410 research outputs found

    Sequence analysis of an HIV-1 subtype C acutely infected cohort from Durban, South Africa.

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    Masters Degree. University of KwaZulu-Natal, Durban.The Human Immunodeficiency Virus is a global public health concern. The Joint United Nations Programme on HIV/AIDS estimated that 36.9 million people were infected with HIV globally at the end of 2017. Almost 20% of these resided in South Africa, making this the highest global HIV burden held by any one country. It is thus important that HIV infection be detected early as this may have important implications in the control of the pandemic. The early recognition of acute HIV infection could present early treatment options that could alter the natural history of the disease, or even eliminate infection. Detecting acute infection early could also provide a unique opportunity to understand HIV transmission and pathogenesis, including early host-virus interactions. In the present study, blood samples were collected from 18-23 year old HIV-1 subtype C acutely infected women from Umlazi Township in KwaZulu-Natal, South Africa, that had participated in a study called Females Rising through Education, Support and Health (FRESH). Eleven blood samples from this cohort, collected within 24 hours of onset of plasma viremia, were used for this study. The aim of the present research was to identify sites within pol that were experiencing positive selective pressure and the likely implications of these mutations on viral functional domains and host cytotoxic T-lymphocyte (CTL) epitopes. The study also sort to observe the loss of drug resistant mutations (DRM) in the viral sequences of participants who had multiple timepoints and to correlate mutation loss to structural changes. Datamonkey and Phylogenetic Analysis by Maximum Likelihood (PAML) were used to detect positively selected sites. Putative functional domains were detected using Prosite and CTL epitopes were identified using the Los Alamos Molecular Immunology Database. Ancestral reconstruction was performed using PAML and Bayesian Evolutionary Analysis by Sampling Trees (BEAST) was used to calculate the time to the most recent common ancestor. Altogether 16 unique positively selected sites were identified in this cohort. Putative functional domains were highly conserved in protease, while positive mutations in reverse transcriptase resulted in either a loss of functional domains in conserved regions or in the gain of functional sites in non-conserved regions. Owing to the important role that protease plays in viral maturation and infectivity, mutations within these conserved regions could possibly lead to defective viral particles with reduced viral infectivity. The K103N in reverse transcriptase, observed in one participant, was the only DRM inherited from its common ancestor. The major limitation of this study was the small sample size

    Development and characterization of molecular tools for microbial forensics

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    Scope and Method of Study:The anthrax attacks of 2001 prompted the rapid establishment and growth of the fields of microbial and plant pathogen forensics. A complete forensic capability includes the ability to discriminate between a natural and an intentional disease outbreak, collection of forensic evidence, generation of genetic profiles for use during attribution and storage of samples. This document describes (i) the molecular characterization of plant virus populations derived from plants that were naturally and mechanically-inoculated with a model plant virus, (ii) the application of microarray-based technologies to genetically fingerprint plant viruses, (iii) the characterization of a previously-designed microarray platform for the identification and diagnosis of known and novel plant viruses, and (iv) the use of FAME profiles to aid in the discrimination of media components used to prepare Bacillus cereus T-strain spores. Though all of these projects are not directly related, they all fall within the scope of microbial forensics.Findings and Conclusions:The molecular characterization of plant virus populations derived from a natural inoculation event and those from mechanically-inoculated plants displayed minor differences in haplotype and pair-wise nucleotide diversities. Additionally, the number of recombination events was found to be lower in the mechanically-inoculated plants than those collected from the natural disease outbreak. These results indicate that differences between the two types of inoculation events exist and may be a direct function of the infection time, source(s) of inoculum(a) or environmental effects.The solution-based minisequencing and capture array technique demonstrated reproducibility at the same concentration of targets, but was less accurate using variable amounts of synthetic targets. The use of solution-based minisequencing followed by tag-array capture appears to be a promising approach to genotyping plant viruses.A significant amount of cross-hybridization was observed using the universal plant virus microarray (Virochip). The microarray platform failed to strongly hybridize to most of the known plant viruses that were applied to the array. Hybridization with Wheat streak mosaic virus-infected material indicated that the system strongly hybridized with the negative-sense strand, but not the corresponding positive-sense strands.Discrimination of individual media components was achieved by analyzing fatty acids derived from Bacillus cereus T-strain spores prepared in different media. One FAME biomarker, oleic acid, was found to be exclusively associated with media supplemented with blood

    Next-generation development and application of codon model in evolution

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    To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine

    Multilocus phylogeny and ecological differentiation of the "Eupelmus urozonus species group" (Hymenoptera, Eupelmidae) in the West-Palaearctic

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    Background: The ecological differentiation of insects with parasitic life-style is a complex process that may involve phylogenetic constraints as well as morphological and/ or behavioural adaptations. In most cases, the relative importance of these driving forces remains unexplored. We investigate here this question for the “ Eupelmus urozonus species group ” which encompasses parasitoid wasps of potential interest in biological control. This was achieved using seven molecular markers, re liable records on 91 host species and a proxy of the ovipositor length. Results: After using an adequate partitioning scheme, Maximum likelihood and Bayesian approaches provide a well-resolved phylogeny supporting the monophyly of this species group and highlighting its subdivision into three sub-groups. Great variations of both the ovipositor length and the host range (specialist versus generalist) were observed at this scale, with these two features being not significantly constrained by the phylogeny. Ovipositor length was not shown as a significant predictor of the parasitoid host range. Conclusions: This study provides firstly the first evidence for the strong lability of both the ovipositor's length and the realised host range in a set of phylogeneticall y related and sympatric species. In both cases, strong contrasts were observed between sister species. Moreover, no significant correlation was found between these two features. Alternative drivers of the ecological differentiation such as interspecific interactions are proposed and the consequences on the recruitment of these parasitoids on native and exotic pests are discussed

    Evolutionary and structural aspects of Solanaceae RNases T2

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    Plant RNases T2 are involved in several physiological and developmental processes, including inorganic phosphate starvation, senescence, wounding, defense against pathogens, and the self-incompatibility system. Solanaceae RNases form three main clades, one composed exclusively of S-RNases and two that include S-like RNases. We identified several positively selected amino acids located in highly flexible regions of these molecules, mainly close to the B1 and B2 substrate-binding sites in S-like RNases and the hypervariable regions of S-RNases. These differences between S- and S-like RNases in the flexibility of amino acids in substrate-binding regions are essential to understand the RNA-binding process. For example, in the S-like RNase NT, two positively selected amino acid residues (Tyr156 and Asn134) are located at the most flexible sites on the molecular surface. RNase NT is induced in response to tobacco mosaic virus infection; these sites may thus be regions of interaction with pathogen proteins or viral RNA. Differential selective pressures acting on plant ribonucleases have increased amino acid variability and, consequently, structural differences within and among S-like RNases and S-RNases that seem to be essential for these proteins play different functions

    Reconstructing the functions of endosymbiotic Mollicutes in fungus-growing ants

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    International audienceMollicutes, a widespread class of bacteria associated with animals and plants, were recently identified as abundant abdominal endosymbionts in healthy workers of attine fungus-farming leaf-cutting ants. We obtained draft genomes of the two most common strains harbored by Panamanian fungus-growing ants. Reconstructions of their functional significance showed that they are independently acquired symbionts, most likely to decompose excess arginine consistent with the farmed fungal cultivars providing this nitrogen-rich amino-acid in variable quantities. Across the attine lineages, the relative abundances of the two Mollicutes strains are associated with the substrate types that foraging workers offer to fungus gardens. One of the symbionts is specific to the leaf-cutting ants and has special genomic machinery to catabolize citrate/glucose into acetate, which appears to deliver direct metabolic energy to the ant workers. Unlike other Mollicutes associated with insect hosts, both attine ant strains have complete phage-defense systems, underlining that they are actively maintained as mutualistic symbionts

    Comparative genomics of early animal evolution

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    The explosion of genomics permits investigations into the origin and early evolution of the Metazoa at the molecular level. In this thesis, I am particularly interested in investigating the molecular foundation of the animal senses (i.e. how animals perceive their world). To understand the directionality of evolutionary innovation a well-developed phylogenetic framework is necessary. On one hand, the combination of molecular and morphological data sets has revolutionized our views of metazoan relationships over the past decades, but on the other hand, a number of nodes on the metazoan tree remain uncertain. Uncertainty is particularly high with reference to the taxa generally named “early branching metazoans”. Unfortunately, understanding the relationships among these taxa is key to understanding the evolution of sensory perception (Nielsen 2008). In this thesis I will investigate both animal phylogenetics (to attempt to resolve the phylogeny among the early branching Metazoa) and the evolution of the metazoan sensory receptors. The G-protein coupled receptor superfamily (GPCR) superfamily is the main family of metazoan surface receptors. In this thesis, after an initial introduction (Chapter 1), I address and substantially clarify the relationship among the early branching animals (Chapter 2) using novel genomic data and publicly available expressed sequence tags (ESTs). I then move forward (Chapter 3) to use network-based methods to study the early evolution of the GPCR superfamily in Eukaryotes and animals. Finally (Chapter 4), I focus on the study of a specific subset of GPCRs (the a-group, Rhodopsin-like receptors). This GPCR group is particularly interesting as it includes the best studied and, arguably, one of the most interesting among the GPCR families: the Opsin family. Opsins are key proteins used in the process of light detection, and the origin and early evolution of this family are still substantially unknown. Chapter 4 addresses both these problems. The thesis is then concluded by a general discussion (Chapter 5) and a future directions (Chapter 6) section. Overall, this thesis provides new insights into the origin and early evolution of the Metazoa and their senses

    The discovery of novel recessive genetic disorders in dairy cattle : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at AL Rae Centre of Genetics and Breeding, Massey University, Palmerston North, New Zealand

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    The selection of desirable characteristics in livestock has resulted in the transmission of advantageous genetic variants for generations. The advent of artificial insemination has accelerated the propagation of these advantageous genetic variants and led to tremendous advances in animal productivity. However, this intensive selection has led to the rapid uptake of deleterious alleles as well. Recently, a recessive mutation in the GALNT2 gene was identified to dramatically impair growth and production traits in dairy cattle causing small calf syndrome. The research presented here seeks to further investigate the presence and impact of recessive mutations in dairy cattle. A primary aim of genetics is to identify causal variants and understand how they act to manipulate a phenotype. As datasets have expanded, larger analyses are now possible and statistical methods to discover causal mutations have become commonplace. One such method, the genome-wide association study (GWAS), presents considerable exploratory utility in identifying quantitative trait loci (QTL) and causal mutations. GWAS' have predominantly focused on identifying additive genetic effects assuming that each allele at a locus acts independently of the other, whereas non-additive effects including dominant, recessive, and epistatic effects have been neglected. Here, we developed a single-locus non-additive GWAS model intended for the detection of dominant and recessive genetic mechanisms. We applied our non-additive GWAS model to growth, developmental, and lactation phenotypes in dairy cattle. We identified several candidate causal mutations that are associated with moderate to large deleterious recessive disorders of animal welfare and production. These mutations included premature-stop (MUS81, ITGAL, LRCH4, RBM34), splice disrupting (FGD4, GALNT2), and missense (PLCD4, MTRF1, DPF2, DOCK8, SLC25A4, KIAA0556, IL4R) variants, and these occur at surprisingly high frequencies in cattle. We further investigated these candidates for anatomical, molecular, and metabolic phenotypes to understand how these disorders might manifest. In some cases, these mutations were analogous to disorder-causing mutations in other species, these included: Coffin-Siris syndrome (DPF2); Charcot Marie Tooth disease (FGD4); a congenital disorder of glycosylation (GALNT2); hyper Immunoglobulin-E syndrome (DOCK8); Joubert syndrome (KIAA0556); and mitochondrial disease (SLC25A4). These discoveries demonstrate that deleterious recessive mutations exist in dairy cattle at remarkably high frequencies and we are able to detect these disorders through modern genotyping and phenotyping capabilities. These are important findings that can be used to improve the health and productivity of dairy cattle in New Zealand and internationally
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