Lignin is a highly abundant aromatic biopolymer deposited during the final stages of secondary cell wall formation in plants and it constitutes a substantial proportion of the dry weight of woody plant stems. Lignin contributes structural support to xylem cell walls and hydrophobisity to water-conducting vessels and forms a defence mechanism against pathogen invasion. Although being an essential part of normal plant cell development, lignin content and composition are targets for tree improvement, because residual lignin in paper pulp has negative effects on paper quality and lignin therefore has to be removed using treatments that are expensive and often detrimental to the environment. At present, little is known about the amount of allelic diversity in lignin biosynthetic genes and whether such diversity may be associated with variation in lignin content and composition. However, the identification of alleles associated with desirable lignin phenotypes is dependent on a detailed understanding of the molecular evolution and population genetics of these genes. This M.Sc. study was aimed at analysing nucleotide and allelic diversity in two lignin biosynthetic genes of Eucalyptus trees. Additionally, the study aimed to develop single nucleotide polymorphism (SNP) markers that could be used to assay allelic diversity for these genes in populations of two target species, E. grandis and E. smithii. Orthologues of the tobacco LIM-domain1 (NtLIM1) transcription factor gene involved in the regulation of lignin biosynthesis were isolated from E. grandis and E. smithii. Approximately 3 kb of genomic sequence including the promoter and full-length gene regions were isolated for the two orthologues, respectively labeled EgrLIM1 and EsLIM1. The predicted amino acid sequences of EgrLIM1 and EsLIM1 were 99.4% identical to each other and indicated that LIM1 is a small protein of only 188 residues in eucalypt trees and has a predicted molecular weight of 21.0 kDa. Quantitative, real-time RT-PCR analysis confirmed the expression of LIM1 in wood-forming tissues undergoing lignification. Ten putative cis-regulatory elements were observed in the promoter regions of EgrLIM1 and EsLIM1including a GA-dinucleotide microsatellite that appears to be specific to LIM1 promoters of Eucalyptus tree species. The full-length LIM1 gene sequences could subsequently be used in the assessment of nucleotide and allelic diversity, together with the full-length CAD2 sequences that were already available in the public domain. The level of nucleotide and allelic diversity and the distribution and decay of linkage disequilibrium (LD) were surveyed in 5’ and 3’ derived gene fragments of CAD2 and LIM1 obtained from 20 E. grandis and 20 E. smithii individuals. Each gene displayed a unique genetic diversity profile, but for the most part, nucleotide diversity (π) was estimated at approximately 0.0010 except for the E. grandis LIM1 gene where π lower than 0.0040 was observed. Generally, except for the high amounts of LD observed in the CAD2 gene of E. grandis (> 2.5 kb), LD decayed within 500 bp. A large number (13 to 45) of SNP sites (defined as single nucleotide changes with minor allele frequencies of at least 0.10 in each species) were observed in each gene of each species. The high SNP density (ranging from one per 45 to one per 155 bp) observed in the two genes facilitated the efficient development of SNP markers to be used in future aspects of LD mapping, association genetics and marker-assisted breeding. The allele sequences obtained for the CAD2 and LIM1 genes were used as templates for the development of SNP marker panels (a series of six or seven SNP markers analysed together) for the analysis (tagging) of SNP haplotype diversity in species-wide reference populations (100 E. grandis and 137E. smithii individuals) of the two species. Each tag SNP was assayed using a single base extension assay and capillary gel electrophoresis. High polymorphism information content (average PIC of 0.836) was observed for the SNP marker panels. Four SNPs in the CAD2 and two in the LIM1 genes were found to be polymorphic in E. grandis and E. smithii (i.e. trans-specific SNPs), suggesting a possible ancestral origin for these polymorphisms. Assessment of candidate gene variation in the genomes of forest trees is of importance to ultimately be able to predict the amount and structure of nucleotide diversity available for the future design of SNP assays at the whole-genome level. Such assays will be useful to study differentiation among tree species and populations, to associate nucleotide polymorphisms with desirable phenotypes and to increase the efficiency of tree improvement approaches. / Dissertation (MSc (Genetics))--University of Pretoria, 2009. / Genetics / unrestricted

Le carcinome à cellules rénales (CCR) se caractérise par une résistance importante aux thérapies. Notre hypothèse était que des voies signalétiques prolifératives, anti-apoptotiques et/ou angiogéniques sont mises en jeu dans la résistance aux thérapies. Il s’agissait de mesurer la sensibilité de lignées cellulaires de CCR humain à différentes classes thérapeutiques in vitro et in vivo. Une étude pilote a été réalisée sur la base de xénogreffes de la lignée A498 chez la souris nude, puis exploitée pour des analyses sur biopuces à protéines afin d’identifier les voies de signalisation induites par le sunitinib. In vitro, les lignées cellulaires de CCR se sont révélées sensibles aux thérapies indépendamment du statut VHL. In vivo, la lignée A498 est apparue résistante au sunitinib. L’approche par biopuces a montré que plusieurs protéines de l’angiogenèse sont modulées sous l'effet du traitement, notamment l’angiogénine. Il n’y a pas de modification de l’expression des protéines de l’apoptose testées. Les formes phosphorylées d’Akt sont également augmentées dans les tumeurs traitées, de même que Lim1 alors que la forme phosphorylée de NFκB est diminuée. Ce travail a ainsi identifié de potentielles cibles impliquées dans les mécanismes de résistance et devraient permettre de définir de nouvelles options thérapeutiques dans le cancer du rein. / The renal cell carcinoma is characterized by a high resistance to therapies. Our working hypothesis was that proliferative signaling pathways, anti-apoptotic and / or angiogenic are involved in resistance to therapies. Thus, as part of this thesis, we measured the sensitivity to chemotherapy and targeted therapies in kidney cancer cell lines in vitro as well in vivo.A pilot study was conducted on the basis of the A498 cell line xenografts in nude mice, and then used for analysis on proteome arrays to identify the signaling pathways induced by sunitinib. In vitro, the cell lines of RCC were sensitive to therapy regardless of the VHL status. In vivo, the line A498 appeared resistant to sunitinib. The approach using the proteome array has shown that several angiogenesis proteins are modulated as a result of treatment, including angiogenin. There was no change in the expression of proteins of apoptosis. Phosphorylated forms of Akt were also increased in the treated tumors, as well as Lim1 whereas the phosphorylated form of NFkB was reduced. This work has identified potential targets involved in resistance mechanisms and should define new therapeutic options in renal cancer.

Le carcinome à cellules rénales claires métastatique (CCC) demeure résistant aux thérapies actuelles. Les travaux précédents ont montré des similitudes mécanistiques entre tumorigenèse et néphrogenèse. Parmi les cibles de la voie oncogénique Sonic Hedgehog-Gli, le facteur développemental Lim1 a été identifié comme un nouvel oncogène dans le CCC. Les études préliminaires suggèrent que Lim1 aurait un rôle dans l’invasion cellulaire. Aucun inhibiteur de Lim1 n’est disponible; l’ARN interférence reste l’outil le plus efficace et le plus spécifique pour l’extinction des gènes. Dans le but de développer un nouvel outil d’inhibition de Lim1 applicable en clinique, basée sur des siRNAs véhiculés par des systèmes nanométriques, une nouvelle génération de véhicules de siRNAs a été étudiée. Il s’agit de polymères diacétyléniques photo-polymérisables sous forme de nanofibres (PDA-Nf). Ces travaux démontrent le rôle invasif de Lim1 dans la dissémination métastatique et identifient les PDA-Nf comme un nouvel outil de délivrance de siRNAs très prometteur en clinique. L’avantage du ciblage de Lim1 avec cette approche, est l’absence de son expression à l’âge adulte. / Clear cell renal cell carcinoma (CCC) remains resistant to current therapies, despite the development of anti-angiogenic and the new immunotherapeutic approaches. Previous work of the laboratory has shown mechanistic similarities between tumorigenesis and nephrogenesis. Among the targets of the Sonic Hedgehog-Gli pathway which is found oncogenic in CCC, the developmental factor Lim1 has been identified as a new oncogene in CCC. Preliminary studies suggest that Lim1 would have a role in cell invasion. No Lim1 inhibitors are available; RNA interference remains the most effective and specific tool for gene silencing. In order to develop a new clinically applicable inhibition tool for Lim1, based on siRNAs carried by nanoparticles, a new generation of siRNA vehicles has been investigated. These are photo-polymerizable diacetylenic polymers in the form of nanofibers (PDA-Nf). These works demonstrate the invasive role of Lim1 in metastatic dissemination and identifies PDA-Nf as a new promising siRNA delivery tool in clinical practice. The advantage of targeting Lim1 with this nano-carrier approach is that Lim1 is not expressed in adulthood.

<p>Horizontal cells are retinal interneurons that modulate the output from photoreceptors. Two horizontal cell (HC) subtypes are commonly identified in the vertebrate retina: axon-bearing and axon-less HCs. In this work, we have identified Isl1 as a novel HC marker and demonstrated that Lim1 and Isl1 distinguish axon-bearing and axon-less HCs, respectively. In the chick retina, axon-less HCs are furthermore split into two different subtypes based on the expression of GABA and TrkA.</p><p>We have demonstrated that during early chick retinogenesis, HCs expressing either Lim1 or Isl1 are generated consecutively as two equally large sub-groups at different time points. Moreover, these newborn HCs undertake an unexpected bi-directional migration before settling in their final laminar position. Different HC subtypes complete this migration at different times.</p><p>We investigated the role of activin signaling during HC subtype generation. Activin or its inhibitor follistatin was administrated during the main phase of HC generation and analyzed when HCs had completed migration. Activin caused a significant decrease in both HC subtypes and decreased the proliferation of retinal precursor cells. Follistatin increased the number of late born (Isl1+) HCs, which migrated to the HC-layer during a prolonged migration period. Both treatments affected retinal histology, but only activin influenced the generation of retinal populations other than HCs. These effects were most likely mediated by altered proliferation in certain retinal precursor cells.</p><p>The data on HC subtype ratios, birth-dates, migration, apoptosis and extrinsic activin modulation favor a scenario where the mature proportions of HC subtypes are generated sequentially from a specific HC-precursor cell lineage early in development and remain stable thereafter. These proportions are not adjusted by apoptosis, but rather by the combined actions of transcription factors and extrinsic signaling. Our studies on HC subtypes and their development promises to facilitate future studies on HC development, evolution and function.</p>

Horizontal cells are retinal interneurons that modulate the output from photoreceptors. Two horizontal cell (HC) subtypes are commonly identified in the vertebrate retina: axon-bearing and axon-less HCs. In this work, we have identified Isl1 as a novel HC marker and demonstrated that Lim1 and Isl1 distinguish axon-bearing and axon-less HCs, respectively. In the chick retina, axon-less HCs are furthermore split into two different subtypes based on the expression of GABA and TrkA. We have demonstrated that during early chick retinogenesis, HCs expressing either Lim1 or Isl1 are generated consecutively as two equally large sub-groups at different time points. Moreover, these newborn HCs undertake an unexpected bi-directional migration before settling in their final laminar position. Different HC subtypes complete this migration at different times. We investigated the role of activin signaling during HC subtype generation. Activin or its inhibitor follistatin was administrated during the main phase of HC generation and analyzed when HCs had completed migration. Activin caused a significant decrease in both HC subtypes and decreased the proliferation of retinal precursor cells. Follistatin increased the number of late born (Isl1+) HCs, which migrated to the HC-layer during a prolonged migration period. Both treatments affected retinal histology, but only activin influenced the generation of retinal populations other than HCs. These effects were most likely mediated by altered proliferation in certain retinal precursor cells. The data on HC subtype ratios, birth-dates, migration, apoptosis and extrinsic activin modulation favor a scenario where the mature proportions of HC subtypes are generated sequentially from a specific HC-precursor cell lineage early in development and remain stable thereafter. These proportions are not adjusted by apoptosis, but rather by the combined actions of transcription factors and extrinsic signaling. Our studies on HC subtypes and their development promises to facilitate future studies on HC development, evolution and function.