Present study was planned to compare the phenotypic variation of performances traits among commercial (CC) and heritage varieties of turkeys. Information about heritage turkey varieties continues to be limited. In addition, the emerging turkey genome sequence provides a unique opportunity to understand the DNA sequence variation and its associations with performance traits. The turClock, turPer3, turCry1 and turCry2 genes were screened and evaluated for its association with their performance traits. As expected, CC turkeys were superior to heritage birds in performance for most of the traits evaluated. However, heritage turkeys showed better reproductive performances compared to CC turkeys. A total of 41 SNPs were identified from the genes that screened. The haplogroups in the turClock gene were significantly associated with body weight (BW) at 309 d of age, feed conversion ratio (FCR) for 34 - 68 d and 69 - 159 d, egg production and average egg weight (P " 0.05). The haplogroups developed from turPeriod-3 gene were significantly associated with BW at 231 d of age, average daily gain (ADG) for 160 - 231 d, FCR for 69 - 159 d and 160 - 231 d, egg production traits, semen quality traits and plasma melatonin concentration (P " 0.05). In the turCry1 gene, haplogroups were significantly associated with ADG for 35 - 68 d, FCR for 160 - 231 d and 34 - 231 d, egg production and ejaculate volume (P " 0.05). The haplogroups identified from turCry2 gene were significantly associated with BW at 34, 68 and 231 d of age, ADG for 160 - 231 d, FCR for 34 - 68 d, average egg weight (P " 0.05). These findings reveal that phenotypic variation observed in growth and reproductive parameters among turkeys could be used for selecting birds for future breeding programs. DNA sequence variations at the nucleotide and haplotype levels are associated with some of growth, reproductive parameters and plasma melatonin of turkeys. Thus DNA sequence variations that identified of the circadian genes may have some regulatory role in the molecular mechanism of the circadian clock which may affect the circadian rhythm of the animal. / Ph. D.

Plant-associated microbes (collectively the microbiome) are important contributors to plant health. They are known to play roles in increasing yield via improving stress tolerance, promoting growth, and suppressing the activity of plant pathogens. We investigated the wheat seed-head microbiome (phytomicrobiome) as a potential source of resistance to Fusarium head blight (FHB), or scab. FHB is a devastating disease in wheat, and other cereal grains, that causes losses in both quantity, through reduced yield, and quality of grain, through the production of toxins such as Deoxynivalenol. Efforts to combat FHB have focused primarily on breeding cultivars with resistance and applying fungicides. However, new resources for combatting FHB may lie in microbiome-plant interactions. To explore host-microbiome-pathogen interactions, we used field trials to characterize the seed head bacterial community (16S rRNA gene amplicons) across planting locations, host resistance genotypes, varieties, and plant development stages. We identified bacterial amplicon sequence variants (ASVs) present in each sample and then examined ASV community composition based on our variables. Characterizing bacterial relative abundance across samples, we identified 9,063 ASVs. These ASVs clustered according to plant developmental stages or maturity plant, location, and host genotype, but not by variety or maturity group. First, comparing plants at the pre-flowering versus mature grain-head stage, we found that both bacterial community richness and evenness changed significantly. In addition to these developmental changes, we found that bacterial community structure changes across locations, even between locations. Finally, we found that, in the presence of the pathogen, ASVs cluster by host resistance genotype, and that there are important taxonomic groups that are differentially abundant in the presence of the pathogen. Overall, we found that the wheat grain-head microbiome is shaped by environment-host-pathogen interactions, and that these interactions lead to differential abundance of particular community members that may be important in the management of FHB. / Master of Science in Life Sciences / Plant associated microbes are important contributors to plant health. They are known to play roles in increasing yield via improved stress tolerance, promoting growth, and suppressing plant disease. We investigated the wheat grain-head microbial communities as a source of disease resistance. The disease is called Fusarium Head Blight (FHB) and is caused by Fusarium graminaerum. FHB is a devastating disease in wheat and other cereals, causing losses, through reduced yield and quality through the production of toxins that prohibit use of the grain. To combat FHB, research has focused on developing plants that have resistance and the application of chemical fungicides. However, new resources for combating FHB may lie in the interactions between plants and microbes. This research is focused on identifying microbes that naturally interact with the plant, and how the pathogen, Fusarium, interacts with these beneficial microbes. In field trials, we characterized the microbial community by DNA sequencing technologies across locations, wheat with varying levels of genetic resistance, and wheat developmental stages. First, between the wheat kernel samples of pre-flowering and maturity, we found significant differences in microbial community. Consistent with other studies we found that the largest changes in microbial community composition across different growing locations. Finally, we found an interaction between the grain head microbiome and host resistance state when plants were exposed to the pathogen. Overall, we find that the wheat grain head microbiome is shaped by growing location and through interactions with the plant host and pathogen.

The influence of genotype variation on phenotype has been a longstanding question in biology but it is now one of the greatest challenges of the post-genomics era. Discovering the link between common gene variants that affect phenotypes within and between populations is likely to provide insight into the molecular physiology of phenotypic traits and the mechanisms by which they evolve. The overall goal of this thesis is to link naturally occurring genotypic variation with the organism??s phenotype. The specific goal of this thesis is to connect natural variation in the mitochondrial genotype with the organismal phenotype using the model organism Drosophila simulans. Mitochondria are intracellular organelles found in most eukaryotes and produce over 90% of the energy needed by cells. Determining the connection of mitochondrial genotype to whole organism phenotype is of particular interest because of the broad use of mitochondrial (mt) DNA as a molecular marker in evolutionary biology and population genetics, the organelle??s central role in cellular energy production, the potential for the mitochondria to influence organismal distribution particularly in the face of climate change and in human degenerative disease. I use the model organism D. simulans because it has high genetic variability, can be easily sampled from the wild and manipulated in the lab, and the energy producing reactions that take place in its mitochondria are highly conserved among metazoa. I studied naturally occurring mutations to understand the influence of these changes in natural populations. The four studies in this thesis have employed a Genotype-Biochemistry-Phenotype (GBP) model to link naturally occurring variation in the mitochondrial genotype with organism phenotype in D. simulans mitochondria. Three major conclusions can be drawn from the thesis that follow the genotype to biochemistry to phenotype model. Firstly, a subset of the mutations in genes that comprise the mitochondrial genotype is functionally significant. Secondly, the biochemical efficiency of OXPHOS is regulated by mitochondrial homeostasis. Thirdly, key organismal life history traits influenced by the mitochondrial genotype and this is mediated through the biochemistry of OXPHOS.

Les paraplégies spastiques héréditaires (PSH) sont des maladies cliniquement et génétiquement hétérogènes, qui se manifestent par la présence de signes pyramidaux (spasticité, réflexes myotatiques vifs et diffusés) et d’un déficit moteur des membres inférieurs. On distingue des formes pures et complexes de PSH, ces dernières étant associées à la présence de signes additionnels tels que troubles cognitifs, neuropathie périphérique, signes cérébelleux, etc. Les mécanismes physiopathologiques des PSH sont également hétérogènes, incluant une anomalie du transport axonal (SPG3A, SPG4, SPG10, SPG20), du métabolisme mitochondrial (SPG7, SPG13), une anomalie de la formation de la myéline (SPG1) ou un dysfonctionnement du développement neuronal (SPG2). Elles peuvent se transmettre selon le mode autosomique dominant (AD), récessif (AR), ou récessif lié au chromosome X. Actuellement, 13 loci dont 9 gènes de PS-AD sont connus, mais seulement 5 gènes responsables de PS-AR ont été identifiés, alors que 14 loci sont connus. De par leur hétérogénéité clinique, génétique et physiopathologique, les PSH sont encore des maladies mal connues. Une meilleure connaissance du phénotype associé à chaque locus/gène permettrait aux cliniciens de mieux orienter les analyses moléculaires pour un diagnostic rapide. L’établissement de corrélations génotype-phénotypes et de la fréquence des gènes impliqués dans les PSH permettrait tant aux cliniciens qu’aux biologistes de cibler les gènes, les exons à analyser ou les mutations à rechercher en priorité. L’identification des mécanismes physiopathologiques des mutations est une première étape vers des études fonctionnelles et des traitements spécifiques. Nous avons montré que la forme de PS AD liée à des mutations dans le gène SPG3A était caractérisée par un début très précoce, avant l’âge de 10 114 ans. Cette forme en générale pure de PS peut se compliquer, notamment par une neuropathie périphérique ou un syndrome cérébelleux après une longue durée d’évolution de la maladie. Ces résultats permettent d’orienter les analyses moléculaires vers le gène SPG3A avant le gène SPG4, devant tout patient qui a débuté la maladie précocement, quelque soit le tableau clinique. Nous avons montré que les mutations dans le gène SPG3A, dont les mutations récurrentes p.R239C et p.R495W dans les exons 7 et 12 peuvent apparaître de-novo, justifiant l’analyse de ce gène chez des patients isolés. Nous avons étendu le phénotype des PS AD liées à des mutations dans le gène SPG4, qui doit être analysé chez les patients présentant une PS associée à un retard mental sans malformation cérébrale. De plus, nous avons montré que les délétions de ce gène ne sont pas rares, atteignant une fréquence de 20% chez les patients présentant une PS-AD sans mutation retrouvée par DHPLC. Ceci entraîne un changement des stratégies d’analyses moléculaires utilisées chez les patients atteints de PS, avec l’instauration systématique d’un MLPA chez chaque patient. Nous avons précisé le tableau clinique des paraplégies spastiques AR liées aux loci SPG26 et 27. Nous avons réduit l’intervalle génomique de ces loci. L’identification d’autres familles liées à ces loci permettra de réduire encore plus leurs intervalles génomiques, voire d’identifier les gènes responsables de ces maladies.

Aggregatibacter actinomycetemcomitans is an oral bacterium that is mainly associated with aggressive forms of periodontitis, which most often starts at an early age. Amongst the virulence factors of A. actinomycetemcomitans, two exotoxins, the leukotoxin (LtxA) and the cytolethal distending toxin (Cdt), are suggested to play an important role in the pathogenicity of aggressive periodontitis. There is also a genetic diversity of the different strains of A. actinomycetemcomitans, and a variation in the ability of different strains to express and release exotoxins has been suggested. Of the different genotypes of A. actinomycetemcomitans, the highly leukotoxic JP2 genotype, which is prevalent in individuals of African origin, seems to be the genotype that is most strongly associated with localized aggressive periodontitis. This thesis is built upon studies of a West African adolescent population. The aim was to study the virulence characteristics of A. actinomycetemcomitans genotypes with a specific focus on the LtxA and the Cdt in relation to the progression of attachment loss (AL). The specific aim was first, to investigate cross-sectionally the presence of the JP2 and non-JP2 genotypes of A. actinomycetemcomitans in relation to the prevalence of AL and then prospectively to assess the progression of AL in a Ghanaian adolescent population. Second, in clinical isolates of A. actinomycetemcomitans obtained from the participants of the study, the serotypes and the virulence characteristics related to the two exotoxins were studied and associated with the progression of AL at the individual level. In Paper I, based on the study population consisting of 500 adolescents (mean age 13.2 years; SD ±1.5), it was shown that the overall carrier rate of A. actinomycetemcomitans was high (54.4%) and that the presence of this bacterium was associated with AL ≥ 3 mm. The JP2 genotype was prevalent (8.8%) in this population. In Paper II, 397 (79.4%) of the study participants were periodontally examined again at a 2-year follow-up. The presence of the JP2 genotype of A. actinomycetemcomitans in subgingival plaque was strongly associated with the progression of AL. This study also provided support for an enhanced estimated risk (odds ratio, OR=3.4), though less pronounced, for the progression of AL in individuals positive for the non-JP2 genotypes of A. actinomycetemcomitans. In Paper III, all three cdt genes (a, b and c) were detected in 79% of the examined A. actinomycetemcomitans isolates, all of which expressed an active toxin. The distribution of the cdt genes showed a serotype-dependent pattern. In particular, the presence of the b serotypes (both JP2 and non-JP2 genotypes) was associated with the disease progression, whereas the expression of Cdt was not particularly related to the disease progression.  In Paper IV, it was shown that the presence of of A. actinomycetemcomitans isolates with high leukotoxicity, also those of the non-JP2 genotypes of A. actinomycetemcomitans, were associated with an increased risk of the progression of AL in relation to the reference group. The main proportion of the serotype b isolates was distributed in the category of highly leukotoxic isolates. The analyses of the non-JP2 genotypes of serotype b indicated a diversity linked to the level of leukotoxicity. In conclusion, A. actinomycetemcomitans in general was associated with the progression of AL. Individuals with an increased risk of developing progression of AL mainly harboured isolates of A. actinomycetemcomitans with a high leukotoxicity, which suggests that the LtxA is an important virulence factor. Of the two exotoxins, the pathogenic potential was mainly associated with the LtxA, while the role of the Cdt is unclear.

The influence of genotype variation on phenotype has been a longstanding question in biology but it is now one of the greatest challenges of the post-genomics era. Discovering the link between common gene variants that affect phenotypes within and between populations is likely to provide insight into the molecular physiology of phenotypic traits and the mechanisms by which they evolve. The overall goal of this thesis is to link naturally occurring genotypic variation with the organism??s phenotype. The specific goal of this thesis is to connect natural variation in the mitochondrial genotype with the organismal phenotype using the model organism Drosophila simulans. Mitochondria are intracellular organelles found in most eukaryotes and produce over 90% of the energy needed by cells. Determining the connection of mitochondrial genotype to whole organism phenotype is of particular interest because of the broad use of mitochondrial (mt) DNA as a molecular marker in evolutionary biology and population genetics, the organelle??s central role in cellular energy production, the potential for the mitochondria to influence organismal distribution particularly in the face of climate change and in human degenerative disease. I use the model organism D. simulans because it has high genetic variability, can be easily sampled from the wild and manipulated in the lab, and the energy producing reactions that take place in its mitochondria are highly conserved among metazoa. I studied naturally occurring mutations to understand the influence of these changes in natural populations. The four studies in this thesis have employed a Genotype-Biochemistry-Phenotype (GBP) model to link naturally occurring variation in the mitochondrial genotype with organism phenotype in D. simulans mitochondria. Three major conclusions can be drawn from the thesis that follow the genotype to biochemistry to phenotype model. Firstly, a subset of the mutations in genes that comprise the mitochondrial genotype is functionally significant. Secondly, the biochemical efficiency of OXPHOS is regulated by mitochondrial homeostasis. Thirdly, key organismal life history traits influenced by the mitochondrial genotype and this is mediated through the biochemistry of OXPHOS.

Thesis (M. A. (Agricultural Management)) -- University of Limpopo, 2020 / Field experiments were conducted at two locations; University of Limpopo (Syferkuil) and University of Venda (Thohoyandou) during 2015 and 2016 winter cropping seasons. The objectives of this study were to determine; the effect of genotype (ACC# 1, 3, 4 and 7) and planting density (33, 25 and 20 plants/m2) on four chickpea genotypes having contrasting growth patterns and also to determine the effect genotype and planting density on water use and water use efficiency of four chickpea genotypes having contrasting growth patterns. The experimental design was randomized complete block design in factorial arrangement with three replications. Plant height, number of primary and secondary branches, grain yield and yield components (number of pods per plant, number of seeds per pod, Harvest Index and 100 seed weight [100-SW] and above ground biomass, and were determined at different growth stages. Data obtained was subjected to analyses of variance using the general linear model of Genstat 17th edition. Significant differences between the treatments means were compared using the standard error of difference (LSD) of the means at 5% level. Correlation analyses were performed to assess the relationship between parameters. Plant height varied with genotype from 41 cm (84 DAE) to 44 cm (118 cm) at Syferkuil and 41 (56 DAE) to 44 cm (63 DAE) at Thohoyandou. Primary branches was not significantly affected by genotype and planting density at both locations and seasons. Planting density had significant effect on number of secondary branches, greater number was recorded at low (32, 6) density at Syferkuil in 2016. Above ground biomass was significantly affected by planting density at Syferkuil during in 2015 (5344 kg ha-1) and 2016 (3701 kg ha-1) growing seasons. Genotype and planting density did not affect number of pods plant-1, number of seeds plant-1, 100 SW (100 seed weight), and Harvest index were not significant at both locations and seasons. Grain yield was significantly affected by planting density at Syferkuil in 2015 and Thohoyandou in 2016. Grain yield increased with the increase in planting density at both locations. Two field experiments were conducted at University of Venda (Thohoyandou) during 2015 and 2016 winter cropping seasons. This study aimed at assessing the effect of genotype v and planting density on water use efficiency of four chickpea genotypes with contrasting growth patterns. Crop water use (WU) was determined by monitoring soil water content at 7-day intervals using a neutron probe and, water use efficiency (WUE) was determined as a ratio of crop biomass and grain yield to WU. Genotype and planting density had no significant effect on WU in 2015 and 2016. Genotype and planting density had no significant effect on biomass production (WUEb) and grain yield production (WUEg) in 2015. In contrast, WUEb and WUEg was significantly affected by planting density in 2016. WUEb was 43.2% greater at high density compared to low density. Similarly, WUEg was 39.3% greater at high density compared to low density. WUEb and WUEg increased with the increase with planting density. Therefore, manipulation of management practices such as planting density may increase chickpea production. Keywords: Planting density, genotype, grain yield and yield components, water use efficiency. / National Research Foundation (NRF) and University of Venda Capacity Development

No description available.

No description available.

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2009. / Dissertation presented for the degree of Doctor of Philosophy at Stellenbosch University. / ENGLISH ABSTRACT: This study describes the molecular epidemiology of Mycobacterium tuberculosis strains with the Beijing genotype. This genotype has received clinical prominence due to its global distribution and the hypothesis that these strains have acquired the ability to evade the protective effect of BCG vaccination, spread more readily, acquire drug resistance and cause severe forms of disease. Molecular biological techniques were used in a series of studies to elucidate the genetic evolutionary mechanisms underlying the success of this genotype in Cape Town, South Africa. Using a collection of 40 different markers it was possible for the first time to construct a phylogenetic history of Beijing genotype strains. This phylogeny was characterized by the consecutive evolution of 7 sublineages. Analysis of epidemiological data in relation to these sublineages showed an association between more recently evolved Beijing strains and an increased ability to transmit and cause disease. From these findings it was hypothesized that the pathogenic characteristics of the Beijing genotype were not conserved but rather that strains representative of the different sublineages had evolved unique properties. In order to determine whether these socalled unique properties were associated with either the host population or the genetic background of strains from sublineage 7, a meta-analysis of published Mycobacterial Interspersed Repetitive-Unit (MIRU) typing data (East Asia) was compared with MIRU typing data from the South African strains in the context of their phylogenetic histories. This study showed that Beijing genotype strains in South Africa originated in East Asia following their introduction during the early 18th century. A significant association was observed between the frequency of occurrence of strains from defined Beijing sublineages and the human population from whom they were cultured (p <0.0001). Based on these findings it was proposed that either the host population (South African) had selected for a particular Beijing sublineage (i.e. sublineage 7) or that strains from that sublineage had adapted to be more successful in the South African population. In a subsequent study, using the methodology developed in the above studies, it was shown that strains from the ancestrally positioned lineage (termed “atypical” Beijing genotype) were over-represented in drug resistant isolates in the Eastern Cape region. This contradicts current dogma which suggests that “atypical” Beijing genotype strains are attenuated in their ability to transmit. However, this phenomenon may be ameliorated in immune-compromised patients as review of the clinical records showed that transmission was associated with HIV co-infection. These findings highlight the need to improve tuberculosis control in vulnerable populations as strains which would normally not contribute significantly to the epidemic now become a cause for concern especially if they are associated with drug resistance. To improve our understanding of the evolution of the Beijing genotype, the genomic stability of an additional 27 polymorphic markers were analysed. These markers have recently been proposed as the new standard in molecular epidemiological studies and were based on MIRU-Variable Number Tandem-Repeats (VNTR) sequences. Superimposition of the MIRU-VNTR data onto the phylogenetic tree showed excellent concordance thereby demonstrating that these alleles were largely stable over time. It is currently not known how the alleles that do change could influence pathogenicity. The results of this study also demonstrated discordance between strains defined by IS6110 DNA fingerprinting and those defined by MIRU-VNTR typing thereby demonstrating that these markers evolve independently and at different rates. Furthermore, the MIRU-VNTR typing method was unable to predict transmission of drug resistant strains which contradict previous reports from low incidence settings. This has significant implications for the use of this typing method in high incidence settings. Using an improved PCR-based method it was possible for the first time, to identify the 5 most prominent phylogenetic lineages in primary cultures of adult tuberculosis patients resident in a high HIV/TB co-infection setting. The results of this study showed that 15% of the study population was infected with two or more strains and Beijing genotype strains were over-represented in these mixed infections. Furthermore, drug susceptibility tests showed that one patient was co-infected with both a drug sensitive and a drug resistant strain. Since mixed infections have been implicated in treatment failure, these findings demonstrate the epidemiological importance of detecting mixed infections in vulnerable populations. This PCR-based method was further applied to cultures of paediatric tuberculosis patients to classify strains which spoligotyping was unable to define. The result of this study showed three mixed infections which otherwise would have been missed. In order to determine whether clinical disease presentation of patients infected with strains of the Beijing genotype were different from that of patients infected with non-Beijing genotype strains, clinical and demographic data of these two groups were analysed. This study showed that patients infected with strains of the Beijing genotype were highly infectious as defined by the increased bacterial load in sputum specimens. However, this finding could not be validated by lung pathology according to chest radiographs of infected patients. / AFRIKAANSE OPSOMMING: Hierdie studie beskryf die molekulêre epidemiologie van Mycobacterium tuberculosis rasse met die Beijing genotipe. Hierdie genotipe is van groot kliniese belang weens hul globale verspreiding en die hipotese dat hierdie rasse die vermoë ontwikkel het om die beskermende effek van BCG vaksinasie te vermy, om meer geredelik te versprei, middelweerstandigheid te ontwikkel en erger vorms van siekte te veroorsaak. Molekulêre biologiese tegnieke is gebruik in ‘n reeks studies om die genetiese evolusionêre meganismes onderliggend tot die sukses van hierdie genotipe in Kaapstad, Suid-Afrika te verklaar. Deur ‘n versameling van 40 verskillende merkers te gebruik, was dit moontlik om vir die eerste keer ‘n filogenetiese stamboom van die Beijing ras genotipe te skep. Hierdie filogenie word gekenmerk deur die opeenvolgende evolusie van 7 ras sublyne. Met die analise van epidemiologiese data in verhouding tot hierdie ras sublyne, is ‘n assosiasie tussen die mees onlangs ontwikkelde Beijing rasse en die verhoogde vermoë om te versprei en siekte te veroorsaak, getoon. Vanweë hierdie bevindinge, is ‘n hipotese daargestel dat die patogeniese kenmerke van die Beijing genotipe nie in alle raslyne voorkom nie, maar eerder dat verteenwoordigende rasse van die verskillende sublyne unieke eienskappe deur evolusie ontwikkel het. ‘n Metaanalise van gepubliseerde MIRU tipering data van Oos-Asië is vergelyk met MIRU tipering data van Suid-Afrikaanse rasse in die konteks van hul filogenetiese geskiedenis om te bepaal watter van hierdie sogenoemde unieke eienskappe geassosieer is met die gasheerpopulasie en watter eienskappe geassosieer is met die genetiese agtergrond van die sublyn 7 rasse. Hierdie studie het getoon dat die Beijing ras genotipe van Suid-Afrika hul oorsprong gekry het van Oos-Asië en vir die eerste keer waargeneem is in die vroeë 18de eeu. ‘n Betekenisvolle assosiasie is waargeneem tussen die frekwensie waarteen die rasse van ‘n bepaalde Beijing sublyn voorkom en die menslike populasie van wie hulle geïsoleer is (p < 0.0001). Gebaseer op hierdie bevindinge is dit voorgestel dat die menslike populasie (Suid-Afrikaners) vir ‘n spesifieke Beijing sublyn geselekteer het (bv. Sublyn 7) of dat rasse van hierdie sublyn aangepas het om meer suksesvol te wees in die Suid-Afrikaanse populasie In ‘n daaropvolgende studie is, deur gebruik te maak van die metodiek wat ontwikkel is vir die bogenoemde studies, getoon dat die voorouerlike sublyn (bekend as die“atipiese” Beijing genotipe) die mees verteenwoordigende sublyn was onder middelweerstandige isolate van die Oos-Kaap gebied. Dit is teenstrydig met die bestaande dogma wat bepaal dat die “atipiese” Beijing genotipe rasse hulle vermoë om te versprei verloor het. Hierdie verskynsel kan egter versterk word in immuun inkompetente pasiënte aangesien hersiening van die kliniese rekords aangedui het dat verspreiding geassosieer was met HIV ko-infeksie. Hierdie bevindinge bring die behoefte om TB beheer in vatbare populasies te verbeter, na vore, omrede rasse wat gewoonlik `n onbetekenisvolle bydrae tot die epidemie lewer, nou ‘n rede vir kommer is veral as hulle met middelweerstandigheid geassosieer is. Om ons insig rakende die evolusie van die Beijing genotipe te verbeter, is die genomiese stabiliteit van ‘n addisionele 27 polimorfiese merkers geanaliseer. Daar is onlangs voorgestel dat hierdie merkers, wat gebaseer is op MIRU-VNTR volgordes,die nuwe standaard vir molekulêre studies is. Die MIRU-VNTR data is op die filogenetiese boom geplaas en het uitstekende ooreenstemming getoon wat die allele se stabiliteit oor tyd gedemonstreer het. Dit is tans nie duidelik hoe van die allele wat wel verander, die patogenisiteit beïnvloed nie. Die resultate van die studie wys ook onenigheid tussen rasse wat deur IS6110 DNA tipering gedefinieer is en dié wat deur MIRU-VNTR tipering gedefinieer is. Dit impliseer dus dat die evolusie van merkers onafhanklik van mekaar plaasvind en teen verskillende tempos. Verder was die MIRU-VNTR tipering metode nie in staat om verspreiding van middelweerstandige rasse te voorspel nie, wat teenstrydig is met vorige verslae waar lae insidensie omgewings bestudeer is. Dit het noemenswaardige implikasies vir die gebruik van hierdie tipering metode in hoë insidensie omgewings. ‘n Verbeterde PKR-gebaseerde metode is vir die eerste keer gebruik om die 5 mees prominente filogenetiese sublyne in primêre kulture van volwasse tuberkulose pasiënte van ‘n hoë MIV/TB ko-infeksie omgewing, te identifiseer. Die resultate van hierdie studie het gewys dat 15% van die studiepopulasie geïnfekteer is met twee of meer rasse en dat die Beijing genotipe ras die meeste voorgekom het in gemengde infeksies. Verder het middelweerstandige toetse gewys dat een pasiënt geïnfekteer was met beide ‘n middelsensitiewe en ‘n middelweerstandige ras. Gemengde infeksies is al vantevore gekoppel aan onsuksesvolle behandeling en dus demonstreer hierdie bevindinge die epidemiologiese belang van die opsporing van gemengde infeksies in vatbare populasies. Hierdie PKR-gebaseerde metode is verder gebruik om rasse wat voorkom in kulture van pediatriese pasiënte, wat spoligotipering nie kon klassifiseer nie, te klassifiseer. Die resultate het drie gemengde infeksies gewys wat sonder die PKR-gebaseerde metode, nie geïdentifiseer sou gewees het. Om te bepaal of die kliniese beeld van pasiënte wat geïnfekteer is met rasse van die Beijing genotipe verskil van dié van pasiënte wat geïnfekteer is met rasse van die nie-Beijing genotipe, is die kliniese en demografiese data van die twee groepe pasiënte geanaliseer. Hierdie studie wys dat pasiënte wat geïnfekteer is met rasse van die Beijing genotipe hoogs aansteeklik is (gedefinieer op grond van hoë bakteriële lading in sputum monsters). Hierdie bevindinge kon egter nie met behulp van long patologie op borskas X-strale bevestig word nie.