Quarks charm são criados em estágios iniciais da colisão de íons pesados em processos de espalhamento duro. Portanto eles são sondas ideais para o Plasma de Quarks e Glúons (QGP), que é um estado da matéria em que os partons contidos em hadrons, em condições de alta temperatura (150 MeV) ou densidade (cerca de cinco vezes a densidade da matéria ordinária), passam para um estado livre de quarks e glúons. A fragmentação de quarks charm pode produzir mésons D. Jatos contendo um méson D como um de seus constituentes podem ser identificados como originados de uma fragmentação de quark pesado. Jatos contendo mésons D são valiosas ferramentas para caracterizar interações de quarks charm com o plasma. Jatos de charm podem fornecer informações para o estudo da perda de energia dependente da massa pela medida da modificação da produção de jatos de charm em colisões de núcleos de chumbo com respeito a colisões entre prótons em função do momento transversal dos jatos. Além disso, uma visão mais profunda pode ser obtida com a medida da distribuição da fração de momento, que é de particular interesse para investigar a possível influência do meio na fragmentação de quarks charm em jatos. Mésons D são reconstruídos através da análise de massa invariante de seu canal de decaimento hadrônico, rejeitando uma grande quantidade de fundo combinatório com seleções topológicas e explorando o tempo de vida relativamente longo de mésons D e as capacidades de identificação de partículas do detector ALICE. Jatos são reconstruídos com o algoritmo anti-kT usando candidatos a mésons D e partículas carregadas. A medida do espectro de momento transversal de jatos contendo mésons D em colisões de núcleos de chumbo a energias de sNN = 5.02 TeV será apresentada. Esses resultados levam a novas possibilidades de sondagem das propriedades do QGP quando comparados com medidas de referência. Por fim, os métodos desenvolvidos podem ser empregados no estudo das funções de fragmentação de quarks charm em colisões de íons pesados. / Charm quarks are created in the early stages of heavy-ion collisions in hard-scattering processes. Therefore, they are ideal probes of the Quark-Gluon Plasma (QGP), which is a state of matter where partons contained in hadrons, at high temperatures (150 MeV) or density (about five times the density of ordinary matter), change to a deconfined state of quarks and gluons. The fragmentation of charm quarks can produce D mesons. Jets containing a D meson as one of their constituents can be identified as originating from heavy-quark fragmentation. These jets are a valuable tool to characterize the charm interaction with the QGP. Charmed jets can provide information to the study the mass-dependent energy loss by the measurement of the modification of the charm-jet yield in Pb-Pb collisions with respect to pp collisions as a function of the jet transverse momentum. Moreover, a further insight can be obtained with the measurement of the momentum-fraction distribution, which is of particular interest to investigate the possible influence of the medium in the charm-jet fragmentation. D mesons are reconstructed through an invariant mass analysis of their hadronic decay channels, rejecting the large combinatorial background with topological selections exploiting the relatively large lifetime of D mesons and the particle identification capabilities of the ALICE detector. Jets are reconstructed with the anti-kT algorithm using D-meson candidates and charged tracks. The measurement of the transverse momentum spectrum of jets containing D mesons in Pb-Pb collisions at sNN = 5.02 TeV will be presented. These results lead to new possibilities of probing the QGP properties when compared to baseline measurements. Furthermore, the methods developed can be employed in the study of charm-quark fragmentation functions in heavy-ion collisions.

In dieser Arbeit werden einige zukünftige Aspekte der Higgs-Messungen ein Jahrzehnt nach seiner Entdeckung untersucht, wobei der Schwerpunkt auf dem Potenzial für zukünftige Läufe des Large Hadron Collider (LHC) liegt. Insbesondere sollen anspruchsvolle Kopplungen des Higgs, wie seine Selbstkopplung und die Wechselwirkung mit leichten Quarks, untersucht werden. Der erste Teil gibt einen Überblick über die Higgs-Physik innerhalb der effektiven Feldtheorie des Standardmodells (SMEFT). Der zweite Teil befasst sich mit der Single-Higgs-Produktion, beginnend mit einer Zweischleifenberechnung der Gluonenfusionskomponente von Zh, um deren theoretische Unsicherheiten zu reduzieren. Dann wird das Potenzial für die Einschränkung der trilinearen Higgs-Selbstkopplung aus Einzel-Higgs-Raten erneut untersucht, indem ebenso schwach eingeschränkte Vier-Schwer-Quark-Operatoren einbezogen werden, die bei der nächsthöheren Ordnung in die Einzel-Higgs-Raten eingehen. Diese Operatoren korrelieren in hohem Maße mit der trilinearen Selbstkopplung, was sich auf die Anpassungen auswirkt, die für diese Kopplung anhand von Einzel-Higgs-Daten vorgenommen wurden. Der dritte Teil konzentriert sich auf die Higgs-Paarproduktion, einen wesentlichen Prozess zur Messung der Higgs-Selbstkopplung, und setzt eine multivariate Analyse ein, um ihr Potenzial zur Untersuchung der leichten Yukawa-Kopplungen zu untersuchen; dadurch wird die Empfindlichkeit der Higgs-Paarproduktion für die leichten Quark-Yukawa-Wechselwirkungen erforscht. Schließlich werden im vierten Teil einige Modelle vorgestellt, die darauf abzielen, die jüngsten Flavour-Anomalien im Lichte einer globalen SMEFT-Bayesian-Analyse zu erklären, die Flavour- und elektroschwache Präzisionsmessungen kombiniert. / This thesis investigates some future aspects of Higgs measurements a decade after its discovery, focusing on the potential for future runs of the Large Hadron Collider (LHC). In particular, it aims to probe challenging couplings of the Higgs like its self-coupling and interaction with light quarks. The first part provides an overview of Higgs physics within the Standard Model Effective Field theory (SMEFT). The second part is about single-Higgs production, starting with a two-loop calculation of the gluon fusion component of Zh to reduce its theoretical uncertainties. Then, the potential for constraining the Higgs trilinear self-coupling from single Higgs rates is revisited; by including equally weaklyconstrained four-heavy-quark operators entering at the next-to-leading order in single Higgs rates. These operators highly correlate with the trilinear self-coupling, thus affecting the fits made on this coupling from single Higgs data. The third part focuses on the Higgs pair production, an essential process for measuring Higgs-self coupling, employing multivariate analysis to study its potential for probing light Yukawa couplings; thereby exploring the sensitivity of Higgs pair production for the light-quark Yukawa interactions. Finally, the fourth part showcases some models aiming to explain the recent flavour anomalies in the light of a global SMEFT Bayesian analysis combining flavour and electroweak precision measurements.

Thesis (PhD)--Stellenbosch University, 2004. / ENGLISH ABSTRACT: Yeasts produce a broad range of aroma-active volatile esters and higher alcohols during alcoholic fermentation. Some of these esters and higher alcohols are important for the fruity flavors and therefore the final quality of wine and other fermented beverages. Esters are produced and hydrolyzed by alcohol acetyltransferases and esterases, respectively. In yeast, ester-synthesizing activities are represented by two alcohol acetyltransferases encoded by the ATFI and ATF2 genes, and by an ethanol hexanoyl transferase encoded by the EHTI gene. Atfl p and Atf2p appear responsible for the production of ethyl acetate and isoamyl acetate, while Ehtl p synthesizes ethyl hexanoate from ethanol and hexanoyl-CoA. Although a fair amount of information is available regarding the ATF 1 gene, limited information is available on the remaining alcohol acetyltransferases. Only two genes that code for esterases have been identified in yeast, namely lAHI and TIPI. It has also been shown that the balance between alcohol acetyltransferases and esterases is important for the net rate of ester accumulation. Higher alcohols are synthesized from the a-keto-acids in the branched-chain amino acid metabolic pathway by decarboxylation and reduction. The transamination of the amino acid to the respective a-keto-acid is catalyzed by mitochondrial and cytosolic branched-chain amino acid transferases, which are encoded by the BATI and BAT2 genes, respectively. In recent years, a strong scientific and industrial interest in the metabolism of flavoractive compounds has emerged, but information regarding the roles of specific enzymes and the physiological relevance of their metabolism remains limited. The aim of this project was to investigate the physiological and metabolic consequences of changes in the expression levels of some of the key enzymes involved in aroma compound production. The consequences of these changes on the chemical composition and the fermentation bouquet of wines and distillates were also investigated. The first part of the section on the results in this dissertation reports on the role and relative importance of the Saccharomyces cerevisiae enzymes involved in ester metabolism, namely Atflp, Atf2p, Ehtlp, Iahlp and Tiplp. The corresponding genes were overexpressed in a laboratory strain of S. cerevisiae, BY4742, and in a widely used commercial wine yeast strain, VIN13. Table wine and base wines for distillation were prepared with these VIN13 transformed strains. The ester concentrations and aroma profiles of the wines and distillates were analyzed and compared. The data indicated that the overexpression of ATF 1 and ATF2 increased the concentrations of ethyl acetate, isoamyl acetate, 2-pheylethyl acetate and ethyl caproate, while the overexpression of JAHI resulted in a significant decrease in the concentrations of ethyl acetate, isoamyl acetate, hexyl acetate and 2-phenylethyl acetate. The overexpression of EHTI resulted in a marked increase in the concentrations of ethyl caproate, ethyl caprylate and ethyl caprate, while the overexpression of TJP1 did not decrease the concentrations of any of the esters. In most cases, there was a correlation between the increase in esters and the decrease in higher alcohols. The data suggest that yeast balances the amount of different esters produced through alcohol acetyltransferases and esterases, and that, in some cases, these enzymes appear to overlap in function and/or influence each other's activity. In the second part of the results section, the consequences of the deletion and the overexpression of two genes, BATl and BAT2, which encode transaminases that contribute to the metabolism of higher alcohols, were investigated. The genes were both disrupted in a S. cerevisiae BY4742, and overexpressed in both this laboratory strain and in the VIN13 wine yeast strain. The effects of these modifications on the general physiology of the corresponding yeast strains and on higher alcohol metabolism were assessed in a range of growth conditions, including aerobic and anaerobic growth conditions, in the presence of glucose or raffinose as sole carbon source and growth in the presence of various concentrations of amino acids. Table wine and base wines for distillation were prepared with the modified industrial strains and the concentrations of the higher alcohols and the aroma profiles of the wine and distillates were analyzed and compared. Batl deletion seemed to be lethal under the conditions that were created, and therefore only the bat2!:!.strain, together with the BATI and BAT2 overexpression strains, were investigated. These modifications did not appear to significantly affect the general physiology of the strains. The results obtained indicated that the overexpression of BATI increased the concentrations of isoamyl alcohol and isoamyl acetate, and, to a lesser extent, the concentrations of isobutanol and isobutyric acid. The overexpression of the BAT2 gene resulted in a substantial increase in the levels of isobutanol, isobutyric acid and propionic acid production, and a modest increase in the level of propanol and isovaleric acid. Interestingly, the overexpression of BAT2 led to a decrease in isoamyl alcohol and isoamyl acetate concentrations. Sensory analyses indicated that the wines and distillates produced with the strains in which the BATl and BAT2 genes were overexpressed had more fruity characteristics (peach and apricot aromas) than the wines produced by the wild-type strains. This study offers new prospects for the development of wine yeast starter strains with optimized ester and higher alcohol-producing capability that could assist winemakers in their efforts to consistently produce wine to definable specifications and styles and a predetermined flavor profile. / AFRIKAANSE OPSOMMING: Gedurende fermentasie produseer giste 'n wye verskeidenheid vlugtige aromatiese esters en hoër alkohole. Sommige van hierdie esters en hoër alkohole is belangrik vir die vrugtige geure en dra dus by tot die finale kwaliteit van wyn en ander gefermenteerde drankies. Esters word onderskeidelik deur alkoholasetieltranferases en esterases geproduseer en gehidroliseer. In giste word die ester-sintetiserende aktiwiteite deur twee alkoholasetieltransferases verteenwoordig wat deur die ATFI-en ATF2-gene, asook 'n etanolheksanoïeltransferase wat deur die EHTl-geen, gekodeer word. Dit blyk dat ATFlp en ATF2p verantwoordelik is vir die produksie van etielasetaat en isoamielasetaat, terwyl Ehtl p-etielheksanoaat vanaf etanol en heksanoïel-CoA sintetiseer. Alhoewel daar 'n redelike hoeveelheid inligting t.o.v die ATF I-geen beskikbaar is, is daar weinig inligting oor die res van die aloholasetieltransferases. Slegs twee gene wat vir esterases kodeer, is in gis geïdentifiseer, naamlik IAHI en TIPI. Daar is ook bewys dat 'n balans tussen die alkoholasetieltransferases en esterases baie belangrik is vir die netto-tempo van ester-akkumulasie. Hoër alkohole word gesintetiseer vanaf a-keto sure in die vertakte-ketting aminosuur metaboliese pad deur dekarboksilasie en reduksie. Die transaminasie van die aminosuur na die onderkeidelike a-ketosuur word deur vertakte-ketting aminosuur transferases, geleë in die mitochondrion en sitosol, en gekodeer deur BATl- en BAT2-gene, gekataliseer. In die laaste paar jare het daar 'n sterk wetenskaplike, asook industrïele, belangstelling in die metabolisme van aroma-aktiewe komponente te voorskyn gekom, maar inligting in verband met die rol van spesifieke ensieme en die fisiologiese belangrikheid van hul metabolisme is egter beperk. Die doel van hierdie projek was om die fisiologiese en metaboliese gevolge van veranderinge in die ekspressievlakke van sommige sleutelensieme betrokke by aromakomponent-produksie te ondersoek. Die gevolge van hierdie veranderinge op chemiese vlakke, asook hoe die fermentasie-aroma van die wyne en distillate beïnvloed word, is ook bestudeer. Die eerste gedeelte van die resultate rapporteer oor die rol en relatiewe belangrikheid van die Saccharomyces cerevisiae-ensieme betrokke by estermetabolisme, naamlik Atfl p, Atf2p, Ehtlp, Iahlp en Tiplp. Die gene was ooruitgedruk in 'n laboratoriurnras van S. cerevisiae, BY4742, asook in 'n kommersïele wyngisras, VIN13. Tafelwyne en basiswyne vir distillasie is gemaak met die getransformeerde VIN13-rasse. Die esterkonsentrasies en aromaprofiele van die wyne en distillate is ontleed en vergelyk. Die data het gewys dat die ooruitdrukking van ATFI- en ATF2-gene 'n verhoging in etielasetaat, isoamielasetaat, 2-fenieletielasetaat en etielkaproaat veroorsaak het, terwyl ooruitdrukking van !AHI 'n betekenisvolle afname in etielasetaat-, isoamielasetaat-, heksielasetaat- en 2-fenieletielasetaat-konsentrasies veroorsaak het. Die ooruitdrukking van EHTI het 'n duidelike verhoging in etielkaproaat, etielkaprilaat en etielkapraat veroorsaak en die ooruitdrukking van TIPIhet geen van die esterkonsentrasies verander nie. In die meeste gevalle was daar nie 'n korrelasie tussen die toename in esters en afname in hoër alkohole nie. Die data stelook voor dat die gis 'n balans tussen die verskillende esters handhaaf deur middel van die alkoholasetieltrasferases en esterases, en in sommige gevalle blyk dit dat die ensieme dieselfde funksies het en/of mekaar se aktiwiteit beïnvloed. In die tweede gedeelte van die resultate is die oorsake van delesie en ooruitdrukking van twee gene, BAT1 en BAT2, wat kodeer vir transaminases wat tot hoër alkohol metabolisme bydra, bestudeer. Die gene is uitgeslaan in S. cerevisiae BY4742 en ooruitgedruk in BY4742 en in die wyngisras VIN13. Die effekte van hierdie modifikasies op die algemene fisiologie van die verskillende gisrasse en op hoëralkoholmetabolisme is onder 'n verskeidenheid kondisies bestudeer, naamlik aërobies en anaërobiese groeikondisies, in die teenwoordigheid van glukose of raffinose as die enigste koolstofbron, asook in die teenwoordigheid van 'n verskeidenheid konsentrasies aminosure. Tafelwyne en basiswyne vir distillasie is gemaak met die gemodifiseerde industrïele rasse en die konsentrasies van die hoër alkohole en aromaprofiele van die wyne en distillate is ontleed en vergelyk. Bat1-delesie was dodelik onder die kondisies, daarom is slegs die batlts-tes tesame met die BAT1 en BAT2 wat in die rasse ooruitgedruk is, bestudeer. Die modifikasies het nie 'n beduidende effek op die algemene fisiologie van die rasse getoon nie. Die data het wel getoon dat die ooruitdrukking van BAT1 'n verhoging in isoamielalkohol- en isoamielasetaatkonsentrasies, en tot 'n mindere mate isobutielalkohol- en isobottersuur-konsentrasies, veroorsaak het. Die ooruitdrukking van BAT2 het 'n beduidende toename in isobutanol-, isobottersuur- en propioonsuurkonsentrasies en 'n kleinere toename in propanol- en isovaleriaansuur veroorsaak. Die ooruitdrukking van BAT2 het ook gelei tot 'n afname in isoamielalkohol- en isoamielasetaatkonsentrasies. Sensoriese analises het getoon dat die wyne en distillate wat geproduseer is met die rasse waarin die BAT1 en BAT2 gene ooruitgedruk is meer vrugtige eienskappe (perske- en appelkoos-aromas) getoon het as die wyne wat deur die wildetipe rasse geproduseer is. Die studie lewer nuwe vooruitsigte vir die ontwikkeling van wyngiste met geoptimiseerde ester en hoër alkohol produserende eienskappe wat die wynmakers in staat kan stelom wyne te produseer met gedefinieerde spesifikasies en style en 'n voorafbepaalde aromaprofiel.

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: During wine fermentation, numerous grape must constituents serve as nutrients to wine yeast (Saccharomyces cerevisiae), which enable their growth and successful completion of alcoholic fermentation. Many of these nutritional factors, in particular nitrogen, also act as precursors for yeastderived flavour compounds such as higher alcohols, esters and volatile fatty acids. Yeast nitrogen metabolism thus plays a determining role in wine aroma and quality. Not only is the nitrogen source, concentration and supplementation timing important, but various environmental factors and the genetic constitution of the yeast strain used for fermentation will also contribute to fermentation outcomes. The main goal of this work was to explore the complex interactions between a number of contributing factors; namely nitrogen source, timing of addition, yeast strain and fermentation matrix. Broadly, this study assessed the impact of seven different nitrogen combinations, added either to the initial grape must or after the onset of fermentation, on fermentation performance and aroma compound production by nine commercial wine yeast strains. Fermentations were done in synthetic grape must, and validated for a subset of parameters in real grape must. The nitrogen treatments were designed according to the generally established order of preference of S. cerevisiae for individual amino acids as source of nitrogen under fermentative conditions, and the potential of certain amino acids to participate in metabolic pathways that produce specific aroma compounds. The results reveal that different nitrogen combinations can lead to unexpected aroma outcomes, depending strongly on the genetic background of individual yeast strains and the timing of nitrogen addition. Certain nitrogen treatments consistently resulted in significant increases or decreases in specific aroma compound concentrations in comparison to the treatment fermented on ammonium as only nitrogen source, for multiple yeast strains. These compounds were classified as nitrogen treatment dependent. Other aroma compounds were produced similarly for all nitrogen treatments and were designated as nitrogen treatment independent. The presence of specific amino acid groups (for example the branched-chain and aromatic amino acids) could be correlated to significantly altered production patterns of related (such as higher alcohols) or unrelated (diethyl succinate) aroma compounds relative to the other nitrogen treatments. Taken together, a number of interesting and novel hypotheses regarding the metabolic pathways involved could be derived from the data. Ultimately, this initial assessment of interactive effects during fermentation will contribute to practical guidelines for winemakers to allow matching grape must constituents (such as nutrients) with the intrinsic aroma production capabilities of specific yeast strains in order to modulate wine aroma, style and quality. / AFRIKAANSE OPSOMMING: Tydens wynfermentasie dien talle druiwemosbestanddele as voedingstowwe vir wyngis (Saccharomyces cerevisiae) wat hul groei bevorder en hul in staat stel om alkoholiese fermentasie suksesvol te voltooi. Baie van hierdie voedingstowwe, veral stikstof, dien ook as voorlopers vir geurkomponente afkomstig van gismetabolisme, soos hoër alkohole, esters en vlugtige vetsure. Die stikstofmetabolisme van gis speel dus ‘n bepalende rol in wynaroma en -kwaliteit. Nie net is die stikstofbron, konsentrasie en tydsberekening van stikstof toevoeging belangrik nie, maar verskeie omgewingsfaktore, asook die genetiese samestelling van die gisras aangewend vir fermentasie, sal bydra tot die fermentasie uitkomste. Die hoofdoel van hierdie werk was om die komplekse interaksies tussen ‘n aantal bydraende faktore te ondersoek; naamlik die stikstofbron, tyd van stikstof toevoeging, gisras en fermentasiematriks. Breedweg het hierdie studie die impak van sewe verskillende stikstofkombinasies, toegedien tot die druiwemos voor of na die aanvang van fermentasie, op die suksesvolle verloop van fermentasie en die produksie van aromakomponente deur nege kommersiële wyngisrasse bepaal. Fermentasies is in sintetiese druiwemos uitgevoer, en ‘n deelversameling van die fermentasies in regte druiwesap te herhaal. Die stikstofbehandelings is ontwerp in ooreenstemming met die algemeen vasgestelde voorkeurvolgorde van S. cerevisiae vir individuele aminosure as stikstofbron onder fermentatiewe kondisies, en die potensiaal van sekere aminosure om mee te doen in metaboliese paaie wat spesifieke aromaverbindings produseer. Die resultate toon dat verskillende stikstofkombinasies tot onverwagte aroma-uitkomste kan lei wat sterk afhanklik is van die genetiese agtergrond van individuele gisrasse en die tyd van stikstof byvoeging. Sekere stikstofbehandelings het konsekwent, vir veelvuldige gisrasse, tot beduidende toenames of afnames in die konsentrasies van spesifieke aromakomponente gelei in vergelyking met die behandeling wat ammonium as enigste stikstofbron bevat het. Hierdie verbindings is as stikstofbehandeling afhanklik geklassifiseer. Ander aromaverbindings is soortgelyk vir alle stikstofbehandelings geproduseer en is aangewys as stikstofbehandeling onafhanklik. Die teenwoordigheid van spesifieke aminosuurgroepe (byvoorbeeld die vertakte-ketting en aromatiese aminosure) kon gekorreleer word met beduidende veranderings in produksiepatrone van verwante (soos hoër alkohole) of onverwante (dietielsuksinaat) aromakomponente relatief tot die ander stikstofbehandelings. Alles inaggenome kon ‘n aantal interessante en nuwe hipoteses rakende die betrokke metabolise padweë van die data afgelei word. Uiteindelik sal hierdie aanvaklike bepaling van interaktiewe effekte tydens fermentasie bydra tot praktiese riglyne vir wynmakers, wat hulle in staat sal stel om druiwesapbestanddele (soos nutriënte) te strook met die intrinsieke aromaproduksie kapasiteite van spesifieke gisrasse, en sodoende wynaroma, styl en kwaliteit te moduleer. / Oenobrands and THRIP for funding this project

Thesis (MSc)--Stellenbosch University, 2003. / ENGLISH ABSTRACT: Spoilage, be it due to microbial actions, chemical reactions or both, poses a serious threat to the food and beverage industries. Not only can spoilage lead to great economic losses, but it can also cause industries to lose their competitive edge in the economic and consumer market. Considering all the modern technologies and the range of preservation techniques that are available, it is surprising that spoilage is still an economic problem. Wine spoilage due to unpalatable bitterness, and the role of lactic acid bacteria (LAB) in causing this bitterness, have received much attention over the years, but no definite understanding has yet emerged. The first objective of this study was to isolate, enumerate and identify the LAB from three red grape varieties, viz. Pinotage, Merlot and Cabernet Sauvignon. The LAB populations on the grapes of all three varieties ranged from 102 to 104 cfu/ml during the 2001 and 2002 harvest seasons. The Cabernet Sauvignon grapes had slightly higher numbers than the Pinotage and Merlot. The LAB population in the Cabernet Sauvignon, Pinotage and Merlot wines after completion of the alcoholic fermentation ranged from 102 to 105 cfu/ml, while during 2002 the numbers in wine undergoing malolactic fermentation (MLF) ranged from 104 to 108 cfu/ml. The isolated LAB were divided into the three metabolic groups, with 59% belonging to the facultatively heterofermentative group, 26% to the obligately heterofermentative group and 15% to the obligately homofermentative group. The isolates were identified by means of species-specific primers as Leuconostoc mesenteroides (4), Oenococcus oeni (28), Lactobacillus brevis (15), Lb. hilgardii (15), Lb. plantarum (98), Lb. pentosus (12), Lb. paraplantarum (3), Lb. paracasei (28), Pediococcus acidilactici (2) and Pediococcus spp. (35). The most predominant species isolated was Lb. plantarum, followed by Pediococcus spp. The results suggest that Pinotage carries a more diverse LAB population in comparison to Merlot and Cabernet Sauvignon. The second objective of this study was to determine the presence of the glycerol dehydratase gene in the LAB strains by using the G01 and G02 primers. Twenty-six strains tested positive, namely Lb. plantarum (15), Lb. pentosus (1), Lb. hilgardii (5), Lb. paracasei (2), Lb. brevis (2) and a Pediococcus spp. (1). Interestingly, 62% of these strains were isolated from Pinotage. The strains all had the ability to degrade glycerol by more than 90%, and no significant differences were observed between the species. The GO-possessing strains exhibited varying degrees of inhibition towards Gram-positive and Gram-negative bacteria, and the results suggest that this inhibition activity may be similar to that of reuterin, which is produced by Lb. reuteri. This study can form the foundation for unravelling the causes of bitterness in red wines. Combining the results of this study with analytical, sensory and molecular data may very well provide the industry with valuable tools with which to combat the occurrence of bitterness. / AFRIKAANSE OPSOMMING: Bederf as gevolg van mikrobiese aksies, chemiese reaksies of beide, hou 'n groot bedreiging vir die voedsel- en drankbedrywe in. Nie net kan bederf lei tot groot ekonomiese verliese nie, maar dit kan ook veroorsaak dat bedrywe hul kompeterende voordeel in die ekonomiese en verbruikersmarkte verloor. As die moderne tegnologie en die reeks preserveringstegnieke wat beskikbaar is, in ag geneem word, is dit verbasend dat bederf steeds 'n ekonomiese probleem is. Wynbederf as gevolg van oormatige bitterheid en die rol van melksuurbakterieë (MSB) in die ontwikkeling van hierdie bitterheid het oor die jare heen baie aandag geniet, maar geen definitiewe verklaring is nog daarvoor gevind nie. Die eerste doelwit van hierdie studie was om MSB vanaf drie rooidruifvariëteite, nl. Pinotage, Merlot en Cabernet Sauvignon, te isoleer, te kwantifiseer en te identifiseer. Die MSB-populasies op die druiwe van al drie variëteite het gedurende die 2001- en 2002-parsseisoene tussen 102 en 104 kvu/ml gevarieer. Die Cabernet Sauvignon-druiwe het effens hoër getalle as die Pinotage- en Merlot-druiwe gehad. Die MSB-populasies in die Cabernet Sauvignon-, Pinotage- en Merlot-wyne aan die einde van die alkoholiese fermentasie het tussen 102 en 1055 kvu/ml gevarieer. Gedurende 2002 het die MSB-getalle in die wyne waarin appelmelksuurgisting (AMG) aan die gang was tussen 104 en 108 kvu/ml gevarieer. Die geïsoleerde MSB was onderverdeel in die drie metaboliese groepe, met 59% wat behoort aan die fakultatiewe, heterofermentatiewe groep, 26% aan die obligate, heterofermentatiewe groep en 15% aan die obligate, homofermentatiewe groep. Die isolate is geïdentifiseer as Leuconostoc mesenteroides (4), Oenococcus oeni (28), Lactobacillus brevis (15), Lactobacillus hi/gardii (15, Lactobacillus p/antarum (98), Lactobacillus pentosus (12), Lactobacillus parap/antarum (3), Lactobacillus paracasei (28), Pediococcus acidi/actici (2) en Pediococcus spp. (35) deur middel van spes iespesifieke inleiers. Die mees algemeen geïsoleerde spesies was Lb. p/antarum, gevolg deur Pediococcus spp. Die resultate impliseer dat Pinotage 'n meer uiteenlopende MSB-populasie in vergelyking met Merlot en Cabernet Sauvignon dra. Die tweede doelwit van hierdie studie was om die teenwoordigheid van die gliseroldehidratase-geen in die MSB-isolate deur middel van die GD1- en GD2- inleiers te bepaal. Ses-en-twintig isolate was positief, nl. Lb. p/antarum (15), Lb. pentosus (1), Lb. hi/gard;; (5), Lb. paracasei (2), Lb. brevis (2) en 'n Pediococcus spp. (1). 'n Interessante resultaat was dat 62% van hierdie isolate vanaf Pinotage geïsoleer is. Die isolate was almal in staat om meer as 90% van die gliserol te gebruik en geen noemenswaardige verskille is tussen die isolate waargeneem nie. Die GD-bevattende isolate het verskillende grade van inhibisie teenoor Grampositiewe en Gram-negatiewe bakterieë getoon, en die resultate impliseer dat hierdie inhiberende aktiwiteit dieselfde is as dié van reuterin wat deur Lb. reuteri geproduseer word. Hierdie studie kan dus die basis vorm vir die ontrafeling van die oorsake van bitterheid in rooiwyne. Deur die resultate van hierdie studie met analitiese, sensoriese en molekulêre data te kombineer, kan die wynbedryf voorsien word van waardevolle metodes om die voorkoms van bitterheid mee te bekamp.

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Nitrogen composition of grape must is highly variable and impacts on the health of the fermenting yeast population as well as the formation of aroma and flavour compounds in wine. Insufficient yeast assimilable nitrogen (YAN), mostly consisting of amino acids and ammonium, can lead to stuck or sluggish fermentations as well as the formation of undesirable compounds such as H2S. Furthermore, it is well established that the total concentration of YAN and the specific amino acid composition have a significant impact on the final aroma and flavour of wines. However, the impact of individual amino acids and of specific amino acid compositions on fermentation kinetics and on the production of aroma and flavour impact compounds under winemaking conditions is not well understood. The first goal of this study was to evaluate the effect of single amino acids on growth kinetics and major volatile production of two industrial wine yeast strains under conditions resembling wine fermentations. To facilitate these fermentation conditions while also allowing for easy reproducibility and manipulation of the initial components, a synthetic grape media was utilized. Biomass formation, exponential growth rate, lag phase, and fermentation duration were utilized to evaluate the efficiency of single amino acids. The data show that previously observed trends in laboratory strains mostly apply to these conditions and strains. In general, the efficiency of amino acids to be used as nitrogen sources and the production of major volatiles due to their presence followed the same patterns for both industrial yeast strains. However, the production of the secondary metabolites butanol, propanol, acetic acid, and ethyl acetate were found to be produced in different final concentrations dependent upon the yeast strain. The branched-chained and aromatic amino acids (BCAAs) treatments were observed to have the most dramatic effects on major volatile production. Investigating the relationships between the initial concentration of the BCAAs and the final concentrations of major volatile compounds, it was found that the production of fusel alcohols and fusel acids due to the degradation of BCAAs by S. cerevisiae could be predicted from the initial concentration of BCAAs. While under simple nitrogen conditions the production of several other secondary metabolites such as butanol, propionic acid, valeric acid, decanoic acid and 2-phenylethyl acetate were found to be correlated to the initial concentration of BCAAs in the media. Future studies should focus on the validation of these trends in aroma production in real grape musts under various fermentation temperatures for a number of industrial wine yeast strains. / AFRIKAANSE OPSOMMING: Die stikstof samestelling van druiwemos is hoogs veranderlik en impakteer op die kerngesondheid van die fermenterende gis populasie asook die produksie van aroma- en geurverbindings in wyn. Onvoldoende assimileerbare stikstof (ook genoem “yeast assimilable nitrogen” (YAN)), wat meestal bestaan uit aminosure en ammonium, kan aanleiding gee tot steek- of slepende fermentasies, asook die vorming van ongewensde verbindings soos H2S. Dit is alombekend dat die totale konsentrasie van YAN en dan ook die spesifieke aminosuur samestelling ‘n noemenswaardige impak op die finale aroma en smaak van wyn het. Die invloed van individuele am inosure en spesifieke aminosuur samestellings op die fermentasie kinetika, asook die produksie van verbindings met ‘n impak op die wyn aroma en smaak, word egter nie deeglik verstaan nie. Die eerste doelwit van die studie was om twee industriële gisrasse te gebruik om die effek van enkel aminosure op die groei-kinetika en produksie van die vername vlugtige verbindings onder wynmaak toestande te bepaal. Kunsmatige, gedefinieerde druiwermosmedium is gebruik om wynmaak toestande te simuleer en ook herhaalbaarheid en manipulering van die aanvanklike samestelling van die medium te verseker. Die studie het vorige tendense wat opgemerk is in die evaluasie van laboratorium rasse onder soortgelyke toestande bevestig. Die doeltreffendheid waarmee aminosure oor die algemeen gebruik word as stikstofbron, asook die produksie van die vernaamste vlugtige verbindings wat gekoppel is aan hulle teenwoordigheid, het ‘n vergelykbare patroon vir beide rasse gevolg. Die sekondêre metaboliete butanol, propanol, asetaat en etiel-asetaat is egter wel in verskillende eindkonsentrasies geproduseer deur die verskillende gisrasse. Die vertakte-ketting en aromatiese aminosuur (“branched-chained and aromatic amino acids” (BCAAs)) behandelings het die mees dramatiese effek op die produksie van die vernaamste vlugtige komponente gehad. Ondersoek na die verwantskap tussen die aanvanklike konsentraies van die BCAAs en die finale konsentrasies van dié verbindings het aangedui dat die produksie van hoër alkohole en sure, as gevolg van die afbraak van BCAAs deur S. cerevisiae, met behulp van die aanvanklike konsentrasie van die BCAAs voorspel kon word. Terselfdertyd is gevind dat onder eenvoudige stikstoftoestande, verskeie ander sekondêre metaboliete soos butanol, propionaat, valeriaat, dekanoësuur en 2-fenieletielasetaat, gekorreleer kan word met die aanvanklike BCAAs in die media. Verdere studies moet poog om hierdie tendense ten opsigte van aromaproduksie te bevestig en wel deur gebruik te maak van ware druiwemos, verskeie fermentasietemperature, asook ’n verskeidenheid van wyngisrasse.

Thesis (MScAgric)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Wine is a product of the fermentation of grape juice. Alcoholic fermentation is mainly conducted by the yeast Saccharomyces cerevisiae which metabolises grape sugars to mainly ethanol, CO2 and glycerol. Aside from these primary fermentation compounds, the yeast also produces many secondary metabolic by-products that are important to wine quality and style. Malolactic fermentation (MLF) is a secondary fermentation that normally occurs after alcoholic fermentation. Lactic acid bacteria (LAB) are responsible for the conversion of malic acid to lactic acid and CO2 during MLF, which is important for wine deacidification and also contributes to microbial stability. Malolactic fermentation and LAB strains can also influence the aroma profile of wines. The main genera associated with this process are Oenococcus, Lactobacillus, Pediococcus and Leuconostoc. Oenococcus oeni is the main species associated with MLF because it is able to survive the harsh physiochemical environment of winemaking. Recently L. plantarum has also been introduced as a commercial MLF starter culture. Research has started to focus on the potential of wine yeast and LAB interactions or combinations to alter the wine aroma profile via the production and/or degradation of aroma compounds. The overriding goal of this study is to unravel the interactions between wine yeast and different LAB strains and their impact on wine aroma and flavour. The first aim was to assess LAB growth during co- and sequential inoculation strategies, the ability to complete MLF and the impact on the production of aroma compounds in combination with two different yeast strains in a medium containing full complement of nitrogen supplementation. Malolactic fermentation was successful in the different inoculation strategies and the bacterial combination (L. plantarum and O. oeni) completed MLF in the shortest time. The impact of the bacterial strains on the modification of aroma compounds was bigger in co- than sequential inoculation. A general increase in total esters (contributing to the fruity character of wines) especially ethyl lactate and ethyl acetate was observed. The production of esters, volatile fatty acids and higher alcohols proved to be dependent on either the yeast strain used and/or the LAB strains used. The second aim of the research was to assess the effect of NH4Cl (ammonium) and amino acids supplementation on yeast and LAB strains (both in co- and sequential inoculation strategies) and the impact on the aroma profile of the fermented must. Fermentations supplemented with ammonia as sole nitrogen source showed the highest total bacterial growth in terms of cell numbers. Malolactic fermentation was completed in the shortest time with O. oeni and the bacterial combination inoculums. The co-inoculated strategies in combination with amino acids supplementation showed the biggest impact on the aroma compound profiles of the different fermentation strategies and bacterial treatments. A general increase in total esters was observed for NH4Cl additions with ethyl lactate and ethyl acetate showing the highest concentrations. The concentration of esters, volatile fatty acids and higher alcohols were strongly influenced by the yeast and the single LAB strains used. The results generated from this study showed that the chemical composition of the fermentation medium and the selection of yeast and LAB strains are important because these factors have an influence on the aroma and flavour profiles of wines. / AFRIKAANSE OPSOMMING: Wyn is die produk van gefermenteerde druiwe. Die gis, Saccharomyces cerevisiae is verantwoordelik vir alkoholiese fermentasies waar druiwe suikers na hoofsaaklik etanol, CO2 en gliserol gemetaboliseer word. Die gis produseer ook sekondêre metaboliete wat ‘n belangrike bydrae lewer tot wynstyl en kwaliteit. Appelmelksuurgisting (AMG) is ‘n sekondêre fermentasie wat gewoonlik na alkoholiese fermentasie plaasvind. Melksuurbakterieë (MSB) speel ‘n sleutel rol in die omskakeling van appelsuur na melksuur en CO2 gedurende AMG. Hierdie fermentasie lei tot ‘n afname in die suurheidsgraad en verbeter die mikrobiese stabiliteit van die wyn. Appelmelksuurgisting en MSB rasse kan die aroma- en geurprofiel van wyne beïnvloed. Die belangrikste genera wat met AMG geassosieer word is Oenococcus, Lactobacillus, Pediococcus en Leuconostoc. Oenococcus oeni is die mees algemene ras wat vir AMG gebruik word omdat dit in uiterste wyn toestande kan oorleef. Mees onlangs is Lactobacillus plantarum as kommersiële aanvangskultuur vir AMG geïdentifiseer. Navorsing het onlangs meer begin fokus op gis en MSB interaksie of kombinasies as ‘n strategie om die aroma profiele van wyne te verander. Die hoofdoel van die studie is om die interaksie tussen wyngiste en verskillende MSB rasse en die effek op die aroma profile van wyne te bestudeer. Die eerste doelwit was om die impak van die twee giste op die groei en AMG vermoeë van MSB gedurende ko- en sekwensiële inokulasie praktyke en die impak op die produksie van aroma komponente, in ‘n medium wat die volledige stikstof aanvullings bevat, te bestudeer. Appelmelksuurgisting was suksesvol in die verskillende inokulasie praktyke en die bakteriese kombinasie (L. plantarum en O. oeni) het AMG in die kortste tyd voltooi. Die impak van die bakteriese rasse op die modifikasie van die aroma komponente was groter met ko- as sekwensiële inokulasies. Daar was ‘n toename in die totale esterkonsentrasies veral in etiellaktaat en etielasetaat. Die produksie van esters, vlugtige vetsure en hoër alkohole word beïnvloed deur die gisras en MSB rasse wat gebruik word. Die tweede doelwit was om die impak van NH4Cl (ammonium) en aminosure aanvullings op die gis- en MSB rasse gedurende ko- en sekwensiële inokulasie strategieë te bepaal. Melksuurbakterieë se groei was beter met die ammonium aanvulling. Appelmelksuurgisting was in die kortste tyd voltooi met O. oeni en die bakteriese kombinasie. Die ko-inokulasie praktyke in kombinasie met die kompleks aminosure aanvulling het die grootste impak op die produksie van aroma komponente gehad. Daar was weereens ‘n toename in die totale esterkonsentrasies vir die NH4Cl aanvulling, veral in etiellaktaat en etielasetaat. Die gis en MSB rasse speel ‘n rol by die produksie en konsentrasies van esters, vlugtige vetsure en hoër alkohole. Die resultate van hierdie studie bewys dat die chemiese samestelling van die fermentasie medium, die seleksie van gis- en MSB rasse is belangrik omdat hierdie faktore die aroma en geur profiele van wyne beïnvloed.

A central goal of flavour physics is a precise determination of the elements of the CKM matrix, which quantifies the strength of charged-current weak interactions between quarks. Of particular interest is the angle γ in the 'b-d' unitarity triangle parameterisation of the CKM matrix. One of the most promising methods to determine γ directly is to measure CP violation in interfering B±->DK± decays, where D indicates a coherent superposition of D0 and D0bar, both of which decay to the same final state. When using this method it is essential to determine the hadronic decay parameters of the D precisely in order to reduce the systematic uncertainties on the measurement of γ. One such parameter is the strong-phase difference between D0 and D0bar decays, which must be accurately known across the entire kinematic phase space. In this thesis we present measurements related to the determination of γ at both the CLEO-c experiment at Cornell University and the LHCb experiment at CERN. Firstly, we describe a model-independent determination of the D->KsKK strong-phase difference using 818pb-1 of quantum-correlated D0-D0bar data collected by CLEO-c at the ψ(3770) resonance. We reconstruct D->KsKK decays tagged with a variety of final states. By studying these decays we determine the weighted cosine and sine of the strong-phase difference in bins across the Dalitz plane. We run simulations to estimate the impact of these measurements on a determination of γ using B±->D(KsKK)K± decays. The resulting uncertainty on γ due to the CLEO-c inputs is between 3.2° and 3.9°, depending on how the Dalitz plane is binned. Furthermore, we present a model-independent measurement of the CP content of the decay D0->KsKK in the kinematic region of the φ->KK resonance. The fraction of CP-odd events in this region is 0.76 or higher at the 90% C.L. We also present an analysis of data recorded by LHCb in 2010, corresponding to an integrated luminosity of 36.5pb-1. We reconstruct the decays B±->D(Kπ)h± and B±->D(KK)h±, where h± indicates either K± or π±. Although there are not enough events in this dataset to measure γ, we are able to measure other observables related to CP violation in the B±->Dh± system. We measure B(DK,Fav)/B(Dπ,Fav), the ratio of the branching fraction of B±->D(Kπ)K± to that of B±->D(Kπ)π±, to be 0.066 ± 0.005 ± 0.004, and B(DK,CP)/B(Dπ,CP), the ratio of the branching fraction of B±->D(KK)K± to that of B±->D(KK)π±, to be 0.093 ± 0.019 ± 0.005. We determine several CP asymmetries: A(CP+,DK), the CP asymmetry in B±->D(KK)K± decays, is measured as 0.06 ± 0.17 ± 0.07; A(CP+,Dπ), the CP asymmetry in B±->D(KK)π± decays, is found to be 0.009 ± 0.042 ± 0.011; and A(Fav,DK), the CP asymmetry in B±->D(Kπ)K± decays, is measured as -0.109 ± 0.085 ± 0.019. Finally we calculate R(CP+), the ratio of the branching fraction of B±->D(KK)K± to that of B±->D(Kπ)K±, to be 1.41 ± 0.31 ± 0.11. These results indicate that LHCb is in a strong position to make a world-leading measurement of γ with a larger data sample.

Two analyses are performed using data collected by the LHCb experiment during 2011. Both consider decays of charged B mesons reconstructed in the π±μ+μ− final state. Decays involving dimuons provide an experimentally clean signature, even in the high-background environment of the √s = 7 TeV proton-proton collisions at the LHC. The first analysis measures the CP asymmetry of B±→Ψπ± decays using 0.37 fb-1 of data, where the dimuon decays of two resonances are considered, J/ψ→μ+μ− and ψ(2S)→μ+μ−. The branching fraction is measured relative to the Cabibbo favoured B±→ΨK± mode. The second analysis uses 1 fb-1 of data to make the first observation of the non-resonant B±→π±μ+μ− decay. The branching fraction is measured relative to that of B±→K±μ+μ−, and measurements of the CP asymmetry and the ratio of CKM matrix elements Vtd/Vts are obtained. The branching fractions of the decays of interest are found to be B(B±→J/ψ π±) = (3.88 ± 0.11 ± 0.15) x 10-5, B(B±→ψ(2S) π±) = (2.52 ± 0.26 ± 0.15) x 10-5 and B(B±→π±μ+μ−) = (2.48 + 0.57 −0.52 ± 0.17) x 10-8, where the first uncertainty is related to the statistical size of the sample and the second quantifies systematic effects. The measured CP asymmetries in these modes are A CP (J/ψ π) = 0.005 ± 0.027 ± 0.011, A CP (ψ(2S) π) = 0.048 ± 0.090 ± 0.011 and A CP (μμπ) = -0.045 ± 0.220 ± 0.066, with no evidence of direct CP violation seen. The ratio of matrix elements is measured as Vtd/Vts = 0.274 + 0.031 − 0.028 ± 0.008, which is in agreement with previous results.

The angle γ, with an uncertainty of approximately 10° is the least well constrained angle of the unitary triangle. Better experimental constraints on this parameter are required in order to provide a consistency check on the standard model description of CP violation. A promising strategy for measuring γ involves exploiting interference effects present in B^± → DK^± decays where the D subsequently decays to a three or four body final state. The three body decay D → K_S ⁰p⁺p^- and the four body decay D⁰ → K⁺K^-p⁺p^- are suitable candidates for making such a measurement. However independent knowledge of the decay structure of these decays is required. The impact of the model, used to describe the p⁺p^- S wave, in the D⁰ → K⁺K^-p⁺p^- decay, on the uncertainty in the measurement of γ is estimated via a simulation study. It is determined that the uncertainty on a gamma measurement would be compromised by this model uncertainty within one year of LHCb data running. The four body decay D⁰ → K⁺K^-p⁺p^- also provides a candidate for making a γ measurement. This decay is expected to display a rich resonant structure. An understanding of this decay may also provide an insight into low energy QCD in addition to allowing a search for CP violation. Only one previous amplitude analysis has been performed on this decay. Using data collected at the CLEO-II.V, CLEO-III and CLEO-c experiments an amplitude model is developed for the D⁰ → K⁺K^-p⁺p^- decay. This model is qualitatively similar to that produced in the previous analysis although the model presented in this thesis considers higher orbital angular momentum states and distinguishes between conjugate states that the previous model did not. A search for CP violation is also carried out using the D⁰ → K⁺K^-p⁺p^- decay data. A positive confirmation of CP violation at the level of sensitivity provided by this decay data would provide evidence for a level of CP violation which could not be accounted for within the standard model. No significant evidence for CP violation is observed in this decay. A toy MC study was carried out in order to determine the sensitivity to γ which may be achieved using this decay. In this study, sets of 1000 B⁺ and B^- events are generated and the decay model developed for the D → K⁺K^-p⁺p^- decay is used to describe the D decay. The sensitivity to γ determined in this study is 11°.