Chapter 1: The unique chemical and biological properties of porphyrins have led to increased interest in the development of porphyrin-based materials. Metal organic frameworks (MOFs) can act as a scaffold for the immobilization of porphyrins in desired arrangements. The crystalline nature of MOFs allows for control over spatial arrangement of porphyrins and the local environment of the porphyrin molecules. This opens up the possibility of conducting systematic studies aimed at exploring structure-property relationships. Several strategies for the design and synthesis of porphyrin-based frameworks have been developed over the last two decades, such as, the pillared-layer strategy, construction of nanoscopic metal-organic polyhedrals (MOPs), post-synthetic modification, etc. These strategies provide an opportunity to engineer porphyrin-based MOFs that can target a specific application or serve as multi-functional assemblies. Porphyrin-based MOFs provide a tunable platform to perform a wide variety of functions ranging from gas adsorption, catalysis and light harvesting. The versatile nature of these frameworks can be exploited by incorporating them in multi-functional assemblies that mimic biological and enzymatic systems. Nano-thin film fabrication of porphyrin-based MOFs broadens their application range, making it possible to use them in the construction of photovoltaic and electronic devices. Chapter 2: The reaction of zirconium salts with meso-tetracarboxyphenylporphyrin (TCPP) in the presence of different modulators results in the formation of a diverse set of metal-organic frameworks (MOFs), each displaying distinct crystalline topologies. However, synthesis of phase-pure crystalline frameworks is challenging due to the concurrent formation of polymorphs. The acidity and concentration of modulator greatly influence the outcome of the MOF synthesis. By systematically varying these two parameters, selective framework formation can be achieved. In the present study, we aimed to elucidate the effect of modulator on the synthesis of zirconium-based TCPP MOFs. With the help of powder X-ray diffraction (PXRD) and scanning electron microscopy (SEM), modulator candidates and the optimal synthetic conditions yielding phase-pure PCN-222, PCN-223 and MOF-525 were identified. 1H NMR analysis, TGA and N2 gas adsorption measurements were performed on select MOFs to gain insight into the relationship between their defectivity and modulator properties. Chapter 3: Singlet-singlet energy transfer in PCN-223(free-base), a highly stable Zr-MOF based on meso-tetrakis(4-carboxyphenyl)porphyrin was investigated, using diffuse reflectance spectroscopy, steady-state emission spectroscopy, time-correlated single photon counting (TCSPC) spectroscopy and nanosecond transient absorption spectroscopy. The effects of the surrounding media and temperature on the excited-state properties of PCN-223(fb) were explored to understand the mechanistic aspects of energy transfer. Stern-Volmer photoluminescence quenching of PCN-223(fb) suspensions was performed to extract quenching rate constants and gain insight into the efficiency of energy transfer. Chapter 4: The fourth chapter of this thesis is adapted from chapter 14 of the book "Elaboration and Applications of Metal-Organic Frameworks" authored by Jie Zhu, Shaunak Shaikh, Nicholas J Mayhall and Amanda J Morris. This chapter summarizes the fundamental principles of energy transfer in MOFs and provides an overview of energy transfer in lanthanide-Based luminescent MOFs, Ru/Os-Based MOFs, porphyrin- and metalloporphyrin-based MOF materials, and nonporphyrinic, organic chromophore-based MOFs. / Master of Science / Metal Organic frameworks (MOFs) composed of Zirconium-oxo clusters connected through meso-tetra(4-carboxyphenyl)porphyrin (TCPP) linker molecules have emerged as promising solid-state materials because of their unique structural features and diverse applications. Although these MOFs have demonstrated great potential over the years, synthesizing them in phase-pure form has proven to be very challenging as they are susceptible to polymorphism. Syntheses of these frameworks often result in phase mixtures and have poor reproducibility. To address, this issue, we conducted a systematic exploration of the synthetic parameter landscape to identify reaction conditions for the synthesis of phase-pure Zirconium-based porphyrin MOFs, and to gain deeper insights into the factors governing the formation of these MOFs. We also investigated the defectivity of pristine Zr-TCPP MOFs using a variety of techniques, including 1H NMR spectroscopy, thermogravimetric analysis (TGA), inductively coupled plasma mass spectrometry (ICP-MS), and Nitrogen gas adsorption/desorption measurements. The long-term goal of this project is to use phase-pure Zr-based porphyrin MOFs as model systems to study energy transfer in three dimensional structures. To achieve this goal, we characterized the photophysical properties of PCN-223(fb) (a Zr-based porphyrin MOF) using a variety of techniques including steady-state photoluminescence spectroscopy, time-resolved photoluminescence spectroscopy, nanosecond transient absorption spectroscopy and femtosecond transient absorption spectroscopy. Understanding the mechanistic aspects of energy transfer in PCN-223(fb) can pave the way for the design of a new generation of solar energy conversion devices.

Gametophytic self-incompatibility limits the ability to derive inbred lines of potato through self-pollination and is prevalent in diploid potato. Within a population of F1 hybrids between two genotypes used in potato genome sequencing, we observed fruit set on many greenhouse-grown plants. Subsequently, after controlled self-pollinations, we confirmed fruit set in 32 of 103 F1 plants. Our goal was to identify genes responsible for self-compatibility in this population and to advance selfed progeny to develop highly homozygous inbred lines. The F1 population was genotyped using a single nucleotide polymorphism (SNP) array. Polymorphic and robust SNPs were analyzed by Fisher\'s Exact Test to identify allelic states segregating with the self-compatible phenotype. Filtering 1966 SNPs to retain only those with p-values less than 0.0001 yielded 95 highly significant SNPs, with all SNPs on anchored scaffolds located on chromosome 12. Candidate genes encoding for multiple notable proteins including an S-protein homologue were identified near highly significant SNPs on the Potato Genome Browser. Seeds obtained after self-pollination of self-compatible individuals were used to advance the population for three generations. SNP chip genotyping of the S3 generation revealed entirely different SNPs segregating for self-compatibility on nine different chromosomes. Comparison of the allelic state of SNPs in the F1 and S3 generations revealed a heterozygosity reduction by 80%, with fixation of many SNPs including those surrounding the S-protein homologue. We conclude that the genes responsible for segregation of self-compatibility in the S3 generation are different from those in the F1 generation. / Master of Science

No / The relationship between molecular self-assembly processes and nucleation during crystallization from solution is an important issue, both in terms of fundamental physical chemistry and for the control and application of crystallization processes in crystal engineering and materials chemistry. This contribution examines the extent to which the occurrence of crystal polymorphism can be used as an indicator of the nature of molecular aggregation processes in supersaturated solutions. For the specific case of 2,6-dihydroxybenzoic acid a combination of solubility, spectroscopic, crystallization, and molecular modeling techniques are used to demonstrate that there is a direct link between the solvent-induced self-assembly of this molecule and the relative occurrence of its two polymorphic forms from toluene and chloroform solutions.

No / We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their first ranked choice, albeit at a considerable computational expense. The results reflect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules.

Yes / Polymorphism of crystalline drugs is a common phenomenon. However, the number of reported polymorphic cocrystals is very limited. In this work, the synthesis and solid state characterisation of a polymorphic cocrystal composed of sulfadimidine (SD) and 4- aminosalicylic acid (4-ASA) is reported for the first time. By liquid-assisted milling, the SD:4-ASA 1:1 form I cocrystal, the structure of which has been previously reported, was formed. By spray drying, a new polymorphic form (form II) of the SD:4-ASA 1:1 cocrystal was discovered which could also be obtained by solvent evaporation from ethanol and acetone. Structure determination of the form II cocrystal was calculated using high resolution X-ray powder diffraction. The solubility of the SD:4-ASA 1:1 cocrystal was dependent on the pH and predicted by a model established for a two amphoteric component cocrystal. The form I cocrystal was found to be thermodynamically more stable in aqueous solution than form II, which showed transformation to form I. Dissolution studies revealed that the dissolution rate of SD from both cocrystals was enhanced when compared to a physical equimolar mixture and pure SD. / Science Foundation Ireland (SFI) under Grant Number 07/SRC/B1158 and SFI/12/RC/2275.

Amplified fragment length polymorphism (AFLP) markers allow a rapid assessment of the level of genetic variation that would be difficult to evaluate using a limited number of morphological markers. AFLP was used to assess the level of genetic variation among 16 different Phalaenopsis species and hybrids. Ten AFLP primer combinations were used for genetic analysis of these Phalaenopsis and 95% of polymorphism in 16 Phalaenopsis species and hybrids was detected. The genetic similarity among Phalaenopsis species and hybrids ranged from 0.298 to 0.774 based on Dice coefficient. The dendrogram derived by UPGMA analysis clustered into two main groups. A significant linear relationship (r² = 0.524, P < 0.0001) was observed between known pedigrees and AFLP-derived genetic similarity for 136 pairwise comparisons of Phalaenopsis species and hybrids. The results indicate that there is an abundance of genetic diversity among within Phalaenopsis and that AFLP can be used to distinguish morphologically similar genotypes. In a second study, the effect of gametophytic selection on genetic diversity in Phalaenopsis was examined by AFLP analysis. Sixteen F1 seedlings resulting from cross-pollination that occurred within high (30 ºC) and low (14 ºC) temperature incubators between two hybrid Phalaenopsis [P. (Taisoco Windian à Sogo Yukidian) by P. hybrid unknown], were subjected to genetic analysis by AFLP. A total of 651 fragments ranging in size from 100 to 350 bp were detected using six primer combinations, of which 387 (59.4%) were polymorphic. Seedlings derived from different temperature treatments exhibited 25.5% to 35.9% polymorphism. The genetic similarity among 16 F1 seedlings ranged from 0.825 to 0.946 based on the Dice coefficient. A dendrogram based on 387 polymorphic markers was derived by UPGMA analysis resulting in three major groups and one subgroup. The dendrogram analysis showed clear clustering in Phalaenopsis hybrids pollinated under different temperature treatments, suggesting that several loci may have been selected during the divergent temperature stress treatments during pollination and early pollen tube growth. / Master of Science

Melanoma, a forma mais agressiva de câncer de pele, é um tumor maligno dos melanócitos. Além dos riscos ambientais tais como a radiação UV e fenótipo de pele do indivíduo, a genética também tem sido descrita como um fator de risco para o desenvolvimento de melanoma. Recentemente foi relatado que a malignidade do melanoma está diretamente relacionada com a secreção constitutiva da citocina inflamatória IL-1? em melanócitos transformados, sugerindo o envolvimento do inflamassoma na progressão tumoral. Com a finalidade de avaliar se a genética do inflamassoma poderia contribuir para a susceptibilidade ao desenvolvimento do melanoma maligno esporádico no presente trabalho analisamos 10 polimorfismos de nucleotídeos únicos (SNPs) em cinco genes do inflamassoma (NLRP1, NLRP3, CARD8, IL1B, IL18) numa coorte brasileira caso/controle de melanoma. Além disso, a expressão de genes do inflamassoma foi avaliada em biópsias de tumores de melanomas e nevos benignos. Para tanto recrutamos 198 pacientes de melanoma e 142 doadores saudáveis. As biópsias de tumores/nevos foram obtidas de 15 dos 198 pacientes de melanoma e de cinco dos 142 controles saudáveis, respectivamente. Utilizamos a técnica de PCR em tempo real com alelo e sondas específicas em ensaios com TaqMan® para os ensaios de genotipagem de amostras de DNA dos casos/controles de melanoma e para estudos de expressão de genes específicos do inflamassoma, em amostras de biopsias de tumores e nevos, respectivamente. Verificamos que o SNP rs6509365 em CARD8 foi significativamente mais comum em controles saudáveis do que em pacientes de melanoma, sugerindo um efeito protetivo da variante para o desenvolvimento de melanoma. Corroborando com este achado, a expressão de CARD8 foi encontrada aumentada em biópsias de melanoma em comparação com a expressão em nevo. Além disso, a estratificação dos dados mostrou que a variante rs11651270 em NLRP1 associada com melanoma nodular; rs1143643 em IL1B, amplificado em níveis baixos, foi associado com invasividade (índice de Breslow) e rs5744256 em IL18 foi associado com desenvolvimento de melanoma em pessoas sensíveis ao sol. A análise em biópsias dos tumores ainda mostrou que a expressão de IL-1beta foi regulada positivamente, especialmente em amostras de indivíduos que apresentaram metástases, enquanto que IL-18 foi negativamente regulada comparada com a expressão em nevos. Em conjunto nossos resultados demonstram, pela primeira vez, a contribuição dos genes do inflamassoma CARD8, IL1B e IL18 ao melanoma / Melanoma, the most aggressive form of skin cancer, is a malignant melanocyte tumor. In addition to environmental risks such as UV radiations, individual\'s skin phenotype and genetics has also been described as potential risk factors for the development of melanoma. It has recently been reported that malignant melanoma is directly related to the constitutive secretion of the inflammatory cytokine, IL-1?, in transformed melanocytes suggesting the involvement of the inflammasome in tumor progression. In order to evaluate if the genetics of the inflammasome could contribute to the susceptibility to the development of malignant melanoma, we analyzed 10 single nucleotide polymorphisms (SNPs) in five inflammation related genes (NLRP1, NLRP3, CARD8, IL1B, IL18) in a case/control Brazilian cohort of melanoma. In addition, the expression of inflammatory genes was evaluated in biopsies of melanoma and nevus tumors. We recruited 198 melanoma patients and 142 healthy donors. Tumor/nevus biopsies were obtained from 15 of 198 melanoma patients and five of 142 healthy controls, respectively. We used the real-time PCR technique for specific allele with specific probes using TaqMan ® assays for genotyping of DNA samples from melanoma cases/controls and for studies of expression of specific genes of inflammasome from RNA samples of tumor biopsy and nevus, respectively. We have found that SNP rs6509365 in CARD8 was significantly more common in healthy controls than in melanoma patients, suggesting a protective effect of this variant for the development of melanoma. Corroborating this finding, CARD8 expression was found to be increased in melanoma biopsies compared to nevus expression. In addition, stratification of the data showed that variant rs11651270 in NLRP1 was associated with nodular melanoma; rs1143643 in IL1B at low levels was associated with invasiveness (Breslow score) and rs5744256 in IL18 was associated with melanoma development in sun sensitive individuals. Biopsy analysis of tumors further showed that IL-1? expression was up-regulated, especially in samples from individuals who had metastases, whereas IL-18 was down-regulated compared to expression in nevus. Together our results demonstrated for the first time the contribution of the inflammation related genes CARD8, IL1B and IL18 to melanoma

Depuis que Parsons et col. ont découvert en 2008 que le gène de l’isocitrate déhydrogénase 1 (IDH1) est fréquemment muté dans les glioblastomes (12%), de nombreuses équipes ont étudié la prévalence et les caractéristiques des mutations des gènes IDH1 et 2 dans les gliomes.Les mutations du gène IDH1 sont observées dans environ 40% des gliomes. La mutation d’IDH1 la plus fréquentes dans les gliomes (>90% des cas) est la mutation R132H. La fréquence des mutations IDH1 et 2 est inversement corrélée au grade des gliomes (grade II ~80%, III ~50%, and IV ~10%). Les mutations IDH1/2 ont une valeur diagnostique ainsi que pronostique (associées à une meilleure survie). Pendant ce travail de thèse nous avons dans une première partie analysé la distribution de ces mutations IDH1/2 dans les différents gliomes, leur association avec d’autres altérations génétiques, ainsi que leur valeur diagnostique et pronostique dans une cohorte de 1332 patients atteints de gliomes. Nous confirmons sur cette très grande cohorte les données de la littérature et affinons la valeur pronostique des mutations IDH1/2. Dans une seconde partie, nous avons mis en évidence dans les gliomes un polymorphisme (SNP) du gène IDH1 (SNP rs 11554137; C (cytosine) substituted by T (thymin)) précédemment observé dans les leucémies myéloïdes aigues. Ce SNP, codon 105, est localisé dans le même exon que le codon 132 fréquemment muté, et nous avons montré qu’il est associé à une moins bonne survie des patients atteints de gliomes. Les mutations du codon 132 causent une baisse de l’activité enzymatique normale d’IDH1/2 qui est remplacé par le gain d’une nouvelle. Les protéines IDH1/2 mutés, au lieu de produire de l’alpha-cétoglutarate de façon NADP dépendante, réduisent de façon NADPH dépendante l’alpha-cétoglutarate en 2-hydroxyglutarate (2HG). Une forte concentration de 2HG et une baisse de la quantité de NADPH peuvent sensibiliser les tumeurs au stress oxidatif et donc potentialiser l’effet de la radiothérapie, ce qui pourrait expliquer la meilleure survie de ces patients. Nous avons donc dans une troisième partie étudié in vitro l’impact de la mutation IDH1R132H sur la survie après radiothérapie de cellules tumorales exprimant de façon stable ce gène muté. Les résultats obtenus montrent que dans certaines conditions ces cellules pourraient être plus radiosensibles que les mêmes cellules exprimant le gène IDH1 non-muté.Dans ce travail de thèse, nous avons donc étudié le gène IDH1 dans les gliomes de patients et tenté par une approche fonctionnelle in vitro d’évaluer l’impact de la mutation IDH1R132H sur la radiosensibilité des cellules tumorales. / Since Parsons et al. (2008) found the frequent mutations of IDH1 (12%) in GBMs, various reports have studied the prevalence and characteristic of IDH1 and IDH2 mutations.The mutations in the isocitrate dehydrogenase 1 (IDH1) gene occur in nearly 40% of gliomas. The frequency of IDH1 mutations are inversely connected with grade II (~80%), III (~50%), and IV (~ 10%) gliomas. Importantly, the status of IDH1 mutations is associated with a better outcome and demonstrated a diagnostic value. We analyzed also these mutations in distribution, association with tumor-derived other genetic alterations and the diagnostic and prognostic value in a cohort of 1332 glioma patients.A synonymous single nucleotide polymorphism [SNP rs 11554137; C (cytosine) substituted by T (thymin)] has been studied in gliomas patients. The SNP rs 11554137 (in codon 105) are located in the same exon with the IDH1 R132 mutations (in codon 132). And gliomas patients with SNP rs 11554137: C>T had a poorer outcome than patients without SNP rs 11554137. This was observed a similarly adverse effect in survival in patients with AML. Mutations in codon 132 can cause a decrease of IDH1/2 activity and also gain a new enzyme function for the NADPH dependent reduction of alpha-ketoglutarate to 2-hydroxyglutarate. High 2HG and low NADPH levels might sensitize tumors to oxidative stress, potentiating response to radiotherapy, and may account for the prolonged survival of patients harboring the mutations. So we studied further the alterations of function in IDH1R132H mutant cells in vitro. Based on the decrease of defence and the increase of impairing factors in tumor cells, we found that the tumors harbouring IDH1 mutations may have an elevated radiosensitivity. In the present study, we described the impact of IDH1 mutations in gliomas and search for new perspectives for the treatment strategy.

Melanoma, a forma mais agressiva de câncer de pele, é um tumor maligno dos melanócitos. Além dos riscos ambientais tais como a radiação UV e fenótipo de pele do indivíduo, a genética também tem sido descrita como um fator de risco para o desenvolvimento de melanoma. Recentemente foi relatado que a malignidade do melanoma está diretamente relacionada com a secreção constitutiva da citocina inflamatória IL-1? em melanócitos transformados, sugerindo o envolvimento do inflamassoma na progressão tumoral. Com a finalidade de avaliar se a genética do inflamassoma poderia contribuir para a susceptibilidade ao desenvolvimento do melanoma maligno esporádico no presente trabalho analisamos 10 polimorfismos de nucleotídeos únicos (SNPs) em cinco genes do inflamassoma (NLRP1, NLRP3, CARD8, IL1B, IL18) numa coorte brasileira caso/controle de melanoma. Além disso, a expressão de genes do inflamassoma foi avaliada em biópsias de tumores de melanomas e nevos benignos. Para tanto recrutamos 198 pacientes de melanoma e 142 doadores saudáveis. As biópsias de tumores/nevos foram obtidas de 15 dos 198 pacientes de melanoma e de cinco dos 142 controles saudáveis, respectivamente. Utilizamos a técnica de PCR em tempo real com alelo e sondas específicas em ensaios com TaqMan® para os ensaios de genotipagem de amostras de DNA dos casos/controles de melanoma e para estudos de expressão de genes específicos do inflamassoma, em amostras de biopsias de tumores e nevos, respectivamente. Verificamos que o SNP rs6509365 em CARD8 foi significativamente mais comum em controles saudáveis do que em pacientes de melanoma, sugerindo um efeito protetivo da variante para o desenvolvimento de melanoma. Corroborando com este achado, a expressão de CARD8 foi encontrada aumentada em biópsias de melanoma em comparação com a expressão em nevo. Além disso, a estratificação dos dados mostrou que a variante rs11651270 em NLRP1 associada com melanoma nodular; rs1143643 em IL1B, amplificado em níveis baixos, foi associado com invasividade (índice de Breslow) e rs5744256 em IL18 foi associado com desenvolvimento de melanoma em pessoas sensíveis ao sol. A análise em biópsias dos tumores ainda mostrou que a expressão de IL-1beta foi regulada positivamente, especialmente em amostras de indivíduos que apresentaram metástases, enquanto que IL-18 foi negativamente regulada comparada com a expressão em nevos. Em conjunto nossos resultados demonstram, pela primeira vez, a contribuição dos genes do inflamassoma CARD8, IL1B e IL18 ao melanoma / Melanoma, the most aggressive form of skin cancer, is a malignant melanocyte tumor. In addition to environmental risks such as UV radiations, individual\'s skin phenotype and genetics has also been described as potential risk factors for the development of melanoma. It has recently been reported that malignant melanoma is directly related to the constitutive secretion of the inflammatory cytokine, IL-1?, in transformed melanocytes suggesting the involvement of the inflammasome in tumor progression. In order to evaluate if the genetics of the inflammasome could contribute to the susceptibility to the development of malignant melanoma, we analyzed 10 single nucleotide polymorphisms (SNPs) in five inflammation related genes (NLRP1, NLRP3, CARD8, IL1B, IL18) in a case/control Brazilian cohort of melanoma. In addition, the expression of inflammatory genes was evaluated in biopsies of melanoma and nevus tumors. We recruited 198 melanoma patients and 142 healthy donors. Tumor/nevus biopsies were obtained from 15 of 198 melanoma patients and five of 142 healthy controls, respectively. We used the real-time PCR technique for specific allele with specific probes using TaqMan ® assays for genotyping of DNA samples from melanoma cases/controls and for studies of expression of specific genes of inflammasome from RNA samples of tumor biopsy and nevus, respectively. We have found that SNP rs6509365 in CARD8 was significantly more common in healthy controls than in melanoma patients, suggesting a protective effect of this variant for the development of melanoma. Corroborating this finding, CARD8 expression was found to be increased in melanoma biopsies compared to nevus expression. In addition, stratification of the data showed that variant rs11651270 in NLRP1 was associated with nodular melanoma; rs1143643 in IL1B at low levels was associated with invasiveness (Breslow score) and rs5744256 in IL18 was associated with melanoma development in sun sensitive individuals. Biopsy analysis of tumors further showed that IL-1? expression was up-regulated, especially in samples from individuals who had metastases, whereas IL-18 was down-regulated compared to expression in nevus. Together our results demonstrated for the first time the contribution of the inflammation related genes CARD8, IL1B and IL18 to melanoma

Thesis (M.S.)--University of Texas Health Science Center at Houston, School of Public Health, 2007. / Source: Masters Abstracts International, Volume: 46-01, page: 0238. Adviser: Marsha Frazier. Includes bibliographical references.