Digital Commons Network^™

Methylation-Based Enrichment Facilitates Low-Cost, Noninvasive Genomic Scale Sequencing Of Populations From Feces, Kenneth L. Chiou, Christina M. Bergey

United States Public Health Resources

Obtaining high-quality samples from wild animals is a major obstacle for genomic studies of many taxa, particularly at the population level, as collection methods for such samples are typically invasive. DNA from feces is easy to obtain noninvasively, but is dominated by bacterial and other non-host DNA. The high proportion of non-host DNA drastically reduces the efficiency of high-throughput sequencing for host animal genomics. To address this issue, we developed an inexpensive capture method for enriching host DNA from noninvasive fecal samples. Our method exploits natural differences in CpG-methylation density between vertebrate and bacterial genomes to preferentially bind and isolate …

Biological Study On Novel Coumarinyl 1,3,4-Oxadiazoles, Maja Molnar, Ana Amic, Valentina Pavic, Tihomir Kovac, Marija Kovac, Elizabeta Has-Schön

Turkish Journal of Chemistry

Coumarinyl 1,3,4-oxadiazoles were synthesized from Schiff bases and acetic anhydride. All compounds were characterized by melting points and their structures confirmed by mass and $^{1}$H and $^{13}$C NMR spectrometry. These novel coumarinyl derivatives were subjected to antibacterial, antifungal, anta atoxigenic, and antioxidant activity. Their activity varied depending on their structure, where 2-(3-acetyl-5-(((4-methyl-2-oxo-2H-chromen-7-yl)oxy)methyl)- 2,3-dihydro-1,3,4-oxadiazol-2-yl)-1,4-phenylene diacetate showed significant antioxidant and antibacterial activity on B. subtilis. 4-(3-Acetyl-5-(((4-methyl-2-oxo-2H-chromen-7-yl)oxy)methyl)-2,3-dihydro-1,3,4-oxadiazol-2-yl)-1,2-phenylene diacetate was found to possess excellent antifungal and antia atoxigenic activity.

Synthesis And Evaluation Of Novel 1,3,4-Thiadiazole--Fluoroquinolone Hybrids As Antibacterial, Antituberculosis, And Anticancer Agents, Asli Demi̇rci̇, Kaan Gökçe Karayel, Esra Tatar, Si̇nem Öktem Okullu, Ni̇han Ünübol, Paki̇ze Nesli̇han Taşli, Zühtü Tanil Kocagöz, Fi̇kretti̇n Şahi̇n, İlkay Küçükgüzel

Turkish Journal of Chemistry

A series of 5-substituted-1,3,4-thiadiazole-based fluoroquinolone derivatives were designed as potential antibacterial and anticancer agents using a molecular hybridization approach. The target compounds 16-25 were synthesized by reacting the corresponding $N$-(5-substituted-1,3,4-thiadiazol-2-yl)-2-chloroacetamides with ciprofloxacin or norfloxacin. The purity and identity of the synthesized compounds were determined by the use of chromatographic and spectral techniques (NMR, IR, MS, etc.) besides elemental analysis. Antibacterial, antituberculosis, and anticancer activity of the target compounds were evaluated against selected strains and cancer cell lines. Compound 20 was appreciated as the most active agent representing antibacterial activity against Escherichia coli and Staphylococcus aureus with MIC values of 4 …

Nitric Oxide Sensors For Biological Applications, Nicole M. Iverson, Eric M. Hofferber, Joseph A. Stapleton

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Nitric oxide (NO) is an essential signaling molecule within biological systems and is believed to be involved in numerous diseases. As a result of NO’s high reaction rate, the detection of the concentration of NO, let alone the presence or absence of the molecule, is extremely difficult. Researchers have developed multiple assays and probes in an attempt to quantify NO within biological solutions, each of which has advantages and disadvantages. This review highlights many of the current NO sensors, from those that are commercially available to the newest sensors being optimized in research labs, to assist in the understanding and …

The Effects Of Emerging Technology On Healthcare And The Difficulties Of Integration, Skyler J. Pavlish-Carpenter

Honors Undergraduate Theses

Background: Disruptive technology describes technology that is significantly more advanced than previous iterations, such as: 3D printing, genetic manipulation, stem cell research, innovative surgical procedures, and computer-based charting software. These technologies often require extensive overhauls to implement into older systems and must overcome many difficult financial and societal complications before they can be widely used. In a field like healthcare that makes frequent advancements, these difficulties can mean that the technology will not be utilized to its full potential or implemented at all.

Objective: To determine the inhibiting factors that prevent disruptive technology from being implemented in conventional healthcare.

Methods: …

Progress Toward Controlled Disulfide Formation To Access Neuroactive Conotoxins, Thilini Kondasinghe

Wayne State University Dissertations

"Conotoxins are mini proteins isolated from marine snails of the Conus family. They have shown activity in the selective inhibition of various ion channels. Therefore, they present an opportunity as possible therapy for a myriad of neurological ailments. The synthesis of conotoxins would enable both biological studies and evaluation of these structures as lead targets for therapeutics. However, establishing a reliable method to consistently folding disulfide rich proteins, including conotoxin, into their native structure has been challenging over few decades. In this research project, it is shown the progress towards a mild, efficient, and broadly applicable methods to generate the …

Synthesis And Application Of Photoreactive Collagen Peptides, And Antiparasitic Agents, Alfredo Ornelas

Open Access Theses & Dissertations

Since the introduction of solid phase peptide synThesis in 1963, peptides and post-translationally modified peptides can be conveniently synthesized in the chemistry laboratory. In the past decade, there has been a remarkable increase in bioactive peptide research and the therapeutic peptide market value is expected to hit $25 billion this year. Peptides can also provide structural and biological functions and have emerged as promising novel biomaterials in tissue engineering. Here we will describe three different projects, which deal with different aspects of peptide chemistry, i.e. synthetic method development, exploration of new peptide biomaterials, and the use of cell penetrating peptides …

Universal Swine Influenza Antigen And Vaccine, Zhao Wang

Electronic Theses and Dissertations

Swine influenza A viruses pose a serious concern for global health and worldwide swine industry considering their evasion from vaccine-induced immune responses. Formulation of effective influenza vaccines can be complicated by both antigenic shift to a different subtype of hemagglutinin (HAs) and antigenic drift within a particular HA subtype. To address these concerns, we employed a systematic approach to determine the antigenic determinants of swine influenza A viruses by focusing on H1 and H3 subtypes. In parallel, we used a cross-disciplinary approach including structural biology and modeling, virology, and immunology to identify swine influenza A virus-derived HA fusion intermediates broadly …

A Pcr/Sequencing Technique To Identify Species And Genotypes Of Haemonchus From Mixed Trichostrongyle Egg Dna Recovered From Livestock Fecal Samples, Pratiksha Khanal

Electronic Theses and Dissertations

Six primer pairs, each with a pair of genus-specific and universal second internal transcribed spacer (ITS2) primers were evaluated to amplify and sequence the ITS2 region of nuclear ribosomal DNA to identify the species and genotypes of Haemonchus from livestock fecal samples containing mixtures of trichostrongyle nematode eggs. Based upon the use of universal ITS2 primers on Haemonchus adults, the ITS2 region has been shown to contain three fixed single-nucleotide differences between H. placei and H. contortus. It is clinically useful to identify the species and genotypes of Haemonchus infecting livestock, but it has not been possible in fecal …

The Colomoto Interactive Notebook: Accessible And Reproducible Computational Analyses For Qualitative Biological Networks, Aurelien Naldi, Celine Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loic Pauleve

Department of Biochemistry: Faculty Publications

Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together,many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users’ learning curve of these technologies. The framework …

The Role Of Prrx1 And Snai2 As Master Regulators Of Fibroblast Identity, Huda A. Alzahrani

Masters Theses

Mammalian development involves a complex system of regulatory signals and reactions, leading to the creation of distinct tissues with specific structures and functions controlled by various gene expression profiles. Tissue-specific gene expression is by controlled specific combinations of transcription factors and cofactors that dictate cell differentiation via activation and repression of genes in mammalian cells.

Whole genome microarray analyses of fibroblasts have revealed candidate genes that may serve as master regulators of fibroblast identity, such as Prrx1 and Snai2, that activate downstream genes such as Bmp3, Twist, Shox2, Cfos, Slug, Sema3A, Spp1, and Col1a1. A previous study showed that Prrx1 …

Resolution Of Proximal Oxidative Base Damage And 3′-Phosphate Termini For Nonhomologous End Joining Of Free Radical-Mediated Dna Double-Strand Breaks, Sri Lakshmi Chalasani

Theses and Dissertations

Clustered damage to DNA is a signature mark of radiation-induced damage, which involves damage to the nucleobases and/or DNA backbone. Double-strand breaks created by damaging agents are detrimental to cell survival leading to chromosomal translocations. Normal cells employ Non-homologous end-joining because of its faster kinetics, to suppress chromosomal translocations. However, the presence of complex DNA ends constitutes a significant challenge to NHEJ. Location of Thymine glycol (Tg) at DSB ends was a potential hindrance to end joining. The substrate with Tg at the third position (Tg3) from the DSB joined better than when present at the fifth position (Tg5). However, …

Quantitation Without Calibration: Response Profile As An Indicator Of Target Amount, Mrittika Debnath

Graduate Research Theses & Dissertations

Quantitative assessment of biomarkers is essential in numerous contexts from decision-making in clinical situations to food quality monitoring to the interpretation of life-science research findings. However, appropriate quantitation techniques are not as widely addressed as detection methods. One of the major challenges in biomarker’s quantitation is the need to have a calibration for correlating a measured signal to a target amount. The step complicates the methodologies and makes them less sustainable. In this work, we addressed the issue via a new strategy: relying on the position of response profile rather than absolute signal for assessment of a target nucleic acid’s …

Surface Modification Of Titanium For Hard-Tissue Engineering Applications, Murali Krishna Duvvuru

Graduate Research Theses & Dissertations

Titanium (Ti) and its alloys are widely used in dental and orthopedic applications due to their advantages such as biocompatibility, excellent corrosion resistance and mechanical properties like low Young’s modulus, low density and high strength as compared to other metallic implants. However, lack of interaction with host tissue (e.g. bioinertness), higher modulus of elasticity as compared to that of bone and resultant stress shielding cause fibrous tissue formation around the implant where the interaction with tissue is minimized. These will eventually cause the implant loosening and revision surgery is needed. Surface modification of Ti by increasing surface roughness and/or incorporation …

Development Of Biclustering Techniques For Gene Expression Data Modeling And Mining, Juan Xie

Electronic Theses and Dissertations

The next-generation sequencing technologies can generate large-scale biological data with higher resolution, better accuracy, and lower technical variation than the arraybased counterparts. RNA sequencing (RNA-Seq) can generate genome-scale gene expression data in biological samples at a given moment, facilitating a better understanding of cell functions at genetic and cellular levels. The abundance of gene expression datasets provides an opportunity to identify genes with similar expression patterns across multiple conditions, i.e., co-expression gene modules (CEMs). Genomescale identification of CEMs can be modeled and solved by biclustering, a twodimensional data mining technique that allows clustering of rows and columns in a gene …

The Great Potential Of Redox Active Ligands: Applications In Cancer Research And Redox Active Catalysis, Meredith Miles

Browse all Theses and Dissertations

Metal N-heterocyclic carbene (NHC) complexes have recently gained much popularity due to their tunable, steric, and electronic properties. Applications for such versatile molecules include organocatalysis, olefin metathesis, sundry cyclization reactions, and materials chemistry. Redox active NHCs are of special interest due to their ability to alter the electronic properties of the metal centers they are ligated to. In the first chapter, Au(I)-NHC complexes were synthesized and tested for biological activity in human cancer cell lines. Increasing reactive oxygen species (ROS) in cellular systems has proven to be a successful pathway for treating cancer. The redox active group in this case …

Methylation-Based Enrichment Facilitates Low-Cost, Noninvasive Genomic Scale Sequencing Of Populations From Feces, Kenneth L. Chiou, Christina M. Bergey

Open Access Publications

No abstract provided.

Type I General Exponential Class Of Distributions, Gholamhossein G. Hamedani, Haitham M. Yousof, Mahdi Rasekhi, Morad Alizadeh, Seyed Morteza Najibi

Mathematics, Statistics and Computer Science Faculty Research and Publications

We introduce a new family of continuous distributions and study the mathematical properties of the new family. Some useful characterizations based on the ratio of two truncated moments and hazard function are also presented. We estimate the model parameters by the maximum likelihood method and assess its performance based on biases and mean squared errors in a simulation study framework.

Embryological Studies On Trichloris (Poaceae, Chloridoideae), Geraldina Alicia Richard, María Carolina Cerino, Beatriz G. Galati, Eliana De Luján Exner, José Francisco Pensiero

Turkish Journal of Botany

The present study provides information on the development of the female and male gametophytes and seed ontogeny characteristics for Trichloris, and it discusses their taxonomic significance to the family Poaceae. Trichloris species are characterized by having 2?3 stamens per floret, tetrasporangiate anthers, a monocotyledonous development of the anther wall, a single middle layer of common origin with the tapetum, fibrous thickening in the cell walls of the endothecium, and a secretory tapetum. These characteristics are constant within Poaceae. The possession of bitegmic and tenuinucellate ovules, laterally positioned antipodals prior to their degeneration, a free exocarp, and an epiblast in the …

Synthetic Investigation Of Natural Products Causing Dopaminergic Neurodegeneration, Michael John Cunningham

Electronic Theses and Dissertations

The terrestrial organisms Streptomyces venezuelae and Rhaponticum repens produce toxic secondary metabolites that likely function as chemical deterrents. The polyketide SV-6 from S. venezuelae and the sesquiterpene lactone repin from R. repens both produce dose-dependent and selective degeneration of dopaminergic neurons. These molecules represent two possible tools that can be used to explore chemotoxic induction of Parkinson’s disease. In the case of SV-6, a newly isolated metabolite, total synthesis was undertaken to confirm its structure and biological activity. The natural product was produced from methacrolein and Roche ester starting materials that were elaborated to their respective fragments, a vinyl iodide …

Proceedings Of The 2018 Undergraduate Research Conference, Ryan C. Winters, Courtney A. Suire, Dillard University, Mcneese State University, Northwestern State University Of Louisiana, Southeastern Louisiana University, University Of New Orleans, University Of Louisiana At Lafayette

Advance: Student Research Experience

Proceedings of the 2018 Undergraduate Research Conference, University of Louisiana at Lafayette, November 16-17, 2018. Supported by the University Honors Program, Office of the Vice-President for Research, LaCOEUR, College of Liberal Arts, College of Sciences, and College of Engineering.

Identification Of Qtl Modifying The Activity Of The Tcb1-S Locus And Characterization And Sequencing Of Two Plutonium-Beryllium Induced Reduced Gametophyte Transmission Mutants In Maize, Merritt Bryer Burch

Electronic Theses and Dissertations

This thesis is split into two independent projects both involving the male gametophyte generation of maize. The first project looks at how pollen interacts with the female gametophyte to reduce its transmission in cross-incompatible reactions controlled by the unilateral cross-incompatibility system, teosinte crossing barrier 1. The second project explores two plutonium-beryllium induced male gametophyte mutants and attempts to uncover their genetic basis.

Identification of QTL Modifying the Activity of the Tcb1-s Locus
Teosinte crossing barrier 1 (Tcb1) is a unilateral cross-incompatibility system present in maize that provides a pre-zygotic pistil barrier to plants carrying Tcb1-s (strong allele) from pollen …

Statistical Algorithms And Bioinformatics Tools Development For Computational Analysis Of High-Throughput Transcriptomic Data, Adam Mcdermaid

Electronic Theses and Dissertations

Next-Generation Sequencing technologies allow for a substantial increase in the amount of data available for various biological studies. In order to effectively and efficiently analyze this data, computational approaches combining mathematics, statistics, computer science, and biology are implemented. Even with the substantial efforts devoted to development of these approaches, numerous issues and pitfalls remain. One of these issues is mapping uncertainty, in which read alignment results are biased due to the inherent difficulties associated with accurately aligning RNA-Sequencing reads. GeneQC is an alignment quality control tool that provides insight into the severity of mapping uncertainty in each annotated gene from …

Using Induced Pluripotent Stem Cell-Derived Hepatocyte-Like Cells To Study Liver Development And Diseases, Ran Jing

MUSC Theses and Dissertations

Studies on liver development and disease traditionally relied on using animal models. However, the difference in liver biology between human and animals prevented the animal models from fully recapitulating human liver dieases. Human induced pluripotent stem cells (iPSC) reprogramed from human somatic cells can self-renew and are capable of being differentiated into various cell types that originate from endoderm, mesoderm or ectoderm. Our lab previously developed a procedure to differentiate iPSCs into cells that resemble mature human hepatocytes. Here we aim to explore the application of iPSC-derived hepatocyte-like cells for the study of basic developmental biology, the generation of new …

Hyperthermia As A Cancer Treatment- From Theory To Practice, Graham Fullerton

CMC Senior Theses

Using iron super-paramagnetic and ferromagnetic nanoparticles composed of Fe₃O₄ molecules, scientists analyze the effectiveness and practicality of this new treatment theory, hyperthermia. The problems of magnetic particle density, isothermal barriers/cellular cooling thresholds, and nanoparticle specific targeting are addressed in this review.

Iron magnetic nanoparticles were chosen due to their relatively low biological reactivates and lack of subsequent cellular toxicity. However, there are significant heating problems associated with these magnetic nanoparticles due to their relative size and short thermal time constants or thermal half-lives. Effectively, these aforementioned issues create a phenomenon where cancerous cells, surrounded by unheated healthy …

Crystallographically Defined Silicon Macropore Membranes, Shannon C. Knight, Bret A. Unger, Kurt W. Kolasinski

Chemistry Faculty Publications

Laser ablation with nanosecond-pulsed Nd:YAG laser irradiation combined with anisotropic alkaline etching of Si wafers creates 4–20 µm macropores that extend all the way through the wafer. The walls of these macropores are crystallographically defined by the interaction of the anisotropy of the etchant with the orientation of the single-crystal silicon substrate: rectangular/octagonal on Si(001), parallelepiped on Si(110), triangular/hexagonal on Si(111). Laser ablation can create pillars with peak-tovalley heights of over 100 µm. However, with nanosecondpulsed irradiation at 532 nm, the majority of this height is created by growth above the original plane of the substrate whereas for 355 nm …

Synthesis And Biological Evaluation Of Novel Drug Candidates To Address Drug Resistance In Tuberculosis And Fungal Diseases, Huy Ngo

Theses and Dissertations--Pharmacy

Tuberculosis (TB) and fungal infections are two of the most lethal infectious diseases worldwide due to the emergence of drug-resistant Mycobacterium tuberculosis (Mtb) and fungal strains that can resist the most potent antimicrobial drugs currently employed. Due to the rise of these drug resistant strains, effective treatment options for these two infections are limited. This dissertation aims at exploring novel drug scaffolds to help combat drug resistance in TB and fungal infections.

TB caused by the pathogenic Mtb is, alongside with human immunodeficiency virus acquired immunodeficiency virus (HIV), the deadliest infectious disease worldwide with approximately 2-3 billion people …

Novel Computational Methods For Sequencing Data Analysis: Mapping, Query, And Classification, Xinan Liu

Theses and Dissertations--Computer Science

Over the past decade, the evolution of next-generation sequencing technology has considerably advanced the genomics research. As a consequence, fast and accurate computational methods are needed for analyzing the large data in different applications. The research presented in this dissertation focuses on three areas: RNA-seq read mapping, large-scale data query, and metagenomics sequence classification.

A critical step of RNA-seq data analysis is to map the RNA-seq reads onto a reference genome. This dissertation presents a novel splice alignment tool, MapSplice3. It achieves high read alignment and base mapping yields and is able to detect splice junctions, gene fusions, and circular …

Ultra-Fast And Memory-Efficient Lookups For Cloud, Networked Systems, And Massive Data Management, Ye Yu

Theses and Dissertations--Computer Science

Systems that process big data (e.g., high-traffic networks and large-scale storage) prefer data structures and algorithms with small memory and fast processing speed. Efficient and fast algorithms play an essential role in system design, despite the improvement of hardware. This dissertation is organized around a novel algorithm called Othello Hashing. Othello Hashing supports ultra-fast and memory-efficient key-value lookup, and it fits the requirements of the core algorithms of many large-scale systems and big data applications. Using Othello hashing, combined with domain expertise in cloud, computer networks, big data, and bioinformatics, I developed the following applications that resolve several major …

Spectroscopic Study Of Excited Molecular Nitrogen Generation Due To Interactions Of Metastable Noble Gas Atoms, Laurence Scally, James Lalor, Miroslav Gulan, Patrick J. Cullen, Vladimir Milosavljevic

Articles

This work provides an insight into the generation of excited nitrogen species by allowing noble gases to interact both with one another and ambient air. He and Ar were utilized to generate the optimum selectivity process to create reactive nitrogen species. An optimum setting for the generation of excited molecular nitrogen species, based on their excited energy levels, was obtained when using a mixture of Ar-He at a ratio of 10:1. At that point, when a voltage of 27 kV is applied to the system, it reached the maximum efficiency for selectivity processes to occur which allowed for a greater …