La vigne est une plante cultivée dans le monde entier dont l’importance économique est principalement liée à la production de vin. La baie de raisin est également l’un des principaux modèles d’étude pour les fruits non-climatériques notamment pour l’étude des mécanismes contrôlant le mûrissement des baies. Le développement de la baie de raisin est caractérisé par deux phases de croissance séparées par une phase de latence se produisant au moment de la véraison. La baie de raisin est composée de trois tissus principaux: la peau, la pulpe et les graines. La peau et la pulpe présentent une structure et une composition en métabolites distinctes et contribuent de manière différente à la qualité du vin, la pulpe fournissant essentiellement le sucre, les acides aminés et organiques alors que la peau est riche en anthocyanes. A l'heure actuelle, les mécanismes moléculaires impliqués dans le contrôle de la maturation des baies de raisin sont encore mal compris. Si l'ABA, le sucre et différents facteurs de transcription jouent un rôle important dans le contrôle de cette phase de développement, les mécanismes épigénétiques, en particulier la méthylation de l’ADN, apparaissent aussi comme des régulateurs importants du développement et du mûrissement des fruits charnus. Dans ce contexte, Le projet de thèse présenté vise à analyser le rôle de la méthylation de l’ADN (1) dans la maturation des baies de raisin et (2) dans la synthèse des anthocyanes en utilisant comme système modèle des cellules de baie de raisin cultivées in vitro.La culture in vitro de baies de raisin en présence d’inhibiteurs de la méthylation de l'ADN, aboutit à une inhibition de la maturation, suggérant que la méthylation de l’ADN joue un rôle crucial pour cette étape du développement chez la vigne. La pellicule et la chair de baies de raisin récoltées à divers stades de développement ont ensuite été analysées séparément pour déterminer les variations des transcriptomes, de l’abondance de différents métabolites, et de la méthylation de l'ADN. Les principaux résultats indiquent des variations des métabolites et du transcriptome, avec des spécificités liés au tissu analysé. En outre, l'analyse des variations de méthylation de l'ADN à deux stades de développement dans chacun de ces deux tissus révèle l’existence de variations de méthylation spécifiques à chaque tissu, tandis que les variations communes aux deux tissus restent limitées. Ces résultats suggèrent un contrôle de la méthylation de l’ADN spécifique à chaque tissu lors de la maturation de la baie. Cependant les régions différentiellement méthylées identifiées dans chaque tissu, ne sont pas associées à des gènes exprimés différentiellement au cours de la maturation des baies, ce qui pose la question du rôle de la méthylation de l’ADN dans le contrôle de l’expression génique dans les baies.Pour analyser le rôle de la méthylation de l’ADN dans le contrôle de la synthèse des anthocyanes, nous avons utilisé des suspensions de cellules de raisin du génotype Gamay Teinturier (GT), connues pour accumuler des anthocyanes lorsqu’elles sont cultivées à la lumière. L’utilisation de la zébularine, un inhibiteur de la méthylation d’ADN, permet de stimuler l’accumulation d'anthocyanes dans les cellules GT en présence de lumière, et de l’induire à l’obscurité. Les traitements à la zébularine provoquent en outre une limitation de la croissance cellulaire, une modification de l’accumulation des sucres solubles et acides organiques ainsi qu’une reprogrammation importante du transcriptome. Ces résultats suggèrent un effet général de la zébularine sur les cellules GT plutôt qu’un effet spécifique sur l’accumulation d’anthocyanes.Dans l'ensemble, les résultats indiquent que la méthylation de l'ADN est importante pour le contrôle de la maturation des fruits de la vigne, bien que les mécanismes qui sous-tendent les variations de la méthylation et leurs rôles dans les différents tissus de la baie de raisin restent à préciser. / Grapevine is a worldwide cultivated fruit crop with high economic importance mainly because of its usage for vine production. Grape berry is also one of the main models for non-climacteric fruits to study the mechanisms controlling the ripening process. Grape berry development is characterized by two phases of rapid size increase separated by a lag phase at the time of ripening induction. Grape berries are composed of three main tissues, the peel, the pulp and the seeds. Peel and pulp present distinct structure and metabolite composition and contribute in a different way to wine quality, the pulp providing sugar, amino and organic acids whereas the peel is important for anthocyanins and other phenolic compound abundance. At the present time, the molecular mechanisms involved in the control of grape berry ripening are still poorly understood. Recent results indicate that both ABA and sugar may be important signals together with various transcription factors. In addition, epigenetic mechanisms are now emerging as important regulators of fleshy fruit development, DNA methylation being critically important for tomato, sweet range and strawberry ripening.The present project aims at analyzing the potential role of DNA methylation in the control grape berry ripening. It also investigates the potential role of DNA methylation in the synthesis of anthocyanins, a compound of primary importance in peel of red grape berries, using in vitro grown fruit cells. To address these questions, grape berries cultivated in vitro were treated with DNA methylation inhibitors. Treatments resulted in delayed and reduced grape berry ripening, therefore sustaining the idea that DNA methylation plays critical roles at this developmental step. Grape berries harvested at various developmental stages were then dissected and each tissue was separately analyzed for transcriptomic, metabolic and DNA methylation variations. Main results indicate significant and distinct metabolic and transcriptomic variations consistent with each tissue following specific modifications during ripening. In addition, analysis of DNA methylation variations at two developmental stages in each tissue indicates both common and tissue specific changes in DNA methylation patterns during fruit ripening. A very small proportion of DMRs is found similarly in the pup and the peel, but most are tissue specific, also consistent with tissue specific control at this developmental phase. Of note, among the different DMRs identified in each tissue, only a few were associated with differentially expressed genes (DEG) during ripening, whereas most were not, questioning the general role of DNA methylation in the control of gene expression at this developmental transition in grape.As Anthocyanins are the most abundant polyphenolic compounds in the skin of red grape berries, we used grape cell suspensions of the Gamay Teinturier genotype, that are known to accumulate anthocyanins when grown in light conditions, to analyze the potential role of DNA methylation in their synthesis. GT cells cultivated in light conditions were treated with the DNA methyltransferase inhibitor zebularine, they accumulate higher quantities of anthocyanins. Of note, GT cells grown in the absence of light do not accumulate anthocyanins. However, zebularine was sufficient to induce anthocyanin accumulation in the absence of light. Zebularine treatments had significant additional effects on grape cells including, cell growth limitation, and modification of soluble sugar, organic acid or stilbene accumulation, together with important transcriptomic reprogramming, consistent with a general effect on cells rather than a specific effect on anthocyanin accumulation.Taken together, results are consistent with DNA methylation being important in the control of grape fruit ripening, although the precise mechanisms underlying methylation variations and roles in grape berries remain to be deciphered.

Protein is an important fraction within bovine milk. This milk protein is not only vital for calf growth and development, but also includes bioactive proteins and peptides that have been shown to enhance the health of animals and humans. Research efforts are focusing on factors, such as nutrition, that can influence the quantity and profile of proteins within the bovine milk proteome. The research outlined herein investigated the impact of diet on the bovine milk proteome. The first experiment examined whether dietary inclusion of grape marc (GM), a condensed tannin (CT) containing by-product from the viticulture industry, could alter the bovine milk proteome through altered nitrogen (N) metabolism. In this experiment, 10 lactating Holstein cows were fed either 2.0 kg dry matter (DM)/ cow/ day of beet pulp: soy hulls in a 50% mixture (control), or 1.5 kg DM/ cow/ day of GM as part of a balanced dairy cow ration for a 28-d trial. Milk samples were obtained for analysis of the high- and low-abundance protein fractions. Skimmed milk samples collected for high-abundance protein analysis were measured using high performance liquid chromatography (HPLC), and liquid-chromatography tandem mass spectrometry (LC-MS/MS) was used to identify proteins in the low-abundance protein enriched fraction. Skimmed milk samples collected for low-abundance milk protein analysis were fractionated and enriched to remove higher abundance proteins. Enriched milk samples were then digested and labeled with isobaric tandem mass tags (TMT) prior to protein identification using LC-MS/MS analysis. There were no changes in the high-abundance protein fraction in response to diet; however, 16 of 127 low-abundance proteins were identified at different relative-abundances due to diet (P ≤ 0.05). While there were no alterations in the metabolic or N status of animals due to GM supplementation, the 12% change in the low-abundance milk protein fraction highlighted the potential for dietary alteration of the bovine milk proteome. A second experiment evaluated the inclusion of alternative forage crops (AFC) as a means to alter the bovine milk proteome. In this experiment, both the skimmed milk and milk fat globule membrane (MFGM) protein fractions were included in analysis. Milk samples were collected from 16 lactating Jersey cattle included in a 21-d grazing experiment, where cows were offered one of two diets. The control group (CON, n=8) grazed a grass-legume pasture mixture containing orchardgrass (Dactylis glomerata), timothy (Phleum pratense), Kentucky bluegrass (Poa pratensis), and white clover (Trifolium repens). The treatment group (AFC, n=8) grazed a similar base pasture that was strip-tilled with oat (Avena sativa), buckwheat (Fagopyrum esculentum), and chickling vetch (Lathyrus sativus) so that the AFC species comprised 10% of the AFC group’s pasture DM intake (DMI). Milk samples were collected for HPLC analysis of the high abundance milk proteins, and LC-MS/MS analysis of the low abundance protein enriched skim milk fraction and MFGM-associated protein fraction. Cows that grazed pastures containing AFC had higher αs1-CAS content (P = 0.005), and higher relative-abundances of 7 low-abundance proteins within the skim milk and MFGM fractions (P ≤ 0.05). While it is plausible that the inclusion of AFC in pasture increased nutrient availability to the mammary gland, the specific mechanisms that could have caused the shifts observed remain unclear. Further investigation is necessary to fully understand the role of diet and the milk protein profile.

Natural, plant-based tannin antioxidants are capable of inhibiting lipid oxidation in ground beef and may be possible alternatives to industry synthetic and natural standards of BHA/BHT and rosemary extract, respectively. Ground beef was purchased on three different days, each defining a batch during study 1. Treatments, added based on meat weight, included a control, 0.2 percent rosemary (RM), 0.02 percent BHA/BHT, 0.5 percent Chardonnay grape seed flour (CG), 0.1 percent and 0.25 percent chestnut wood flour (CN), and 0.25 percent and 0.5 percent of four sorghum bran varieties: black (BS), black with tannin (BTS), white (WS), and high tannin (TS). Patties, formed in duplicate, were randomly designated as cooked or raw and by 0 to 5 day storage, and were aerobically stored at 4 degrees C. Cooked patties were analyzed using the TBARS method. Raw patties were analyzed for subjective and objective color, number of ingredient specks, and pH. In study 2, six treatments were chosen for sensory evaluation including a control, 0.2 percent RM, 0.02 percent BHA/BHT, 0.5 percent CG, 0.1 percent CN, and 0.5 percent BTS. Preparation, and raw and cooked analysis occurred similar to study 1. Additional patties were made for day 1 consumption by consumer panelists. In study 1, all treatments except 0.25 percent WS reduced TBARS values over time compared to 0.2 percent RM. Four treatments (0.5 percent BTS, 0.5 percent CG, 0.25 percent CN, and 0.1 percent CN) showed no significant increase in TBARS values over storage. BS and BTS yielded the lowest color space values (CIE L*, a*, and b*; P<0.0001). Ingredient specks were possible color measurement influences. In both studies antioxidant addition reduced TBARS values over time compared to the control (P<0.0001), and percent discoloration was highest in patties containing a sorghum treatment (P<0.0001). Patties containing 0.1 percent CN were significantly favored in terms of overall like (P<0.0002) and flavor like (P<0.0001). Patties containing 0.2 percent RM were ranked lowest in overall and flavor like, and ground beef-like bite. Patties containing 0.5 perent CG were least liked according to tenderness level (P<0.005). These results indicate that CG, CN, and certain varieties of sorghum bran can be added to pre-cooked ground beef products and provide better antioxidant protection than currently used ingredients of BHA/BHT and rosemary extract.

The genus Vitis (the grapevine) is a group of highly diverse, diploid woody perennial vines consisting of approximately 60 species from across the northern hemisphere. To gain insights into the use of wild Vitis species during the past century of interspecific grape breeding and to provide a foundation for marker- assisted breeding programmes, we present a principal components analysis based ancestry estimation method to calculate admixture proportions of hybrid grapes in the United States Department of Agriculture grape germplasm collection using genome-wide polymorphism data. We find that grape breeders have backcrossed to both the domesticated V. vinifera and wild Vitis species and that reasonably accurate genome-wide ancestry estimation can be performed on interspecific Vitis hybrids using a panel of fewer than 50 ancestry informative genetic markers.

Landscape characteristics affect vineyard microclimates and influence the quality of grapes produced. There is currently a lack of research examining the microclimatological conditions of vineyards and how they affect grape quality. This study utilizes qualitative methods to explore the relationship between vineyard microclimates and grape quality in Madeira, Portugal. Semi-structured interviews have been conducted with local participants involved in the production of wine grapes and are used to reveal the factors affecting grape quality. Interviews accompany a physical inventory of landscape characteristics in the vineyards, and are guided by where interviewees observe changes in grape quality. The findings suggest there is a strong relationship between microclimates and grape quality. These results are utilized to make recommendations for methods of site selection and the microclimatic design of vineyards.

Hormones control plant development by coordinating changes in the expression of numerous genes at crucial times in a tissue and organ-specific manner. They have been implicated in controlling various aspects of grape berry development, in particular, the important process of ripening and are used in some crops to control growth and ripening. Abscisic acid (ABA), is associated in grapevine with the response to water stress but may also have a role in berry ripening. We have shown over three seasons that ABA levels in Cabernet Sauvignon berries increase dramatically at veraison, consistent with it being involved either as a trigger for ripening or as a response to the increase in sugars that occurs at this time. Net ABA accumulation doesn't occur until veraison, the decrease in ABA concentration in the first phase of berry development being due to berry expansion. The decrease in ABA that occurs later in development is likely to be due to a combination of catabolism and sequestration into the bound form. The genes crucial to ABA synthesis, 9-cis-epoxycarotenoid dioxygenase (NCED) and zeaxanthin epoxidase (ZEP), were expressed throughout berry development and no clear correlation was found between their levels and that of ABA. Laboratory studies have shown that isolated berries respond to the presence of sucrose through an increase in ABA biosynthesis pathway gene expression (NCED and ZEP). This resulted in de novo synthesis of ABA as inhibition of the carotenoid synthesis pathway by a phytoene desaturase inhibitor prevented ABA accumulation. Replicated field trials clearly showed that ABA treatments can be effective in significantly enhancing ripening when applied in at or near the end of the first period of berry expansion. Colour accumulation in the skins commenced earlier in ABA-treated fruit as did the increase in sugar levels. ABA treatment also advanced the timing of the second phase of berry expansion as it appeared to eliminate the lag phase of berry growth. Taken together these data demonstrate that ABA is likely to play some part in the control of berry ripening and can be used to advance the timing of ripening. Further investigation into the characteristics of ABA-treated fruit will be needed to investigate the compositional character of treated fruit and to gauge its suitability for winemaking. An ability to control the timing of ripening may provide considerable benefits to the wine industry in terms of wine style/quality and for winery scheduling. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1278807 / Thesis (Ph.D.) - The University of Adelaide, School of Agriculture, Food & Wine, 2007.

Hormones control plant development by coordinating changes in the expression of numerous genes at crucial times in a tissue and organ-specific manner. They have been implicated in controlling various aspects of grape berry development, in particular, the important process of ripening and are used in some crops to control growth and ripening. Abscisic acid (ABA), is associated in grapevine with the response to water stress but may also have a role in berry ripening. We have shown over three seasons that ABA levels in Cabernet Sauvignon berries increase dramatically at veraison, consistent with it being involved either as a trigger for ripening or as a response to the increase in sugars that occurs at this time. Net ABA accumulation doesn't occur until veraison, the decrease in ABA concentration in the first phase of berry development being due to berry expansion. The decrease in ABA that occurs later in development is likely to be due to a combination of catabolism and sequestration into the bound form. The genes crucial to ABA synthesis, 9-cis-epoxycarotenoid dioxygenase (NCED) and zeaxanthin epoxidase (ZEP), were expressed throughout berry development and no clear correlation was found between their levels and that of ABA. Laboratory studies have shown that isolated berries respond to the presence of sucrose through an increase in ABA biosynthesis pathway gene expression (NCED and ZEP). This resulted in de novo synthesis of ABA as inhibition of the carotenoid synthesis pathway by a phytoene desaturase inhibitor prevented ABA accumulation. Replicated field trials clearly showed that ABA treatments can be effective in significantly enhancing ripening when applied in at or near the end of the first period of berry expansion. Colour accumulation in the skins commenced earlier in ABA-treated fruit as did the increase in sugar levels. ABA treatment also advanced the timing of the second phase of berry expansion as it appeared to eliminate the lag phase of berry growth. Taken together these data demonstrate that ABA is likely to play some part in the control of berry ripening and can be used to advance the timing of ripening. Further investigation into the characteristics of ABA-treated fruit will be needed to investigate the compositional character of treated fruit and to gauge its suitability for winemaking. An ability to control the timing of ripening may provide considerable benefits to the wine industry in terms of wine style/quality and for winery scheduling. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1278807 / Thesis (Ph.D.) - The University of Adelaide, School of Agriculture, Food & Wine, 2007.

Hormones control plant development by coordinating changes in the expression of numerous genes at crucial times in a tissue and organ-specific manner. They have been implicated in controlling various aspects of grape berry development, in particular, the important process of ripening and are used in some crops to control growth and ripening. Abscisic acid (ABA), is associated in grapevine with the response to water stress but may also have a role in berry ripening. We have shown over three seasons that ABA levels in Cabernet Sauvignon berries increase dramatically at veraison, consistent with it being involved either as a trigger for ripening or as a response to the increase in sugars that occurs at this time. Net ABA accumulation doesn't occur until veraison, the decrease in ABA concentration in the first phase of berry development being due to berry expansion. The decrease in ABA that occurs later in development is likely to be due to a combination of catabolism and sequestration into the bound form. The genes crucial to ABA synthesis, 9-cis-epoxycarotenoid dioxygenase (NCED) and zeaxanthin epoxidase (ZEP), were expressed throughout berry development and no clear correlation was found between their levels and that of ABA. Laboratory studies have shown that isolated berries respond to the presence of sucrose through an increase in ABA biosynthesis pathway gene expression (NCED and ZEP). This resulted in de novo synthesis of ABA as inhibition of the carotenoid synthesis pathway by a phytoene desaturase inhibitor prevented ABA accumulation. Replicated field trials clearly showed that ABA treatments can be effective in significantly enhancing ripening when applied in at or near the end of the first period of berry expansion. Colour accumulation in the skins commenced earlier in ABA-treated fruit as did the increase in sugar levels. ABA treatment also advanced the timing of the second phase of berry expansion as it appeared to eliminate the lag phase of berry growth. Taken together these data demonstrate that ABA is likely to play some part in the control of berry ripening and can be used to advance the timing of ripening. Further investigation into the characteristics of ABA-treated fruit will be needed to investigate the compositional character of treated fruit and to gauge its suitability for winemaking. An ability to control the timing of ripening may provide considerable benefits to the wine industry in terms of wine style/quality and for winery scheduling. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1278807 / Thesis (Ph.D.) - The University of Adelaide, School of Agriculture, Food & Wine, 2007.

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La digestion anaérobie représente un élément clé dans la dynamique de développement durable contribuant à la valorisation verte des déchets organiques sous forme de biogaz et d'engrais. Dans le cadre de ce travail de thèse franco-libanais, nous cherchons à valoriser le marc de raisin, déchet majeur et principal sous-produit issu de la viniculture, par la digestion anaérobie, afin de générer de l’énergie dite verte sous forme de méthane. Dans un premier temps, le potentiel méthane du marc de raisin est démontré, validant notre biomasse végétale comme source potentielle d’énergie. Des informations détaillées sur les productions maximales de méthane à partir du marc entier, des pulpes et des pépins, séparément, sont obtenues en mode batch à 37 °C. La faisabilité technique du procédé est alors validée suite à une extrapolation au mode continu. De plus, des essais d’acclimatation du digesteur continu à la température moyenne de la vallée de la Bekaa (25 °C) permettent de simuler et d’adapter le système au milieu libanais. D’autre part, nous avons mené une caractérisation bio-physico-chimique de différents cépages de marcs de raisins en provenance de différentes régions viticoles. La diversité du contenu lignocellulosique et du potentiel méthanogène des substrats choisis a été mise en évidence. Une corrélation négative existe, en particulier, entre le potentiel méthane et les teneurs en lignine et en cellulose. Afin d’intensifier la production de méthane, le dimensionnement des digesteurs anaérobies en mode continu est optimisé en déterminant un optimum de fonctionnement pour une charge appliquée de 3,7 kg DCO m-3 j-1 et un temps de séjour de 20 jours. Enfin, nous évaluons les effets d’une variété de prétraitements (congélation, traitement alcalin, traitement acide, ultrasons et champs électriques pulsés) sur la production de méthane et sur la biodégradabilité des fractions. Le couplage du traitement alcalin à 10% NaOH avec la congélation à -20 °C s’avère être le meilleur procédé d’intensification. / Anaerobic digestion is considered to be a crucial part of a sustainable development strategy, contributing to the green valorization of organic waste as biogas and fertilizers. As part of this doctoral thesis, we explored the valorization of grape pomace, the major waste and main by-product of winemaking, by anaerobic digestion, to generate green energy in the form of methane. Firstly, the methane potential of grape pomace is demonstrated, validating our vegetal biomass as a potential source of energy. Detailed information on the maximum production of methane from whole pomace, pulps and seeds are obtained in batch mode at 37 °C. The technical feasibility of the process is then validated following an extrapolation to the continuous mode. Moreover, the acclimation of the continuous digester at the average temperature of the Beqaa valley (25 °C) allowed to simulate and adapt the current system to the Lebanese environment. On another note, we carried out a bio- physico-chemical characterization of different grape varieties from different wine-growing areas. The diversity of the lignocellulosic content and the methane potential of the selected substrates was highlighted. A negative correlation exists, in particular, between the methane potential and the lignin and cellulose fractions. In order to intensify methane production, we conducted an optimization of anaerobic digesters dimensioning in continuous mode by determining an optimum of operation for an applied load of 3.7 kg COD m-3 d-1 and a residence time of 20 days. Finally, we evaluated the effects of a variety of pretreatments (freezing, alkaline treatment, acid treatment, ultrasounds and pulsed electric fields) on the methane production and the biodegradability of lignocellulosic fractions. The coupling of the alkaline treatment using 10% NaOH with freezing at -20 °C seems to be the best intensification process.