Tato diplomová práce se zabývá vlivem zaplňovacích činidel na interakce v systému DNA-tenzid. DNA o velikosti 4017 párů bází byla připravena polymerázovou řetězovou reakcí, jako templát byl použit plasmid pSB-E1g. Polyetylen glykol (PEG) byl použit jako zaplňovací činidlo a jeho vliv na DNA-tenzid interakce byl zkoumán experimenty založenými na fluorescenci a gelové elektroforéze. Také byl studován vliv iontové síly za použití NaBr na interakce DNA-tenzid za použití zaplňovacího činidla. Data byla vyhodnocena a evaluována v této práci. V úvahu byl brán i možný vliv polyetylen glykolu na kritickou micelarní koncentraci (CMC) tenzidu, bylo provedeno měření CMC pomocí ultrazvuku s vysokým rozlišením, avšak nebyl zjištěn žádný značný vliv zaplňovacího činidla na CMC tenzidu. Část této práce bude zahrnuta v publikaci s anglickým názvem Combined role of macromolecular crowding and cationic surfactant in efficient DNA condensation.

Stomata are small pores that are located on the surface of epidermal leaves, and they can regulate the uptake of CO2 and prevent water lose by opening and closing the pores. Stomata of plants can be regulated by external condition such as CO2, biotic and abiotic stresses and internal factors. CAM (crassulacean acid metabolism) plants adapt to hot and dry environments by closing stomata during the day and opening stomata during the cool night. However, it is still unclear how CAM plants open their stomata during the night and close them during the day. In this study, a number of factors were evaluated for their potential roles in promoting stomatal opening in the model CAM plant Kalanchoe laxiflora. Citrate is an important organic acid and it accumulates during the night in CAM plants. It is shown in this study that citrate promoted stomatal opening in detached leaf epidermis of Kalanchoe laxiflora. Further, the cytokinin zeatin is also shown to stimulate stomatal opening in detached leave of Kalanchoe laxiflora. Melatonin is an important regulator of circadian rhythms in mammals and has been implicated in regulation of plant abiotic stress responses. Melatonin was detected in the leaves of Kalanchoe laxiflora. It promoted stomatal opening in detached epidermis of Kalanchoe laxiflora. Together, these results suggest that stomata of Kalanchoe laxiflora respond to citrate and malate which are the main organic acids accumulate during nighttime and also to some signaling molecules (zeatin, melatonin, and serotonin) by opening stomata during dark period.

Rice (Oryza sativa L.) is an important crop cultivated worldwide, and abiotic stresses limit its productivity. Different approaches were carried out to understand the mechanisms of rice defense responses against abiotic stresses, mainly drought. The NADPH-generating enzymes engaged in response to dehydration and salt stresses during the seedling stage of Nipponbare cultivar were analyzed. Enzyme activities of 6-phosphogluconate dehydrogenase (6PGDH), NADP-dependent aldehyde dehydrogenase, NADP-malic enzyme (NADP-ME) in leaves, and 6PGDH in roots were significantly increased in response to dehydration stress. NADP-ME and NADP-glutamate dehydrogenase activities in roots increased significantly in response to salt stress. These results suggest the involvement of NADPH-generating enzymes in plant responses to dehydration and salinity stresses, and the increased demands of NADPH in plants under abiotic stress can be furnished by enhanced activities of NADPH-producing enzymes. Also, a dehydration-induced protein was detected and identified as serine-hydroxymethyltransferase. This result indicates that serine-hydroxymethyltransferase can play a key role in regulating dehydration response in rice. Moreover, comparative proteomic analyses of CL163 (drought-tolerant), Cheniere (drought-sensitive), and Rex (moderately-drought-sensitive) rice varieties were performed. Drought-responsive proteome changes were profiled in leaves and roots at the seedling stage in response to drought stress imposed by polyethylene glycol (PEG-6000). Eighteen significantly differentially expressed proteins were identified by mass spectrometry. Elongate factor1 alpha and 17.9-kDa classI heat shock protein appear to have different expression patterns between CL163 and Cheniere, which may be attributable to the difference in drought response of the two rice varieties. Furthermore, a compendium of 103 drought resistance genes in rice was compiled to construct and analyze networks formed by associations between genes/proteins and to identify the most significant genes, biological processes/pathways. Genes were classified based on gene ontology and protein class into 26 groups. Forty-two genes were classified as transcription factors. Proteins encoded by the genes were localized in 8 subcellular locations and classified into three classes. Two pathways from KEGG whose genes were overrepresented in the compendium were identified. Gene expression, network presenting pairwise interactions between genes/proteins, and co-expression network were constructed. This study provides a systematic view of the crucial genes that can be contributing collectively to drought tolerance.

Indiana University-Purdue University Indianapolis (IUPUI) / The single cell gel electrophoresis assay (comet assay) is a useful tool for monitoring individuals who may be at risk of DNA damage and the ensuing process of carcinogenesis or other disease states. Leukocytes in blood samples provide a means of obtaining cells for use in the comet assay. However instances may arise when samples must be stored for later analysis. The present study investigated the effects of storage conditions on DNA damage in the form of strand breaks and oxidized bases in rat and human leukocytes using the comet assay. Whole blood and buffy coat samples were stored at room temperature or 4ºC for 1, 2, 24, and 48 hours or cryopreserved at -80ºC for 1 day and 1, 2, 3, and 4 weeks. The results show that the time of storage is limited if the whole blood or buffy coat samples are stored at room temperature or 4ºC. However, if cryopreserved using glycerol or DMSO as the cryoprotectant, the samples may be stored for at least 4 weeks without DNA strand breaks or oxidative damage deviating significantly from the fresh samples.

No description available.

No description available.

A mesocosm experiment was carried out in a Norwegian fjord near Bergen in May 2006, with the main objective being the study of the effects of increasing concentrations of atmospheric CO2 (and associated effects such as increased acidification) on blooms of natural marine coastal plankton. Three mesocosms were bubbled with CO2(g) to achieve a high (~700ppm) CO2 concentration (pH ~7.8) to simulate predicted future conditions as a result of rising atmospheric CO2 concentrations. Another three mesocosms were treated as controls and bubbled with ambient air to represent a near pre-industrial scenario (atmospheric CO2 concentration ~300ppm, surface seawater pH ~8.15). Blooms in the mesocosms were stimulated by the addition of nutrients at a near-Redfield ratio ([N:P] ≈ [16:1]), and scientific measurements and analyses were carried out over the course of the blooms for approximately one month. Of particular interest in this study were the autotrophic plankton. The diversity and activities of these microorganisms under the two treatments was therefore investigated. By designing and using new degenerate primers specifically targeting ‘Green-type’ (Form IA and IB), ‘Red-type’ (Form IC and ID) and Form II RuBisCO, analysis of primary producers was carried out using PCR and either gDNA or cDNA (mRNA) templates from key time points spanning the complete duration of the blooms throughout the mesocosm experiment. Over 1250 novel RuBisCO large subunit sequences have been fully annotated and deposited in the NCBI GenBank® database. These sequences revealed distinct changes in the diversity of primary producers both over the courses of the blooms and between treatments. Particularly striking was the effect of acidification on the community structure of the eukaryotic picoplankton, Prasinophytes. A clade of prasinophytes closely related to Micromonas pusilla showed a distinct preference for the high CO2 conditions; a laboratory-based experiment confirmed the high tolerance of Micromonas pusilla to lower pH. Conversely, a clade related to Bathycoccus prasinos was almost entirely excluded from the high CO2 treatments. Clades of form II RuBisCO-containing dinoflagellates were also abundant throughout the experiment in both treatments. The high similarity of some of these clades to the toxin-producing species Heterocapsa triquetra and Gonyaulax polyedra, and apparent high tolerance of some clades to high CO2 conditions, is perhaps cause for concern in a high CO2 world and demands further research. In parallel with the RubisCO work, new primers were designed that target the gene encoding the Fe protein of nitrogenase (NifH). 82 Bergen genomic nifH sequences have been annotated and submitted to GenBank®. These sequences include those from organisms related to Alpha, Beta, and Gammaproteobacteria, and Cluster II and Cluster III sequences that align most closely with anaerobic Bacteria, Gram positive, and/or sulphur-reducing Bacteria. The biggest surprise, however, was the apparent abundance and significance of a Rhodobacter sphaeroides-like microorganism throughout the duration of the experiment in both treatments. Whilst this clade was unsurprisingly absent in the RuBisCO cDNA libraries, all but two of 128 nifH cDNA clones analysed were identical to the gene from Rhodobacter sphaeroides. This shows that this clade was potentially fixing N2 throughout the entire experiment, even in the presence of combined N added to both sets of mesocosms at the start of the experiment. A group of Rhodobacter sphaeroides-like microorganisms present at Bergen may therefore have been an unexpected source of new N during the experiment and contributed to the maintenance of the mesocosm communities as nutrients became depleted. One organism dominated the autotrophic communities after the blooms in both treatments. Synechococcus spp. Form IA rbcL clones most closely related to the coastal strain Synechococcus sp. strain CC9902 were recovered throughout the experiment but were particularly numerous toward the end of the experiment and dominated the “Green-type” libraries at this time. Initially, rbcL clones from these cyanobacteria were mostly derived from the ambient CO2 mesocosms but were equally distributed between treatments by the end of the experiment. This suggests that cyanobacteria related to strain CC9902 may be less tolerant of elevated CO2 (which was greatest at the beginning rather than the end of the experiment). However, despite the mesocosms being Pi-limited at the end of the experiment, several Synechococcus species (including those related to strain CC9902 and another coastal strain, CC9311) thrived. Following on from this observation, Pi uptake and assimilation mechanisms in a Synechococcus species were investigated in the laboratory. This led to the sequencing and characterisation of a pstS gene from the marine cyanobacterium Synechococcus sp. WH 8103. Unlike conventional pstS, it was discovered that the pstS II gene in this organism is constitutively expressed and unresponsive to or only weakly regulated by Pi supply. The use of PstS/pstS as a marker for P-limitation in natural samples, therefore, should be interpreted with caution.

No description available.

On retrouve dans le complexe Chrosomus eos-neogaeus une forme cybride ayant le génome nucléaire de C. eos et le génome mitochondrial de C. neogaeus. Ce modèle particulier fournit une occasion unique d’étudier l’influence d’une mitochondrie exogène sur le métabolisme et la physiologie d'organismes vivant en milieu naturel, et s'étant donc adaptés à cette situation cellulaire atypique. La mitochondrie jouant un rôle fondamental vital, nous nous attendons à ce que la présence d’une mitochondrie exogène chez la forme cybride ait un impact sur l’expression de son génome et du protéome qui en découle. L’objectif de ce projet est d’étudier les différences au niveau protéomique entre des individus C. eos purs (forme sauvage) et des cybrides provenant d'habitats similaires afin de faire ressortir au maximum les différences dues à la présence de mitochondries C. neogaeus chez la forme cybride. Pour ce faire, nous avons comparé les protéomes des formes cybride et sauvage en utilisant l'électrophorèse en deux dimensions. Un sous-groupe de protéines produisant un signal spécifique révélé par l’analyse comparative a été identifié et analysé par spectrométrie de masse (LC/MS). Les résultats indiquent que la présence de mitochondries C. neogaeus chez le cybride influence fortement la régulation génique chez ce dernier. De plus, les protéines identifiées apportent des pistes intéressantes supportant l'hypothèse que la présence de mitochondries C. neogaeus chez le cybride rendrait ce biotype plus résistant au froid que la forme sauvage. / The Chrosomus eos-neogaeus genetic complex regroups different forms of hybrids of these two species, among which a cybrid form, that harbours the nuclear genome of C. eos and the mitochondria of C. neogaeus. This peculiar model is thus a unique opportunity to study the influence of an exogenous mitochondria on the metabolism and cellular physiology in a living animal in the wild, and thus perfectly adapted to this atypical cellular environment. Mitochondria being at the core of fundamental biological processes, we expect that the presence of foreign mitochondria will modify gene expression and the resulting proteome of these fishes. The overall goal of this master thesis is thus to compare the proteome of pure (wild type) C. eos with the cybrid form sampled in similar lakes from the same geographical area so that most differences could be attributed to the different mitochondrial genomes. To achieve this goal, we used two dimensional electrophoresis. We selected a sub-group of proteins that showed the most extreme expression differences and identified these spots by mass spectrometric analyses (LC/MS). Results demonstrate that C. neogaeus mitochondria has a strong influence on gene expression in cybrid. Proteins identified bring new clues supporting the hypothesis that cybrid are more cold tolerant than the wild type biotype.

A Doença Reumática Cardíaca (DRC) é uma séria complicação de orofaringite causada por determinados sorotipos de Streptococcus pyogenes não tratada adequadamente em indivíduos suscetíveis. É um grande problema de saúde pública, principalmente nos países não desenvolvidos e em desenvolvimento, como Brasil, Índia, países da África, regiões de população aborígine da Austrália, e Egito. É altamente debilitante e com alta taxa de mortalidade devido ao comprometimento cardíaco. As lesões miocárdicas iniciais regridem, mas as lesões valvares, principalmente a mitral e a aórtica, são irreversíveis e progressivas. Muitos estudos já caracterizaram a resposta imune celular (linfócitos T) e humoral nos indivíduos acometidos pela doença. Mimetismo molecular e espalhamento de epítopo são os principais mecanismos que se pensa estar envolvidos na patogênese da DRC. Avaliamos, nesta pesquisa, o perfil de expressão proteica em valvas mitrais de indivíduos acometidos por DRC. Para detectar alterações específicas desta doença, comparamos as expressões de proteínas nos grupos portadores de DRC com insuficiência (DRC-INS) e com estenose (DRC-EST) a um grupo de indivíduos com degeneração mixomatosa de valva mitral (DMX) e outro sem valvulopatias (CTL). Alterações especificamente observadas em tecido mitral na DRC-INS ou DRC-EST em fases avançadas da doença podem explicar o mecanismo de desenvolvimento desses dois tipos de lesão. Foram encontradas 25 \"spots\", correpondendo a 29 proteínas diferencialmente expressas nos grupos com valvulopatias, refletindo principalmente alterações na matriz extracelular. Encontramos importante clivagem diferencial da vimentina, cuja proteína íntegra possui 54 kDa, formando fragmentos com ~40 e ~45 kDa, aumentados na DRC, principalmente na DRC-INS. O colágeno do tipo VI, com aproximadamente 95 kDa, encontrou-se com expressão diminuída exclusivamente no grupo DRC-INS. A Vitronectina foi encontrou-se aumentada em na DMX e na DRC-EST, em relação ao grupo controle, principalmente na DRC-EST. Lumican, por sua vez, teve expressão diminuída na DMX e na DRC-EST, apesar de possuir um único \"spot\" com expressão aumentada na DRC. Utilizando métodos de análise de padrões de expressão protéica in silico foram identificados conjuntos de proteínas capazes de discriminar as amostras de valva mitral por etiologia da doença. O presente trabalho pode auxiliar na elucidação dos mecanismos de desenvolvimento da doença e de alterações estruturais do tecido mitral em resposta às lesões autoimunes, bem como no diagnósticoda DRC. / Rheumatic Heart Disease (RHD) is a serious complication of oropharingitis caused by some serotypes of Streptococcus pyogenes not properly treated in susceptible individuals. It is a public health concern, mainly for undeveloped and developing countries, such as Brazil, India, some countries in Africa, aboriginal regions in Australia, and Egypt. It is highly debilitating with a high mortality rate due to cardiac commitment. Initial myocardial lesions disappear, but valvar lesions, mainly mitral and aortic, are irreversible and progressive. Many studies have characterized cellular (T lymphocytes) and humoral responses in individuals affected by the disease. Molecular mimicry and epitope spreading are the main mechanisms thought to be involved in the pathogenesis of RHD. We evaluated, in this research, the profile of protein expression in mitral valves from individuals affected by RHD. To detect alterations specific of this disease, we compared protein expression in the group of RHD with regurgitation (RHD-RGT) and stenosis (RHD-STN) to a group of individuals with mitral valve myxomatous degeneration (MXD) and another group without valvulopathies (CTL). Alterations specifically observed in the mitral tissue of RHD-RGT and RHD-STN in advanced stages of the disease can explain the mechanism of development for these two kinds of lesions. Twenty-five spots, corresponding to 29 proteins were found to be differentially expressed in the valvulopathy groups, reflecting mainly alterations in extracellular matrix. We found important differential cleavage of vimentin, the whole protein having 54 kDa, in fragments with ~40 and ~45 kDa, increased in RHD, mainly in RHD-RGT. Collagen type-VI, with approximatelly 95 kDa, was found to have decreased expression exclusivelly in the RHD-RGT group. Increased expression of Vitronectin was detected in DMX and RHD-EST groups, compared to the CTL group, mainly in the RHD-STN. Lumican, in turn, had decreased expression in the MXD and RHD-STN groups. By using in silico methods for analysis of patterns of protein expression, we identified sets of proteins capable of discriminating mitral valve samples by disease etiology. The present study might help elucidating the mechanisms of disease development and structural alterations in the mitral tissue in response to the autoimmune lesions, as well as in the diagnosis of RHD.