Caracterização de genes de reparo de DNA em cana-de-açúcar

Sugarcane is an important culture for Brazil that holds almost half of all worldwide productivity. Plants face many challenges, because of biotic and abiotic stresses presents in the production field, which could prevent plants from reaching their genetic potential. As consequence, those stresses can generate Reactive Oxygen Species – ROS – that can cause damages on DNA. Another consequence of stress is the early-flowering process, which contributes for a reduction on yield. In this context, the aim of this work is to characterize ScMUTM1 and ScMUTM2, two DNA glycosylases belonging to base excision repair pathway; and identify genes potentially related to stress and DNA repair in two sugarcane cultivars with contrasting flowering phenotypes. The characterization of the DNA glycosylases included the construction of vector to over express the recombinant proteins ScMUTM1 and ScMUTM2; they will be used in a near future to purification of these proteins and use in enzymatic assays. It was also made a phylogenetic reconstruction of this gene in plants and analysis of its promoter. With the phylogenetic analysis, it is possible to observe the presence of these genes grouped inside a branch with monocots and another one with dicots. This suggests that the duplication of this gene probably occurred after the separation of these two groups. The analysis of the promotor of MUTM shows of the presence of stress-related regulatory motifs at ScMUTM2 promoter, when compared with ScMUTM1. This may suggests that ScMUTM1 might be suffering sub functionalization process. After the analysis of microarrays data, it is observed an up-regulation from some stress-related genes in one of the conditions analyzed, related to early flowering process.

Caracterização de genes de reparo de DNA em cana-de-açúcar

Sugarcane is an important culture for Brazil that holds almost half of all worldwide productivity. Plants face many challenges, because of biotic and abiotic stresses presents in the production field, which could prevent plants from reaching their genetic potential. As consequence, those stresses can generate Reactive Oxygen Species – ROS – that can cause damages on DNA. Another consequence of stress is the early-flowering process, which contributes for a reduction on yield. In this context, the aim of this work is to characterize ScMUTM1 and ScMUTM2, two DNA glycosylases belonging to base excision repair pathway; and identify genes potentially related to stress and DNA repair in two sugarcane cultivars with contrasting flowering phenotypes. The characterization of the DNA glycosylases included the construction of vector to over express the recombinant proteins ScMUTM1 and ScMUTM2; they will be used in a near future to purification of these proteins and use in enzymatic assays. It was also made a phylogenetic reconstruction of this gene in plants and analysis of its promoter. With the phylogenetic analysis, it is possible to observe the presence of these genes grouped inside a branch with monocots and another one with dicots. This suggests that the duplication of this gene probably occurred after the separation of these two groups. The analysis of the promotor of MUTM shows of the presence of stress-related regulatory motifs at ScMUTM2 promoter, when compared with ScMUTM1. This may suggests that ScMUTM1 might be suffering sub functionalization process. After the analysis of microarrays data, it is observed an up-regulation from some stress-related genes in one of the conditions analyzed, related to early flowering process.

Cyclostratigraphy and eccentricity tuning of the early Oligocene through early Miocene record from Walvis Ridge

Few astronomically calibrated high-resolution (<=5 kyr) climate records exist that span the Oligocene-Miocene time interval. Notably, available proxy records show responses varying in amplitude at frequencies related to astronomical forcing, and the main pacemakers of global change on astronomical time-scales remain debated. Here we present newly generated X-ray fluorescence core scanning and benthic foraminiferal stable oxygen and carbon isotope records from Ocean Drilling Program Site 1264 (Walvis Ridge, southeastern Atlantic Ocean). Complemented by data from nearby Site 1265, the Site 1264 benthic stable isotope records span a continuous ~13-Myr interval of the Oligo-Miocene (30.1-17.1 Ma) at high resolution (~3.0 kyr). Spectral analyses in the stratigraphic depth domain indicate that the largest amplitude variability of all proxy records is associated with periods of ~3.4 m and ~0.9 m, which correspond to 405- and ~110-kyr eccentricity, using a magnetobiostratigraphic age model. Maxima in CaCO3 content, d18O and d13C are interpreted to coincide with ~110 kyr eccentricity minima. The strong expression of these cycles in combination with the weakness of the precession- and obliquity-related signals allow construction of an astronomical age model that is solely based on tuning the CaCO3 content to the nominal (La2011_ecc3L) eccentricity solution. Very long-period eccentricity maxima (~2.4-Myr) are marked by recurrent episodes of high-amplitude ~110-kyr d18O cycles at Walvis Ridge, indicating greater sensitivity of the climate/cryosphere system to short eccentricity modulation of climatic precession. In contrast, the responses of the global (high-latitude) climate system, cryosphere, and carbon cycle to the 405-kyr cycle, as expressed in benthic d18O and especially d13C signals, are more pronounced during ~2.4-Myr minima. The relationship between the recurrent episodes of high-amplitude ~110-kyr d18O cycles and the ~1.2-Myr amplitude modulation of obliquity is not consistent through the Oligo-Miocene. Identification of these recurrent episodes at Walvis Ridge, and their pacing by the ~2.4-Myr eccentricity cycle, revises the current understanding of the main climate events of the Oligo-Miocene.

Identification de transcrits modulés par ETV6 : un gène candidat suppresseur de tumeur

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Host gene expression classifiers diagnose acute respiratory illness etiology.

Acute respiratory infections caused by bacterial or viral pathogens are among the most common reasons for seeking medical care. Despite improvements in pathogen-based diagnostics, most patients receive inappropriate antibiotics. Host response biomarkers offer an alternative diagnostic approach to direct antimicrobial use. This observational cohort study determined whether host gene expression patterns discriminate noninfectious from infectious illness and bacterial from viral causes of acute respiratory infection in the acute care setting. Peripheral whole blood gene expression from 273 subjects with community-onset acute respiratory infection (ARI) or noninfectious illness, as well as 44 healthy controls, was measured using microarrays. Sparse logistic regression was used to develop classifiers for bacterial ARI (71 probes), viral ARI (33 probes), or a noninfectious cause of illness (26 probes). Overall accuracy was 87% (238 of 273 concordant with clinical adjudication), which was more accurate than procalcitonin (78%, P < 0.03) and three published classifiers of bacterial versus viral infection (78 to 83%). The classifiers developed here externally validated in five publicly available data sets (AUC, 0.90 to 0.99). A sixth publicly available data set included 25 patients with co-identification of bacterial and viral pathogens. Applying the ARI classifiers defined four distinct groups: a host response to bacterial ARI, viral ARI, coinfection, and neither a bacterial nor a viral response. These findings create an opportunity to develop and use host gene expression classifiers as diagnostic platforms to combat inappropriate antibiotic use and emerging antibiotic resistance.

Transcriptomic Analysis of the Host Response and Innate Resilience to Enterotoxigenic Escherichia coli Infection in Humans.

BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) is a globally prevalent cause of diarrhea. Though usually self-limited, it can be severe and debilitating. Little is known about the host transcriptional response to infection. We report the first gene expression analysis of the human host response to experimental challenge with ETEC. METHODS: We challenged 30 healthy adults with an unattenuated ETEC strain, and collected serial blood samples shortly after inoculation and daily for 8 days. We performed gene expression analysis on whole peripheral blood RNA samples from subjects in whom severe symptoms developed (n = 6) and a subset of those who remained asymptomatic (n = 6) despite shedding. RESULTS: Compared with baseline, symptomatic subjects demonstrated significantly different expression of 406 genes highlighting increased immune response and decreased protein synthesis. Compared with asymptomatic subjects, symptomatic subjects differentially expressed 254 genes primarily associated with immune response. This comparison also revealed 29 genes differentially expressed between groups at baseline, suggesting innate resilience to infection. Drug repositioning analysis identified several drug classes with potential utility in augmenting immune response or mitigating symptoms. CONCLUSIONS: There are statistically significant and biologically plausible differences in host gene expression induced by ETEC infection. Differential baseline expression of some genes may indicate resilience to infection.

Identification de transcrits modulés par ETV6 : un gène candidat suppresseur de tumeur

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Sedimentology, geochemistry and ostracodes from Lake Ohrid

Ancient Lake Ohrid, located in the southern Balkan Peninsula in Macedonia and Albania is characterized by a high degree of endemism and it is considered to be the oldest lake in Europe. But its exact age (between one and ten million years) and also its origin are so far not known. To unravel these uncertainties an ICDP (International Continental Scientific Drilling Program) drilling project (Scientific Collaboration On Past Speciation Conditions in Ohrid (SCOPSCO)), started in April 2013. In addition to the investigations about the age and origin, other paleolimnological studies, e.g., the reconstruction of past climate and of past lake level changes, should be performed with the drilled cores. Used proxies in such paleolimnological studies are, e.g., ostracodes because they respond sensitively to environmental changes but an accurate knowledge of their preferences and tolerances to specific environmental conditions is necessary for this purpose. So far, this knowledge about the, mostly endemic, Ohrid ostracodes was limited. Thus, within the framework of this thesis, ostracodes and a multiplicity of environmental data were collected in Lake Ohrid and its adjacent waters during four field campaigns. In a total of 47 ostracode species could be detected in the entire study area and 32 of them were found alive in Lake Ohrid. Multivariate statistic identified that water depth, salinity, conductivity, pH, and dissolved oxygen were the main determining factors for ostracode distribution in the entire study area. In Lake Ohrid, the distribution was mainly controlled by water depth, water temperature, and pH. Some ostracodes were identified as strong indicator species for important environmental variables, e.g., water temperature and water depth. A distinctive feature of Lake Ohrid was the finding of the ostracode genus Amnicythere whose species normally inhabit oligo-(meso-)haline waters and this could point to a marine origin of the lake. So far, the specialized endemic ostracodes show the highest abundances and the greatest spatial distribution in Lake Ohrid but during the sampling eight widespread species were found for the first time in the lake. They inhabited mainly the northern part of the lake, where two cities are located and industry and agriculture play a major role, and they were limited to water depths above 50 m and this could be an evidence for an increasing anthropogenic pressure because widespread ostracode species often replace endemic species. To unravel the human impact on Lake Ohrid during the last decades short sediment cores were taken and the multi-proxy study indicated that the lake productivity between the early 1920s and the late 1980s was relatively low. Diatom assemblages indicate a rising productivity in the southern part of Lake Ohrid since the mid 1970s and geochemical proxies and ostracodes point to an increasing productivity since the late 1980s in the southern and in the northern part. A slight increase in the productivity continued until 2009. Noticeable is the fact that since the early 1990s, the increasing productivity and the increasing concentrations of heavy metals correspond to a decreasing number of ostracodes in the northern part of Lake Ohrid. Perhaps, this indicates that living conditions in this lake part became less favorable for the mostly endemic ostracode species. Furthermore, the sediment samples from the cores show relatively high concentrations of arsenic, iron, and nickel. Fluctuations in ostracode assemblages from three longer sediment cores, the longest spans approximately 136 ka, taken in Lake Ohrid, correspond to fluctuations in the productivity, in the carbonate content, of the lake level, and of climate changes. Between the marine isotope stage (MIS) 6 and MIS 2 the number of ostracode valves is very low or the valves were completely absent. This corresponds to a low lake productivity, a low carbonate content, and a low lake level. At the onset of the Holocene, the number of valves increased markedly and this correlates with an increased productivity and carbonate content and a warmer climate. But during the Little Ice Age (LIA), the number of valves dropped again and species which prefer warmer waters disappeared completely. This drop corresponds also to a low productivity. After the LIA, the number of species increased again but since 1895 AD a strong and abrupt decrease is visible. A reason for this could be an increase in the heavy metal concentrations.

(Appendix) Stable carbon and oxygen isotopes, and Mg/Ca ratios of foraminifera from ODP Hole 154-925A

To better understand the links between the carbon cycle and changes in past climate over tectonic timescales we need new geochemical proxy records of secular change in silicate weathering rates. A number of proxies are under development, but some of the most promising (e.g. palaeoseawater records of Li and Nd isotope change) can only be employed on such large samples of mono-specific foraminifera that application to the deep sea sediment core archive becomes highly problematic. "Dentoglobigerina" venezuelana presents a potentially attractive target for circumventing this problem because it is a typically large (> 355 ?m diameter), abundant and cosmopolitan planktic foraminifer that ranges from the early Oligocene to early Pliocene. Yet considerable taxonomic and ecological uncertainties associated with this taxon must first be addressed. Here, we assess the taxonomy, palaeoecology, and ontogeny of "D." venezuelana using stable isotope (oxygen and carbon) and Mg/Ca data measured in tests of late Oligocene to early Miocene age from Ocean Drilling Program (ODP) Site 925, on Ceara Rise, in the western equatorial Atlantic. To help constrain the depth habitat of "D." venezuelana relative to other species we report the stable isotope composition of selected planktic foraminifera species within Globigerina, Globigerinoides, Paragloborotalia and Catapsydrax. We define three morphotypes of "D." venezuelana based on the morphology of the final chamber and aperture architecture. We determine the trace element and stable isotope composition of each morphotype for different size fractions, to test the validity of pooling these morphotypes for the purposes of generating geochemical proxy datasets and to assess any ontogenetic variations in depth habitat. Our data indicate that "D." venezuelana maintains a lower thermocline depth habitat at Ceara Rise between 24 and 21 Ma. Comparing our results to published datasets we conclude that this lower thermocline depth ecology for the Oligo-Miocene is part of an Eocene-to-Pliocene evolution of depth habitat from surface to sub-thermocline for "D." venezuelana. Our size fraction data advocate the absence of photosymbionts in "D." venezuelana and suggest that juveniles calcify higher in the water column, descending into slightly deeper water during the later stages of its life cycle. Our morphotype data show that d18O and d13C variation between morphotypes is no greater than within-morphotype variability. This finding will permit future pooling of morphotypes in the generation of the "sample hungry" palaeoceanographic records.

Abundance of organic-walled dinoflagellate cysts of sediment core GeoB3603-2

Here, we reconstruct the varying influence of the Agulhas Current (AgC), the South Atlantic Current and the Antarctic Circumpolar Current on the Agulhas Retroflection (AgR) in the eastern South Atlantic Ocean for the last 160,000 years on the basis of the dinoflagellate cysts, pollen and spores present in a sediment core (GeoB 3603-2) from the southeastern Cape Basin offshore South Africa, where the Agulhas Current enters the Atlantic Ocean. Our analyses reveal strong orbital forcing on the heat exchange between the Indian Ocean and the South Atlantic Ocean during the Late Quaternary. Maxima in local productivity appear to be primarily related to a strengthening of the ocean circulation as a result of the high seasonal contrast during precession maxima. During precession minima, seasonal contrast was low and stratified, oligo- to mesotrophic conditions prevailed, notably when these minima coincided with the glacial terminations. The clear presence of periodicities on a sub-Milankovitch scale as well as modulations of the primary frequencies demonstrate that the Agulhas Retroflection furthermore is modulated substantially by complex interactions between the subtropical, 'precession-driven', climate and ocean circulation systems, and the southern, 'obliquity-driven', high latitudes.

Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing

Chromatin immunoprecipitation (ChIP) provides a means of enriching DNA associated with transcription factors, histone modifications, and indeed any other proteins for which suitably characterized antibodies are available. Over the years, sequence detection has progressed from quantitative real-time PCR and Southern blotting to microarrays (ChIP-chip) and now high-throughput sequencing (ChIP-seq). This progression has vastly increased the sequence coverage and data volumes generated. This in turn has enabled informaticians to predict the identity of multi-protein complexes on DNA based on the overrepresentation of sequence motifs in DNA enriched by ChIP with a single antibody against a single protein. In the course of the development of high-throughput sequencing, little has changed in the ChIP methodology until recently. In the last three years, a number of modifications have been made to the ChIP protocol with the goal of enhancing the sensitivity of the method and further reducing the levels of nonspecific background sequences in ChIPped samples. In this chapter, we provide a brief commentary on these methodological changes and describe a detailed ChIP-exo method able to generate narrower peaks and greater peak coverage from ChIPped material.

Fasciola hepatica surface tegument: glycoproteins at the interface of parasite and host

Fasciola hepatica, commonly known as liver fluke, is a trematode which causes Fasciolosis in ruminants and humans. The outer tegumental coat of F. hepatica (FhTeg) is a complex metabolically active biological matrix that is continually exposed to the host immune system and therefore makes a good vaccine target. F. hepatica tegumental coat is highly glycosylated and helminth-derived immunogenic oligosaccharide motifs and glycoproteins are currently being investigated as novel vaccine candidates. This report presents the first systematic characterisation of FhTeg glycosylation using lectin microarrays to characterise carbohydrates motifs present, and lectin histochemistry to localize these on the F. hepatica tegument. We discovered that FhTeg glycoproteins are predominantly oligomannose oligosaccharides that are expressed on the spines, suckers and tegumental coat of F. hepatica and lectin blot analysis confirmed the abundance of N- glycosylated proteins. While some oligosaccharides are widely distributed on the fluke surface other subsets are restricted to distinct anatomical regions. We selectively enriched for FhTeg mannosylated glycoprotein subsets using lectin affinity chromatography and identified 369 proteins by mass spectrometric analysis. Among these proteins are a number of potential vaccine candidates with known immune modulatory properties including proteases, protease inhibitors, paramyosin, Venom Allergen-like II, Enolase and two proteins, nardilysin and TRIL, that have not been previously associated with F. hepatica Furthermore, we provide a comprehensive insight regarding the putative glycosylation of FhTeg components which could highlight the importance of further studies examining glycoconjugates in host-parasite interactions in the context of F. hepatica infection and the development of an effective vaccine.

MMSET deregulation affects cell cycle progression and adhesion regulons in t(4;14) myeloma plasma cells

BackgroundThe recurrent immunoglobulin translocation, t(4;14)(p16;q32) occurs in 15% of multiple myeloma patients and is associated with poor prognosis, through an unknown mechanism. The t(4;14) up-regulates fibroblast growth factor receptor 3 (FGFR3) and multiple myeloma SET domain (MMSET) genes. The involvement of MMSET in the pathogenesis of t(4;14) multiple myeloma and the mechanism or genes deregulated by MMSET upregulation are still unclear.Design and MethodsThe expression of MMSET was analyzed using a novel antibody. The involvement of MMSET in t(4;14) myelomagenesis was assessed by small interfering RNA mediated knockdown combined with several biological assays. In addition, the differential gene expression of MMSET-induced knockdown was analyzed with expression microarrays. MMSET gene targets in primary patient material was analyzed by expression microarrays.ResultsWe found that MMSET isoforms are expressed in multiple myeloma cell lines, being exclusively up-regulated in t(4;14)-positive cells. Suppression of MMSET expression affected cell proliferation by both decreasing cell viability and cell cycle progression of cells with the t(4;14) translocation. These findings were associated with reduced expression of genes involved in the regulation of cell cycle progression (e.g. CCND2, CCNG1, BRCA1, AURKA and CHEK1), apoptosis (CASP1, CASP4 and FOXO3A) and cell adhesion (ADAM9 and DSG2). Furthermore, we identified genes involved in the latter processes that were differentially expressed in t(4;14) multiple myeloma patient samples.ConclusionsIn conclusion, dysregulation of MMSET affects the expression of several genes involved in the regulation of cell cycle progression, cell adhesion and survival.

Effets préventifs et thérapeutiques des polyphénols dans un modèle in vitro et in vivo de maladie inflammatoire de l’intestin : caractérisation des polyphénols de la pelure de pomme et de la canneberge par spectrométrie de masse

La muqueuse intestinale est exposée à des agents oxydants provenant de l’ingestion d’aliments modifiés, de cellules immuno-inflammatoires et de la flore intestinale. Une diète élevée en fruits et légumes peut diminuer le stress oxydant (SOx) ainsi que l’inflammation via plusieurs mécanismes. Ces effets bénéfiques peuvent être attribuables à leur contenu élevé en polyphénols. La première étude de mon doctorat consistait à tester l’hypothèse que les polyphénols extraits de pelures de pomme (DAPP) pouvaient diminuer le stress oxydant et l'inflammation impliqués dans les maladies inflammatoires de l'intestin (MII). Nous avons caractérisé les polyphénols des DAPP par spectrométrie de masse (LC-MS) et examiné leur potentiel antioxydant et anti-inflammatoire au niveau des cellules intestinales. L’identification des structures chimiques des polyphénols a été effectuée par LC-MS. Le SOx a été induit par l’ajout du complexe fer/ascorbate (Fe/Asc, 200 µM/2 mM) et l’inflammation par la lipopolysaccharide (LPS, 200µg/mL) à des cellules intestinales Caco-2/15 pré-incubées avec les DAPP (250 µg/mL). L’effet du SOx est déterminé par le dosage du malondialdéhyde (MDA), de la composition des acides gras polyinsaturés et de l’activité des enzymes antioxydantes endogènes (SOD et GPx). L’impact des DAPP sur l’inflammation a été testé par l’analyse de l’expression des marqueurs inflammatoires: cyclooxygénase-2 (COX-2), le facteur de nécrose tumorale alpha (TNF-a et l’interleukine-6 (IL-6) et les facteurs de transcription NF-KB, Nrf-2 et PGC1α par immunobuvardage. Nos données ont montré que les flavonols et les flavan-3-ols constituent les composés polyphénoliques majoritaires des DAPP. L’ajout de Fer2+/Asc a provoqué une augmentation de la peroxidation lipidique comparativement aux cellules contrôles, un appauvrissement des acides gras polyinsaturés n-3 et n-6, et une modulation des enzymes antioxydantes, se traduisant par une augmentation de l’activité de la SOD et une diminution de la GPx. En contrepartie, les DAPP ont exhibé leur potentiel à corriger la plupart des perturbations, y compris l’expression protéique anormalement élevée du COX-2 et la production de la prostaglandine E2 (PGE2), ainsi que l’inflammation telle que réflétée par les facteurs NF-κB, TNF-α et IL-6. Par ailleurs, les mécanismes sous-jacents à ces changements bénéfiques des DAPP ont fait intervenir les facteurs de transcription antioxydants (Nrf-2, PGC1α). Vraisemblablement, cette première étude a permis de démontrer la capacité des DAPP à amoindrir le SOx et à réduire l’inflammation, deux processus étroitement impliqués dans les MII. Dans la deuxième étape de mon doctorat, nous avons voulu comparer les résultats de DAPP à ceux des polyphénols dérivant de la canneberge qui est considérée par la communauté scientifique comme le fruit ayant le plus fort potentiel antioxydant. À cette fin, nous avons caractérisé l’effet des composés polyphénoliques de la canneberge (CPC) sur le SOx, la défense antioxydante et l’inflammation au niveau intestinal tout en définissant leur métabolisme intraluminal. Les différents CPC ont été séparés selon leur poids moléculaire par chromatographie et leurs structures chimiques ont été identifiées par LC-MS. Suite à une pré-incubation des cellules Caco-2/15 avec les extraits CPC (250 µg/mL), le Fe/Asc et la LPS ont été administrés comme inducteurs du SOx et de l’inflammation, respectivement. La caractérisation globale des CPC a révélé que les acides phénoliques composaient majoritairement l’extrait de canneberge de petit poids moléculaire (LC) alors que les flavonoïdes et les procyanidines dimériques/trimériques représentaient l’extrait de poids moléculaire moyen (MC) tout en laissant les procyanidines oligo et polymériques à l’extrait de haut poids moléculaire (HC). Les CPC ont permis de restaurer la plupart des perturbations engendrées dans les Caco-2/15 par le Fe/Asc et le LPS. Les CPC exhibaient le potentiel d’abaisser les niveaux de MDA, de corriger la composition des acides gras polyinsaturés n-3 et n-6, d’augmenter l’activité des enzymes antioxydantes (SOD, GPx et CAT) et d’élever l’expression de Nrf2 et PGC1α. En outre, les CPC pouvaient aussi réduire les niveaux élevés des protéines inflammatoires COX-2, TNF-α et IL-6 ainsi que la production des PGE2 par un mécanisme impliquant le NF-κB. Au niveau mitochondrial, les procyanidines oligomériques ont réussi à corriger les dysfonctions reliées à la production d’énergie (ATP), l’apoptose (Bcl-2, Cyt C et AIF) et le statut des facteurs de transcription mitochondriaux (mtTFA, mtTFB1, mtTFB2). Dans le but de bien comprendre les mécanismes d’action des CPC, nous avons défini par LC-MS les composés polyphénoliques qui ont été transportés ou absorbés par l’entérocyte. Nos analyses soulignent le transport (i) des acides cinnamiques et benzoïques (LC); (ii) la quercétine glycosylée et conjuguée et les procyanidines dimériques de type A (MC); et (iii) l’épicatéchine et les procyanidines oligomériques (HC). Les processus de métabolisation (méthylation, glucuronidation et sulfatation) au niveau de l’entérocyte ont probablement permis le transport de ces CPC surtout sous leur forme conjuguée. Les procyanidines oligomériques ayant un degré de polymérisation supérieur à 2 (HC) ont semblé adhérer aux cellules Caco-2/15. L’épicatéchine suivi par les procyanidines dimériques de type A ont été trouvés majoritaires au niveau des mitochondries. Même si nous ignorons encore l’action biologique de chaque composé polyphénolique, nous pouvons suggérer que leurs effets combinatoires exercent des fonctions antioxydantes, anti-inflammatoires et mitochondriales dans le modèle intestinal Caco-2/15. Dans une troisième étape, nous avons procédé à l’évaluation des aspects préventifs et thérapeutique des DAPP tout en sondant les mécanismes sous-jacents dans une étude préclinique. À cette fin, nous avons exploité le modèle de souris avec colite expérimentale provoquée par le Dextran Sulfate de Sodium (DSS). L’induction de l’inflammation intestinale chez la souris C57BL6 a été effectuée par l’administration orale de DSS à 2.5% pendant 10 jours. Des doses physiologiques et supra-physiologiques de DAPP (200 et 400 mg/kg/j, respectivement) ont été administrées par gavage pendant 10 jours pré- et post-DSS. L’inflammation par le DSS a provoqué une perte de poids, un raccourcissement du côlon, le décollement dystrophique de l’épithélium, l’exulcération et les infiltrations de cellules mono et polynucléaires au niveau du côlon. De plus, le DSS a induit une augmentation de la peroxidation lipidique, une régulation à la baisse des enzymes antioxydantes, une expression protéique à la hausse de la myéloperoxidase (MPO), du COX-2 et de la production des PGE2. Par ailleurs, les DAPP ont permis de corriger ou du moins d’alléger la plupart de ces anomalies en situation préventive ou thérapeutique, en plus d’abaisser l’expression protéique de NF-κB et des cytokines inflammatoires (TNF-a et l’IL-6) tout en stimulant les facteurs de transcription antioxydants (Nrf-2, PGC1α). Conséquemment, les polyphénols des DAPP ont exhibé leur puissant pouvoir antioxydant et anti-inflammatoire au niveau intestinal dans un modèle in vivo. Leurs actions sont associées à la régulation des voies de signalisation cellulaire et des changements dans la composition du microbiote. Ces trois projets de recherche permettent d’envisager l’évaluation des effets préventifs et thérapeutiques des DAPP cliniquement chez les patients avec des désordres inflammatoires de l’intestin.

Saccharomycotin transcriptomics by next-generation sequencing

The non-standard decoding of the CUG codon in Candida cylindracea raises a number of questions about the evolutionary process of this organism and other species Candida clade for which the codon is ambiguous. In order to find some answers we studied the transcriptome of C. cylindracea, comparing its behavior with that of Saccharomyces cerevisiae (standard decoder) and Candida albicans (ambiguous decoder). The transcriptome characterization was performed using RNA-seq. This approach has several advantages over microarrays and its application is booming. TopHat and Cufflinks were the software used to build the protocol that allowed for gene quantification. About 95% of the reads were mapped on the genome. 3693 genes were analyzed, of which 1338 had a non-standard start codon (TTG/CTG) and the percentage of expressed genes was 99.4%. Most genes have intermediate levels of expression, some have little or no expression and a minority is highly expressed. The distribution profile of the CUG between the three species is different, but it can be significantly associated to gene expression levels: genes with fewer CUGs are the most highly expressed. However, CUG content is not related to the conservation level: more and less conserved genes have, on average, an equal number of CUGs. The most conserved genes are the most expressed. The lipase genes corroborate the results obtained for most genes of C. cylindracea since they are very rich in CUGs and nothing conserved. The reduced amount of CUG codons that was observed in highly expressed genes may be due, possibly, to an insufficient number of tRNA genes to cope with more CUGs without compromising translational efficiency. From the enrichment analysis, it was confirmed that the most conserved genes are associated with basic functions such as translation, pathogenesis and metabolism. From this set, genes with more or less CUGs seem to have different functions. The key issues on the evolutionary phenomenon remain unclear. However, the results are consistent with previous observations and shows a variety of conclusions that in future analyzes should be taken into consideration, since it was the first time that such a study was conducted.