [M(L^1)](X)_2 \cdot yH_2O (where M = Co(II), Zn(II), UO_2(II), X = Cl, AcO or NO_3, …

Chemistry Of Bicyclic Endoperoxides Derived From Dihydropyridine Derivatives: Attempted Synthesis Of Polyhydroxypiperidine Derivatives, Emi̇ne Salamci, Beyhan Bayram, Meti̇n Balci

Turkish Journal of Chemistry

To achieve the synthesis of azasugar derivatives with the utilization of singlet oxygen, pyridine was used as the starting material. The reduction of pyridine followed by a singlet oxygen reaction afforded cyclic aza-endoperoxides (14 and 16). However, many attempts were made to convert the aza-endoperoxides to the corresponding di- and triacetates without success. However, the base-catalyzed rearrangement of 14 gave unprecedented rearrangement products 23 and 24.

The Synthesis Of 4-Phenoxyphenylglyoxime And 4,4'-Oxybis(Phenylglyoxime) And Their Complexes With Cu(Ii), Ni(Ii) And Co(Ii), Ahmet Coşkun

Turkish Journal of Chemistry

4-Acetyldiphenyl ether and 4,4'-diacetyldiphenyl ether were synthesized from diphenyl ether and acetyl chloride in the presence of AlCl_3 used as catalyst. Subsequently, their keto oxime and glyoxime derivatives were prepared. The metal complexes of the glyoximes such as Cu(II), Ni(II) and Co(II) were also prepared. The structures of these ligands and their complexes were identified by FT-IR, ^1H NMR and ^{13}C NMR spectral data, elemental analysis and magnetic measurements.

Antioxidant Activities Of The Extracts And Components Of Teucrium Orientale L. Var. Orientale, Ahmet Çakir, Ahmet Mavi̇, Cavi̇t Kazaz, Ali̇ Yildirim, Ömer İrfan Küfrevi̇oğlu

Turkish Journal of Chemistry

The effects of the developing stages of Teucrium orientale L. var. orientale on the antioxidant and DPPH radical scavenging activities of the extracts obtained with different organic solvents were investigated. The aerial parts of the plant samples were collected at the budding, flowering and vegetative stages and then the plant samples were extracted separately with petroleum ether, chloroform, acetone and methanol. The antioxidant activities of the extracts were evaluated using 2 different tests: the thiocyanate method and scavenging of the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical. The acetone and methanol extracts of all of the harvesting stages and chloroform extracts of the budding …

Synthesis Of Vic-Dioxime Derivatives With Hydrazone Side Groups And Their Metal Complexes, İlknur Babahan, Hüseyi̇n Anil, Nursabah Sarikavakli

Turkish Journal of Chemistry

Two novel vic-dioxime (L^1H_2, L^2H_2) compounds bearing hydrazone side groups and their transition metal complexes Ni(II), Co(II), Cu(II), and Zn(II) were synthesized. The vic-dioxime ligands bearing hydrazone side groups were synthesized by reacting anti-glyoximehydrazine (GH_2) with 4-nitroacetophenone and 4-methylacetophenenone, respectively. Ligands form mononuclear complexes [(LH)_2M] with a metal to ligand ratio of 1:2 with M=Co(II)(H_2O)_2, Ni(II), and Cu(II). Zn(II) forms complexes [(LH)(H_2O)(Cl)Zn] with a metal to ligand ratio of 1:1. The Co(II) complexes of the ligands are proposed to be octahedral with water molecules as axial ligands, the Ni(II) and Cu(II) complexes are proposed to be square planar, and the …

Synthesis, Crystal Structure And Antifungal/Antibacterial Activity Of Some Novel Highly Functionalized Benzoylaminocarbothioyl Pyrrolidines, H. Ali̇ Döndaş, Yahya Nural, Ni̇zami̇ Duran, Colin Kilner

Turkish Journal of Chemistry

A series of novel highly functionalized benzoylaminocarbothioyl pyrrolidines were prepared from benzoylisothiocyanate and substituted pyrrolidines in excellent yield. The crystal structure of the novel 1-benzoylaminocarbothioyl-5-(naphthyl)- pyrrolidine-2,3,4-tricarboxylicacid trimethyl ester (3a) was determined by X-ray crystal structure analysis. The synthesized compounds were characterized and screened for their in vitro antibacterial and antifungal activities and toxicity. The prepared compounds were tested against the standard strains: Escherichia coli (ATCC 25922), Enterobacter cloacae (ATCC 13047), Enterococcus faecalis (ATCC 29212), Pseudomonas aeruginosa (ATCC 27853), Staphylococcus aureus (ATCC 29213) and Staphylococcus epidermidis (ATCC 12228) and the yeasts Candida albicans (ATCC 90028), Candida krusei (ATCC 6258), Candida parapsilosis …

The Mechanism And Crystal Structure Of 2-Methoxy-2-Methyl-4-Phenyl-3,4,4a, 10b-Tetrahydro-2h,5h-Pyrano[3,2-C]Chromen-5-One. Acetal Of Warfarin Acid, Saira Shahzadi, Saqib Ali, Irum Asif, Rizwana Ashraf, Guo-Xin Jin

Turkish Journal of Chemistry

Acetal of warfarin acid has been synthesized via a hemi acetal intermediate and structurally characterized by X-ray diffraction. The crystal structure shows that the title compound was formed by the hydrolysis of warfarin acid in methanol at pH 3, with space group P2_1/n and unit cell parameters a = 5.859 (17), b =16.745 (5), c = 16.402 (5) Å, \alpha = 90.00; \beta = 94.853 (4), and \gamma = 90.00°.

Trans-Atlantic Correlation Of Upper Cretaceous Marine Sediments, Marcus R. Ross, David E. Fastovsky

Faculty Publications and Presentations

Upper Cretaceous marine deposits from the Mid-Atlantic region of North America (Delaware, Maryland, and New Jersey) and the Maastricht area (southern Netherlands, and nearby Belgium and Gennany) are correlated across the Atlantic using a variety of macro invertebrates, nannofossils, and sequence stratigraphy. Four late Cretaceous Mid-Atlantic sequences, the Marshalltown, Englishtown, Merchantville, and Navesink, span the upper Santonian to lowennost Danian, and have direct correlatives in the Maastricht area. Correlations between the Mid-Atlantic and the Maastricht regions (respectively) are as follows: the upper Santonian to lower Campanian Merchantville and Matawan formations with the Achen and lower Vaals fonnations; the middle Campanian …