Genetics

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Analysis of the gut microbiome sheds insights into breed resilience and the challenges of antimicrobial resistance in Dohne merino sheep.
(2024) Mgaga, Andiswa.; Dzomba, Edgar Farai.; Muchadeyi, Farai Catherine.; Pierneef, Riaan.
This study focused on analysing the gut microbiome of Dohne Merino, one of South Africa’s leading sheep breeds, that is also reared in Australia, New Zealand, and other European countries. Dohne Merino is of high economic importance in South Africa as it maintains livelihoods in many small rural communities. In South Africa, sheep and other livestock are exposed to multiple diseases and parasites. The efforts to manage these diseases and infections while keeping high productivity have led to an increased usage of antimicrobials in agriculture. This has resulted in high prevalence of antimicrobial resistance (AMR), that is a primary global concern demanding surveillance and action. Some sheep breeds and populations are known to be resilient to diseases, harsh production, and environmental conditions and have low AMR prevalence, which could be due to the defense provided by their gut microbiome. Studying the gut microbiome is essential because the gut microbiome contributes to animal nutrition and health. The study investigated the gut microbial environment of South African Dohne merino sheep. Metagenomic sequencing of the rumen, reticulum, omasum, and abomasum of six mature Dohne Merino ewes that were raised on open pasture was performed. Illumina HiSeq2500 was used to generate a total of 15million reads of 150bp illumina base pairs. The members of the microbial population were fully characterised, and the resistome of the gut was analysed. The microbial population was studied at phylum, class, order, genus, and species level, with bacteria being the most abundant and diverse domain. Other present domains included archaea and viruses. Majority of the microbial population was Bacteroides (53,9%) and Firmicutes (25,4%). Two illness-related bacterial phyla were also identified, Actinobacteria and Cyanobacteria. Identified archaea belonged to the phyla Candidatus Asgardarchaeota, Candidatus Thermoplasmatota, and Euryarchaeota. The observed viral population was very diverse with a total of 5 realms, 8 kingdoms,13 phyla, and 21 classes. Many of the viruses were dsDNA phages belonging to the Duplodnaviria realm. Disease-linked RNA viruses belonging to the Riboviria realm were also observed. Riboviria members have been associated with diseases such as influenzae, rabies and the corona virus. The relationships between microbiome composition and AMR prevalence across the four gut compartments were assessed. A total of 12 AMR genes were identified in the gut and were found to confer resistance to 15 antimicrobials. The observed antimicrobial resistance profiles were low compared to those reported for other breeds and species implying breed resilience of the Dohne Merino sheep. The analysis of the resistance profiles within the compartments revealed that, the higher the diversity, the lower the prevalence of AMR. The overall high diversity of the gut microbiome is the probable cause of breed resilience in Dohne Merino sheep. Additionally, the observed AMR high prevalence with no clinical symptoms of AMR in the animals is also indicative of breed resilience. More studies that will investigate the relationships between the gut microbiome and AMR prevalence are required and the knowledge generated can then be applied to overcome the challenges of AMR in livestock species.
Antimicrobial resistance, plasmid profiles and sequence typing of enterotoxigenic escherichia coli isolates causing colibacillosis in neonatal and weaning piglets of South Africa.
(2016) Ranketse, Mary.; Dzomba, Edgar Farai.; Muchadeyi, Farai Catherine.; Madoroba, Evelyn.
Abstract available in PDF file.
Association of genetic polymorphisms in select HIV-1 replication cofactors with susceptibility to HIV-1 infection and disease progression.
(2011) Madlala, Paradise Zamokuhle.; Ndung'u, Peter Thumbi.; Kormuth, Emil.
Objective.Humans differ substantially with respect to susceptibility to human immunodeficiency virus type 1 (HIV-1) infection and disease progression. This heterogeneity is attributed to the interplay between the environment, viral diversity, immune response and host genetics. This study focused on host genetics. We studied the association of single nucleotide polymorphisms (SNPs) in peptidyl prolyl isomerase A (PPIA), transportin 3 (TNPO3) and PC4 or SFRS1 interacting protein 1 (PSIP1) genes with HIV-1 infection and disease progression. These genes code for Cyclophilin A (CypA), Transportin-SR2 (TRN-SR2) and Lens epithelium derived growth factor/p75 (LEDGF/p75) proteins respectively, which are all validated HIV replication cofactors in vitro. Methods. One SNP A1650G in the PPIA gene was genotyped in 168 HIV-1 negative and 47 acutely infected individuals using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). 6 intronic and 2 exonic haplotype tagging (ht) SNPs (rs13242262; rs2305325; rs11768572; rs1154330; rs35060568; rs8043; rs6957529; rs10229001) in the TNPO3 gene, 4 intronic ht SNPs (rs2277191, rs1033056, rs12339417 and rs10283923) and 1 exonic SNP (rs61744944, Q472L) in the PSIP1 gene were genotyped in 195 HIV-1 negative and 52 acutely infected individuals using TaqMan assays. The rs1154330, rs2277191, rs12339417 and rs61744944 were further genotyped in 403 chronically infected individuals. CypA and LEDGF/p75 messenger RNA (mRNA) expression levels in peripheral blood mononuclear cells (PBMCs) were quantified by real-time reverse transcriptase polymerase chain reaction (RT-PCR). The impact of the Q472L mutation on the interaction of LEDGF/p75 with HIV-1 integrase (IN) was measured by AlphaScreen. Results. The minor allele (G) of SNP A1650G (1650G) in the promoter region of PPIA was significantly associated with higher viral load (p<0.01), lower CD4+ T cell counts (p<0.01) and showed a possible association with rapid CD4+ T cell decline (p=0.05). The 1650G was further associated with higher CypA expression post HIV-1 infection. The minor allele (G) of rs1154330 in the intron region of TNPO3 was associated with faster HIV-1 acquisition (p<0.01), lower CD4+ T cell counts, higher viral load during primary infection (p<0.05) and rapid CD4+ T cells decline (p<0.01). The minor allele (A) of rs2277191 (rs2277191A) in the intron region of PSIP1 was more frequent among seropositives (p=0.06). Among individuals followed longitudinally, rs2277191A was associated with higher likelihood of HIV-1 acquisition (p=0.08) and rapid CD4+T cell decline (p=0.04) in the recently infected (primary infection) cohort. In contrast, the minor allele (C) of rs12339417 (rs12339417C) also in the intron region of PSIP1 was associated with higher CD4+ T cell counts during primary infection. The rs12339417C was also associated with slower rate of CD4+ T cell decline (p=0.02) and lower mRNA levels of LEDGF/p75 (p<0.01). Seroconverters had higher preinfection mRNA levels of LEDGF/p75 compared to nonseroconverters (p<0.01) and these levels decreased after HIV-1 infection (p=0.02). The Q472L mutation showed approximately 2-fold decrease in the association constant (Kd), suggesting stronger binding to HIV-1 integrase. Our findings demonstrate, for the first time, that genetic polymorphisms in the TNPO3 and PSIP1 genes may be associated with susceptibility to HIV-1 infection and the disease progression. These data provide in vivo evidence that TRN-SR2 and LEDGF/p75 are important host cofactors for HIV-1 replication. This is also the first study to show the association of genetic polymorphisms in the PPIA gene with disease outcome in a population (South African) with high burden of HIV-1 infection. Conclusions. Genetic variation in HIV-1 replication cofactors may be associated with disease outcome in a South African population. These data strongly support the role of these HIV replication cofactors in disease pathogenesis in vivo and suggest that these factors are possible targets for therapeutic interventions. However, these data will need to be replicated in larger cohorts to confirm the effect of these genetic variants. Further studies on how to target these factors in antiviral strategies are needed.
Autolytic characterization of selected Enterococcal strains, (previously Streptococcal)
(2007) Sukkhu, Melisha.; Beukes, Mervyn.
Autolysins are enzymes that cleave specific structural components within the bacterial cell wall. They contribute to numerous cellular activities such as cell growth, cell division, peptidoglycan recycling and turnover. In this study, twelve Enterococcal isolates (previously from the genus Streptococcus) were examined for susceptibility to the antibiotics Penicillin G and Vancomycin, using a Disk Diffusion and a Microtitre plate assay. In both methods, all twelve strains were resistant to Vancomycin. Six of these strains were susceptible to Penicillin G. The minimum inhibitory concentration (MIC) values were twice that of the disk diffusion assay values. In the presence of antibiotic, the growth rates for the six strains were halved. Autolysins were extracted from the respective cell cultures using a 4% SDS precipitation method. The protein concentrations were calculated and estimated to be within the range of 5.47- to 6.35 μg/μl. Profiles of the SDS precipitate were analyzed on SDS-PAGE. Autolytic proteins were identified and partially analyzed by renaturing SDS-PAGE (zymograms) using gels containing cell wall substrate. Seven lytic bands of molecular weights 25, 30, 50, 63, 75 95 and 145 kDa (designated Autolysin A to G, respectively) were selected for further analysis. The temporal distribution of the enzymes ranged from the mid exponential phase to the early death phase. The seven proteins were blotted onto polyvinylidene difluoride (PVDF) membranes and excised for N-terminal sequencing. Blast analysis of the respective N-terminal sequences showed autolysins A, C, D, E and F to have 100% similarity to the muramidase, amidase and peptidase from S. cremoris, S. suis, S. pneumonia, S. pyogenes and E. faecium, respectively. Biochemical characterization confirmed autolysins A, B, E and F to exhibit muramidase activity, and autolysin C and G to exhibit peptidase activity. Autolysin D displayed 100% similarity to the protein LytA, a peptidoglycan hydrolase that is known to exhibit amidase activity. Blast analysis could not determine any significant similarities for autolysins B and G to previously identified autolysins, thus indicating they may perhaps be novel autolysins.
Behavioural, reproductive and growth studies on Oreochromis mossambicus (Peters 1852)
(2010) Weber, Raimund Michael.; Laing, Mark Delmege.
A major obstacle facing the successful creation of an African aquaculture industry, based upon Oreochromids, is the irregular supply of good quality fish seed. There are several causative biological processes behind its irregular supply. The aim of this research was therefore to determine the basic requirements for the establishment and maintenance of a small breeding facility, for O. mossambicus. The goal was to make a unit that was simple and which could be easily replicated in rural, satellite aquaculture seed stations. The results obtained illustrate that a small reproduction unit can produce large quantities of healthy 90-day fry. Asynchronous hatching of the eggs and spawning asynchrony in female Oreochromis mossambicus are two elements which negatively affect uniformity in the fry produced. Typical fish seed production uses large ponds partitioned into breeding allotments or a series of breeding pools. While the earthen ponds provide a substrate in which a nest can be excavated, its presence is not required for mating success in the closely related O. niloticus (Linneaus 1758). Female mate choice, as well as apparent fecundity, according to nest size has been clearly recorded in related cichlids but no investigations have been made as to nest size and spawning synchrony in O. mossambicus. The main focus of this investigation was to ascertain whether O. mossambicus would accept artificial nest substitutes in preference to their own constructed ones and secondly, whether different alternatives would elicit different levels of acceptance. The observed results indicate a ready acceptance for artificial nest alternatives, with nest lip height being prioritised by the fish . The implications thereof are discussed in relation to the potential for optimization of breeding arenas for O. mossambicus by the provision of artificial nests whose dimensions satisfy both male and female preferences. In established communities, Oreochromis mossambicus display various complex and ritualised behaviours during stable and disruptive events. The aim of this research was primarily to produce a glossary of behaviours defining these interactions, particularly with reference to male-male behaviours. Three males and six females were allowed to acclimatise over one month, with various social groupings being established within the first few days. Results from this study illustrated not only a dynamic social structure, signaled via various chemosensory and visual methods, but also supported recent findings in apparent male-male courtship and the underlying ii causes. Furthermore, the observed male-male activity of the nestholder malesfirmly corroborate the current practice in aquaculture whereby only one male is allocated per breeding arena. The use of artificial incubation of Oreochromis spp. eggs has become widespread in high intensity fish seed production. Various types of incubator exist, and their selection is dependent on the specific attributes of the egg to be incubated. Currently available incubators are typically of a funnel (up-flow) or round bottomed (down-flow) design. Neither permits easy access to the eggs, which is particularly important when dealing with poor quality water as is typically found in rural areas. The aim of this study was to devise and test an easy-to-use incubator, applicable to rural seed production projects, which offers advantages over currently available incubator types. The final design, WETNURSE Type II, offered improved hatching rates over Type I, with a mean hatching success of 75%. While falling short of the desired 80% success rate (Rana 1986), the various other benefits provided by the design justify further optimization and testing. Three distinct populations of O. mossambicus, representing populations of inbred, randomly mated and genetically unknown (wild-caught) pedigree were analysed according to their food conversion efficiency (FCE). The intra- and inter-sample crosses were done with single males in order to produce half-sib progeny batches which allowed for the assessment of sire influences on the FCE of the progeny batches. The results show that the population of unknown pedigree is comparable to that of the randomly mating population, indicating the presence of sufficient genetic variation to permit further selection; the genetic contribution of the males to their respective progeny was insignificant in relation to that made by the female.
Breed effects on the virulence gene profiles and genetic diversity at FUT1, MUC4, MUC13 and MUC20 candidate genes for controlling diarrhoea-causing Escherichia coli.
(2013) Mohlatlole, Ramadimetja Prescilla.; Dzomba, Edgar Farai.; Chimonyo, Michael.
Escherichia (E) coli infections result in diarrhoea and oedema in growing pigs. Enterotoxigenic (ETEC), shigatoxin producing (STEC) and enteroaggregative (EAEC) E. coli have been identified as the principal causes of colibacillosis in most pig production systems. These E. coli use fimbrial and non-fimbrial adhesins to adhere to the intestines and cause infection. Absence or presence of the receptors on the intestinal walls determines the resistance or susceptibility of the host to the E. coli. In other populations, candidate genes linked to the receptors have been found to be associated with resistance/susceptibility to infection and are used in marker-assisted selection programs. This study investigated the presence and prevalence of ETEC, STEC and EAEC and the associated virulence genes in 263 E. coli isolates sampled from Landrace, Large White, Duroc and Indigenous piglets from the Animal Production Institute of the Agricultural Research Council (ARC) in Irene and Middledrift farm in Eastern Cape Province. The study also investigated polymorphisms at six candidate genes associated with two E. coli receptors in the same pig populations. Over 39 % of the isolates tested positive for the E. coli virulent genes investigated. None of the samples had fimbrial adhesins. The mode of attachment of the investigated E. coli was through non-fimbrial adhesins which were found in 49.06% of the isolates. The 106 E. coli isolates were categorized into 25 pathotypes carrying definable and unique combinations of E. coli virulence factors. The resistant allele for Alfa (1) fucosyltransferase 1 (FUT1) M307, a candidate gene for FI8R, was present in less than 1 % of the population. Various mutations of mucin genes MUC4 g.8227, MUC20 c1600 and g.191 were found in the population. Their respective alleles for controlling F4ab/ac E. coli adhesion in pigs were predominant in both breeds. Three loci (FUT1, MUC20 g.191 and MUC20 c.1600) deviated from Hardy Weinberg equilibrium (HWE) in the Indigenous and the Large White breeds. Heterozygotes deficiency and high levels of within breed diversity was observed in these two breeds at the mentioned loci. Overall, the study observed a wide range of toxin and colonisation factors (CFs) giving rise to diverse pathotypes in South African pigs. The absence of fimbrial adhesins suggests a different colibacillosis control program from that previously used. The presence of the resistant alleles in most of the loci investigated was low, however their presence suggest it is possible to use them to generate a resistant population using marker assisted selection. This study serves as a foundation for future pig colibacillosis control and immunity studies in the South African pig herds.
Breeding for disease resistance to the major foliar pathogens of dry beans (Phaseolus vulgaris) in South Africa.
(1994) Edington, Brian Ross.
Resistances to bean common mosaic virus, halo, common and Ascochyta blight, angular leaf spot, anthracnose and rust pathogens of beans in South Africa were combined by reverse dichotomous crossing. Full resistance to Uromyces appendiculatus from Carioca 80 was conditioned by a single dominant gene. Partially dominant resistance to Phaeoisariopsis griseola was conditioned by a single gene in Carioca 80 and two genes in PAl 127. Differences in aggressiveness of isolates of Phoma exigua var. exigua were found. Different levels of Ascochyta blight resistance were found in the glasshouse, but field testing showed little difference after flowering. Inoculations of differential cultivars indicated the presence of at least eight races of U. appendiculatus and the a-Brazil race of Colletotrichum lindemuthianum . Inoculations of the old set of halo blight differential cultivars identified races 1 and 2. Forty-five lines with partial resistance to rust were obtained by recurrent selection. Very highly significant differences were noted between ratings of percentage leaf area affected by rust and yield of 23 cultivars planted in field trials. Significant genotype x environment interaction was noted for rust ratings. Ratings at different dates within a trial were correlated with one another, showing few ratings are required per trial, and a correlation of -0.678 between yield and rust rating was found. Inheritance of partial resistance and improved yield of eight cultivars crossed in a full diallel was mostly due to additive effects but non-additive effects were also very highly significant. Reciprocal effects were not significant for yield and rust ratings. Genotype x environment interactions were significant for rust ratings and yield. High estimates of narrow-sense heritability for rust resistance were obtained. No relationship between resistance and time to flowering, pustule size, leaf hairs and stomata was found. Latent periods in unifoliate leaves did not correlate with resistance but a closer match was found in the fourth trifoliate leaves. Inoculations with three additional single-pustule isolates of the 23 parent cultivars indicated the cultivars had similar levels of resistance. Ring necrosis was found in nine cultivars or crosses with them. The ring reaction was conditioned by a single dominant gene and possibly by the epistatic interaction of two dominant genes in Carioca 80. Differences in symptom severity in plants derived from Epicure indicated the possibility of additional gene interaction.
Breeding of advanced generation of Eucalyptus macarthurii-growth parameters and development of a near infrared (NIR) calibration model to predict whole tree pulp yield using non destructive cores.
(2008) Ndlovu, Zama Thandekile Laureen.; Tongoona, Pangirayi.; Swain, Tammy-Lyn.
Eucalyptus macarthurii is one of the cold tolerant eucalypt species grown in South Africa for pulp and paper. However, little research has been done on this species’ growth performance. A study was therefore initiated to: i) analyse growth characteristics of Eucalyptus macarthurii at two sites and to calculate genetic parameters (genetic and phenotypic correlations, heritabilities and genetic gains), ii) develop a non-destructive near infrared calibration model to predict whole tree pulp yield of Eucalyptus macarthurii, and iii) screen a second generation Eucalyptus macarthurii breeding population, using the developed near infrared calibration model on core samples, to predict screened pulp yield and to rank and identify families with superior pulping properties. Eucalyptus macarthurii population growth data (diameter under bark, diameter over bark, bark thickness, bark stripping, height, basic wood density and stem form) were measured at Pinewoods and Vlakkloof sites and their respective genetic parameters calculated. Genotype by environment interaction was found in this population, indicating that different populations should perhaps be developed independently of each other for the two sites. Genetic and phenotypic correlations between diameter over bark and diameter under bark were, 0.96 and 0.98 for Pinewoods and 0.98 and 0.99 for Vlakkloof, respectively. These correlations indicated that selection of diameter over bark would lead to a positive indirect selection for diameter under bark. The heritability estimates also ranged from 0.03 to 0.23 at both sites, which indicated a reasonable response to selection. The predicted gains for all traits found at Pinewoods were higher than those at Vlakkloof for progeny trials E76/P1, except height for progeny trial E76/P2, which was 2.09m at Pinewoods site and 3.52m at Vlakkloof site which showed that, selection for taller trees will be more effective at Vlakkloof site. A preliminary study was undertaken from eleven second generation trees (2007 tree collection) to investigate if the radial strip core taken at breast height predicts the whole tree wood properties. Correlations found between laboratory Kraft pulping of whole tree wood discs and whole tree NIR spectra with that of the radial strip core NIR spectra were 0.9472 and 0.9506, respectively. These results confirmed that NIR spectra of the radial strip core at breast height predict the whole tree wood properties. A non-destructive near infrared calibration model using wood samples was obtained from Eucalyptus macarthurii felled trees. The wood samples were chipped into wood chips, pulped using Kraft pulping (reference method) and a sub-sample of wood chips of the same trees were ground into sawdust samples and analysed through near infrared spectroscopy for screened pulp yield. The screened pulp yield values obtained from both processes had a narrow screened pulp yield range of 40 to 48%. The Eucalyptus macarthurii screened pulp yield values obtained from both processes, as well as from values obtained from other eucalypt species, were subjected to Vision® Software for calibration and validation of the near infrared calibration model. The results indicated a strong calibration correlation coefficient of 94%, between Kraft pulping and near infrared spectroscopy with a validation coefficient of 89%. The strong correlation and validation coefficient indicated that a reliable non-destructive near infrared model to predict screened pulp yield was successfully developed. The successful development of the valid calibration model required a wider range of other eucalypts species, which improved the development of the model. The developed calibration model was applied to the second generation breeding population planted in KwaZulu-Natal and Mpumalanga provinces, using wood core samples obtained from standing trees for the prediction of screened pulp yield. The highest screened pulp yield achieved was 48%, which compared well to that found for Kraft pulping, which confirmed the success of the development of the calibration model. There was a wide scope of growth variation found amongst traits, which will be useful in selecting superior trees for the next generation. The development of the nondestructive near infrared calibration model was a success due to the strong correlation coefficients found between the screened pulp yields obtained from Kraft pulping and near infrared spectroscopy processes, which was achieved by the inclusion of other eucalypt species in the dataset. The calibration model can be used to select the top performing individual and family trees for the next generation based on screened pulp yield. Tree improvement trials can now be conserved for further breeding, without felling the trees for determination of pulping properties.
Carnivore ecology and diet assessment using DNA-based approaches: the elusive black-footed cat (Felis nigripes) as a case study.
(2024) Siziba, Vimbai Isabel.; Willows-Munro, Sandi.
Information obtained from the assessment of diet has been used to reconstruct food webs of elusive and shy predators that are difficult to observe in their natural habitats. The information from these studies has been crucial in developing conservation strategies. Predator-prey dynamics in particular, can also be used as a proxy of ecosystem health. Traditional approaches for diet analysis often involve direct observation or morphological identification of prey remains from scat. These approaches can be challenging for smaller predators that are difficult to track, and are generalist, opportunistic or scavenging carnivores. This is because traditional methods are not well adapted to analyze and identify such a wide variety of prey species, making them liable to bias and inaccuracy. DNA-based methods for the identification of diet from scats have been shown to provide better resolution, accuracy and consistency when compared to all other methods. Species identification of prey consumed can be achieved using DNA barcoding; identification of species through the amplification of specific genetic markers linked to taxonomically identified species. DNA metabarcoding is a recent technological advancement which allows for identification of multiple species from a single sample using high-throughput sequencing (HTS). Using the shy and elusive black-footed cat (Felis nigripes, Burchell 1824) as a case study, in this dissertation I aimed to determine if DNA-based methods could be used to provide important population-level information (number of individuals in population, relatedness of individuals, dietary components, and parasite load). The first data chapter (Chapter 2) aimed to provide an in-depth review of the state of DNA reference libraries for small South African mammals. Small mammals constitute a large portion of small and medium carnivore diet. As such, the abundance of DNA reference libraries for small mammals gives a good indication if DNA metabarcoding studies are feasible. Analysis of DNA records revealed that the majority of small mammals are represented by at least one of the five mitochondrial genes. This study supports the use of multiple gene regions when performing scat metabarcoding particularly when wanting to determine the small mammal component of the diet. Chapter 3 tested in silico if published metabarcoding primers for 12S rRNA, 16S rRNA, COI and cyt b could reliably delimit common prey items eaten by black-footed cats. Successful species delimitation using metabarcoding rests on the presence of a “DNA barcode gap”. This gap is the difference between intraspecific and interspecific genetic distances within a group of organisms. Eight metabarcoding primer pairs were chosen from the literature. Using an alignment of DNA sequences from South African small mammals, each amplicon produced by the primer pairs was tested to determine if species level identification could be made. An optimal set of primers were developed for use in black-footed cat (and other small and medium carnivores) diet analyses. Chapter 4 assessed if microsatellites previously designed for use in domestic cat (Felis silvestris catus) could be successfully amplified and used to identify individual black-footed cats from scats. All nine microsatellite loci used in this study were amplified successfully and were polymorphic. The loci were found to have sufficient discriminatory power to distinguish individuals and identify clones and could therefore be used in parentage assignments. Chapter 5 aimed at identification of prey items of black-footed cats in the Benfontein Nature Reserve, Kimberley, South Africa using DNA metabarcoding. Of the four DNA regions selected for high-throughput sequencing, the cyt b region did not sequence well and was therefore excluded from the study. The result from this study were compared to a previous study conducted which was based on direct observations of black-footed cat feeding. Unsurprisingly, our DNA data supported previous studies which showed that the diet of black-footed cat consists mainly of rodents. Importantly, the DNA metabarcoding results identify some prey items that have not been recorded in black-footed cat diet previously highlighting the sensitivity of the DNA-based method. For example larger prey items such as antelope were also identified suggesting that the cats may also opportunistically scavenge. Chapter 6 assessed the presence of parasites found in black-footed cat wild populations. Five pathogens known to be of veterinary importance in domestic cats were found in the black-footed cat scats. These pathogens had previously not been documented in wild African felids, but are well documented in other taxa. These results add to the growing knowledge of diseases that could possibly contribute to the declining populations of black-footed cats in South Africa. In conclusion, DNA based methods have been shown to improved species resolution when compared to traditional methods of diet assessments. More so when coupled with highthroughput sequencing technologies. The results of this study show that DNA metabarcoding can be applied successfully to study the diet of South Africa carnivores. The results also indicate that DNA metabarcoding can be used in identification of species that are endemic to southern Africa.
Characterisation of antibiotic resistance in Streptococcus, Enterococcus and Staphylococcus using a bioinformatics approach.
(2005) Ramsuran, Veron.; Beukes, Mervyn.
The rate at which bacterial pathogens are becoming resistant to antibiotics is quite alarming, and therefore much attention has been focussed on this area. The mechanism whereby the bacterial cells acquire resistance is studied in order to determine how this process works as well as to determine if any future resistance mechanisms can be circumvented. In this study three different genera and the antibiotics that are resistant to them were used, namely, penicillin resistant Streptococcus, vancomycin resistant Enterococcus and methicillin resistant Staphylococcus. The results prove that the active sites SXXK, SXN and KT(S) G in the penicillin resistance Streptococcus plays a major role in resistance. It is seen in this study that the SXXK active site is found in all the resistant and most of the intermediate strains, therefore proving to be an important component of the cell wall resistance. It was subsequently noticed the greater the number of mutations found in the sequences the higher the resistance. Three dimensional structures showed the actives sites and their binding pockets. The results also show the change in conformation with a mutation in the active site. The results also proved that the Penicillin Binding Protein (PBP) genes essential for resistance are PBP Ia, PBP 2b and PBP 2x. The results obtained, for the vancomycin resistance in Enterococcus study, proved that the VanC and VanE cluster are very much alike and VanE could have evolved from VanC. There is also close similarity between the different ligase genes. The VanX 3D structure shows the position of the critical amino acids responsible for the breakdown of the D-Ala-D-Ala precursors, and the VanA ligase 3D structure shows the amino acids responsible the ligation of the D-Ala-D-Lac precursors. The analysis performed on the methicillin resistance in Staphylococcus study showed that the genes used to confer resistance are very similar between different strains as well as different species.
Characterisation of the divergence of the Elsenburg Merino resource flock.
(2012) Naidoo, Pavarni.; Dzomba, Edgar Farai.; Cloete, Schalk Willem P.
The Elsenburg Merino flock has been divergently selected for the ability of ewes to rear multiple offspring since 1986. Updated genetic trends for reproduction are reported for the Elsenburg Merino resource flock. The objective was to determine whether genetic trends estimated previously for the Elsenburg Merino Resource flock changed significantly with the introduction of genetic material from the industry to the high (H) line. All analyses included the full pedigree file, consisting of 6547 individuals. Heritability estimates were 0.08 ± 0.02 for number of lambs weaned and 0.11 ± 0.02 for corrected weight of lamb weaned. The ewe permanent environment variance was estimated at 0.09 ± 0.02 and 0.11 ± 0.02 for number of lambs weaned and for corrected weight of lamb weaned, respectively. Genetic trends for the H and low (L) lines were divergent (P < 0.05) for all reproduction traits during the period prior to the observed breakpoints. Progress for number of lambs weaned in the H line stabilised after 1999 while a decline in response for weight of lamb weaned in the H line occurred after 2003. The change points may result from reduced selection intensity during the formation of reciprocal crossbred lines, or the introduction of unrelated industry sires in the H line. The pedigree was analysed and inbreeding trends computed for the H and L lines with the aim to test the significance of inbreeding within the lines. The software packages used for the statistical analyses were ENDOG v4.8 and POPREP web analysis software. The average inbreeding coefficients (F) were 1.47% and 0.73% for the divergently selected H and L lines. The rate of inbreeding (ΔF) per generation was 0.5% for the H line and 0.6% in the L line. The overall rates of inbreeding per generation were different in the H and L lines but within acceptable levels. The L line, however, showed an unwanted recent increase in inbreeding that will need to be considered in future. Since 2003, part of the Elsenburg Merino breeding flock was subjected to structured reciprocal within-breed crossing. Lamb survival traits and ewe reproductive performance of purebred (H and L) and reciprocal crosses (HxL and LxH) were evaluated using least squares analyses. Levels of heterosis were also assessed. The mean survival of the two crossbred lines was notably superior to the midparent value in absolute terms, although the contrast did not reach statistical significance (P = 0.098). Further research is required to establish whether this within breed heterosis for lamb survival can be exploited to decrease lamb losses. Reproduction, number of lambs born (NLB) and number of lambs weaned (NLW) in the H line was higher than in the L line (P < 0.05) while the two crossbred lines were intermediate and different from both the H line and the L line (P < 0.05) from the analyses of annual reproduction and overall “lifetime” reproduction across three lambing opportunities. Individual heterosis for annual reproduction was estimated at 2.2% for NLB, 13.8% for NLW and 8.5% for corrected weight of lamb weaned (TWW), with the estimate for NLW reaching significance (P < 0.05). Corresponding estimates for total production over three lambing opportunities were 8.7% for TNLB, 19.1% for TNLW and 13.8% for TTWW, with the estimate for NLW reaching significance (P < 0.05). Ten RAPD markers were used to study molecular divergence between the H and L lines. Phenotypic data on the lifetime reproduction of ewes born in 1999 and 2000 indicated that reproduction in the H line ewes was markedly higher than that of L line contemporaries (P < 0.01). The RAPD assay, conducted on 15 ewes from each line, used eight primers and produced 87% polymorphic loci. The mean coefficient of genetic differentiation between lines (Gst) was estimated to be 0.25. In conclusion, the H and L lines were shown to be divergent for genetic trends and levels of inbreeding. The derived estimates of heterosis may also be used to infer divergence between the lines and significant molecular divergence proven using RAPD assays.
Characterization of streptococcal infections in KwaZulu-Natal Durban by random amplified polymorphic DNA anaylsis and DNA macrorestriction analysis.
(2004) Madlala, Paradise Zamokuhle.; Beukes, Mervyn.
A collection of 29 clinical streptococcal isolates obtained from the University of KwaZulu-Natal, Medical School, Durban Metro area (South Africa) were studied to establish their penicillin G susceptibility patterns often refered to as minimal inhibitory concentration (MIC) and to determine the genetic diversity among them using two genotyping methods, randomly amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE) analysis. All isolates with MIC less than or equal to 0.12 µg/ml were considered susceptible, intermediate resistant if MIC was between 0.25 µg/ml and 4 µg/ml and resistant if greater than 4 µg/ml, The percentage of isolates with resistance was relatively high (75.9%), only 10.3% of isolates showed intermediate resistance and 13.8% of the isolates were completely susceptible to penicillin G. Some of the resistant isolates were highly resistant reaching penicillin G MIC levels of 5000 µ/ml. They were speculated to contain Path altered penicillin binding proteins and high level of crosslinking cell wall induced by the gene products of the MurMN operon. RAPD analysis was performed using three primers, MBPZ-1, MBPZ-2, and MBPZ-3, respectively. RAPD analysis allowed for the identification of 27 RAPD types with MBPZ-1 and MBPZ-3 and 26 RAPD types with MBPZ-2. Ninety-eight percent of these isolates were clustered into two groups, group I and group II, with 90% to 100% dissimilarity among them. Fifty two percent of the isolates of MBPZ-1 group I were in MBPZ-2 group I, 72% isolates of MBPZ-1 group I were in MBPZ-3 group I, and 72% of the isolates of MBPZ-2 group I were in MBPZ-3 group 1. This shows the discriminatory ability of the primers used in this study. Despite clustering of isolates, relatively high diversity was seen. PFGE analysis of macrorestriction fragments obtained after digestion of chromosomal DNA by restriction enzyme, SmaI showed 24 PFGE patterns. The 24 PFGE patterns were divided into three groups (I, II and III) of isolates, with an average of 85% dissimilarity (15% homology) among them. At 25% homology, four clusters, A (13 isolates), B (9 isolates), C (4 isolates), and D (4 isolates) were observed. Two pairs of isolates in group I, cluster A, showed 100% homology. This suggested that each represent the same strain. Four isolates of group I, cluster B, also exhibited 100% homology. This study showed that most of streptococcal isolates with the same penicillin G susceptibility patterns grouped together in a phylogenetic tree by both RAPD and PFGE analysis. There was also some similarity between the results obtained by RAPD analysis and PFGE analysis. Seventeen and nine of the 29 isolates grouped into group I and group II, respectively, two pairs of isolates were indistinguishable, and two pairs of islates were closely related by both RAPD (using MBPZ-3) and PFGE analysis. Although, RAPD analysis is sensitive, specific, faster and cost effective, the ease with which PFGE analysis can be performed, high discriminatory power, reproducibility of the results, and the polymorphism seen in the patterns, suggests that PFGE method has the potential to be very useful for epidemiological evaluations of nosocomial streptococcal infections in KwaZulu-Natal.
Characterization of the autolytic systems in selected streptococcal species.
(2005) Naidoo, Kershney.; Beukes, Mervyn.
Autolysins are endogenous enzymes responsible for the cleavage of specific bonds in the bacterial sacculus resulting in damage to the integrity and protective properties of the cell wall. The true biological functions of these enzymes are largely unknown. However, they have been implicated in various important biological synthesis processes making their characterization important. Antibiotic susceptibility testing showed these streptococcal strains to have broad spectrum inhibitory concentrations. The major autolysins of selected streptococcal strains were detected and partially characterized by renaturing sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis with substrate-containing gels (zymograms). The autolysins were isolated from the specific culture supematants using 4% SDS precipitation and were shown to have apparent molecular masses ranging from 60kDa to 20kDa. Four major autolysins named A, B, C, and D from the Streptococcus milleri 77 strain were characterized. Lytic enzymes were blotted onto polyvinylidene difluoride (PVDF) membrane and N-terminally sequenced. Sequences showed between 100% and 80% similarity to that of a muramidase, glucosaminidase and a peptidase from S. mutans, S. pyogenes and S. pneumonia respectively. Biochemical characterization confirmed autolysin A to exhibit muramidase activity with both autolysin Band C exhibiting endopeptidase activity. Autolysin D showed an 80% N-terminal sequence similarity to Millericin B, a peptidoglycan hydrolase that is known to exhibit peptidase activity. Autolysis was determined using different buffers at two optimal pHs. Assaying for autolytic activity at different growth stages showed autolysis to be moderate during the lag and early exponential phases of the growth cycle. The activities of autolysins were the highest in the late exponential phase and the stationary phase of growth. Zymogram analysis showed that the Streptococcal milleri strains had moderate autolytic expression during the early and late exponential phases of the growth cycle. Control regulatory mechanisms of autolysins were determined in the presence or absence of specific charged groups, such as teichoic acids. In each case the absence of these charged groups inhibited the rate of autolysis, suggesting that the absence of teichoic acids could play a role in the regulation of the autolysins. Two-dimensional-SDS and zymographic-electrophoresis was used to determine total protein profiles for each strain. This is the first report using twodimensional zymography. Specific proteins which were either up- or down-regulated were identified.
Cloning, expression and purification of the immunity factor associated with leucocin A production.
(2004) Pillay, Kovashni.; Beukes, Mervyn.
Leucocin A is a bacteriocin produced by Leucoconostoc gelidium UAL 187-22. Bacteriocin producer strains possess an immunity protein, which enables the strain to protect itself against its own bacteriocin. The immunity gene from Leucoconostoc gelidium was isolated via PCR from a recombinant clone pJF5.5. This fragment was cloned by amplifying the immunity gene from pJF5.5 and ligating it into pMALc2. The resulting recombinant plasmid pKP1 was then transformed into Escherichia coli strain JM103. The clone putative, was confirmed by DNA sequencing and southern blot hybridization using the primers EAL-2 and EAL-3. It was shown to contain an insert of 3.6 kb. Expression analysis showed the construct as an in frame malE fusion protein expressed within E. coli. The fusion construct was isolated by affinity chromatography. Leucocin A was purified to 90% purity, from the supernatant of Leucocnostoc gelidium UAL 187-22 by ion-exchange chromatography and HPLC. It was found to elute from a C18 reverse phase column at 55% actetonitrile, 0.1% TFA. Binding interaction and the stability of the immunity gene fusion protein were compared using a Biacore 2000. The supernatant and cytoplasmic extract isolated from Leucocnostoc gelidium UAL 187-22 were tested for interaction with the fusion construct. Surface Plasmon resonance studies indicated that there was no binding partner present in the supernatant which would influence the immunity process. However, a stable interaction was found between the immunity protein and an orphan ligand within the cytoplasm.
Cloning, expression and purification of the subunits of the Mannose PTS Permease of Listeria monocytogenes EGD.
(2010) Mia, Rizwana.; Beukes, Mervyn.; Watson, Gregory M. F.
The disease listeriosis is caused by Listeria monocytogenes. This common food-borne disease has been responsible for about 0.1 to 10 cases per million inhabitants per year. However, this disease is serious with its high fatality rates of 20% - 30%, and 40% of all cases reported have been in pregnant women suffered from a foetal abortion. Recently the organism has acquired resistance to antibiotic treatment and the development of an alternative treatment is necessary. Class IIa bacteriocins such as leucocin A have been shown to be active against L. monocytogenes. However, the leucocin A receptor molecule responsible for growth inhibition within L. monocytogenes remains unclear. Various studies have implicated the mannose PTS permease (EIIt Man) of L. monocytogenes as the putative receptor for class IIa bacteriocins. The results from studies reviewed indicate that the EIIt Man of L. monocytogenes could be the chiral receptor needed for bacteriocin interaction at the surface of targeted cells. Specifically, the membrane associated IIDMan and IICMan subunits were implicated in direct interaction with class IIa bacteriocins. Our study focused on cloning, expression and purification of the subunits of the mannose PTS permease of L. monocytogenes EGD. Primers were designed to amplify the subunit genes of the mptACD operon. The mptC, mptD and mptAB genes which were then successfully cloned into pET28a expression vector and transformed into E. coli JM109(DE3) host strain. Recombinant plasmids were screened using colony PCR. Subsequently recombinant pET28-C, pET28-D and pET28-AB was once again transformed and expressed in the E. coli BL21(DE3) pLysS expression host strain. After an induction at 30°C for 5 hours, IICMan and IIDMan were found to be expressed in the cell membrane, whilst IIABMan was expressed in the cytosol of the host expression strain. Membrane proteins His-IICMan, His- IIDMan, and cytosol associated His-IIABMan were purified using Ni2+-NTA affinity chromatography. Results for His-IICMan yielded a 28 kDa protein and a 55 kDa co-purified protein. Results for His-IIDMan yielded a 31 kDa protein and a 60 kDa co-purified protein. Results for His-IIABMan yielded a 35 kDa protein and a 68 kDa co-purified protein. A western blot analysis revealed that all proteins purified carried an attached His-tag as detected by an anti-mouse peroxidase conjugate anti-His-tag antibody.
A comparative socio-economic impact analysis of the 2010 Comrades Marathon on the cities of Durban and Pietermaritzburg.
(2015) Maharajh, Ashok.; Van Heerden, Johan.
Sport has always been a significant component of society but is now becoming an increasingly significant component of the economy. Recent years have seen the staging of hallmark and mega-events in sport as increasingly important in the development of a tourist product centered on large cities (Jones, 2001). Studies that assess the impact of hallmark and mega-events often focus on the economic impact of the host economy. Such events are often rationalised as an economic initiative of the host governing authority. This study aspires to estimate the economic and social impacts of a large one-day international sporting event viz. the 2010 Comrades Marathon on the economies of two cities viz. Pietermaritzburg and Durban. A secondary objective is to demonstrate the value of such a major sporting event to the regional and provincial governments as well as formal and informal businesses in the said cities. This study also addresses the social impact of the event on the residents and communities in KwaZulu-Natal. According to Matheson (2006) the role of sports in a society such as South Africa in driving the developmental agenda cannot be over-emphasised. He stated that sporting events do not only play an important economic role but are also useful catalysts in forging social cohesion and nation building. This study also seeks to investigate the socio-economic impact of the 2010 FIFA World Cup that was hosted in South Africa on the Comrades Marathon. Durban was one of the nine cities that hosted games whilst Pietermaritzburg was utilised as a training venue by one of the international teams. It is important to note that the first World Cup match was played eleven days after the Comrades Marathon was run. The study also seeks to investigate the regional origins of visitors to the event and the relationship between the visitors both national and international and the expenditure generated at the event. Durban and Pietermaritzburg like other key cities in the world are and will increasingly be confronted by two vital and related challenges. Firstly, there is need to successfully compete in a universal economy characterised by increased competition and globalisation. Secondly, there is need to eliminate poverty and address issues of inequality and marginalisation. Thus, the Comrades Marathon, as a hallmark sporting event, can be seen as a primary driver to create jobs and contribute to competitiveness. The organisation of major sporting events is a crucial time in the lives of large cities. It provides them with an opportunity to promote themselves, their energy and creativity and, increasingly, their competitiveness. However, it also involves exchanging experiences in this field so as to control the effects, minimise possible risks and guarantee positive results as far as possible. Measuring the effect of an event on the development of a city is a complex and demanding task. This exercise spreads over a variety of different spheres viz. the economy, society, tourism, public finance, organisation capacity, infrastructures, public confidence and international reputation. Much of the analysis in this study was undertaken using a questionnaire survey to interview the key interest groups at the registration venues in both the cities prior to the event and on race day at the finish venue in Durban. The data collected was then analysed using a specialist statistical software package viz. SPSS to calculate the additional expenditure in the host cities. In certain instances, face-to-face interviews were employed to collect the data. The questionnaire requested data on places of residence, the age, gender, occupations, income, spending patterns, features of the cities, unsavoury incidents experienced and the types of activities that the population found attractive. The population comprised of foreign runners and supporters, domestic runners and supporters that reside in other provinces of South Africa, residents of the cities, stall holders at the registration venues, representatives of the sponsors of the event, the organizer of the Bonitas Comrades Experience, vendors, the organisers of the event and representatives of selected shopping malls and hotels in the cities. A truly great sports event is an event where the impact and spin-offs for all those involved viz. the organisers, the community within which the event takes place, the participants and possibly the government, is a positive one when clear benefit is acquired from the event. The Statistical Package for the Social Sciences (SPSS) was used to analyse the data collected. The Chi-Square Test and the Analysis of Variance were applied in this study. The chi-square test was used to determine whether there is a significant difference between the expected frequencies and the observed frequencies in one or more categories. The ANOVA (Analysis of Variance) was used to analyse the differences between group means and their associated procedures. It provides a statistical test of whether or not the means of several groups are equal and is useful in comparing/testing three or more means i.e. groups or variables for statistical significance. The p-value of 0.001 that was computed revealed that there was a significant difference in terms of the racial groups amongst the respondents who resided in Durban and Pietermaritzburg. This can be attributed to the substantial increase in the number of participants and their supporters and family members that arrived in the cities because of the aggressive marketing campaign that the CMA had conducted both internationally and nationally and the fact that the 2010 FIFA World Cup was hosted by South Africa. The p-value regarding the income earned by the respondents was calculated to be 0.001 which showed that there was a significant difference in the income of the respondents who visited the registration venues in Durban and Pietermaritzburg. The p-value of 0.8 revealed that there was no significant difference in the age categories of the respondents that resided in both the cities. A p-value of 0.001 confirmed that there was a significant difference in the items the respondents purchased in the cities. The p-value of 0.20 verified that there was no significant difference in the various types of accommodation establishments that the respondents utilized in both cities. The p-value of 0.001 indicated that there was a significant difference in the duration of stay of the respondents who resided in Durban and those who resided in Pietermaritzburg. The findings of this study revealed that a grand total of R130 978 314 was new income that was generated by the participants, their families and friends. This amount comprised of R110 340 612 that was generated in Durban and R20 637 702 in Pietermaritzburg. A closer examination of the amount generated in Durban showed that R93 397 920 was the average daily expenditure of the participants, their families and friends and that R16 942 692 was the expenditure spent on accommodation. The findings also revealed that of the total amount spent in Pietermaritzburg the sum of R16 283 266 was the average daily expenditure by the participants, their families and friends and R4 354 436 represented the expenditure spent by the afore-mentioned on accommodation. This bodes well for the event, the organisers and the Cities of Durban and Pietermaritzburg. It must also be noted that the Comrades Marathon also brings additional intangible benefits for the local and South African fraternity. The event is also likely to have significant yet unquantifiable benefits for the local economy by presenting Durban and Pietermaritzburg in a positive light to the South African television audience and to its potential participants and their supporters. In addition to the quantifiable impacts related to the Comrades Marathon that was previously discussed, the event also engendered significant intangible benefits to the communities of Durban and Pietermaritzburg in terms of lifestyle improvements. Examples of the intangible benefits are: • significant national and international exposure for the cities as sport fans who enjoyed their visits to the cities may return later thereby raising future tourist revenues • enhancing community pride, self-image, exposure, reputation and prestige associated with hosting a world-famous event and in this way creating a climate of optimism • enhancing the national and international image of the cities so that they become world-class cities and travel destinations • enhancing economic growth and ancillary private sector development spurred on by the operations and activities associated with the Comrades Marathon • providing assets in the cities e.g. the International Convention Centre (ICC) in Durban that can augment their world-class attractions, accommodations and international airport • increase in tourism • promoting the cultural diversity of the population in terms of race, ethnicity and religion • motivate the community to develop active healthy lifestyles and in so doing reduce absenteeism and increase productivity in the work place Furthermore, there is escalating evidence that the media coverage of the race has improved. Gerretsen (2006) reported that Tourism KZN confirmed that the race was viewed by millions because of the television coverage. It is envisaged that television viewers might decide to take a trip to the city at some time in the future based on what they see during the broadcast of the event. This is an exceptional way to showcase the province’s scenic beauty and the warmth and hospitality of its inhabitants. The potential of the Comrades Marathon to attract more visitors and for the visitors to stay longer is indicated by the number of visitors who expressed an interest in existing activities and/or attractions which are related to sport and recreation. The Comrades Marathon is an excellent example of a hallmark sporting event that attracts “outsiders” to the region and the cities. These tourists thus generate “new money” into the economies of the cities and the province.
Computer simulation of marker-assisted selection utilizing linkage disequilibrium.
(2006) Keildson, Sarah.; Hancock, Carolyn Elizabeth.
The face of animal breeding has changed significantly over the past few decades. Traditionally, the genetic improvement of both plant and animal species focussed on the selective breeding of individuals with superior phenotypes, with no precise knowledge of the genes controlling the traits under selection. Over the past few decades, however, advances in molecular genetics have led to the identification of genetic markers associated with genes controlling economically important traits, which has enabled breeders to enhance the genetic improvement of breeding stock through linkage disequilibrium marker-assisted selection. Since the integration of marker-assisted selection into breeding programmes has not been widely documented, it is important that breeders are able to evaluate the advantages and disadvantages of marker-assisted selection, in comparison to phenotypic selection, prior to the implementation of either selection strategy. Therefore, this investigation aimed to develop deterministic simulation models that could accurately demonstrate and compare the effects of phenotypic selection and marker-assisted selection, under the assumption of both additive gene action and complete dominance at the loci of interest. Six computer models were developed using Microsoft Excel, namely 'Random Mating,' 'Phenotypic Selection,' 'Marker-Assisted Selection,' 'Selection with Dominance,' 'Direct Selection' and 'Indirect selection.' The 'Random Mating' model was firstly used to determine the effects of linkage disequilibrium between two loci in a randomly mating population. The 'Phenotypic Selection' and 'Marker-Assisted Selection' models focused primarily on examining and comparing the response to these two selection strategies over five generations and their consequent effect on genetic variation in a population when the QTL of interest exhibited additive gene action. In contrast, the 'Selection with Dominance' model investigated the efficiency of phenotypic selection and marker-assisted selection under the assumption of complete dominance at the QTL under selection. Finally, the 'Direct Selection and 'Indirect Selection' models were developed in order to mimic the effects of marker assisted selection on two cattle populations utilizing both a direct and indirect marker respectively. The simulated results showed that, under the assumption of additive gene action, marker-assisted selection was more effective than phenotypic selection in increasing the population mean, when linkage disequilibrium was present between the marker locus and the QTL under selection and the QTL captured more than 80% of the trait variance. The response to both selection strategies was shown to decrease over five generations due to the decrease in genetic variation associated with selection. When the QTL under selection was assumed to display complete dominance, however, marker-assisted selection was markedly more effective than phenotypic selection, even when a minimal amount of linkage disequilibrium was present in the population and the QTL captured only 60% of the trait variance. The results obtained in this investigation were successful in simulating the theoretical expectations of markerassisted selection. The computer models developed in this investigation have potential applications in both the research and agricultural sectors. For example, the successful application of a model developed in this investigation to a practical situation that simulated markerassisted selection, was demonstrated using data from two Holstein cattle populations. Furthermore, the computer models that have been developed may be used in education for the enhancement of students understanding of abstract genetics concepts such as linkage disequilibrium and marker-assisted selection.
Conservation genetics of the Hooded vulture Necrosyrtes monachus.
(2023) Le Roux, Rynhardt.; Willows-Munro, Sandi.; Van Vuuren, Bettine.; Thompson, Lindy Jane.
African vulture species have experienced rapid population declines, due to many anthropogenic threats. Hooded vultures are no exception and have experienced dramatic declines and are now listed as Critically Endangered on the IUCN Red Data list. Two subspecies of Hooded vulture have been described : Necrosyrtes monachus monachus which occurs in West Africa and Necrosyrtes monachus pileatus which occurs in East and southern Africa. The two subspecies differ in their feeding behaviour and morphology supporting the validity of the subspecies status. However, the validity of this taxonomic grouping is still being questioned. Clarifying the taxonomic status of the subspecies is important as if the two subspecies are genetically distinct then they should not be managed as a single species and current conservation policies would need to be updated. In addition, there is limited information available on many aspects of Hooded vulture life history including the factors affecting reproduction in the wild. In Chapter 2 I use microsatellite data collected from across the distributions of the two subspecies and Approximate Bayesian Computation (ABC) to test the hypothesis that the two subspecies are genetically distinct and should be elevated to separate species. In Chapter 3 I examine the genetic variation present in the South African Hooded vulture population. This population only includes 100-200 individuals and is at the edge of the southern range of the species. The conservation value of peripheral populations is debatable as these populations are often isolated and smaller with genetic drift and inbreeding leading to reduced genetic variability. In contrast, studying the genetic diversity in range-edge populations is important for understanding range shifts and adaptive capacity under climate change. These edge populations could potentially also retain unique genetic diversity which helps with the adaptation of species to different environments. Vulture colonies act as “food finding information hubs” allowing for the exchange of information regarding potential food resources. This explains, in part, the high-levels of relatedness often found within colonies as close relatives are more likely to tolerate the cost of sharing food by increasing their inclusive fitness. Hooded vultures are tree nesters with a single breeding pair per tree. In Chapter 4 I use the genetic data to test if individuals nesting close to each other are closely related and if the same individuals use the same nest over multiple years. The analyses conducted in Chapter 2 did not support the existence of the two subspecies classification, due to different demographic events experienced between the two groups. The next factor indicating that there is no subspeciation is the contemporary gene flow that is still seen between the population (m = 0.188) and the little variance seen between the two subspecies (11.9%). Structure analysis also does not support the formation of two distinct subspecies. Thus, this study supports the claim made by Mundy 2021 that it is size cline and not speciation. In Chapter 3 the genetic data did not support the hypothesis that the small South African population was genetically depauperate, instead the results show that the South African population contained similar levels of genetic diversity (Ho = 0.495) to that recorded for the Ghanaian population (Ho = 0.315) where Hooded vultures are more abundant. Levels of heterozygosity were similar to those recorded for other species of Old World vultures such as Cape Vultures (Gyps coprotheres, Ho = 0.380), and Bearded vultures (Gypaetus barbatus Ho = 0.400 – 0.480), but differed from the Griffon Vulture (Gyps fulvus Ho = 0.530 – 0.600) found in Europe. Worryingly, both populations of Hooded vultures show elevated levels of inbreeding and relatedness. The bottleneck analysis for both populations show no sign of a recent bottleneck and a normal L shaped distribution for both populations. In Chapter 4 breeding pairs were not found to reuse the same nests over multiple years. A negative correlation was seen between genetic distance and geographical distance (R2 = 0.0117; p-value = 0.012) the closer related individuals thus tend to nest further away from each other. The spatial autocorrelation shows a positive correlation between genetic and geographical distance between distance classes 8 km – 16km, 32 km – 40km and then between 88 km – 112km, but no clear support for increased relatedness between closer nesting individuals. Thus no support is seen for the formation of loose colonies to function as food finding information sharing hubs. African vultures are facing a number of challenges and most species are considered of conservation concern. Despite this limited genetic data is available for many species. This study aimed to fill this knowledge gap by generating and analysing microsatellite data for the Critically Endangered Hooded vulture to answer a number of key hypotheses. As such this study makes an important contribution towards the conservation of Hooded vultures across Africa.
Designing T-cell epitope-based vaccine against Eimeria infection in chicken using immunoinformatics approach.
(2021) Madlala, Thabile.; Adeleke, Matthew Adekunle.; Okpeku, Moses.
Chicken coccidiosis is the most significant ubiquitous, intestinal parasitic disease known to infect chickens globally. It is recognised for incurring significant production loss to the poultry industry, caused by single or multiple Eimeria spp. infections which threaten chicken welfare and productivity. The emergence of drug resistance in parasites and pathogenicity reversion has put pressure on the poultry industry to reduce chemoprophylactic drugs and live vaccines as preventive measures against coccidiosis. Recombinant DNA vaccines have shown promising results as an alternative option, but complete protection has not been reported highlighting the need for the design of new vaccine against this disease. In this study, Eimeria antigens Immune Mapped Protein-1(IMP1) and Microneme Protein-2(MIC2) were explored using reverse vaccinology and immunoinformatics tool to predict and design potential multiepitope vaccine candidate against coccidiosis. A total of 28 and 19 antigenic T-cell epitopes were predicted and used to construct two multiepitope vaccines with 610 and 512 amino acids for IMP1 and MIC2, respectively. The produced vaccines exhibited favoured characteristics for an ideal vaccine candidate; they were antigenic (Vaxijen score of 0.5989 and 0.5103), immunogenic (scores: 10.15 and 9 419), thermostable (instability index <40 ), and non-allergic. The presence of IFN-gamma and IL-4 inducing epitopes in the constructed vaccine enables vaccine to trigger a cellular and humoral response within the host. Molecular docking of designed vaccines with toll-like receptors (TLR4 and TLR5) to determine vaccine interaction and stability was confirmed by molecular dynamics simulation root-mean square deviation (RMDS) and root-mean-square fluctuation (RMSF) analysis. The designed vaccines induced immune response through production of cytokines and antibodies associated with tertiary response. When exposed to online immune simulation C-ImmSim, both vaccines produced potent immune response through production of IgG, Tc and Th cell and memory Bcells. The constructed multiepitope vaccine in this present study is highly promising and as such further experimental work should be done to confirm its suitability against chicken coccidiosis.
The development of a white clover for use in the eastern high potential areas of South Africa.
(1988) Smith, Albert.; Reusch, J. Dieter H.
The problems associated with the use of white clover in pastures in the eastern high potential areas of South Africa i.e. high P requirements, low tolerance to high Al levels and low pH in the soil as well as a limited survival time of approximately 30 months, were identified and found to be related to the inadequate root system of white clover cultivars. During the improvement programme cultivars available on the world market were introduced and evaluated under dryland conditions. Selections were made from these introductions on the basis of root conformation in high AI, low pH soils, their response to grazing and induced moisture stress. A laboratory technique for the improvement of Al tolerance was developed and the tolerance of white clover plants to high levels of Al was improved but due to the complexity of pasture plant improvement it was decided that the selection for tolerance to Al could be more effectively carried out in the field. The effectiveness of vesicular arbuscular mycorrhizas as phosphate gatherers indicated that local strains of mycorrhizas combined as effectively with white clover as the imported strains. As no seed production of white clover is undertaken in South Africa guidelines for local seed production were also established. As a result of the improvement programme, Trifolium repens cv. DUSI was developed as an open pollinated synthetic variety, based on thirty eight selected mother lines. DUSI has a greater tolerance to high AI, low pH, low P in the soil and due to an improved root system with a high percentage of secondary taproots produces better under dryland conditions and has a longer stand life than any of the cultivars of white clover available on the local market. Plant Breeders Rights were obtained for cv. DUSI and the cultivar was inscribed on the South African variety list. Limited amounts of Breeders seed have been made available to the South African Forage Seed Association for commercial seed production.

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