Biosensors monitor physiological activities for diagnosis and treatment of disease. Molecularly imprinted polymers (MIPs) are a viable synthetic approach for molecular recognition in biosensing. For biosensing purposes, the most important properties in MIP optimization are sensitivity and selectivity towards a desired analyte. This study aims to optimize MIP sensitivity and selectivity by varying the amount and type of cross-linker used in the synthesis of cortisol and melatonin. The four cross-linkers tested were trimethylpropane trimethacrylate (TRIM), ethyleneglycodimethacrylate (EGDMA), divinylbenzene (DVB), and pentaerythritol triacrylate (PETRA). Based on literature, the following ratios were used for the template molecule to functional monomer to cross-linker in MIP synthesis: for EGDMA cross-linked polymers, 1:6:30; for TRIM and PETRA cross-linked polymers, 1:8:8, 1:6:3, and 1:8:35; for DVB cross-linked polymers, 1:6:30, 1:4:16, and 4:1:60. The polymers were ground and washed, then suspended in a polyvinyl matrix which was spin-coated onto an organic electrochemical transducer (OECT). The device performance was evaluated using electrochemical impedance spectroscopy. For each device, the impedance was measured in electrolyte solutions containing target molecules in concentrations ranging from 1 pM to 100 uM. The impedance was plotted against the analyte concentration to give the sensing slope, which is a measurement for the binding affinity of the polymer. For a device to be considered sensitive, its sensing slope should be greater than its non-imprinted counterpart by a factor above the error margin (+/- 1.79). Of the devices tested, CM1835T (highly cross-linked with TRIM) showed sensitivity towards cortisol, but lacks selectivity towards cortisol over its structural analog, estradiol. Of the melatonin selective polymers, MM163T (low cross-linking with TRIM), MM1630D, and MM4160D (both highly cross-linked with DVB) all showed promising results in sensitivity to melatonin. Overall, the results indicate that high degrees of cross-linking in MIPs improve sensitivity for large, rigid, non-aromatic molecules such as cortisol; however there is no correlation between selectivity and the degree of cross-linking. Meanwhile, divinylbenzene as a cross-linker improves sensitivity and selectivity towards aromatic analytes such as melatonin and estradiol. This study could be improved upon by further characterization of imprinted and non-imprinted polymers, investigation of molecular dynamics, and optimization of devices.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19271号 / 医博第4035号 / 新制||医||1011(附属図書館) / 32273 / 京都大学大学院医学研究科医学専攻 / (主査)教授 妻木 範行, 教授 松田 秀一, 教授 萩原 正敏 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 新制・課程博士 / 博士(工学) / 甲第24234号 / 工博第5062号 / 新制||工||1790(附属図書館) / 京都大学大学院工学研究科材料化学専攻 / (主査)教授 大塚 浩二, 教授 沼田 圭司, 教授 大内 誠 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

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Estudos recentes demonstraram que a variação de expressão alelo-específica é mais comum do que se imaginou, podendo chegar, em humanos, a 50% dos genes. Identificar os genes submetidos ao controle de expressão alelo-específica é muito importante para o entendimento de várias doenças, incluindo o câncer. A identificação dos alvos desse tipo de regulação diferencial é difícil, principalmente devido à dificuldade de se avaliar a expressão de cada alelo individualmente. Neste trabalho, abordamos este problema com uma estratégia de análise in-silico, fundamentada na integração de dados públicos do genoma humano, dados de expressão (como cDNAs, SAGE e MPSS) e dados sobre polimorfismos (SNPs). Desenvolvemos um banco de dados de polimorfismos de base única (Single-Nucleotide Polymorphism - SNPs) associados a etiquetas alternativas de SAGE (Serial Analysis of Gene Expression) e MPSS (massively parallel signature sequencing). SAGE e MPSS são técnicas desenvolvidas para análise da expressão de genes em larga escala. Ambas as técnicas têm como princípio a produção de pequenas seqüências marcadoras (etiquetas), adjacentes aos sítios de enzimas de restrição que estiverem mais próximo da cauda poli-A do RNA mensageiro. Tais etiquetas são seqüenciadas em grande escala e a quantidade de etiquetas é usada para medir a abundância relativa dos RNAs mensageiros correspondentes. A presença de SNPs nos sítios de restrição ou nas seqüências das etiquetas pode gerar etiquetas distintas para alelos do mesmo gene, que denominamos etiquetas alternativas. Neste trabalho, empregamos o banco de dados de etiquetas alternativas associadas a SNPs para identificar genes com expressão alélica diferencial. Usando esta estratégia, identificamos 812 genes com expressão monoalélica, Estudos anteriores comprovaram que, dentre os 812 genes identificados, cinco estão sujeitos ao fenômeno de imprinting genômico. Durante o decorrer deste estudo, trabalhos realizados por outros grupos apontaram outros 73 genes do nosso repertório como genes que apresentam variação no nível de expressão dos alelos em heterozigotos. Com objetivo de confirmar a expressão alélica diferencial dos nossos candidatos, selecionamos 29 genes para validação experimental. Para 12 destes genes não achamos indivíduos heterozigotos, impossibilitando a análise da expressão dos alelos. Dentre os outros 17 genes, três apresentaram expressão bialélica e 14 apresentaram expressão alélica diferencial nos indivíduos heterozigotos, sendo que 3 deles apresentaram expressão monoalélica. Estes resultados sugerem que nossa estratégia pode contribuir significativamente na identificação de genes com expressão alélica diferencial. / Recent studies have shown that variation of allelic-specific gene expression is more common than previously thought, reaching up to 50% of human genes. To identify genes displaying differential expression among alleles it is important for the understanding of several diseases, including the cancer. Identification of genes submitted to allelic-specific differential expression is hard, mostly due to the difficulty in evaluating the expression levels of each allele independently. In this work, we developed an in-silico approach, based on the integration of public data about the human genome, gene expression data (such as cDNAs, SNPs, SAGE and MPSS) and data on polymorphisms (SNPs). We developed a database of Single Nucleotide Polymorphisms (SNPs) associated to alternative SAGE (Serial Analysis of Gene Expression) and MPSS (Massively Parallel Signature Sequencing) tags. SAGE and MPSS are genome-wide techniques developed for analysis of gene expression. Both techniques rely on the production of short marker sequences (known as tags), adjacent to restriction sites closer to the poly-A tail of messenger RNAs. Such tags are sequenced in a large scale and tag counts are used to measure the relative abundance of their corresponding transcripts. The presence of SNPs in the restriction sites or in the tag sequences might generate allelic-specific tags for the same gene, which we call alternative tags. In this work, we used the database of SNPs and associated alternative tags to identify genes submitted to allelic-specific differential gene expression. Using this approach, we identified 812 genes showing allelic-specific differential gene expression. Previous studies have shown that, among the 812 candidates, five genes are targets for genomic imprinting. While this study was being performed, work done by other groups suggested other 73 genes in our candidates list to have different expression levels for alleles in heterozygous. Aiming to verify whether variations in the expression levels of alleles existed among our candidate genes, we submitted 29 genes for experimental validation. For 12 genes, we couldnt find heterozygous individuals, thus rendering it impossible to ascertain whether the supposed expression variation was true. Among the other 17 genes analyzed, three genes presented bi-allelic expression and 14 genes have shown clear differential expression among alleles, three of the last ones displaying strict mono-allelic expression. These results suggest that our approach may contribute significantly to the identification of genes with allelic-specific differential expression.

Advantages such as chemical, mechanical and thermal stability together with high selectivity for the templated analyte render molecularly imprinted polymers MIPs interesting alternatives to routinely applied separation materials or antibodies. Nevertheless, many factors such as the choice of functional monomer, cross-linker, and porogenic solvent, as well as the ratio between template, functional monomer, and cross-linker will affect the resulting imprinting efficiency and polymer particle size and morphology. The research described in this thesis contributes to the development of new synthetic strategies for the generation of imprinted micro- and nanospheres for 17beta-estradiol (E2) focusing on accurate control and optimization of the governing parameters for precipitation polymerization, including the polymerization temperature and the cross-linker, yielding a one-step synthetic approach with superior control on the bead diameter, shape, monodispersity and imprinting efficiency. Thus synthesized imprinting materials for E2 were successfully applied in HPLC separation, solid phase extraction and radioligand binding assays. As the optimization of imprinted materials is based on fundamental understanding of the binding site properties, the investigations is aimed at establishing a more rational basis for further tailoring imprinted materials to the desired analytical application. The relationships between the particle porosity and rebinding properties were detailed, providing useful guidelines for controlling the particle properties for the desired application including, SPE pre-concentration, HPLC separations, and biomimetic binding assays. Furthermore, analytical techniques (1H-NMR and IR, etc.) and molecular modeling were combined in this thesis to facilitate advanced understanding of the fundamental principles governing selective recognition of molecularly imprinted polymers at a molecular level. The molecular interactions involved in the templating process of molecularly imprinted polymers based on the self-assembly approach were simulated in molecular dynamic simulation model by building a modeling system include all the imprinting components with correct ratio, which has never been reported before. Molecular level interactions such as hydrogen bonding, π-π stacking interactions as well as the free energy governing complex formation of E2 with the functional monomers 4-vinylpyridine (4VP) and methacrylic acid (MAA), and the cross-linker divinylbenzene (DVB) were discussed.

Estudos recentes demonstraram que a variação de expressão alelo-específica é mais comum do que se imaginou, podendo chegar, em humanos, a 50% dos genes. Identificar os genes submetidos ao controle de expressão alelo-específica é muito importante para o entendimento de várias doenças, incluindo o câncer. A identificação dos alvos desse tipo de regulação diferencial é difícil, principalmente devido à dificuldade de se avaliar a expressão de cada alelo individualmente. Neste trabalho, abordamos este problema com uma estratégia de análise in-silico, fundamentada na integração de dados públicos do genoma humano, dados de expressão (como cDNAs, SAGE e MPSS) e dados sobre polimorfismos (SNPs). Desenvolvemos um banco de dados de polimorfismos de base única (Single-Nucleotide Polymorphism - SNPs) associados a etiquetas alternativas de SAGE (Serial Analysis of Gene Expression) e MPSS (massively parallel signature sequencing). SAGE e MPSS são técnicas desenvolvidas para análise da expressão de genes em larga escala. Ambas as técnicas têm como princípio a produção de pequenas seqüências marcadoras (etiquetas), adjacentes aos sítios de enzimas de restrição que estiverem mais próximo da cauda poli-A do RNA mensageiro. Tais etiquetas são seqüenciadas em grande escala e a quantidade de etiquetas é usada para medir a abundância relativa dos RNAs mensageiros correspondentes. A presença de SNPs nos sítios de restrição ou nas seqüências das etiquetas pode gerar etiquetas distintas para alelos do mesmo gene, que denominamos etiquetas alternativas. Neste trabalho, empregamos o banco de dados de etiquetas alternativas associadas a SNPs para identificar genes com expressão alélica diferencial. Usando esta estratégia, identificamos 812 genes com expressão monoalélica, Estudos anteriores comprovaram que, dentre os 812 genes identificados, cinco estão sujeitos ao fenômeno de imprinting genômico. Durante o decorrer deste estudo, trabalhos realizados por outros grupos apontaram outros 73 genes do nosso repertório como genes que apresentam variação no nível de expressão dos alelos em heterozigotos. Com objetivo de confirmar a expressão alélica diferencial dos nossos candidatos, selecionamos 29 genes para validação experimental. Para 12 destes genes não achamos indivíduos heterozigotos, impossibilitando a análise da expressão dos alelos. Dentre os outros 17 genes, três apresentaram expressão bialélica e 14 apresentaram expressão alélica diferencial nos indivíduos heterozigotos, sendo que 3 deles apresentaram expressão monoalélica. Estes resultados sugerem que nossa estratégia pode contribuir significativamente na identificação de genes com expressão alélica diferencial. / Recent studies have shown that variation of allelic-specific gene expression is more common than previously thought, reaching up to 50% of human genes. To identify genes displaying differential expression among alleles it is important for the understanding of several diseases, including the cancer. Identification of genes submitted to allelic-specific differential expression is hard, mostly due to the difficulty in evaluating the expression levels of each allele independently. In this work, we developed an in-silico approach, based on the integration of public data about the human genome, gene expression data (such as cDNAs, SNPs, SAGE and MPSS) and data on polymorphisms (SNPs). We developed a database of Single Nucleotide Polymorphisms (SNPs) associated to alternative SAGE (Serial Analysis of Gene Expression) and MPSS (Massively Parallel Signature Sequencing) tags. SAGE and MPSS are genome-wide techniques developed for analysis of gene expression. Both techniques rely on the production of short marker sequences (known as tags), adjacent to restriction sites closer to the poly-A tail of messenger RNAs. Such tags are sequenced in a large scale and tag counts are used to measure the relative abundance of their corresponding transcripts. The presence of SNPs in the restriction sites or in the tag sequences might generate allelic-specific tags for the same gene, which we call alternative tags. In this work, we used the database of SNPs and associated alternative tags to identify genes submitted to allelic-specific differential gene expression. Using this approach, we identified 812 genes showing allelic-specific differential gene expression. Previous studies have shown that, among the 812 candidates, five genes are targets for genomic imprinting. While this study was being performed, work done by other groups suggested other 73 genes in our candidates list to have different expression levels for alleles in heterozygous. Aiming to verify whether variations in the expression levels of alleles existed among our candidate genes, we submitted 29 genes for experimental validation. For 12 genes, we couldnt find heterozygous individuals, thus rendering it impossible to ascertain whether the supposed expression variation was true. Among the other 17 genes analyzed, three genes presented bi-allelic expression and 14 genes have shown clear differential expression among alleles, three of the last ones displaying strict mono-allelic expression. These results suggest that our approach may contribute significantly to the identification of genes with allelic-specific differential expression.

The research described in this thesis contributes to the development of new strategies facilitating advanced understanding of the fundamental principles governing selective recognition of molecularly imprinted polymers (MIPs) at a molecular level for the rational optimization of biomimetic materials. The nature of non-covalent interactions involved in the templating process of molecularly imprinted polymers based on the self-assembly approach were investigated with a variety of analytical techniques addressing molecular level interactions. For this purpose, the concerted application of IR and 1H-NMR spectroscopy enabled studying the complexation of the template molecules 2,4-dichlorophenoxyacetic acid, quercetin, and o-, m-, and p-nitrophenol with a variety of functional monomers in the pre-polymerization solution by systematically varying the ratio of the involved components. In aqueous and non protic porogenic solvents, information on the interaction types, thermodynamics, and complex stoichiometry was applied toward predicting the optimum imprinting building blocks and ratios. Molecular dynamics simulations of 2,4-dichlorophenoxyacetic acid and its interactions with the functional monomer 4-vinylpyridine in aqueous and aprotic explicit solvent allowed demonstrating the fundamental potential of computer MD simulations for predicting optimized pre-polymerization ratios and the involved interaction types. The obtained results clearly demonstrate that the application of rapid IR/NMR pre-screening methods in combination with molecular modeling strategies is a promising strategy towards optimized imprinting protocols in lieu of the conventionally applied labor intensive and time-consuming trial-and-error approach. Furthermore, HPLC characterization of the produced MIPs compared to control polymers enabled a systematic approach to imprinting based on advanced understanding of the factors governing the formation of high-affinity binding sites during the polymerization. In addition, the importance of the combination of size, shape, and molecular functionalities for the selective recognition properties of MIPs was investigated. MIPs for the mycotoxins deoxynivalenol and zearalenone and for the antioxidant quercetin were applied as separation materials for advanced sample preparation in beverage analysis. The obtained results demonstrated the potential of MIPs for rapid one-step sample clean-up and pre-concentration from beverages such as wine and beer.

Orientadores: Susanne Rath, Rogério Custódio / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-27T17:08:24Z (GMT). No. of bitstreams: 1 Barros_LeonardoAugustode_D.pdf: 4314419 bytes, checksum: 93a1b964e0a2949ef6a2379990e2f089 (MD5) Previous issue date: 2014 / Resumo: Esse trabalho teve como objetivo principal otimizar e sintetizar polímeros de impressão molecular (MIP) para serem empregados em processos de extração em fase sólida (SPE), visando a determinação de diuréticos tiazídicos em urina. Cálculos teóricos de modelagem molecular, usando o programa computacional Gaussian 09 e os métodos DFT e PCM, no nível B3LYP e conjunto de base 6-31G(d), foram realizados para selecionar o monômero funcional (MF) e o solvente porogênico mais adequados para serem utilizados na síntese dos MIP. Para o desenvolvimento dos MIP compatíveis com água, foi utilizado hidroclorotiazida, clorotiazida ou hidroflumetiazida como molde, acrilamida como MF, etilenoglicol dimetacrilato como reagente de ligação cruzada (RLC) e tetraidrofurano como solvente porogênico. Foram avaliados alguns parâmetros que afetam a eficiência do polímero de impressão, tais como a quantidade de MF e a natureza do RLC. Foram construídas as isotermas de adsorção para cada um dos polímeros sintetizados e foi avaliada a seletividade dos MIP frente a análogos estruturais dos moldes. Os polímeros foram caracterizados por infravermelho com transformada de Fourier, 13C RMN, microscopia eletrônica de varredura, porosimetria de sorção de nitrogênio e análise termogravimétrica. Os MIP foram empregados como fase estacionária em SPE para a determinação de diuréticos tiazídicos em urina por cromatografia líquida de alta eficiência e os mesmos apresentaram seletividade cruzada em relação aos análogos estruturais / Abstract: This work aimed to optimize and synthesize molecularly imprinted polymers (MIP) to be employed in processes of solid phase extraction (SPE), for the determination of thiazide diuretics in urine. Theoretical calculations of molecular modeling, using the Gaussian 09 software and the density functional theory and PCM methods, at the B3LYP/6-31G(d) level, were performed to select a the most appropriate functional monomer (FM) and porogenic solvent for the synthesis of the molecularly imprinted polymers (MIP). For the development of a water-compatible MIP chlorothiazide, hydrochlorothiazide or hydrfoflumethiazide were used as template, acrylamide as FM, ethyleneglycol dimethacrylate as cross-linker and tetrahydrofuran as porogenic solvent. Parameters that affect thepolymer efficiency, such as the amount of the monomer and nature of the cross-linker were evaluated. The adsorption isotherms for each of the synthesized polymers were constructed and the selectivities of the MIPs in relation to structural analogues of the templates were evaluated. The polymers were characterized by Fourier transform infrared, 13C NMR, scanning electron microscopy, nitrogen sorption porosimetry and thermogravimetric analysis. The MIPs were employed as stationary phase in SPE for the determination of thiazide diuretics in urine by high performance liquid chromatography and they showed cross-selectivity in relation to their structural analogues / Doutorado / Quimica Analitica / Doutor em Ciências

Bacterial infections are an increasing problem for human health. In fact, an increasing number of infections are caused by bacteria that are resistant to most antibiotics and their combinations. A new solution to fight bacteria and infectious diseases, without promoting antimicrobial resistance, is required. A promise strategy is the disruption or attenuation of bacterial Quorum Sensing (QS), a refined system that bacteria use to communicate. In a QS event, bacteria produce and release specific small chemicals, signal molecules - autoinducers (AIs) - into the environment. AIs regulate gene expression as a function of cell population density. Phenotypes mediated by QS (QS- phenotypes) include virulence factors, toxin production, antibiotic resistance and biofilm formation. In this work, two polymeric materials (linear polymers and molecularly imprinted nanoparticles) were developed and their ability to attenuate QS was evaluated. Both types of polymers should be able to adsorb bacterial signal molecules, limiting their availability in the extracellular environment, with expected disruption of QS. Linear polymers were composed by methyl methacrylate as backbone and itaconic acid or methacrylic acid as functional monomer. IA and MAA monomers were identified by computer modelling to have strong interactions with the AIs produced by Gram-negative bacteria. Cont/d.