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A Nested Pcr Strategy For Recovering Highly Discriminatory Y-Str Dna Profiles From Trace Male Dna Samples, Anna Kimball

Electronic Theses and Dissertations, 2020-2023

DNA profiling is an effective method of identifying individuals in forensic casework. In sexual assault cases in particular, male donor DNA can be genotyped using Y chromosome short tandem repeat (Y-STR) analysis even in the presence of significant levels of female DNA. The recently released recommended national standard for sexual assault evidence collection from the victim is within 5 days after the sexual assault, with the probability of obtaining a male DNA profile diminishing significantly thereafter due to degradation and/or loss of sperm. The present study was designed to develop a method of obtaining a highly probative DNA profile with …

Total Synthesis Of Natural Products From Oxidative Dearomatization, Nameer Ezzat

Electronic Theses and Dissertations, 2020-2023

The goal of our research is to prepare natural products and related core structures through oxidative dearomatization. The development of a stereoselective iron (III)-mediated intramolecular cascade dearomatization of phenol allowed access to various spirocyclohexadienones and tropons in one step using potassium ferricyanide via single electron transfer (SET). Using this oxidative dearomatization reaction, the thesis focuses on three main parts. The first part is the synthetic efforts toward total synthesis of Harringtonolide. The second part focused on the synthesis of spiro[4.5]decane, a core structure in multiple natural products. The spiro compounds were prepared from ortho hydroxyphenyl nitroalkanes using SET reaction with …

Studies On The Synthesis Of Unusual Amino Acids And Their Incorporation Into New Peptide Antibiotics, Agnieszka Wadolowska

Doctoral

As microorganisms continue to develop resistance and survive against many different forms of antimicrobial solutions, such as antibiotics, there is urgent need for new classes of antimicrobial peptides to mitigate the threat. Bacteria are a rich source of ribosomally-synthesized antimicrobial peptides known as bacteriocins, which are produced by one bacterial species to kill other bacterial strains. Lanthionine-containing lantibiotics and sactibiotics are post-translationally modified bacteriocins which display extremely potent antibacterial activity.

Thuricin CD, a two-peptide system belonging to the sactibiotic family, shows high activity, but most importantly excellent selectivity, against C. difficile infection. The Thuricin CD peptides contain a number of …

Ratiometric Near-Infrared Fluorescent Probes For The Sensitive Detection Of Intracellular Ph And Bio-Thiols In Live Cells, Shuai Xia

Dissertations, Master's Theses and Master's Reports

In the past twenty years, fluorescence sensing and imaging based on fluorescent probes has been developed as an imperative technique due to the merits including excellent sensitivity, operational simplicity, instant time effectiveness and outstanding selectivity in the research areas such as mineralogy, gemology, biological medicine, materials and environmental engineering. Protons act as a significant role in a variety of pathological and physiological processes, and there are obvious differences in the pH among organelles: the pH in lysosomes is acid within the range of 4.5–5.5, whereas mitochondrial pH is basic that can be as high as 8.0. Abnormal intracellular pH is …

Gravity-Drawing Flexible Silicone Filaments As Fiber Optics And Model Foldamers, Katherine Snell

CMC Senior Theses

Here, we present a method of gravity-drawing polydimethylsiloxane (PDMS) silicone fibers with application as fiber optics and as model foldamers. Beginning as a viscous liquid, PDMS is cured using heat until its measured viscosity reaches 4000 mPa•s. The semi-cured elastomer is then extruded through a tube furnace to produce thin (diameters on the order of hundred micrometers) filaments with scalable lengths. PDMS is biocompatible, gas-permeable, flexible, and hydrophobic. Additionally, the PDMS surface hydrophobicity can be modified via UV exposure, O2 plasma, and corona discharge. We demonstrate the patternibility (i.e patterns of hydrophobicity) of PDMS fibers, adding complexity to potential foldamer …

Improving The Value Of The Coconut With Biotechnology, Fabian M. Dayrit, Quang Nguyen

Chemistry Faculty Publications

The fruit of the coconut tree is perhaps the most useful plant resource in the tropics. All parts of the coconut fruit have traditional uses that have been developed commercially in recent times (Foale 2003, Dayrit and Dayrit 2013). Due to its widespread household use, trade and industry statistics on coconut products reflect only part of the actual importance of the coconut. Today, coconut-based products have gone beyond the tropics and are consumed in many temperate countries and global regions such as Australia, China, Europe, North America, and the Middle East (Costello 2018). Coconut milk is the basic ingredient of …

Feasibility Of Cyclodextrin-Potassium Ion Assemblies Synthesis And Its Application In Loading Bio-Active Molecules, Yomkippur Perez, Gilbert U. Yu

Chemistry Faculty Publications

In the study, colorless cubic crystals of “green” cyclodextrin (CD)-based assemblies were synthesized and their potential to load bio-active molecules such as drugs and, separately, enzymes were investigated. Busulfan (Bu), an anti-cancer drug widely used to treat chronic myelogenous leukemia (CML), was used as a test drug while trypsin and lipase were used as model enzymes. These porous CD-K+ ion assemblies were prepared by dissolving alkali metal salts and γ-CD in water followed by vapor diffusion in varying solvents for several days. Crystals were activated via dichloromethane dispersion and in vacuo drying. Slow vapor diffusion with ethanol was found to …

Determination Of Samarium And Dysprosium Solubility, Seana Brennan

Theses and Dissertations (Comprehensive)

In recent years, the use of Rare Earth Elements (REE) has rapidly increased, resulting in numerous potential anthropogenic inputs to the environment. As a result, these metals are emerging as microcontaminants and pose a potential threat to aquatic life. However, the toxicity of REE are largely unknown due, in part, to the limited information on their chemical speciation. The purpose of this project was to gain an understanding of REE precipitate formation and solubility as the foundation for the development of the chemical equilibrium component of toxicity prediction models. Solubility experiments were conducted with Samarium, (Sm), a light REE, and …

Nanoparticles As Alternative Ceramic Glaze Colorants, Nathan Dinh

Honors Theses

Metallic nanoparticles, including gold and silver, have been used in wide-ranging applications due to their versatile characteristics. These include catalysis, biosensing, imaging, cancer treatments, and art. Due to the phenomenon called surface plasmon resonance, metallic particles change optical properties when sized in the nanoscale based on their composition, shape, diameters, or aspect ratios. In study, these robust nanoparticle systems are applied as an alternative to traditional bulk metal colorants in ceramic glazes.

In this study, the research goals are two-fold: to understand firing mechanism on the gold nanoparticle size and to develop these processes for wider use by regular artisans. …

Deriving Statistical Inference From The Application Of Artificial Neural Networks To Clinical Metabolomics Data, Kevin M. Mendez

Theses: Doctorates and Masters

Metabolomics data are complex with a high degree of multicollinearity. As such, multivariate linear projection methods, such as partial least squares discriminant analysis (PLS-DA) have become standard. Non-linear projections methods, typified by Artificial Neural Networks (ANNs) may be more appropriate to model potential nonlinear latent covariance; however, they are not widely used due to difficulty in deriving statistical inference, and thus biological interpretation. Herein, we illustrate the utility of ANNs for clinical metabolomics using publicly available data sets and develop an open framework for deriving and visualising statistical inference from ANNs equivalent to standard PLS-DA methods.

Selective Synthesis Of Trans-Fused Lactam-Lactones By Vicinal Difunctionalization Of Readily Affordable Allylic Lactams, Morgan J. Rodriguez

All Master's Theses

With intrinsic versatility and an overwhelming presence in natural products, nitrogen- and oxygen-containing heterocycles boast a plethora of medicinal properties. Specifically, lactams and lactones are the respective luminaries of the antibiotic and flavor worlds. However, the synthesis of fused lactams-lactones, especially those bearing trans-fusion, is challenging from the standpoints of chemoselectivity, stereoselectivity, and regioselectivity. In this thesis, the highly-selective, cost-effective, and high-yielding conversion of readily affordable allylic lactams into trans-fused lactam-lactones by intramolecular vicinal difunctionalization is explored. The approach is highly divergent and requires only two steps, which bodes well for the construction of medicinally pertinent fragments. It …

N‑Linked Glycosylation Prevents Deamidation Of Glycopeptide And Glycoprotein, Joshua Zhu, Ding Liu, Vy P. Tran, Zhigang Wu, Kuan Jiang, He Zhu, Jiabin Zhang, Christopher Gibbons, Bingzhong Xue, Hang Shi, Peng George Wang

Faculty Work Comprehensive List

Deamidation has been recognized as a common spontaneous pathway of protein degradation and a prevalent concern in the pharmaceutical industry; deamidation caused the reduction of protein/peptide drug efficacy and shelf life in several cases. More importantly, deamidation of physiological proteins is related to several human diseases and considered a "timer" for the diseases. N-linked glycosylation has a variety of significant biological functions, and it interestingly occurs right on the deamidation site-asparagine. It has been perceived that N-glycosylation could prevent deamidation, but experimental support is still lacking for clearly understanding the role of N-glycosylation on deamidation. Our results presented that deamidation …

Design Of New Ruthenium Complexes For Photoactivated Chemotherapy, Lindsey Paul

Honors Theses

Photoactivated chemotherapy (PACT) offers a targeted approach to cancer treatment through selective drug activation. Substitutionally labile ruthenium-based prodrugs undergo ligand-loss when irradiated, producing an unbound ligand and a Ru-aqua complex. We report the synthesis and cytotoxicity of several new ruthenium-centered complexes and their irradiation products for use in PACT. A series of complexes were synthesized in order to study the effects of structural differences on cell viability. Cell viability was tested on T47D human breast cancer cells in the presence of compound to determine cytotoxicity and dose-response. While neither the Rucomplexes nor their ligands demonstrated cytotoxicity, their Ru-aqua dissociation complexes …

Correction: Visible-Light Photooxidation In Water By 1o2-Generating Supramolecular Hydrogels, Sankarsan Biswas, Mohit Kumar, Andrew Levine, Ian Jimenez, Rein V. Ulijn, Adam Braunschweig

Advanced Science Research Center

Correction for ‘Visible-light photooxidation in water by ¹O₂-generating supramolecular hydrogels’ by Sankarsan Biswas et al., Chem. Sci., 2020, 11, 4239–4245, DOI: 10.1039/C9SC06481H.

Structural Characterization Of Emerging Synthetic Drugs, Jay Tyler Davidson

Graduate Theses, Dissertations, and Problem Reports (ETD)

The identification of well-characterized seized drugs is performed thousands of times a day in the United States; however, the expanding use of emerging synthetic drugs is creating a growing problem for both toxicological and seized drug analyses. Two of the most rapidly growing areas of emerging synthetic drugs are synthetic cathinones and fentanyl-related compounds (FRCs). In this work we demonstrate the combination of multi-stage mass spectrometry (MSⁿ), accurate mass measurements with high-resolution mass spectrometry (HRMS), and isotopic labeling for the structural characterization of synthetic cathinones and fentanyl analogs. The deliverables of this research include the identification of conserved …

Determination Of Herbicides In Water Samples By Spectroscopic Techniques, Anna Prukjareonchook

Chulalongkorn University Theses and Dissertations (Chula ETD)

Atrazine and paraquat are widely used to control weeds in the agricultural areas. The residue of herbicides can harm the environment and living things. In this research, nanoporous carbon derived from melamine based polybenzoxazine or NPC-PBZ-m was used as an adsorbent for atrazine and paraquat analysis. NPC-PBZ-m was synthesized by sol-gel and pyrolysis processes. The characteristics of sorbent were investigated by FTIR, BET, XPS, and FE-SEM. For atrazine determination, NPC-PBZ-m pre-concentration column combined with a colorimetric detection based on a Konig’s reaction and HPLC-UV at 222 nm were developed. The parameters affecting the adsorption performance were optimized. The reusability of …

Detection Of Hydrogen Peroxide And Persulfate Ion By Gold Nanorod Sensor, Petrada Chunnuan

Chulalongkorn University Theses and Dissertations (Chula ETD)

Gold nanorods (GNRs) multicolor sensor were developed to determine hydrogen peroxide (H2O2) and persulfate (S2O82-) based on the etching of GNRs which was detected from either naked-eye or UV-visible spectroscopic method. The changed size of GNRs was directly related to the concentration of H2O2 and S2O82-. To obtain the optimum conditions for H2O2 and S2O82- determination, CTAB concentration, FeSO4 concentration and detection time were investigated. For H2O2, the working range was 0.20 to 3.0 mM where the good linear working range was in the range of 0.20 to 0.80 mM. LOD was 0.08 mM. Moreover, the GNRs conjugated hydrogel was …

Synthesis, Characterization, And Biological Activity Of Imidazolium Salts, David Weader

Williams Honors College, Honors Research Projects

Nonmuscle invasive bladder cancer (NMIBC) inflicts thousands of Americans annually, and is typically treated with the immunotherapy BCG. However, due to a BCG shortage, there is a new need for novel treatments of NMIBC. Addressing this issue, several imidazolium salt derivatives were synthesized and characterized with the intent of treatment within the bladder. These imidazolium salts were tested against different human bladder cancer cell lines in vitro to determine their reactivity and cytotoxicity. Among these results are GI50 concentrations for each drug, which is the concentration of drug needed to see growth inhibition in 50% of treated cells. Previous published …

Expression, Purification, And Characterization Of Recombinant Human Npas2, Brenda Moreno

Open Access Theses & Dissertations

Many living organisms have biological clocks known as circadian rhythms that control various physiological and behavioral processes, tailored with the day and night. At the cellular level, the circadian clock drives daily rhythms with a transcriptional-translational feedback loop (TTFL) established by multiple transcription factors and genes under their regulation. Circadian Locomotor Output Cycles Kaput (CLOCK) and Brain and Muscle ARNT-like protein 1 (BMAL1) are two of those transcription factors, initiating the TTFL by forming a heterodimeric complex that bind to DNA promoters. Neuronal PAS domain protein 2 (NPAS2) is a functional analog to CLOCK. Less knowledge about NPAS2, in contrast …

Polymer Chemistry Education To Increase Student Awareness Of Plastic Pervasiveness And Environmental Impact, Victoria Hill

Master's Theses and Doctoral Dissertations

A polymer-pollution-focused laboratory sequence was written to teach general chemistry concepts in a course for pre-service elementary teachers. Students experienced the difficulties related to polymer pollution clean-up and made bio-based materials to see possible alternatives. In order to determine whether this laboratory sequence changed student understanding of the importance of polymers and their environmental impact, student opinions were gathered with pre/post-course sequence surveys, observations, post-laboratory surveys, and focus group interviews. These same data collection methods were also used to determine the likelihood that the pre-service elementary teachers would teach these polymer and environmental laboratories or their concepts in the future. …

Quantum Chemical Pka Estimation Of Carbon Acids, Saturated Alcohols, And Ketones Via Quantitative Structure-Activity Relationships, Corey Adam Baldasare

Browse all Theses and Dissertations

Acid dissociation constants, often expressed as pKa values, afford vital information with regards to molecular behavior in various environments and are of significance in fields of organic, inorganic, and medicinal chemistry. Several quantitative structure-activity relationships (QSARs) were developed that correlate experimental pKas for a given class of compounds with a descriptor(s) calculated using density functional theory at the B3LYP/6-31+G** level utilizing the CPCM solvent model. A set of carbon acids provided a good final QSAR model of experimental aqueous pKas versus ΔEH2O (R2 = 0.9647) upon removal of three aldehydes as outliers. A study of saturated alcohols offered a final …

Triflic Acid Mediated Sequential Cyclization Of Ortho-Alkynylarylesters With Ammonium Acetate, Maciej E. Domaradzki, Xiaochen Liu, Jiye Ong, Gyeongah Yu, Gan Zhang, Ariel Simantov, Eliyahu Perl, Yu Chen

Publications and Research

A triflic acid (TfOH) mediated sequential cyclization of ortho-alkynylarylesters and ammonium acetate (NH₄OAc) was reported. The reaction took place via a Brønsted acid-mediated intramolecular cyclization of ortho-alkynylarylesters followed by an ammonium acetate participated substitution reaction, forming isoquinolin-1-ones as the major products. Different from most of the known synthetic methods of isoquinolin-1-ones, no metal catalyst was required in the reported reaction. The regioisomers – isoindolin-1-ones were obtained together with isoquinolin-1-ones in a few cases. The intermediate compounds – isochromen-1-ones and isobenzofuran-1-ones were also isolated. The interconversion experiments showed that the regioisomers formed during the Brønsted acid induced …

Laser Surface Cleaning As A Novel Approach For Genesis Solar Wind Collectors, Martina Schmeling, I. V. Veryovkin, C. E. Tripa

Chemistry: Faculty Publications and Other Works

A new surface cleaning method utilizing lasers has been evaluated for its suitability to Genesis solar wind collectors

Kidney Tissue Preparation For 1h-Nmr Analysis And Colorimetric Activity Assay Of Mitochondria, Savannah Knight, James Wolfsberger

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Metabolomic Study Of The Lew.1wr1 Rat: Serum Artificial Mixture Validation, Jennifer S. Nix

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

The Role Of Influenza Infection On Cell Metabolism, Megha Mokkapati

Williams Honors College, Honors Research Projects

In this particular study global metabolomics LCMS data was analyzed to determine the effect of influenza infection on host metabolic processes. Specifically, wild-type male and female mouse lung samples from mice infected with PR8 (H1N1) or both PR8 and a reinfection of X31 (H3N2) were analyzed. The LC/MS(liquid chromatography-mass spectrometry) based global metabolomics will be performed on the samples using hydrophilic interaction liquid chromatography to separate polar analytes from the tissues (Dettmer, Aronov, 2007). Metabolites impacted by influenza infection in all samples will be analyzed to compare male and female mice, as well as differences between PR8 infection and X31 …

Development Of A Method For The Detection And Quantification Of Various Benzodiazepines And Z-Drugs In Human Blood And Qualitative Identification In Urine Samples Using Liquid Chromatography Mass Spectrometry (Lc-Ms/Ms), Haley Michel

Williams Honors College, Honors Research Projects

This method developed in the toxicology department at the Cuyahoga County Medical Examiner’s Office (CCMEO) detects 40 benzodiazepines and metabolites along with several z-drugs in blood and urine by liquid chromatography tandem mass spectrometry. A sample amount of 0.5 mL was used to detect analytes in postmortem drug facilitated sexual assault and impaired driving cases. Twenty-nine analytes met criteria for quantification while the remaining 14 were used as qualitative indicators. Bias and precision results for quality controls met criteria, staying within ±15% except for clonazolam and etizolam which were within ±20%. Quantitative reporting criteria which included dilution integrity was met …

Targeting Oncogenic K-Ras And Monoamine Oxidase B Utilizing Chalcones Bearing The 3,4,5-Trimethoxyphenyl Motif, Cody Fourman

Browse all Theses and Dissertations

Oncogenic K-Ras is a driver protein found in specific cancers and was once thought to be “undruggable.” However, recent advances have suggested that mislocalizing K-Ras from the plasma membrane could be a viable strategy to target these cancers. The objective of this project was to identify a lead compound and determine a structure-activity relationship from chalcones bearing the 3,4,5-trimethoxy motif towards oncogenic K-Ras and MAO-B. This was accomplished by keeping the trimethoxy group consistent on one ring while varying the electron-donating or -withdrawing groups on the opposite ring. Previous work showed chalcones of this specific archetype exhibiting indiscriminate MAO inhibition, …

Exploring Substrate Specificity Of Fructose Transporters En Route To Glut Specific Probes For Biochemical And Biomedical Applications, Vagarshak Vigenovich Begoyan

Dissertations, Master's Theses and Master's Reports

Carbohydrate Transporters (GLUTs) are responsible for the transportation of sugars into the cell and have been of great interest in research for decades. Alterations or mutations that result in overexpression of GLUTs have been linked to a great number of diseases including, obesity, diabetes, and cancer. Differentiation between transporters has been shown to be incredibly difficult due to the highly conserved nature of the transporter structure, and thus specific targeting of transporters has proven a difficult challenge. Additionally, the GLUTs have been shown to high flexibility in their conformations, so it is difficult to determine what can or cannot pass …

Synthesis, Magnetic And Adsorption Of Dye Onto The Surface Of Nio Nanoparticles, Islam Gomaa, Nasser M. Hosny

Nanotechnology Research Centre

NiO was synthesized simply via thermal decomposition of nickel ascorbate, which resulted from semi-solid reaction of nickel acetate and ascorbic acid. The prepared precursor was characterized by elemental, thermal and spectral analyses. The precursor was decomposed at 700 °C producing cubic NiO with average size 50 nm as indicated from XRD and TEM. FESEM indicated the formation of macroporous NiO. Magnetic parameters (saturation magnetization (Ms), remanence (Mr) and coercivity (Hc)) of NiO nanoparticles and its precursor were determined and compared with the bulk nickel. Zeta potential measurements at different pH values indicated that NiO is negatively charged. Adsorption of ponceau …