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Synthetic Oligodeoxynucleotide Purification Via Catching By Polymerization, Suntara Fueangfung

Dissertations, Master's Theses and Master's Reports - Open

Large quantities of pure synthetic oligodeoxynucleotides (ODNs) are important for preclinical research, drug development, and biological studies. These ODNs are synthesized on an automated synthesizer. It is inevitable that the crude ODN product contains failure sequences which are not easily removed because they have the same properties as the full length ODNs. Current ODN purification methods such as polyacrylamide gel electrophoresis (PAGE), reversed-phase high performance liquid chromatography (RP HPLC), anion exchange HPLC, and affinity purification can remove those impurities. However, they are not suitable for large scale purification due to the expensive aspects associated with instrumentation, solvent demand, and high …

Mercury Methylation Potentials In Sediments An Ancient Cypress Wetland Using Species-Specific Isotope Dilution-Gc-Icp-Ms: Analytical Method Development And The Effect Of Sorbent Amendments, Derek Davin Bussan

Electronic Theses and Dissertations

A novel method was developed to measure mercury (Hg) directly in environmental solids using inductively coupled plasma mass spectrometry (ICP-MS) with online sample ashing. The method combines a direct mercury analyzer (DMA) that is based on sample combustion, Hg pre-concentration by amalgamation with gold, and atomic absorption spectrometry (AAS), with a high resolution ICP-MS. Unlike AAS, the ICP-MS is capable of individual isotope measurements allowing for accurate quantitation by isotope dilution mass spectrometry (IDMS) and for isotope tracer experiments. The method was validated using certified reference materials including sediment (NIST 2709), leaves (NIST 1547), and fish-muscle (DORM-3), with recoveries within …

Introduction To The Modeling And Analysis Of Complex Systems, Hiroki Sayama

Milne Open Textbooks

Keep up to date on Introduction to Modeling and Analysis of Complex Systems at http://bingweb.binghamton.edu/~sayama/textbook/!

Introduction to the Modeling and Analysis of Complex Systems introduces students to mathematical/computational modeling and analysis developed in the emerging interdisciplinary field of Complex Systems Science. Complex systems are systems made of a large number of microscopic components interacting with each other in nontrivial ways. Many real-world systems can be understood as complex systems, where critically important information resides in the relationships between the parts and not necessarily within the parts themselves. This textbook offers an accessible yet technically-oriented introduction to the modeling and …

Synthesis And Anti-Proliferative Activity Of N,N’-Bis(Arylmethyl)Benzimidazolium Salts, Travis M. Williams

Williams Honors College, Honors Research Projects

A series of N,N’-bis(arylmethyl)benzimidazolium salts with hydrophilic and lipophilic substituents have been synthesized, characterized, and tested against select non-small cell cancer cell lines. Substituent variations on the imidazole ring have shown that lipophilicity and hydrophilicity can influence the imidazolium salts’ anti-proliferative activity and aqueous solubility.

The Door At The End Of The Hall Or Why There Is Life On Earth, And Why We Should Have Seen It Coming, Kirk Pearson

The Synapse: Intercollegiate science magazine

No abstract provided.

I. Synthesis Of Ascarosides For Biological Evaluation And Ii. Development Of Visible Light-Promoted Selenofunctionalization And Grafting Of Aryl Iodides, Elizabeth Susan Conner Balapitiya

LSU Doctoral Dissertations

This dissertation focuses on analog synthesis for biological evaluation and visible light promoted method development. Chapter 1 centers upon the synthesis of Caenorhabditis elegans dauer pheromone analogs. C. elegans is a nematode which, in times of environmental stress, enters a dauer stage. Two highly conserved pathways, which play important roles in some diseases in higher organisms, monitor dauer formation: TGF-β and IGF-1. Dauer formation is triggered by the nematode’s chemosensation of the dauer pheromone, consisting of a group of previously-isolated ascarosides. These compounds differ in chain length, saturation, terminal functionality of side chain, ω vs. ω-1 oxygenation and presence of …

Sampling Strategies For Finite Population Using Auxiliary Information, Florentin Smarandache, Rajesh Singh

Branch Mathematics and Statistics Faculty and Staff Publications

The present book aims to present some improved estimators using auxiliary and attribute information in case of simple random sampling and stratified random sampling and in some cases when non-response is present. This volume is a collection of five papers, written by seven co-authors (listed in the order of the papers): Sachin Malik, Rajesh Singh, Florentin Smarandache, B. B. Khare, P. S. Jha, Usha Srivastava and Habib Ur. Rehman. The first and the second papers deal with the problem of estimating the finite population mean when some information on two auxiliary attributes are available. In the third paper, problems related …

Readup Buildup. Thync - Instant Α-Readings, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

No abstract provided.

Development Of New Linking Chemistry With The Fac-{Re(Co)3}+ Core For Eventual Applications In Radiopharmaceuticals In Imaging And Therapy, Aponsu Meregngna Pramuditha Lakmi Abhayawardhana

LSU Doctoral Dissertations

The facile labeling of biomolecules with a radionuclide is a key goal in radiopharmaceutical development. This study explores two different ligand systems for fac-[Re(CO)3L]+ complexes, that could be used in bioconjugation. The first approach uses a tridentate ligand having a sulfonamide linkage and modeled on previously evaluated fac-[Re(CO)3(N(SO2R)dpa)]PF6 complexes. The present goal was to develop new related sulfonamide complexes with more hydrophilic ligands designed to avoid the bioavailability problems that would plague the N(SO2R)dpa ligand system. A series of fac-[Re(CO)3(N(SO2R)dien)]PF6 complexes with different R groups linked to the central nitrogen of a symmetric tridentate sulfonamides were synthesized with the aim …

I. Synthesis Of Ascarosides For Chemical Biology Studies In Caenorhabditis Elegans, Ii. A Photochemical Approach To Delavayine, And Iii. Remote Hydroxylation By Radical Translocation And Polar Crossover, Kyle Allen Hollister

LSU Doctoral Dissertations

The foci of this dissertation are the synthesis of analogs for chemical biology studies, synthetic chemistry method development (with an emphasis on photochemistry), and the application of these methods toward total synthesis. Chapter 1 outlines the synthesis of an array of pheromone analogs that are derivatives of the dideoxy sugar ascarylose. Referred to as ascarosides, such compounds have recently been shown to influence important biological processes in the model organism Caenorhabditis elegans. C. elegans secretes ascarosides into its environment, where the compounds then act as signaling molecules by providing information on factors like population density. Chapter 2 describes the biological …

Nanoscale Gumbos: Size-Control, Characterization, And Applications As Enantioselective Molecularly Imprinted Polymers And Fluorescent Materials, Suzana Hamdan

LSU Doctoral Dissertations

Nanomaterials derived from a group of uniform materials based on organic salts (GUMBOS) have been introduced into the scientific literature through many analytical, biological, and technological applications. These nanomaterials, referred to as nanoGUMBOS, have been shown to display a number of interesting properties including fluorescence, magnetism, tumor targeting, and optoelectronic properties. Herein, we present major studies on nanoGUMBOS including synthesis and size-control, chiral molecular imprinting in polymers, as well as investigation of optical properties and quantum yield of fluorescent semiconductor-based nanoGUMBOS. Various strategies were introduced for production of well-defined nanoGUMBOS. Specifically, several methods based on sonochemistry, microwave, cyclodextrin, and surfactant-assisted …

The Electronic Structure Of Environmentally Persistent Free Radicals Formed On Metal Oxide Surfaces, Chad Allen Thibodeaux

LSU Doctoral Dissertations

We have investigated the electronic structure of environmentally persistent free radicals (EPFRs) formed on two different metal oxides: Cu(II)O and ZnO. Cu(II)O is known to be one of the most active metal oxides to form EPFRs. ZnO, however, forms the longest-lived EPFRs. First, we examined the adsorption of phenol on different crystal faces of ZnO. Ultraviolet photoelectron spectroscopy (UPS) shows direct evidence of charge transfer away from the ZnO to the phenol. This differs from the hypothesized mechanism of EPFR formation that says that an electron is transferred to the metal oxide. UPS difference spectra also shows that the phenol …

Evolution Of Acyl-Substrate Recognition By A Family Of Acyl-Homoserine Lactone Synthases, Quin H. Christensen, Ryan M. Brecht, Dastagiri Dudekula, E. Peter Greenberg, Rajesh Nagarajan

Chemistry and Biochemistry Faculty Publications and Presentations

Members of the LuxI protein family catalyze synthesis of acyl-homoserine lactone (acyl-HSL) quorum sensing signals from S-adenosyl-L-methionine and an acyl thioester. Some LuxI family members prefer acyl-CoA, and others prefer acyl-acyl carrier protein (ACP) as the acyl-thioester substrate. We sought to understand the evolutionary history and mechanisms mediating this substrate preference. Our phylogenetic and motif analysis of the LuxI acyl-HSL synthase family indicates that the acyl-CoA-utilizing enzymes evolved from an acyl-ACP-utilizing ancestor. To further understand how acyl-ACPs and acyl-CoAs are recognized by acyl-HSL synthases we studied BmaI1, an octanoyl-ACP-dependent LuxI family member from Burkholderia mallei, and BjaI, an …

Hydrolytically Stable Analogues Of Sugar Phosphates And A Miniaturized In Situ Enzymatic Screen, Xiang Fei

Department of Chemistry: Dissertations, Theses, and Student Research

The glmS riboswitch undergoes self-cleavage upon binding its metabolic product GlcN6P, thereby providing a negative feedback mechanism limiting translation of the glmS protein when GlcN6P is abundant. As a first step toward the development of novel antimicrobials, we have synthesized a series of GlcN6P analogues bearing phosphatase-inert surrogates in place of the natural phosphate ester functionality. The self-cleavage assay identified two such compounds that display significant riboswitch actuator activity; namely those bearing a 6-phosphonomethyl group or a 6-O-malonyl ether. These two analogues exhibit a 22-fold and a 27-fold higher catalytic efficiency, respectively, than does glucosamine. Docking experiments were …

The Cosm Newsletter

COSM Newsletter

• The College of Science and Mathematics Welcomes New Administration in the Dean’s Office
• COSM Faculty and Staff Recognized at College and University Levels
• College Awards
• University Awards
• Summer SOAR Project: Books for Back Pack Buddies
• COSM Alum Honored in Promotion Ceremony at the Pentagon
• Altrusa partners with Georgia Southern Pre-Vet Students for First Annual Dog Wash
• Two COSM Undergrads selected for Prestigious Summer Research Programs
• The Department of Biology Welcomes New Faculty
• Dr. Ed Mondor Named 2014 Outstanding Advocate for First Year Students
• Distinguished Alumnus Chosen
• Honor’s Day Ceremony Resumes
• Professor Gives Talk at 11th Congress on the Biology of …

Probabilistic Uncertainty Quantification And Experiment Design For Nonlinear Models: Applications In Systems Biology, Vu Cao Duy Thien Dinh

Open Access Dissertations

Despite the ever-increasing interest in understanding biology at the system level, there are several factors that hinder studies and analyses of biological systems. First, unlike systems from other applied fields whose parameters can be effectively identified, biological systems are usually unidentifiable, even in the ideal case when all possible system outputs are known with high accuracy. Second, the presence of multivariate bifurcations often leads the system to behaviors that are completely different in nature. In such cases, system outputs (as function of parameters/inputs) are usually discontinuous or have sharp transitions across domains with different behaviors. Finally, models from systems biology …

Synthesis And Evaluation Of Sensitizer Drug Photorelease Chemistry: Micro-Optic Method Applied To Singlet Oxygen Generation And Drug Delivery, Goutam Ghosh

Dissertations, Theses, and Capstone Projects

This thesis summarizes a new micro-optic method for singlet oxygen generation and sensitizer drug delivery, which include i) synthesis and evaluation of a first generation device for drug delivery from native and fluorinated silica probe tips, ii) synthesis of PEG conjugated sensitizers to study phototoxicity in ovarian cancer cells, and iii) synthesis and evaluation of tris-PEGylated chlorin conjugated fluorinated silica for its future integration into the device to use as a 2nd generation device. A first generation micro-optic device was developed that works by sparging O2 gas and light generating cytotoxic singlet oxygen that cleaves the covalently attached drug (sensitizer) …

The Cosm Newsletter, Georgia Southern University

College of Science & Mathematics: News & Publications (2012-2022)

• The College of Science and Mathematics Welcomes New Administration in the Dean’s Office
• COSM Faculty and Staff Recognized at College and University Levels
• College Awards
• University Awards
• Summer SOAR Project: Books for Back Pack Buddies
• COSM Alum Honored in Promotion Ceremony at the Pentagon
• Altrusa partners with Georgia Southern Pre-Vet Students for First Annual Dog Wash
• Two COSM Undergrads selected for Prestigious Summer Research Programs
• The Department of Biology Welcomes New Faculty
• Dr. Ed Mondor Named 2014 Outstanding Advocate for First Year Students
• Distinguished Alumnus Chosen
• Honor’s Day Ceremony Resumes
• Professor Gives Talk at 11th Congress on the Biology of …

Component Trees For The Exploration Of Macromolecular Structures In Biology, Lucas Oliveira

Dissertations, Theses, and Capstone Projects

Understanding the three-dimensional structure of a macromolecular complex is essential for understanding its function. A component tree is a topological and geometric image descriptor that captures information regarding the structure of an image based on the connected components determined by different grayness thresholds. This dissertation presents a novel interactive framework for visual exploration of component trees of the density maps of macromolecular complexes, with the purpose of improved understanding of their structure. The interactive exploration of component trees together with a robust simplification methodology provide new insights in the study of macromolecular structures. An underlying mathematical theory is introduced and …

Passivation And Functionalization Of Conjugated Polymer Nanoparticles With Head Group Modified Phospholipids And Proteins, Prakash Kandel

All Dissertations

Conjugated polymer nanoparticles (CPNs) possess important characteristics such as high fluorescence brightness, reasonable photostability, and non-toxicity. These properties allow the use of CPNs in fluorescence based cellular and biological applications including cellular labeling, imaging, biosensing, and single particle tracking. To realize the broad applications of CPNs, it is required that CPNs possess functionality to conjugate a recognition moiety and maintain colloidal stability in biological media. In the following Dissertation, we have prepared functionalized CPNs by surface passivation with head group- functionalized poly (ethylene glycol) lipids and proteins. We studied the colloidal stability of CPNs in biological media and investigated their …

Analyses Of 2002-2013 China’S Stock Market Using The Shared Frailty Model, Chao Tang

Electronic Theses and Dissertations

This thesis adopts a survival model to analyze China’s stock market. The data used are the capitalization-weighted stock market index (CSI 300) and the 300 stocks for creating the index. We define the recurrent events using the daily return of the selected stocks and the index. A shared frailty model which incorporates the random effects is then used for analyses since the survival times of individual stocks are correlated. Maximization of penalized likelihood is presented to estimate the parameters in the model. The covariates are selected using the Akaike information criterion (AIC) and the variance inflation factor (VIF) to avoid …

Biophysical Interactions In The Straits Of Florida: Turbulent Mixing Due To Diel Vertical Migrations Of Zooplankton, Cayla Whitney Dean

HCNSO Student Theses and Dissertations

Diel vertical migrations (DVM) comprise the largest animal migration on the planet and are a phenomenon present in all bodies of water on Earth. A strong sound scattering layer undergoing DVM was observed in the Straits of Florida via a bottom-mounted Acoustic Doppler current profiler (ADCP) Workhorse Longranger 75 kHz (Teledyne RD Instruments) located at the 244 m isobath. ADCP average backscatter showed a clear periodicity corresponding with sunrise and sunset times indicating the presence of a nocturnal DVM. Analysis of the ADCP backscatter data indicated zooplankton swimming velocities were faster during sunrise than sunset times. In several cases the …

Exploring The Link Between Otolith Growth And Function Along The Biological Continuum In The Context Of Ocean Acidification, Eric D. Wilcox Freeburg

Graduate Doctoral Dissertations

Oceans are acidifying as atmospheric CO₂ is drawn down. This process, known as ocean acidification (OA), is well known and documented. Over the next 100 years, pH of the surface ocean is projected to decrease by up to 0.35 units. This CO₂ draw down has a direct effect on dissolved inorganic carbon (DIC) balance in the ocean. OA is expected to impact calcifying organisms that rely on constituencies of the DIC system, specifically carbonate ion [CO₃2-]. It is clear that externally calcified structures, such as coral skeletons, bivalve shells, etc., will be significantly affected as pH, …

Branching Into Rnai: Synthesis, Characterization And Biology Of Branch And Hyperbranch Sirnas, Anthony Muriithi Maina

Seton Hall University Dissertations and Theses (ETDs)

The cancer epidemic continues to afflict millions of humans world-wide each year and despite a renewed hope with the development of new and improved forms of therapy, a cure for cancer remains an elusive goal. This is partly related to the rise of resilient forms of tumors that have evolved with resistance towards conventional chemotherapy and radiation treatments. Moreover, these non-specific therapeutic regimens are highly toxic, leading to severe immunosuppressive effects which poisons the body and compromises the road towards remission. In an effort to mitigate these limitations, cancer-targeting approaches are currently experiencing a renaissance in the translation of new …

On Individual, Sex And Age Differentiation Of Indian House Crow (Corvus Splendens) Call: A Preliminary Study In Potohar, Pakistan, Waqas Hameed, Inayat Ullah, Safia Janjua, Fakhar -I- Abbas, Afsar Mian

Journal of Bioresource Management

Considering importance of acoustics studies in population biology, 500 calls of the Indian House Crow (Corvus splendens) were recorded in morning - mid-afternoon hours (January-February, 2009) from 23 sites of urban areas of Potahar (Punjab, Pakistan). Calls were recorded using Sony CFS 1030 S sound records (sampling rate = 48 KHz) and edited using Sound Analysis Pro (Version 1.02). software using FFT method rate 50%, data window 9.27 ms, advanced window 1.36 ms. Through editing of calls, we selected 60 (37 ♂♂, 17 ♀♀, 6 Juvenile ♂♂) good quality spectrograms for detailed analysis. Spectrograms were characterized by rapid frequency modulations …

Synthesis Of N-Heterocycles Through Cyclization-Triggered Tandem Additions To Alkynes And The Study Of Promoters In Ionic Reactions., Junbin Han

Electronic Theses and Dissertations

Our research mainly focused on three parts related to the rapid construction of N-heterocycles and the search for ionic reaction promoters. First, N-heterocycles of different ring sizes and with different substitution patterns constitute extremely important structure classes (e.g., alkaloids) in the search for bioactivity. A contemporary challenge in organic synthesis is the mapping of new chemical spaces through tandem or cascade reactions in an atom economical fashion. Our strategy to access these biologically important heterocycles is through a cyclization-triggered tandem addition to alkynes catalyzed by readily available alkynophilic coinage metals like copper. In this manner, a variety of functional groups …

Understanding The Influence Of Interfacial Chemistry In Core, Core/Shell And Core/Shell/Shell Quantum Dots On Their Fluorescence Properties, Omondi Bernard Omogo

Graduate Theses and Dissertations

Colloidal semiconductor nanocrystals (quantum dots) have received a great deal of attention due to their superior size tunable properties and promising applications in many areas. Some of the most practical areas of their applications include light emitting diodes (LED), photovoltaic and biological studies. Synthetic methods of these crystals is becoming more established with new strategies being reported every now and then. However, quantitative studies connecting the processes at the interface, namely core-ligand, core-shell and shell-shells, to the overall quantum dots fluorescence properties are not well understood. Specifically for cores, relating surface-atoms interactions, solvents, ligands nature, density and functional groups on …

N-Methylmesoporphyrin Ix Fluorescence As A Reporter Of Strand Orientation In Guanine Quadruplexes, Navin C. Sabharwal , '14, V. Savikhin, Joshua R. Turek-Herman , '16, John Michael Nicoludis , '12, V. A. Szalai, Liliya A. Yatsunyk

Chemistry & Biochemistry Faculty Works

Guanine quadruplexes (GQ) are four-stranded DNA structures formed by guanine-rich DNA sequences. The formation of GQs inhibits cancer cell growth, although the detection of GQs invivo has proven difficult, in part because of their structural diversity. The development of GQ-selective fluorescent reporters would enhance our ability to quantify the number and location of GQs, ultimately advancing biological studies of quadruplex relevance and function. N-methylmesoporphyrin IX (NMM) interacts selectively with parallel-stranded GQs; in addition, its fluorescence is sensitive to the presence of DNA, making this ligand a possible candidate for a quadruplex probe. In the present study, we investigated the effect …

Photochemical Elimination Reactions That Proceed Via Triplet Excited State Electrocyclic Ring Closures, Himali Devika Jayasekara

Master's Theses (2009 -)

Cage compounds have become an important tool for the study of biological processes. The research focuses on new cage compounds that can unmask functional groups present in biologically important molecules such as proteins, peptides, and oligonucleosides. The project focuses on certain functional groups that are often difficult to release photochemically. These are the thiolate groups present in cysteine residues of proteins and peptides. Thiolate groups are fairly basic leaving groups, unlike the more labile groups such as the carboxylates that are present in proteins and peptides, or the phosphate groups present in nucleosides. The research takes advantage of the ability …

Modeling Stem Cell Population Dynamics, Samiur Arif

Computer Science Theses & Dissertations

Because of the stochastic nature of biological systems, mathematical and computational modeling approaches have become more acceptable to experimentalists and clinicians in recent years as contributing to new understandings of complicated cell mechanisms and tissue physiology. Indeed, even single cell or small tissue samples are complex dynamic systems that adapt to environmental challenges in space and time which is poorly understood. Mathematical models and computer simulations can explain and uncover unknown aspects of cell behavior and tissue functions. Models based on key biological mechanisms can give interesting insights and formulate predictions that cannot be derived from physical experiments or statistical …