No description available.

Multiple biomarkers of oxidative stress have been measured and used in human medicine to diagnose and monitor airway disease. The purpose of the study was to determine if similar relationships existed between inflammatory and oxidative stress biomarkers in exhaled breath condensate (EBC), bronchoalveolar lavage fluid (BALF), red blood cells, white blood cells, and plasma; and cytokine expression in airway inflammatory cells and mucosal biopsies of RAO-affected horses and their controls. Sixteen horses in pairs were used: 8 non-RAO-affected (controls) and 8 RAO-affected horses. Samples from all horses were collected at remission (S1), during environmental challenge (S2) and at recovery (S3). RAO-affected horses had significant alterations in cellular glutathione peroxidase (cGPx) activity, ascorbic acid and pH in a number of biological samples. Concentrations of 8-isoprostanes, isofurans, amino acids and mRNA expression of interleukin 4 (IL4), gamma interferon (INFγ), inducible nitric oxide synthase (iNOS), extracellular glutathione peroxidase (GPx-3), and cytosolic superoxide dismutase (SOD-1) were not significantly different or were at the limits of detection. Conductivity was measured and assessed as a potential correctional factor for respiratory fluid dilution. The alterations in biomarker concentrations demonstrate that oxidative stress is an important component of airway inflammation in RAO-affected horses. Further research is warranted in the use of biomarkers and the effects of dietary interventions. / Master of Science

No description available.

<p>The Muoio lab studies the interplay between lipid whole body energy balance,</p><p>mitochondrial function and insulin action in skeletal muscle. Data from our lab suggests that lipid-induced insulin resistance in skeletal muscle may stem from excessive incomplete oxidation of fatty acids, which occurs when high rates of &beta;-­oxidation exceed TCA cycle flux (Koves et al., 2005; Koves et al., 2008). Most notably, we have shown that mice with a genetically engineered decrease in mitochondrial uptake and oxidation of fatty acids are protected against diet-­induced insulin resistance (Koves et al., 2008). This</p><p>suggests that an excessive and/or inappropriate metabolic burden on muscle</p><p>mitochondria provokes insulin resistance. Our working model predicts that: 1) high rates of incomplete &beta;-oxidation reflect a state of &rdquo;mitochondrial stress,&rdquo; and 2) that energy-overloaded mitochondria generate a yet unidentified signal that mediates insulin</p><p>resistance. One possibility is that this putative mitochondrial-derived signal stems from redox imbalance and disruptions in redox sensitive signaling cascades. Therefore, we are interested in identifying molecules that link redox balance, mitochondrial function and insulin action in skeletal muscle. The work described herein identifies thioredoxin-interacting protein (TXNIP) as an attractive candidate that regulates both glucose homeostasis and mitochondrial fuel selection.</p><p>TXNIP is a redox sensitive, &alpha;-arrestin protein that has been implicated as a negative regulator of glucose control. Mounting evidence suggested that TXNIP might play a key role in regulating mitochondrial function; however, the molecular nature of this relationship was poorly defined. Previous studies in TXNIP knockout mice reported that deficiency of this protein compromises oxidative metabolism, increases glycolytic activity and promotes production of reactive oxygen species (ROS), while also affording protection against insulin resistance. Therefore, we hypothesized that TXNIP might serve as a nutrient sensor that couples cellular redox status to the adjustments in mitochondrial function. We tested this hypothesis by exploiting loss of function models to evaluate the effects of TXNIP deficiency on mitochondrial metabolism and respiratory function.</p><p>In chapter 3, we comprehensively evaluated oxidative metabolism, substrate</p><p>selection, respiratory kinetics and redox balance in mice with total body and skeletal muscle-­specific TXNIP deficiency. Targeted metabolomics, comprehensive bioenergetics analysis, whole-body respirometry and conventional biochemistry showed that TXNIP deficiency results in reduced exercise tolerance with marked impairments in skeletal muscle oxidative metabolism. The deficits in substrate oxidation were not secondary to decreased mitochondrial mass or increased H₂O₂ emitting potential from the electron transport chain. Instead, the activities of several mitochondrial dehydrogenases involved in branched-chain amino acid and ketone catabolism, the tricarboxylic acid (TCA) cycle and fatty acid &beta;-oxidation were significantly diminished in TXNIP null muscles. These deficits in mitochondrial enzyme activities were accompanied by decreased protein abundance without changes in mRNA expression. Taken together, these results suggest that in skeletal muscle TXNIP plays an essential role in maintaining protein synthesis and/or stability of a subset of mitochondrial dehydrogenase enzymes that permit muscle use of alternate fuels under conditions of glucose deprivation.</p><p>Based on these conclusions, we questioned whether additional regulatory</p><p>mechanisms could contribute to the reduced oxidative metabolism in the absence ofTXNIP. Several metabolic enzymes of the TCA cycle have been shown to be redox-sensitive protein targets regulated by the thioredoxin (TRX1/TRX2) and glutathione (GSH) redox-mediated circuits. TXNIP has been shown to respond to oxidative stress by shuttling to the mitochondria where it binds to TRX2 and/or other proteins, thus affecting downstream signaling pathways, such as the apoptotic cascade. Therefore, we speculated whether there was a role for redox imbalance in mediating the mitochondrial phenotype of the TXNIP knockout (TKO) mice. In chapter 4, we present preliminary evidence that increased glucose uptake promotes non-mitochondrial ROS production, causing a shift in redox balance, decreased GSH/GSSG, and S-glutathionylation of &alpha;-­ketoglutarate dehydrogenase (&alpha-KGD). This post-translational modification protects the protein from permanent oxidative damage, but at the cost of reversible loss of activity and subsequent disruption of TCA cycle flux that contributes, in part, to the diminished oxidative metabolism observed in the TXNIP deficient mice.</p><p>In aggregate, this work sheds new light onto the physiological role of TXNIP in</p><p>skeletal muscle as it pertains to substrate metabolism and fuel switching in response to nutrient availability. This work has important implications for metabolic diseases such as obesity and type 2 diabetes, which are characterized by marked disruptions in fuel selection.</p> / Dissertation

Correct functioning of the brain relies upon the precise connectivity between the billions of neurons that make up this crucial organ. Aberrations in the formation of these elaborate neural networks lead to neurodegenerative and neuropsychiatric disorders. A synapse-spanning molecular triad, involving members of the Neurexin, Cbln and ionotropic glutamate receptor delta families of proteins, is crucial for the accurate formation and proper function of synapses in the cerebellum. This trans-synaptic complex has been implicated in the molecular mechanisms behind motor control and motor learning, and furthermore individual members have been linked to diseases such as Alzheimer’s, autism spectrum disorders and schizophrenia. The major findings presented in this thesis include: crystal structures of the amino-terminal domains (ATD) of the two members of the ionotropic glutamate receptor delta (iGluR-Delta) family, functional characterisation of the effects of disrupting the ATD interface in one member of the iGluR-Delta family, a crystal structure of the C1q domain of Cbln1, biophysical analysis of the molecular interactions within the Neurexin-Cbln1-GluD2 trans-synaptic complex, as well as evidence for the domain arrangement of the ecto-domain of the iGluR-Delta proteins. Together, these data enhance our knowledge of the molecular details of this macro-molecular complex and provide evidence to support models for the mechanisms of their involvement in synapse formation and function, thereby making a contribution to the vast and medically relevant field of molecular neurobiology.

Thesis (PhD (Viticulture and Oenlogy))--University of Stellenbosch, 2008. / Includes bibliography and list of tables and figures. / ENGLISH ABSTRACT: Over the last decade research has shown the importance of small antimicrobial peptides in the innate immunity of plants. These peptides do not only play a critical role in the multilayered defense systems of plants, but have proven valuable in the engineering of disease resistant food crops towards the ultimate aim of reducing the dependency on chemical fungicides. As the lists of isolated and characterized peptides grew, it became clear that other biological activities, in addition to the antimicrobial capacity, could be linked to some of these peptides; these alternative activities could have important applications in the field of medicine. This has made the defensin encoding genes prime targets for the agricultural and medical biotechnology sectors. To this end we set out to evaluate South African flora for the presence of plant defensin sequences and to isolate plant defensin genes that might be useful in biotechnology applications. Moreover, by isolating and characterizing these novel peptides, also in an in planta environment and in interaction with fungal pathogens, important knowledge will be gained of the biological role and importance of the peptides in the plant body. The plant host targets were South Africa Brassicaceae species including indigenous species, as well as Vitis vinifera, as the most important fruit crop in the world and since no defensins have been isolated from this economically important crop plant. The Brassicaceae family has been shown to be abundant in defensin peptides and several of the best characterized peptides with potent activity have been isolated from this family. Based on initial activity screens conducted on selected South African Brassicaceae spp. we concluded that these spp. contain promising antifungal peptide activities, warranting further efforts to isolate the genes and encoding peptides and to characterize them further. The preliminary activity screens used a peptide-enrichment isolation strategy that favored the isolation of basic, heat-stable peptides; these properties are characteristic features of plant antimicrobial peptides. These peptide fractions showed strong antifungal activities against the test organisms. A PCR-amplification strategy was subsequently designed and implemented, leading to the isolation of 14 novel defensin peptide encoding genes from four South African Brassicaceae spp., including the indigenous South African species Heliophila coronopifolia. Amino acid sequence analysis of these peptides revealed that they are diverse in amino acid composition and share only 42% homology at amino acid level. This divergence in amino acid composition is important for the identification of new biological activities within closely related plant defensins. Single amino acid changes have been contributed with the divergent biological activities observed in closely related plant defensin peptides. Phylogenetic analysis conducted on the deduced amino acid sequences revealed that all the new defensins share a close relationship to other Brassicaceae members of the plant defensin superfamily and was furthest removed from the defensins isolated from the families Solanaceae and Poaceae. Classification analysis of these peptides showed that they belong to subgroup A3 of the defensin superfamily. A putative defensin sequence was also isolated from V. vinifera cultivar, Pinotage, and termed Vv-AMP1. Genetic characterization showed that only a single gene copy of this peptide is present within the V. vinifera genome, situated on chromosome 1. Genetic characterization of this peptide encoding gene within the Vitis genus showed that this gene has stayed conserved throughout the divergent evolution of the Vitis genus. Expression studies of Vv-AMP1 revealed that this gene is expressed in a tissue specific and developmentally regulated manner, being only expressed in grape berries and only at the onset of vèraison. Induction of Vv-AMP1 in grapevine leaf material could never be achieved through the external application of hormones, osmotic stress, wounding, or pathogen infection by Botrytis cinerea. Deduced amino acid analysis showed that Vv-AMP1 encoded for a 77 amino acid peptide consisting of a 30 amino acid signal peptide and a 47 amino acid mature peptide, with putative antifungal activity. The Vv-AMP1 peptide grouped with the subclass B type defensins, which have been documented to have both antifungal and antibacterial activities. The Vv-AMP1 signal peptide directed the green fluorescent protein (GFP) reporter gene to the apoplastic regions in cells with high levels of accumulation in the vascular tissue and the guard cells of the stomata. Recombinant Vv-AMP1 peptide was successfully purified from a bacterial host and shown to have a size of 5.495 kDa. Recombinant Vv-AMP1 showed strong antifungal activity at low concentrations against a broad spectrum of fungal pathogens, which included Verticillium dahliae (IC50 of 1.8 μg mL-1) and the necrotrophic pathogen Botrytis cinerea (IC50 of 12-13 μg mL-1). Antifungal activity of Vv-AMP1 did not induce morphological changes in fungal hyphae, but its activity was associated with induced membrane permeabilization in treated hyphae. Vv-AMP1 was successfully introduced into Nicotiana tabacum as confirmed by Southern blot analysis and 20 individual lines were generated. Genetic characterization confirmed the integration and expression of the gene in the heterologous tobacco environment. The peptide was under control of its native signal sequence which has been shown to direct its product to the apoplastic regions of cells. The transgenic lines were analyzed to determine the presence and activity of the grapevine defensin peptide. Western blot analyses of partially purified plant extracts detected a signal of the expected size in both the untransformed control and the transgenic lines. Comprehensive analysis of EST databases identified three highly homologous sequences from tobacco that probably caused the background signal in the control. These crude protein extracts were able to inhibit the growth of V. dahliae in vitro when tested in a microtiter plate assay, but the inhibition could not be conclusively linked to the presence of the transgenic peptide, since non-expressing transgenic lines, included as controls, also showed inhibition. Similar results were obtained with infection studies, clearly showing that despite successful integration and expression of the transgene, the peptides was either not functional in the heterologous environment, or perhaps unstable under the particular regulatory conditions. This peptide belongs to a subclass of peptides known for associated activities that might activate tight control by plant hosts if threshold levels are reached. These aspects need further investigation, specifically since it is in stark contrast to previous results obtained with defensins from a different subclass. This study has also yielded significant other related resources that would be instrumental for further possible biotechnology exploitation of some of the novel peptides, but also to provide genetic constructs and plant material that would be invaluable to address fundamentally important questions such as the regulation and mode of action of defensin peptides, specifically in interaction with pathogen hosts. The novel peptides have been transformed to various hosts, including grapevine and these transgenic populations are available to facilitate the next rounds of research into this extremely promising group of antifungal peptides. / AFRIKAANSE OPSOMMING: In die laaste dekade het navorsing die belangrike rol van klein antimikrobiese peptiede in plantweerstandsmeganismes beklemtoon. Hierdie peptiede speel nie alleenlik 'n belangrike rol in die komplekse lae van plantweerstandstelsels nie, maar het ook hulle ekonomiese potensiaal getoon in die manipulering van siekteweerstandbiedendheid in voedselgewasse met die oorkoepelende doel om landbougewasse minder afhanklik van chemiese spuitstowwe te maak. Soos wat die hoeveelheid geïsoleerde en gekarakteriseerde peptiede toeneem, het dit duidelik geword dat ander biologiese aktiwiteite, bykomend tot die antimikrobiese kapasiteit, met sommige van dié peptiede verbind kan word; hierdie alternatiewe aktiwiteite het belangrike toepassing in veral die mediese veld. Dit het die defensin-koderende gene kernteikens vir die landbou- en mediese biotegnologiesektore gemaak. In die studie is daar begin om die Suid-Afrikaanse blommeryk te evalueer vir die teenwoordigheid van plantdefensingene en om dié gene te isoleer wat van ekonomiese belang vir die biotegnologiebedryf kan wees. Deur die in vitro- én in planta karakterisering van die unieke plantdefensinpeptiede word daar gemik daarna om belangrike inligting in te win oor die biologiese rol van die peptiede binne die plantligggaam. Die plantgashere wat geteiken is sluit in die Suid-Afrikaanse Brassicaceae-spesies, insluitende inheemse spesies, asook Vitis vinifera, wat as die belangrikste vrugtegewas ter wêreld beskou word. Die Brassicaceae-familie is welbekend daarvoor dat dit 'n ryk bron van plantdefensinpeptiede is en verskeie van die bes gekarakteriseerde antifungiese defensinpeptiede is van dié familie afkomstig. Aanvanklike aktiwiteitstoetse het getoon dat die Suid-Afrikaanse Brassicaceae-spesies belowende antifungiese aktiwiteit toon, wat die verdere isolering en karakterisering van dié gene en hul peptiedprodukte regverdig. Die aanvanklike aktiwiteitstoetse het 'n selektiewe peptiedverrykingstrategie gevolg wat die isolering van basiese, hittestabiele peptiede bevoordeel het; hierdie eienskappe is baie kenmerkend van plant-antimikrobiese peptiede. Die peptiedfraksies wat met hierdie metode geïsoleer is, het sterk antifungiese aktiwiteit teen die toetsorganismes getoon. Die resultate het gelei tot die ontwikkeling en toepassing van 'n polimerasekettingreaksie-strategie, wat daartoe gelei het dat 14 nuwe defensingene van vier Suid-Afrikaanse Brassicaceae-genera, insluitend die inheemse spesie Heliophila coronopifolia, geïsoleer kon word. Afgeleide aminosuurvolgorde-analises van die nuwe defensinpeptiede het gewys dat hulle slegs 42% homologie het. Hierdie diversiteit in aminosuurvolgorde is belangrik vir die identifisering van nuwe biologiese aktiwitiete binne die groep van verwante peptiede. Navorsing het verder getoon dat enkel-aminosuurverskille bydra tot die diverse spektrum van biologiese aktiwiteite binne 'n groep van verwante defensinpeptiede. Filogenetiese analise van die aminosuurvolgordes het getoon dat al die nuwe defensinpeptiede 'n sterk verwantskap met plantdefensinpeptiede, wat van ander Brassicaceae-spesies geïsoleer is, toon. Daarteenoor het dit die kleinste verwantskap getoon met plantdefensinpeptiede wat van die Solanaceae- en Poaceae-families geïsoleer is. Klassifikasiestudies het bewys dat die nuwe peptiede saam met subgroep A3 van die plantdefensin-superfamilie groepeer. 'n Moontlike plantdefensingeen, genaamd Vv-AMP1, is ook van die V vinifera-kultivar, Pinotage, geïsoleer. Genetiese karakterisering het aangedui dat slegs 'n enkele kopie van die geen in die V. vinifera-genoom teenwoordig en op chromosoom 1 geleë is. Genetiese karakterisering van Vv-AMP1 binne die Vitus-genus het gewys dat die geen binne die genus evolusionêr gekonserveerd is. Uitdrukkingstudies van Vv-AMP1 het verder bewys dat die geen uitgedruk word op 'n weefselspesifieke, ontwikkelingsgekoppelde wyse, naamlik slegs in druiwekorrels en slegs tydens rypwording. Vv-AMP1-uitdrukking kon nooit geïnduseer word in wingerdblare deur die uitwendige toediening van hormone, osmotiese stres, wonding of patogeeninfeksie deur Botrtys cinerea nie. Ontleding van die afgeleide aminosuurvolgorde het gewys dat Vv-AMP1 kodeer vir 'n 77-aminosuurpeptied, wat uit 'n 30-aminosuurseinpeptied en 'n 47-aminosuur-aktiewe peptied met voorspelde antifungiese aktiwiteit bestaan. Die Vv-AMP1-peptied is gegroepeer met subgroep B van die plantdefensin-superfamilie, 'n subgroep wat vir beide antifungiese en antibakteriese aktiwiteit gedokumenteer is. Die Vv-AMP1-seinpeptied het die groen fluoressensie-indikatorproteïen (GFP) na die apoplastiese areas van die plantselle gelei, met hoë vlakke van lokalisering in die vaatbundelweefsel en sluitselle van die huidmondjies. Die rekombinante Vv-AMP1-peptied is suksesvol geproduseer en uit 'n bakteriese produksieras gesuiwer, en het 'n molekulêre massa van 5.495 kDa gehad. Die gesuiwerde peptide het by lae konsentrasies 'n sterk aktiwiteit getoon teen 'n breë spektrum van fungiese patogene, wat Verticllium dahliae (IC50 van 1.8 μg mL-1) en die nekrotrofiese patogeen, B. cinerea (IC50 van 12-13 μg mL-1), ingesluit het. Vv-AMP1-aktiwiteit het geen ooglopende morfologiese veranderinge in die fungi-hifes veroorsaak nie, maar hulle aktiwiteit is verbind met 'n verhoogde membraandeurdringbaarheid in behandelde fungi-hifes. Suksesvolle intergrasie van Vv-AMP1 in die Nicotiana tabacum-genoom is deur Southern-kladontledings bevestig en 20 individuele transgeniese lyne is ontwikkel. Genetiese karakterisering van die transgeniese lyne het gewys dat Vv-AMP1 suksesvol geïntegreer is en ook in die transgeniese tabakomgewing uitgedruk word. Die peptied is uitgedruk onder beheer van sy eie seinpeptied, wat die aktiewe produk na die apoplastiese areas van die plantselle teiken. Die transgeniese tabaklyne is ook ontleed om te bepaal of die wingerdpeptied suksesvol geproduseer word en sy aktiwiteit in die transgeniese omgewing behou. Western-kladanalise van semi-gesuiwerde plantproteïenekstrakte het 'n positiewe sein gelewer in beide die kontroleplante en die transgeniese plantlyne. Bestudering van tabakgeenuitdrukkings-databasisse het drie nukleotiedvolgordes opgelewer wat homologie met Vv-AMP1 toon en moontlik verantwoordelik kan wees vir die positiewe sein in die ongetransformeerde kontroleplante. Kru proteïenekstrakte van die transgeniese tabaklyne het in vitro-aktiwiteit teen V. dahliae getoon. Geen oortuigende ooreenkoms kon egter gevind word tussen V. dahliae-inhibisie en die teenwoordigheid van die transgeniese Vv-AMP1-peptied nie, aangesien kontroleplante wat Southern-klad-positief is, maar nie geenuitdrukking toon nie, ook inhibisie van V. dahliae veroorsaak het. Soortgelyke resultate is met infeksiestudies verkry. Alle resultate dui daarop dat, al is daar suksesvolle integrasie en uitdrukking van die geen in tabak verkry, dat die Vv-AMP1 peptied óf onaktief óf onstabiel in die transgeniese tabakomgewing is. Die peptied behoort aan 'n subgroep peptiede met aktiwiteite wat, sodra sekere vlakke van peptied oorskry word, die moontlik streng kontrole op proteïenvlak in die gasheerplant kan uitlok. Sekere aspekte van die studie sal verder bestudeer moet word, aangesien die data teenstrydig is met data wat verkry is met soortgelyke plantdefensinpeptiede wat aan 'n ander subgroep behoort. Die studie het baie hulpbronne gegenereer wat vir die biotegnologiesektor belangrik kan wees, veral op ekonomiese gebied. Verder is die geenkonstrukte en plantlyne wat ontwikkel is waardevol om fundamentele vrae rondom die regulering en meganisme van aksie van defensinpeptiede, spesifiek plantpatogeeninteraksie, te beantwoord. Die nuwe plantdefensingene is na verskeie gasheerplante, insluitende wingerd, getransformeer waar die transgeniese lyne die volgende rondte van navorsing oor die bestudering oor die belangrike groep van antifungiese peptiede, sal aanvul.

Thesis (PhD (Wine Biotechnology))--University of Stellenbosch, 2011. / Includes bibliography. / ENGLISH ABSTRACT: Alcoholic fermentation, and especially wine fermentation, is one of the most ancient microbiological processes utilized by man. Yeast of the species Saccharomyces cerevisiae are usually responsible for most of the fermentative activity, and many data sets clearly demonstrate the important impact of this species on the quality and character of the final product. However, many aspects of the genetic and metabolic processes that take place during alcoholic fermentation remain poorly understood, including the metabolic processes that impact on aroma and flavour of the fermentation product. To contribute to our understanding of these processes, this study took two approaches: In a first part, the initial aim had been to compare two techniques of transcriptome analysis, DNA oligo-microarrays and Serial Analysis of Gene Expression (SAGE), for their suitability to assess wine fermentation gene expression changes, and in particular to assess their potential to, in combination, provide combined quantitative and qualitative data for mRNA levels. The SAGE methodology however failed to produce conclusive data, and only the results of the microarray data are shown in this dissertation. These results provide a comprehensive overview of the transcriptomic changes during model wine fermentation, and serve as a reference database for the following experiments and for future studies using different fermentation conditions or genetically modified yeast. In a second part of the study, a screen to identify genes that impact on the formation of various important volatile aroma compounds including esters, fatty acids and higher alcohols is presented. Indeed, while the metabolic network that leads to the formation of these compounds is reasonably well mapped, surprisingly little is known about specific enzymes involved in specific reactions, the genetic regulation of the network and the physiological roles of individual pathways within the network. Various factors that directly or indirectly affect and regulate the network have been proposed in the past, but little conclusive evidence has been provided. To gain a better understanding of the regulations and physiological role of this network, we took a functional genomics approach by screening a subset of the EUROSCARF strain deletion library, and in particular genes encoding decarboxylases, dehydrogenases and reductases. Thus, ten genes whose deletion impacted most significantly on the aroma production network and higher alcohol formation were selected. Over-expression and single and multiple deletions of the selected genes were used to genetically assess their contribution to aroma production and to the Ehrlich pathway. The results demonstrate the sensitivity of the pathway to cellular redox homeostasis, strongly suggest direct roles for Thi3p, Aad6p and Hom2p, and highlight the important role of Bat2p in controlling the flux through the pathway. / AFRIKAANSE OPSOMMING: Alkoholiese fermentasie, en veral die maak van wyn, is een van die vroegste mikrobiologiese prosesse wat deur die mensdom ingespan is. Die gisspesie Saccharomyces cerevisiae is gewoonlik grotendeels verantwoordelik vir die fermentasie and verskeie vorige studies het gedemonstreer dat hierdie spesie ‘n baie belangrike rol speel in die uiteindelike kwaliteit en karakter van die voltooide produk. Nieteenstaande die feit is daar steeds baie aspekte van beide die genetiese en metaboliese prosesse wat plaasvind tydens alkoholiese fermentatsie wat nog swak verstaan word, insluitende metaboliese padweë wat ‘n impak het op die smaak en aroma van die fermentasie produk. Om ons kennis van die veld uit te brei het die studie twee aanslae geneem: In die eerste geval is gepoog om twee tegnieke van transkriptoom analiese, nl. DNA oligomikro- arrays en Serial Analysis of Gene Expression (SAGE) te bestudeer vir hul vermoë om geen ekspressie veranderinge tydens wynfermentasie te ondersoek en meer spesifiek om hul potensiaal om ‘n kombinasie van kwantitatiewe sowel as kwalitatiewe data met betreking to mRNA vlakke te produseer. Die SAGE metode kon egter geen betroubare resultate produseer nie en dus word slegs die resultate van die mikro-array eksperimente in die tesis bespreek. Die resultaat is ‘n geheeloorsig oor die geenekspressie veranderinge wat so ‘n wyngis tydens alkoholiese fermentasie ondergaan en dien as ‘n verwysingsraamwerk vir toekomstige studies met geneties gemodifiseerde gis of selfs verskillende fermentasieparameters. Die tweede deel van die studie het gefokus op die identifikasie van gene wat ‘n impak het op die vorming van belangrike, vlugtige aroma komponente, o. a. Esters vetsure en hoër alkohole d.m.v. ‘n siftingseksperiment. Alhoewel daar redelik baie inligting is oor die onderligende metaboliese netwerke wat lei tot die vorming van die verbindings, is daar min kennis van die genetiese regulasie van die netwerk en die fisiologiese rol van individuele padweë wat die netwerk vorm. Verskeie faktore – wat of die netwerk direk of indirek affekteer – is al voorgestel, meer met min konkrete bewyse. Dus het ons gepoog om meer lig op die onderwerp te laat m.b.v. ‘n funksionele genoom aanslag deur ‘n siftingseksperiment te doen op ‘n subgroep (spesifiek gene wat kodeer vir dekarboksilase, dehidrogenase en reduktase ensieme) van die EUROSCARF delesiebiblioteek. Dus is tien gene geïdentifiseer – die delesie waarvan ‘n merkbare effek het op die aroma produksie netwerk en spesifiek die van hoër alkohole. Ooruitdrukkings en enkel en meervoudige delesie rasse van die tien gene is gemaak om d.mv. genetiese analiese, hulle rol in aroma produksie en die Ehrlich padweh uit te pluis. Die resultate toon dat hierdie padweg sensitief is teenoor die sellulêre redoks balans en dui op direkte rolle vir Thi3p, Aad6p en Hom2p, asook dat Bat2p ‘n baie belangrike rol speel in die werking van die padweg.

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Supply-demand analysis (SDA) is a tool that allows for the control, regulation and behaviour of metabolic pathways to be understood. In this framework, reactions are grouped into reaction blocks that represent the supply and demand of a metabolic product. The elasticities of these supply and demand blocks can be used to determine the degree of control either block has over the flux in the pathway and the degree of homoeostasis of the metabolic product that links the blocks. Rate characteristic plots, on which the rates of supply and demand blocks are plotted as functions of the concentration of the linking metabolite, represent a powerful visual tool in this framework. Generalised supply-demand analysis (GSDA) allows for the analysis of metabolic models of arbitrary size and complexity without prior knowledge of the regulatory structure of the pathway. This is achieved by performing SDA on each variable metabolite in a pathway instead of choosing a single linking metabolite. GSDA also provides other benefits over SDA as it allows for potential sites of regulation and regulatory metabolites to be identified. Additionally it allows for the identification and quantification of the relative contribution of di erent routes of regulation from an intermediate to a reaction block. Moiety-conserved cycles present a challenge in performing in silico SDA or GSDA, as the total concentration of a moiety must remain constant, thereby limiting the range of possible concentrations of the metabolites between which it cycles. The first goal of this thesis was to develop methods to perform GSDA on two-membered and interlinked moiety-conserved cycles. We showed that by expressing the members of a moiety-conserved cycle as a ratio, rather than individual metabolite concentrations, we can freely vary the ratio without breaking moiety conservation in a GSDA. Furthermore, we showed that by linking the concentrations of the members of two interlinked two-membered moiety-conserved cycles to a “linking metabolite”, we could vary the concentration of this metabolite, within constraints, without breaking moiety conservation. The Python Simulator for Cellular Systems (PySCeS) is a software package developed within our group that provides a variety of tools for the analysis of cellular systems. The RateChar module for PySCeS was previously developed as a tool to perform GSDA on kinetic models of metabolic pathways by automatically generating rate characteristic plots for each variable metabolite in a pathway. The plots generated by RateChar, however, were at times unclear when the models analysed were too complex. Additionally, invalid results where steady-states could not be reached were not filtered out, and therefore appeared together with valid results on the rate characteristic plots generated by RateChar. We therefore set out to improve upon RateChar by building plotting interface that produces clear and error-free rate characteristics. The resulting RCFigure class allows users to interactively change the composition of a rate characteristic plot and it includes automatic error checking. It also provides clearer rate characteristics with e ective use of colour. Using these tools two case studies were undertaken. In the first, GSDA was used to investigate the regulation of aspartate-derived amino acid synthesis in Arabidopsis thaliana. A central result was that the direct interaction of aspartate-semialdehyde (ASA), a metabolite at a branch point in the pathway, with the enzyme that produces it only accounts for 7% of the total response in the flux of supply. Instead, 89% of the observed flux response was due to ASA interacting with of the downstream enzymes for which it is a substrate. This result was unexpected as the ASA producing enzyme had a high elasticity towards ASA. In a second case study moiety-conserved cycles in a model of the pyruvate branches in lactic acid bacteria were linearised using the above mentioned method. This served to illustrate how multiple reaction blocks are connected by these conserved moieties. By performing GSDA on this model, we demonstrated that the interactions of these conserved moieties with the various reaction blocks in the pathway, led to non-monotonic behaviour of the rate characteristics of the supply and demand for the moiety ratios. An example of this is that flux would increase in response to an increase in product for certain ranges. This thesis illustrates the power of GSDA as an entry point in studying metabolic pathways, as it can potentially reveal properties of the regulation and behaviour of metabolic pathways that were not previously known, even if these pathways were subjected to previous analysis and a kinetic model is available. In general it also demonstrates how e ective analysis tools and metabolic models are vital for the study of metabolism. / AFRIKAANSE OPSOMMING: Vraag-en-aanbod analise (VAA) is ’n analisemetode wat mens in staat stel om die beheer, regulering en gedrag van metaboliese paaie beter te verstaan. In hierdie raamwerk word reaksies gegroepeer as reaksieblokke wat die aanbod (produksiestappe) en die aanvraag (verbruik-stappe) van ’n metaboliese produk verteenwoordig. Vanaf die elastisiteite van hierdie aanbod- en aanvraag-blokke kan die graad van beheer van elkeen van die blokke oor die fluksie, asook die graad van homeostase van die metaboliese koppelingsintermediaat, bereken word. Snelheidskenmerk-grafieke, waarop die snelhede van die vraag- en aanbod-blokke as funksies van die konsentrasie van die koppelingsmetaboliet uiteengesit word, verteenwoordig ’n kragtige visuele hulpmiddel in hierdie raamwerk. Veralgemeende vraag-aanbod analise (VVAA), die veralgemeende vorm van VAA, maak dit moontlikommetaboliese modelle van arbitrêre grootte en kompleksiteit te analiseer sonder enige vooraf-kennis van die regulatoriese struktuur van die paaie. Die prosedure is om VAA op elk van die veranderlike metaboliete in die pad uit te voer, eerder as om ’n enkele koppelingsmetaboliet te kies. VVAA het ook ander voordele bo VAA aangesien dit potensiële setels van regulering en regulatoriese metaboliete kan identifiseer. Daarbenewens kan dit die relatiewe bydrae van verskillende regulerings-roetes van vanaf ’n intermediaat na ’n reaksieblok identifiseer en hulle kwantifiseer. Groep-gekonserveerde siklusse bied ’n uitdaging vir in silico VAA of VVAA, aangesien die totale konsentrasie van die gekonserveerde groep konstant moet bly. Dit beperk die waardes van moontlike konsentrasies van die metaboliete wat die siklus uitmaak. Die eerste doelstelling van hierdie tesis was dus om metodes te ontwikkel waarmee VVAA op tweeledige en saamgebonde groep-gekonserveerde siklusse uitgevoer kan word. Deur die lede van groep-gekonserveerde siklusse eerder as verhoudings uit te druk in plaas van as individuele metabolietkonsentrasies, het ons gewys dat ons hierdie verhouding vrylik kan varieer sonder om die groep-konservering te breek in ’n VVAA. Ons het ook gewys dat die konsentrasies van die lede van ’n saamgebonde groep-gekonserveerde siklus gekoppel kan word aan ’n “koppelingsmetaboliet”, waarvan die konsentrasie dan binne perke gevarieer kan word sonder om die groep-konservering te breek. Die “Python Simulator for Cellular Systems” (PySCeS) is ’n programmatuur-pakket wat binne ons navorsingsgroep ontwikkel is met die doel om sellulêre sisteme numeries te analiseer. Die RateChar module vir PySCeS was reeds voor die aanvang van hierdie projek ontwikkel om VVAAop kinetiese modelle van metaboliese paaie uit te voer deur outomaties snelheidskenmerke vir elke veranderlikke metaboliet te genereer. Die grafieke wat deur RateChar gegenereer is, was egter soms onduidelik wanneer die modelle te groot of kompleks geraak het. Daarbenewens is ongeldige resultate, waar ’n bestendige toestand nie bereik kon word nie, nie uitgefiltreer nie, en het dus saam met geldige resultate op die snelheidskenmerke verskyn. Een van die doelstellings was dus om RateChar te verbeter deur ’n koppelvlak vir grafieke te ontwikkel wat duidelike en foutlose snelheidskenmerke kon produseer. Dit het gelei tot die RCFigure klas wat outomatiese foutopsporing uitvoer en gebruikers in staat stel om op ’n interaktiewe wyse die samestelling van ’n snelheidskenmerkgrafiek te verander. Dit bied ook duideliker snelheidskenmerke deur e ektief van kleur gebruik te maak. Met hierdie ontwikkelde gereedskap is twee gevallestudies onderneem. In die eerste is VVAA gebruik om die regulering van aspartaat-afgeleide aminosuursintese in Arabidopsis thaliana te bestudeer. Die belangrikste resultaat was dat die direkte interaksie van aspartaat-semialdehied (ASA), ’n metaboliet by ’n vertakkingspunt in die pad, met die ensiem wat dit produseer, slegs vir 7% van die totale respons in die aanbod-fluksie verantwoordelik was. Daarteen was 89% van die waargenome fluksierespons die gevolg van die interaksie van ASA met drie van die stroomafensieme, waarvoor dit ’n substraat is. Hierdie resultaat was onverwag aangesien die ensiem wat ASA produseer ’n hoë elastisiteit teenoor ASA toon. In ’n tweede gevallestudie is die groep-gekonserveerde siklusse in ’n model van die pirovaat-takke in melksuurbakterie-metabolisme gelineariseer deur gebruik te maak van die bo beskrewe metode. Dit illustreer hoe verskeie reaksieblokke verbind word deur hierdie gekonserveerde groepe. M.b.v. ’n VVAA van hierdie model het ons gedemonstreer dat die interaksies van die gekonserveerde groepe met die verskeie reaksieblokke in die pad kan lei tot nie-monotoniese gedrag van die snelheidskenmerke van die vraag- en aanbod-reaksies vir die verhouding van die gekonserveerde groep-komponente. ’n Voorbeeld hiervan is die onverwagte waarneming dat die fluksie toeneem met toenemende produk-konsentrasie oor sekere gebiede. Hierdie tesis illustreer die krag van VVAA as ’n beginpunt vir die studie van metaboliese paaie, aangesien dit onbekende regulatoriese eienskappe en gedragspatrone kan ontbloot, selfs al is die paaie vantevore m.b.v. kinetiese modelle geanaliseer. Oor die algemeen demonstreer dit die noodsaaklikheid van e ektiewe analisegereedskap en metaboliese modelle vir die bestudering van metabolisme. / National Research Foundation

Oxidative stress (OS) plays a critical role in the pathogenesis of atherosclerosis potentially through interaction with nitric oxide (NO) generated by the inducible nitric oxide synthase (iNOS) pathway. Although considerable literature supports a pro-atherogenic role for iNOS-induced NO, recent evidence suggest an anti-atherogenic property for this enzyme where iNOS-induced NO attenuates atherosclerotic lesions after immune injury, enhancing endothelial integrity, survival, protecting against OS-induced apoptosis and necrosis. We therefore hypothesize that iNOS may have a cardio-protective role in the atherosclerotic vessel and that under conditions of OS, expression and function of this enzyme may be impaired, thus contributing to the deleterious consequences of OS. Experiments have therefore been conducted to establish whether pro-oxidants regulate iNOS expression/function in rat cultured aortic smooth muscle cells (RASMCs). These cells were induced for 24 hours with LPS and IFN-γ to mimic inflammatory conditions. Oxidative stress inducers may modulate iNOS-induced NO production through alteration of the expression and/or function of the inducible L-arginine-NO pathway. We examined the effects of hydrogen peroxide (H2O2), antimycin A and diethyl maleate (DEM) on this pathway in vascular smooth muscle cells. H2O2 had little effect on NO production or L-arginine transport while antimycin A and DEM independently caused a concentration dependent inhibition of both processes. Only DEM induced hemeoxygenase-1 (HO-1) expression, monitored by western blotting as a marker of OS. The effects of statins on NO synthesis and L-arginine transport in the presence and absence of OS were also investigated. The benefits of statins therapy in cardiovascular medicine are ascribed in part to their lipid-lowering effect by inhibiting 3-hydroxy-3-methoxyglutaryl coenzyme A (HMG-CoA) reductase, the rate limiting enzyme for cholesterol synthesis. However, statins may possess anti-inflammatory properties and are able to improve endothelial function, stabilize atherosclerotic plaque, and inhibit platelet aggregation, vascular smooth muscle cells proliferation and vessel wall inflammation. These effects may be exerted through novel actions of statins that include interaction with specific signalling pathways in cells which may be associated with the induction of iNOS and/or cationic amino acid transporters (CATs). Thus, we have extended our investigations to include an examination of the effects of statins on both iNOS and CAT function and expression under control conditions and following exposure of cells to OS. Atorvastatin caused a bell shaped response on NO production and iNOS expression and also enhanced L-arginine transport but in a non-concentration dependent manner. Simvastatin only affected NO synthesis without altering transporter activity. Pravastatin was without effect on either system. Further studies demonstrated that that atorvastatin was able to reverse the effects of antimycin A and DEM but only on NO production. These findings confirm that the inducible L-arginine-NO pathway can be downregulated by pro-oxidants. This mechanism may therefore contribute to the deleterious effects observed in disease states associated with OS. Moreover, statins (in particular atorvastatin) appear to be effective in reversing the inhibition of NO production caused by inducers of OS. This, together with the fact that atorvastatin and simvastatin can potentiate iNOS-induced NO production and indeed L-arginine transport (with atorvastatin), highlights a potential novel mechanism through which the cardio-protective actions of these compounds could be mediated.

The mammalian odorant receptor (OR) repertoire is an attractive model to study evolution, because ORs have been subjected to rapid evolution between species, presumably caused by changes of the olfactory system to adapt to the environment. However, functional assessment of ORs in related species remains largely untested. Here we investigated the functional properties of primate and rodent ORs to determine how well evolutionary distance predicts functional characteristics. Using human and mouse ORs with previously identified ligands, we cloned 18 OR orthologs from chimpanzee and rhesus macaque and 17 mouse-rat orthologous pairs that are broadly representative of the OR repertoire. We functionally characterized the in vitro responses of ORs to a wide panel of odors and found similar ligand selectivity but dramatic differences in response magnitude. 87% of human-primate orthologs and 94% of mouse-rat orthologs showed differences in receptor potency (EC50) and/or efficacy (dynamic range) to an individual ligand. Notably dN/dS ratio, an indication of selective pressure during evolution, does not predict functional similarities between orthologs. Additionally, we found that orthologs responded to a common ligand 82% of the time, while human OR paralogs of the same subfamily responded to the common ligand only 33% of the time. Our results suggest that, while OR orthologs tend to show conserved ligand selectivity, their potency and/or efficacy dynamically change during evolution, even in closely related species. These functional changes in orthologs provide a platform for examining how the evolution of ORs can meet species-specific demands. / Dissertation