Araucaria angustifolia é uma conífera nativa do Brasil de importância econômica, que, após intenso desmatamento, possui sua distribuição limitada a aproximadamente 3% da área original. Atualmente está incluída na lista de espécies ameaçadas de extinção, na categoria de perigo crítico de acordo com a IUCN (International Union for Conservation of Nature). A embriogênese somática é um processo em que, através da técnica de cultivo in vitro, células isoladas ou um pequeno grupo de células somáticas dão origem a embriões. Este é um sistema com potencial de aplicação em conservação, reflorestamento, propagação em larga escala, e melhoramento vegetal em espécies arbóreas recalcitrantes e em risco de extinção. Um dos principais fatores limitantes, nos sistemas de embriogênese somática em arbóreas, é a baixa freqüência de maturação e conversão de embriões somáticos em plântulas. Durante a fase de maturação, os embriões somáticos acumulam substâncias de reserva, reduzem a atividade metabólica e adquirem tolerância à desidratação. A suplementação do meio de cultura com determinados reguladores de crescimento e agentes osmóticos, os quais permitem a progressão do desenvolvimento normal dos embriões somáticos, promove um estresse hídrico. Esta situação mimetiza aquela que ocorre durante a embriogênese zigótica quando do desenvolvimento da semente. O óxido nítrico (NO) e espécies reativas de oxigênio (ROS) são moléculas que atuam nas respostas das plantas aos vários estresses ambientais e estão envolvidas em processos de desenvolvimento como embriogênese e germinação de sementes, gravitropismo, formação de raízes. Este trabalho teve como objetivo avaliar o efeito de promotores de maturação, ABA e os agentes osmóticos, PEG e maltose, no conteúdo de NO e ROS em culturas embriogênicas de A. angustifolia. Foi observado que os agentes promotores da maturação reduzem a síntese endógena de NO e ROS. Essa redução é dose dependente. Foram pesquisadas duas linhagens de células com diferentes capacidades de maturação. Para as culturas embriogênicas com competência de maturação esses promotores induzem a maturação e nas culturas que não maturam, promovem a morte celular programada. / Araucaria angustifolia is a native conifer of economic importance in Brazil. Due its massive deforestation, this species is now limited to only 3% of the original area. A. angustifolia is currently on the list of endangered species in the category of critically endangered according to IUCN (International Union for Conservation of Nature). Somatic embryogenesis is a process that, through the technique of in vitro culture, isolated cells or a small group of somatic cells gives rise to embryos. This is a system with potential application in conservation, reforestation, large-scale propagation and breeding of tree species . A limiting factor in the systems of somatic embryogenesis in trees is the low frequency of embryo maturation and conversion into plantlets. During the maturation, somatic embryos accumulate storage substances, reduce metabolic activity and acquire tolerance to dehydration. The water stress is made by supplementation of culture medium with growth regulators and osmotic agents, which allow the normal development of somatic embryos. This situation mimics that occurs during development of the seed. Nitric oxide (NO) and reactive oxygen species (ROS) are molecules that act in plant responses to various environmental stresses and are involved in developmental processes such as embryogenesis and seed germination, gravitropism, root formation. This study aimed to evaluate the effect of promoters of maturation, ABA and osmotic agents, PEG and maltose in the generation of NO and ROS in embryogenic cultures of A. angustifolia. It was observed that the promoters of maturation reduces the endogenous synthesis of NO and ROS. We investigated two cell lines with different maturation capacities. For responsive cell line these promoters induce maturation and for blocked cell line, promote programmed cell death.

O presente trabalho teve como objetivo caracterizar o desenvolvimento da semente de Araucaria angustifolia através da proteômica comparativa, buscando compreender as alterações fisiológicas e metabólicas que ocorrem durante esse processo. Inicialmente, foram avaliados três diferentes metodologias de extração de proteínas. A metodologia composta por solução de extração contendo 7 M de uréia, 2 M de tiouréia, 1% de ditiotreitol, 2% de Triton-100, 1 mM de fluoreto de fenilmetilsulfonil e 5 µM de pepstatina, seguido de precipitação em 20% de ácido tricloroacético apresentou géis de maior resolução e reprodutibilidade, tendo sido escolhida como metodologia de extração protéica para o estudo das alterações no proteoma da semente de A. angustifolia. Uma dificuldade associada ao estudo do proteoma de espécies não sequenciadas é a baixa representatividade nos bancos de dados protéicos, resultando em identificações baseadas em homologia. Estratégias proteômicas baseadas em fracionamento em gel resultam em grandes contaminações por fragmentos de queratina. Sendo assim, foi desenvolvido um programa de remoção de espectros de baixa qualidade para utilização em proteômica baseada em homologia. As análises mostraram que o programa reduz o tempo de busca, melhora a qualidade dos alinhamentos e não resulta em perda de identificações positivas. Finalmente, utilizando as metodologias descritas, foram estudadas as alterações no proteoma durante o desenvolvimento da semente de A. angustifolia. Noventa e seis proteínas foram identificadas e agrupadas de acordo com sua função biológica e padrão de detecção. Os resultados obtidos permitiram o estabelecimento de marcadores protéicos no início e final do desenvolvimento embrionário. A análise das proteínas abundantes no início da embriogênese indica um maior controle no metabolismo oxidativo em relação aos estádios finais. Contrariamente, o final da embriogênese é caracterizado por um alto metabolismo de assimilação de carbono e acúmulo de proteínas de reserva. As implicações dos resultados obtidos no controle e melhoramento de sistemas de embriogênese somática na espécie também foram discutidas. / The aim of the present work was to characterize the seed development of Araucaria angustifolia through proteomics in order to understand the physiological and biochemical changes during this process. For that, initially, three different protein extraction methods were evaluated. The extraction based on protein solubilization in 7 M urea, 2 M thiourea, 1% dithiothreitol, 2% Triton-100, 1 mM phenylmethylsulphonyl fluoride, 5 µM pepstatin, followed by 20% trichloroacetic acid precipitation showed the highest gel resolution and reprodutivity and, thus, was chosen to be used in the analysis of the proteome of A. angustifolia seeds. One aspect that hampers the proteome study of unsequenced species is the low protein representativity in databases. So, protein identification is usually carried out through homology. Strategies based on 2-DE result in high keratin contamination. In the present work a spectra filtering software was developed and evaluated for use in homology driven proteomics. The software reduced the time of search, improved alignment quality and did not result in lost of positive identifications. Finally, using the described strategies, the changes in the proteome of A. angustifolia seeds were studied. Ninety six proteins were identified and classified according to their biological functions and expression profiles during seed development. The identified proteins may be used as protein markers of early and late embryogenesis. Proteins involved in the control of oxidative metabolism were highly expressed during the early stages of seed development; while, carbon metabolism and storage proteins were highly expressed in late stages. Considerations on the improvement and control of somatic embryogenesis through medium manipulation and protein markers screening using data generated are also discussed.

Les cellules positionnent leur plan de division de manière précise et prévisible. En particulier au tout début de l’embryogenèse, la cellule-œuf suit un patron de clivage extrêmement reproductible, mais néanmoins sensible aux perturbations (manipulation de la forme de la cellule,…), ce qui suggère une plasticité intrinsèque du système. Au cours de ma thèse, je me suis intéressée aux signaux qui déterminent la position des plans de division embryonnaires, et à leur compétition. Dans un premier temps, j’ai développé un modèle pour prédire le positionnement du plan de division à partir de la forme de la cellule, et de la présence éventuelle de polarité maternelle à la membrane ou d’une distribution inhomogène de yolk/organelles dans le cytoplasme. Ce modèle est basé sur les forces de traction exercées par les microtubules des astres interphasiques sur le fuseau mitotique/noyau. Sous l’hypothèse que ces forces dépendent de la longueur des microtubules (dynéine dans le cytoplasme) et sont modulées par la polarité membranaire, il est alors possible de trouver la position d’équilibre du fuseau, qui détermine le futur plan de division. J’ai également reproduit les formes et réarrangements des cellules (blastomères) dans l’embryon après la division, à l’aide d’un programme (The Surface Evolver) qui minimise l’énergie de surface sous différentes contraintes : ici les volumes, tensions de surface et éventuels confinements. En bouclant la génération des formes des blastomères avec la prédiction de leurs divisions (les formes permettent de prédire la division, qui permet de générer les formes des cellules filles, etc…), j’ai pu reproduire de manière quantitative quatre patrons de clivage représentatifs (poisson-zèbre, xenope, oursin, ascidie), jusqu’au stade 8 à 16 cellules, in silico. J’ai également testé le modèle sur des expériences classiques de perturbation dans ces quatre systèmes (Hertwig, Hörstadius, ablation de la polarité,…), et reproduit les observations de la littérature. Cette première partie suggère que ces systèmes sont auto-organisés et que la détermination du plan de division dépend principalement d’un nombre restreint de signaux. Dans un second temps, j’ai cherché à caractériser la compétition entre les signaux de forme et de polarité maternelle chez l’embryon d’oursin, de manière quantitative. Ce projet comprend une part importante d’imagerie 3D (position des centrosomes et division, polarité, forme des blastomères), ainsi que des expériences visant à tester le rôle de la forme/taille des blastomères et de la polarité (séparation des blastomères, microchambres de différentes formes, inhibition de la polarité,…). Les résultats obtenus sont comparés aux prédictions du modèle, cette fois basées sur la forme imagée des blastomères. Ces résultats expérimentaux confirment les hypothèses de l’étude in silico, et permettent d’évaluer la robustesse du système biologique pour affiner le modèle. / Cells position their cleavage plane in a precise and predictable way. In particular, during the early embryogenesis, the cleavage pattern of the egg cell is extremely reproducible, yet sensitive to perturbation (shape manipulation,…), which suggests an intrinsic plasticity of the system. My PhD project is about the signals that determine the positions of the cleavage planes in the embryo, and their competition. First, I developed a model to predict division plane positioning from cell shape and possible additional cortical maternal polarity or inhomogeneous yolk/organelles distribution within the cytoplasm. This model is based on pulling forces exerted by interphase astral microtubules on the mitotic spindle/nucleus. Under the hypothesis that these forces depend on microtubule lengths (dynein in the cytoplasm), and are modulated by cortical polarity, it is then possible to find the equilibrium position of the spindle, that sets the future division plane. In addition, I reproduced the shapes and rearrangement of cells (blastomeres) within the embryo, with a program (The Surface Evolver) that minimizes surface energy under various constraints : here cell volumes, surface tensions and possible confinements. The modeling framework I used consisted in a loop between cell shape generation and division plane prediction (cell shape allows to predict cell division, that gives the daughter cells volumes and positions to generate the next cell shapes, and so on…). I could quantitatively reproduce four representative cleavage patterns (zebrafish, xenopus, sea urchin, ascidian), up to the 8 to 16-cell stage, in silico. I also tested the model on classic perturbation experiments in these four systems (Hertwig, Hörstadius, polarity ablation,…), and reproduced the observations of the literature. This first part suggests an auto-organization of these systems, and that the determination of the cleavage plane mainly depends on a limited number of signals. Second, I aimed at characterizing the competition between shape and maternal polarity cues, in a quantitative manner. This project comprises 3D imaging (positions of the centrosomes and division planes, polarity, blastomere shape), as well as experiments assessing the roles of blastomere shape/size and of polarity (blastomere separation, microchambers of different shapes, polarity inhibition,…). The results are compared to the predictions of the model, that now inputs the imaged blastomere shapes. These experimental results confirm the hypotheses of the in silico study, and allow assessing the robustness of the biological system to refine the model.

Signal transducer and activator of transcription (STAT) is a family of intracellular proteins that are responsible for carrying the signal from the cell surface to the nucleus in response to specific ligands. Once in the nucleus, STATs activate the transcription of specific genes. To date, seven human STATs have been identified. Among these STATs, STAT3 is considered as oncogenic. It activates genes that block apoptosis and inhibits antitumor immune responses (1). STAT3 is also essential in early embryogenesis and plays a role in cell growth and survival, differentiation and apoptosis depending on the target tissue. Analysing STAT3 signalling provides insights into pathology and can be used as a tool for diagnosis, prognosis and therapy development. Traditionally, western blot has been used to analyse cell signalling but it is impractical in analysing rare cell populations or providing information at the single cell level. Moreover, it is a demanding and time consuming technique that offers qualitative and less sensitive analysis. The rapid evolution in the multi-parametric flow cytometry and the availability of both epitope specific antibodies and sophisticated software facilitate the wide application of this technology in cell signalling studies. Flow cytometry has the ability to resolve different subcellular sets in a heterogeneous population, collects data at a single cell level and correlates multiple markers simultaneously. However, it requires highly standardized protocols for maximal sensitivity. The aim of this study was to assess the dose and the time response of both total STAT3 and pSTAT3 to in vitro stimulation with either IL-6 or IL-10 in peripheral blood mononuclear cells (PBMC). This assessment was done using both the flow cytometry and the western blot techniques. The results of this study showed that lower doses of IL-6 (1 & 10 ng/ml) were not sufficient to induce phosphorylation of STAT3. However, following stimulation with 100 ng/ml of IL-6, no significant change in the level of total STAT3 could be detected in either lymphocytes or monocytes from 3 different donors using either the FC500 or the Accuri cytometer. Using the FC500 cytometer, a small but insignificant increase in the pSTAT3 was seen in the lymphocytes and monocytes. A significant increase in STAT3 phosphorylation was only observed for monocytes after 15 minutes stimulation with 100 ng/ml of IL-6 using the Accuri flow cytometer. xii When the fluorescent labelled antibodies used in the flow cytometric assays were used for western blot probing, western blot analysis of stimulated cell lysates with 100 ng/ml IL-6 detects proteins of a low molecular weight than STAT3 or pSTAT3 which may explain the flow cytometric results of IL-6 stimulation. In IL-10 stimulation experiments, lower doses (1 and 10 ng/ml) tested by flow cytometric and western blot techniques demonstrated insignificant STAT3 phosphorylation induction. Following stimulation with either 50 or 100 ng/ml IL-10, no significant change in the total STAT3 was seen in either lymphocytes or monocytes when using the Accuri flow cytometer. However, stimulation with 100 ng/ml IL-10 induces STAT3 phosphorylation from 10 minutes through 30 minutes in both lymphocytes and monocytes. Longer times were required and high inter-individual variability was noticed for the activation of STAT3 after stimulation with 50 ng/ml IL-10. By using different antibodies from those used in the flow cytometric assay; the western blot results were comparable with the flow cytometric findings following stimulation with 100 ng/ml IL-10. The addition of phosphatase inhibitors during the flow cytometric protocol didn’t show any increase in the STAT3 phosphorylation. However, using paraformaldehyde for fixation and methanol for permeabilisation significantly decreased the mean fluorescence intensity of the PE conjugated antibodies comparing to the BD commercial fixation and permeabilisation buffers. The onset and the signal intensity of “in house” chemiluminescence mixture for western blot detection of STAT3 were comparable to the commercial ECL reagent used. However, the background of the “in house” mixture increased with time and was higher than with the commercial product. Upon longer exposure, the background increased enough to cause signal loss. In spite of the number of advantages of the flow cytometric assay compared to the western blot assay, these results are highly dependent on the specificity and the selectivity of the used antibodies. Furthermore, flow cytometry requires a highly standardized protocol to be able to assess the normal level of signalling proteins which could be later applied to detect abnormalities. It is suggested that the antibodies used in the flow cytometric assay be tested by western blot to confirm their selective detection of the target protein before their use in the flow cytometric analysis. / Dissertation (MSc)--University of Pretoria, 2013. / gm2014 / Pharmacology / unrestricted

The segregation of progenitor somatic cells from those of the primordial germ cells that sequester and retain elevated levels of DNA during subsequent developmental events, poses an interesting, alternative pathway of chromosome behavior during the reproductive cycle of certain species of cyclopoid copepods and several other organisms. Separation of maternal and paternal chromosome sets during very early cleavages (gonomery) is often a feature following marked elevations of DNA levels in germ cells for some of these species. Here, we report on the accumulation of large amounts of DNA in germ line nuclei of both female and male juveniles and adults of a freshwater copepod, Mesocyclops edax (Forbes, 1890). We also report the robust uptake of 3H-thymidine by germ cells prior to gametogenesis in this species. By using cytophotometric analysis of the DNA levels in both germ line cells and somatic cells from the same specimens we demonstrate that germ cell nuclei accumulate high levels of DNA prior to the onset of gametogenesis. These elevated amounts coincide with the levels of heterochromatic DNA discarded during chromatin diminution. A new model is proposed of major cytological events accompanying the process of chromatin diminution in M. edax.

Selenoprotein H (SELENOH) is a nucleolar oxidoreductase with DNA binding properties whose function is not well understood. To determine the functional and physiological roles of SELENOH, a knockout of SELENOH was generated in cell lines using CRISPR/Cas9-mediated genomic deletion and in mice by targeted disruption. Based on the sequenced genome, the results of deduced protein sequences indicated various forms of mutants in the CRISPR/Cas9-mediated knockout, including a frame-shift by aberrant splicing and truncated SELENOH by early termination of the translation process. Loss of SELENOH in HeLa cells induced slow cell proliferation, the formation of giant multinucleated cells, accumulation of unrepaired DNA damage and oxidative stress, and cellular senescence. SELENOH cells were enlarged and possessed a single large nucleolus. Atomic force microscope showed increased stiffness in the nucleoli of SELENOH knockout cells, which suggests that SELENOH maintains the flexible structure of the nucleolus. Furthermore, the knockout of SELENOH led to a large-scale reorganization of the nucleolar architecture with the movement of nucleolar protein into nucleolar cap regions in response to oxidative stress. The nucleolar reorganization is dependent on ATM signaling. Altogether, results suggest that SELENOH appears to be a sensor of oxidative stress that plays critical roles in redox regulation and genome maintenance within the nucleolus. To determine the physiological role of SELENOH in vivo, Selenoh knockout mice were generated by targeted deletion through homologous recombination. Selenoh+/− mice were fertile and phenotypically indistinguishable from wild-type littermates. Results from matings of Selenoh+/− mice showed a significantly reduced fraction of Selenoh−/− offspring on the basis of Mendelian segregation. Since some Selenoh−/− were born, it is likely that Selenoh is a partially essential gene in mice. Live-born Selenoh−/− mice were viable and born without apparent phenotypes. Selenoh−/− mice at 2-month of age showed increased GPX activity in the lung but not in the brain and liver. Furthermore, loss of Selenoh resulted in the aggravated formation of aberrant crypt foci in the colon of Selenoh+/− mice that were injected with azoxymethane. Altogether, SELENOH has critical roles in embryogenesis and colorectal carcinogenesis.

No description available.

The effect of steady shear stress on somatic embryos were investigated in a flow chamber and evaluated at different time intervals using microscopy technique. The development of meristematic cell clusters, i.e. the immature embryos, into a polarized somatic embryo, and the effect on the localization of the suspensor cells that form during development of the immature embryos, were studied as a function of shear stresses. With the distribution and growth rate of the meristematic and suspensor cells, the effect of stress on the embryo development was established. Furthermore, the effect of shear stress on the cells at molecular level, the reaction of integrin-like proteins, the production of reactive oxygen species and the pore size of the cell walls involved in the shear stress responses, were investigated with molecular techniques. In general, shear stress inhibits meristematic cells growth. Meristematic cells grow fastest at shear rate of 86 s-1 among all the tested shear stress conditions. By combining the results of meristematic cells growth and suspensor cells formation, it suggests that there is a critical shear rate between 86 and 140 s-1, at which no suspensor cells form. The unidirectional flow with different shear stresses helps the polarized growth and the unidirectional alignment of suspensor cells. Reactive oxygen species and integrin-like protein are detected in the stressed cells as cellular responses to shear stresses. By monitoring the pore size and uptake time of cells to macromolecules with solute-exclusive experiments, it suggests that the stressed cells expedite the response to plasmolyzing components that are used to induce maturation treatment thus affect the response to maturation stimuli.

Using the known sequences for serine palmitoyltransferase (SPT) and ceramide kinase (CERK) from Arabidopsis, candidates for the corresponding genes in Loblolly pine were cloned and examined during embryogenesis. The cloned two cDNA sequences from Loblolly pine, which has similarity of 81% and 88% respectively to two subunits of SPT1 and SPT2 in Arabidopsis, were presumed as the Loblolly pine SPT1 and SPT2 (Pt-SPT1 and Pt-SPT2). A few different versions of Pt-SPT1 mRNAs (2223 nts, 756 nts, 822 nts, and 754 nts respectively), most likely the alternative splicing results, were found. Three of these mRNAs are capable of encoding proteins. The long version (2223 nts) encodes a protein with 484 amino acids (Pt-SPT1); two short versions (822 nts, 756 nts) encode a 90 a.a. protein. Another cDNA sequence of 2396 nts encodes a protein of 493 a.a. (Pt-SPT2). Both predicted Pt-SPT1 and Pt-SPT2 proteins possess highly conserved serine palmitoyltransferase functional domains (E value 5.7e-61). Their expression patterns are different between somatic and zygotic embryogenesis. Two different versions of mRNAs, with 2786 nts (long), and 2320 nts (short) respectively, of ceramide kinases in Loblolly pine (Pt-CERKs) have been cloned. The long version encodes a protein with 721 a.a.; the short version with 560 a.a. The expression patterns for these two CERK mRNAs are different during embryo development. The long version is constitutively expressed, while the short one is only expressed in some stages with much lower expression level. Overexpression Pt-CERKL, Pt-CERKS, and Pt-CERKF in E.coli and function analysis in vitro show that all Pt-CERKs appear to have the same catalytic functions as their homologs in human and Arabidopsis, but with different efficiency. The catalytic efficiency was dramatically lower in the short Pt-CERK protein compared with the long Pt-CERK protein and Pt-CERKF. The membrane system is not necessary for the catalytic reactions of these three Pt-CERKs in vitro and Pt-CERKs were less dependent on the Ca2+ ions. Thus, these studies have provided the first information about SPT- and CERK- like proteins in loblolly pine, and open new avenues of investigation for the roles of sphingolipids in embryonic development.

myo-Inositol-1,2,3,4,5,6-hexakisphosphate (InsP6), also called phytic acid, is ubiquitous in eukaryotic cells and the most abundant inositol phosphate derivative. Loblolly pine (LP, Pinus taeda) constitutes the primary commercial species in the southern forest of U.S. Somatic embryogenesis (SE) is an effective technique to maintain the desirable genetic composition of the progeny and to accomplish the efficiency of propagation. SE can also serve as a tool for study of plant development. Unlike angiosperm embryos with attached cotyledons as seed storage organs, the diploid conifer embryo is surrounded by the unattached haploid female gametophyte (FG). In LP SE, FG tissue is absent in the embryogenic tissue culture. We found that extracts from early-stage FG stimulate growth and multiplication of early-stage somatic embryos, whereas FG water extracts from late stage contain substance(s) inhibitory to early-stage somatic embryo growth (DeSilva et al., 2007). We now present the isolation and identification of the inhibitory substance as InsP6 by means of water extraction, two gel filtrations and two ion exchange FPLC chromatographies. The results represent the first complete structural characterization of InsP6 from a natural product using LC/MS, LC/MS/MS, exact MS, 1D- and 2D-NMR analyses. We also report that there is a good correlation between the amount of InsP6 purified from FG tissue (1.3 nmoles per full-term FG) and the amount of InsP6 which inhibits somatic embryo growth. This novel approach of isolating and characterizing InsP6 from plant tissue, and investigating its role on SE can allow us to improve SE technology by circumventing current bottleneck, to elucidate enigmatic functions of InsP6 in plants, and most importantly, to utilize this molecule properly.