A method for the selective concentrating of DNA targets using capillary affinity gel electrophoresis is presented. Complementary ssDNA targets are retained through hybridization with oligonucleotide probes immobilized within polyacrylamide gels while non-complementary targets are removed. The captured DNA targets were concentrated by step elution, where a localized thermal zone was applied in small steps along the capillary. Evaluation of the selective capture of a 150 nt DNA target in a complicated mixture was carried out by factorial analysis. Gels with a smaller average pore size were found to retain a higher amount of complementary targets. This was thought to be due to the ssDNA target migrating through the gel by reptation, eliminating hairpin structures, making the complementary region of the target available for hybridization. This method was applied to a series of DNA targets of different lengths, 19 nt, 150 nt, 250 nt and 400 nt. The recovery of the method ranged from 0.5 to 4% for the PCR targets, and 13 to 18% for the 19 nt oligonucleotide target. The purity was calculated to be up to 44% for the PCR targets and up to 86% for the 19 nt target. This was an improvement in purity of up to 15 times and 1100 times in comparison to the original samples for the PCR targets and 19 nt oligonucleotide, respectively. The 19 nt targets were selective concentrated and delivered into a microfluidic based DNA biosensing platform. The purity of the sample improved from 0.01% to 50% while recovery decreased from 100% to 20% for a sample with 0.5 nM complementary and 1 μM non-complementary targets. An improvement in the response of the sensing platform was demonstrated on 19 nt oligonucleotide targets delivered by selective concentration versus concentration alone into the microfluidic biosensing system.

Thesis (M.S.)--Youngstown State University, 2008. / Includes bibliographical references (leaves 50-53). Also available via the World Wide Web in PDF format.

Honors Project--Smith College, Northampton, Mass., 2009. / Includes bibliographical references.

Thesis (M.S.)--Georgia State University, 2009. / Title from file title page. W. David Wilson, committee chair; Stewart A. Allison, Kathryn B. Grant, committee members. College of Arts and Sciences.Description based on contents viewed July 22, 2009. Includes bibliographical references (p. 85-87).

Thesis (Ph. D.)--University of Texas at Austin, 2003. / Supervisor: Adam Heller. Vita. Includes bibliographical references. Also available from UMI.

Thesis (M.S.)--Rochester Institute of Technology, 2007. / Typescript. Includes bibliographical references (leaves 91-98).

Orientadores: Helena Teixeira Godoy, Roy Edward Bruns / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Alimentos / Made available in DSpace on 2018-08-16T15:04:06Z (GMT). No. of bitstreams: 1 Meinhart_AdrianaDillenburg_D.pdf: 1252628 bytes, checksum: b7a02daccb3ff84e9c4321162440ec4f (MD5) Previous issue date: 2010 / Resumo: Os carboidratos são compostos muito abundantes na natureza. Estão presentes em todas as etapas evolutivas, tanto em vegetais como animais. Quaisquer reações, de anabolismo ou catabolismo envolvem, de alguma forma, algum carboidrato. Na indústria alimentícia são responsáveis por diversos fenômenos que promovem efeitos químicos, físicos e sensoriais nos alimentos. A importância destes compostos acompanha etapas que vão desde a obtenção da matéria-prima, a formulação, o processamento, as características do produto final até o tratamento dos resíduos gerados. São compostos de ações biológicas e tecnológicas distintas, mas de características físico-químicas semelhantes e, por isso, de difícil separação. Diversos métodos já foram desenvolvidos para a análise desses compostos. No entanto, dentre a literatura pesquisada, nenhum método investigou a possibilidade de separação simultânea dos 13 carboidratos geralmente encontrados em alimentos: glicose, frutose, sacarose, lactose, galactose, lactulose, epilactose, arabinose, manose, maltose, xilose, ribose e maltotriose. Nesse estudo, foram avaliados os efeitos de três diferentes metodologias na separação desses compostos, envolvendo eletroforese capilar de zona, cromatografia eletrocinética micelar com tensoativo catiônico e tensoativo aniônico. Foram investigados diversos fatores que possam influenciar na separação, dentre eles, o tipo e a concentração do eletrólito, o pH, a concentração de surfactante, a voltagem, temperatura, adição de outros sais como tetraborato de sódio, fosfato de sódio, acetato de sódio e cloreto de sódio e a adição de solventes orgânicos como etanol e acetonitrila. Foram utilizadas técnicas estatísticas multivariadas para a otimização do pH, da concentração do eletrólito e do tensoativo. Através da função de Derringer e Suich foi possível realizar a avaliação simultânea de várias respostas e prever as condições analíticas das metodologias de separação. Utilizando a eletroforese capilar de zona foi possível obter a separação de 8 compostos, por cromatografia eletrocinética micelar contendo surfactante catiônico foi possível separar 9 compostos (sacarose, lactose, lactulose, glicose, arabinose, manose, frutose, xilose e ribose), enquanto que utilizando tensoativo aniônico foi obtida a separação dos 13 compostos. Os métodos estatísticos multivariados se apresentaram como uma valiosa ferramenta para o tratamento dos dados e a predição matemática das condições ótimas de separação. Além disso, permitiram a redução do número de experimentos aliada a obtenção de um grande número de informações a respeito dos sistemas estudados / Abstract: The carbohydrates are compounds very abundant in nature. They are present in all evolutionary steps, both in vegetables and animals. Any metabolism or synthesis reaction involves, in some way, a carbohydrate. In food industries, carbohydrates are compounds responsible for several phenomena that promote chemical, physical and sensorial effects. These compounds are important in raw material obtention, formulation, processing, final product characteristics and generated residue treatment. They are compounds having different biological and technological actions, but with similar physico-chemical characteristics and, for this reason, are hard of separate. Several methods have been developed for the analysis of these compounds. However, in the research literature, no method investigating the possibility of simultaneous separation of the 13 carbohydrates commonly found in foods: glucose, fructose, sucrose, lactose, galactose, lactulose, epilactose, arabinose, mannose, maltose, xylose, ribose and maltotriose was found. In this work, three different methodologies for the separation of these compounds were evaluated, involving capillary zone electrophoresis, micellar electrokinetic chromatography with cationic and anionic surfactants. Several factors that could influence the separation were assayed, electrolyte type and concentration, voltage, temperature, addition of sodium tetraborate, sodium phosphate, sodium acetate and sodium chloride salts and addition of organic solvents like ethanol and acetonitrile. Multivariate statistical techniques were used to optimize pH and electrolyte and surfactant concentrations. Employing the Derringer and Suich desirability function it was possible to make a simultaneous evaluation of several responses and predict the optimum analytical conditions of separation. Using the method of capillary zone electrophoresis it was possible to obtain the separation of 8 compounds, by micellar electrokinetic chromatography containing cationic surfactant. It was possible to separate 9 compounds (sucrose, lactose, lactulose, glucose, arabinose, mannose, fructose, xylose and ribose), when using an anionic surfactant. it was obtained the 13 compounds separation. The multivariate statistical methods were a valuable tool for data treatment and for mathematical prediction of the optimum separation conditions. Moreover, they allowed a reduction in number of experiments as well as the obtention of a great amount of information concerning the studied systems / Doutorado / Doutor em Ciência de Alimentos

Fishes of the perciform suborder Notothenioidei are found in Antarctic and sub-Antarctic waters that are separated by the Antarctic Polar Front (APF), with some species being distributed on both sides of this front. In this wide latitudinal range, these fishes are exposed to different temperatures ranging from -2 °C in the High Antarctic regions to 12 °C in the sub-Antarctic regions. To survive in icy Antarctic waters, the Antarctic notothenioid species have evolved antifreeze glycoproteins (AFGPs) that prevent their body fluids from freezing. The findings of past research on the AFGP attributes of several notothenioid species inhabiting ice-free sub-Antarctic environments have presented a complex picture. Furthermore, previous taxonomic studies split widely distributed notothenioids into different species and/or subspecies, with other studies disagreeing with these splits. To understand the response of the sub-Antarctic notothenioids to warmer, ice-free environments, it is necessary to have a good understanding of their antifreeze biology and systematics. Therefore, this study aimed to determine the association, if any, between the antifreeze attributes of sub-Antarctic notothenioid fishes and their taxonomic status. And more...

The goal of this research was to design, prepare and study a new class of supermolecules coupling ruthenium and platinum, which would display covalent binding to DNA. Drawing upon the well-established efficacy of cis-diamminedichloroplatinum(II) (cisplatin) and the DNA-binding properties of select ruthenium polyazine complexes, the approach was to bind the cis-PtIICl2 active site of cisplatin to ruthenium light absorbers using the dpq and dpb bridging ligands (where dpq = 2,3-bis(2-pyridyl)quinoxaline, dpb = 2,3-bis(2-pyridyl) benzoquinoxaline). These complexes are potentially bifunctional, capable of DNA intercalation through the bridging ligand and covalent binding to DNA through the cis-PtCl2 site. Synthetic methods were developed to prepare the mixed-metal, bimetallic complexes [(bpy)2Ru(BL)PtCl2](CF3SO3)2 and [(phen)2Ru(BL)PtCl2](CF3SO3)2 (where bpy = 2,2¢-bipyridine, phen = 1,10-phenanthroline) in high purity and good overall yields. The DNA-binding ability of these complexes was probed by reaction with linearized plasmid DNA and subsequent analysis by native and denaturing gel electrophoresis. The known DNA binders, cisplatin and trans-{[PtCl(NH3)2]2(m-H2N(CH2)6NH2)}(NO3)2 (1,1/t,t), were examined under equivalent conditions and used as positive controls. Native gel electrophoresis was used to show that these complexes strongly bind DNA, retarding the migration of DNA through the gel in a fashion inversely proportional to the ratio of DNA base pairs (bp) to metal complex (mc). Analysis by denaturing gel electrophoresis determined that the Ru-Pt complexes bind to DNA in a fashion similar to cisplatin, forming primarily intrastrand adducts. However, these systems also appear to form interstrand adducts at a 10-fold lower metal concentration than cisplatin. In addition to affecting the migration rate, the bimetallic complexes also significantly reduced the fluorescence of DNA-intercalated ethidium bromide for the Ru-Pt reacted samples at low-DNA bp: mc ratios. This was not observed for the cisplatin and 1,1/t,t treated samples. This observation was quantitated by gel densitometry. Precipitation of the DNA by cisplatin, 1,1/t,t and all four Ru-Pt complexes was determined not to be the cause of reduced ethidium bromide fluorescence intensity. Homogenous solution fluorescence quenching studies have revealed that the Ru-Pt complexes quench the emission of ethidium bromide even in the absence of DNA, whereas cisplatin and 1,1/t,t do not. In order to compare the effects on DNA migration produced by cisplatin, 1,1/t,t and the Ru-Pt complexes, Rf values were calculated. This analysis has revealed that all four Ru-Pt complexes retard DNA migration to approximately the same degree. Calculation of theoretical DNA migration distances, based upon the molecular weight change of DNA caused by metal-complex binding, have revealed that the observed affect on DNA migration cannot be accounted for by an increase in molecular weight alone. This indicates that changes in charge and three-dimensional shape of the DNA upon binding of the Ru-Pt complexes may also contribute. / Ph. D.

Plant breeders have focused on improving maize resistance to Aspergillus flavus infection and aflatoxin accumulation by breeding with genotypes having the desirable traits. Various maize inbred lines have been developed for the breeding of resistance. Identification of differentially expressed proteins among such maize inbred lines will facilitate the development of gene markers and expedite the breeding process. Computational biology and proteomics approaches on the investigation of differentially expressed proteins were explored in this research. The major research objectives included 1) application of computational methods in homology and comparative modeling to study 3D protein structures and identify single nucleotide polymorphisms (SNPs) involved in changes of protein structures and functions, which can in turn increase the efficiency of the development of DNA markers; 2) investigation of methods on total protein profiling including purification, separation, visualization, and computational analysis at the proteome level. Special research goals were set on the development of open source computational methods using Matlab image processing tools to quantify and compare protein expression levels visualized by 2D protein electrophoresis gel techniques.