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Search Results: 1 - 10 of 58 matches for " Stothard "
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Future trypanosomatid phylogenies: refined homologies, supertrees and networks
Stothard, JR;
Memórias do Instituto Oswaldo Cruz , 2000, DOI: 10.1590/S0074-02762000000400014
Abstract: there has been good progress in inferring the evolutionary relationships within trypanosomes from dna data as until relatively recently, many relationships have remained rather speculative. ongoing molecular studies have provided data that have adequately shown trypanosoma to be monophyletic and, rather surprisingly, that there are sharply contrasting levels of genetic variation within and between the major trypanosomatid groups. there are still, however, areas of research that could benefit from further development and resolution that broadly fall upon three questions. are the current statements of evolutionary homology within ribosomal small sub-unit genes in need of refinement? can the published phylograms be expanded upon to form `supertrees' depicting further relationships? does a bifurcating tree structure impose an untenable dogma upon trypanosomatid phylogeny where hybridisation or reticulate evolutionary steps have played a part? this article briefly addresses these three questions and, in so doing, hopes to stimulate further interest in the molecular evolution of the group.
Future trypanosomatid phylogenies: refined homologies, supertrees and networks
Stothard JR
Memórias do Instituto Oswaldo Cruz , 2000,
Abstract: There has been good progress in inferring the evolutionary relationships within trypanosomes from DNA data as until relatively recently, many relationships have remained rather speculative. Ongoing molecular studies have provided data that have adequately shown Trypanosoma to be monophyletic and, rather surprisingly, that there are sharply contrasting levels of genetic variation within and between the major trypanosomatid groups. There are still, however, areas of research that could benefit from further development and resolution that broadly fall upon three questions. Are the current statements of evolutionary homology within ribosomal small sub-unit genes in need of refinement? Can the published phylograms be expanded upon to form `supertrees' depicting further relationships? Does a bifurcating tree structure impose an untenable dogma upon trypanosomatid phylogeny where hybridisation or reticulate evolutionary steps have played a part? This article briefly addresses these three questions and, in so doing, hopes to stimulate further interest in the molecular evolution of the group.
Genetic diversity and genetic exchange in Trypanosoma cruzi: dual drug-resistant "progeny" from episomal transformants
Stothard, JR;Frame, IA;Miles, MA;
Memórias do Instituto Oswaldo Cruz , 1999, DOI: 10.1590/S0074-02761999000700027
Abstract: extensive characterisation of trypanosoma cruzi by isoenzyme phenotypes has separated the species into three principal zymodeme groups, z1, z2 and z3, and into many individual zymodemes. there is marked diversity within z2. a strong correlation has been demonstrated between the strain clusters determined by isoenzymes and those obtained using random amplified polymorphic dna (rapd) profiles. polymorphisms in ribosomal rna genes, in mini-exon genes, and microsatellite fingerprinting indicate the presence of at least two principal t. cruzi genetic lineages. lineage 1 appears to correspond with z2 and lineage 2 with z1. z1 (lineage 2) is associated with didelphis. z2 (lineage 1) may be associated with a primate host. departures from hardy-weinberg equilibrium and linkage disequilibrium indicate that propagation of t. cruzi is predominantly clonal. nevertheless, two studies show putative homozygotes and heterozygotes circulating sympatrically: the allozyme frequencies for phosphoglucomutase, and hybrid rapd profiles suggest that genetic exchange may be a current phenomenon in some t. cruzi transmission cycles. we were able to isolate dual drug-resistant t. cruzi biological clones following copassage of putative parents carrying single episomal drug-resistant markers. a multiplex pcr confirmed that dual drug-resistant clones carried both episomal plasmids. preliminary karyotype analysis suggests that recombination may not be confined to the extranuclear genome.
Genetic diversity and genetic exchange in Trypanosoma cruzi: dual drug-resistant "progeny" from episomal transformants
Stothard JR,Frame IA,Miles MA
Memórias do Instituto Oswaldo Cruz , 1999,
Abstract: Extensive characterisation of Trypanosoma cruzi by isoenzyme phenotypes has separated the species into three principal zymodeme groups, Z1, Z2 and Z3, and into many individual zymodemes. There is marked diversity within Z2. A strong correlation has been demonstrated between the strain clusters determined by isoenzymes and those obtained using random amplified polymorphic DNA (RAPD) profiles. Polymorphisms in ribosomal RNA genes, in mini-exon genes, and microsatellite fingerprinting indicate the presence of at least two principal T. cruzi genetic lineages. Lineage 1 appears to correspond with Z2 and lineage 2 with Z1. Z1 (lineage 2) is associated with Didelphis. Z2 (lineage 1) may be associated with a primate host. Departures from Hardy-Weinberg equilibrium and linkage disequilibrium indicate that propagation of T. cruzi is predominantly clonal. Nevertheless, two studies show putative homozygotes and heterozygotes circulating sympatrically: the allozyme frequencies for phosphoglucomutase, and hybrid RAPD profiles suggest that genetic exchange may be a current phenomenon in some T. cruzi transmission cycles. We were able to isolate dual drug-resistant T. cruzi biological clones following copassage of putative parents carrying single episomal drug-resistant markers. A multiplex PCR confirmed that dual drug-resistant clones carried both episomal plasmids. Preliminary karyotype analysis suggests that recombination may not be confined to the extranuclear genome.
A Fresh Insight into Transmission of Schistosomiasis: A Misleading Tale of Biomphalaria in Lake Victoria
Claire J. Standley, Christopher M. Wade, J. Russell Stothard
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026563
Abstract: Lake Victoria is a known hot-spot for Schistosoma mansoni, which utilises freshwater snails of the genus Biomphalaria as intermediate hosts. Different species of Biomphalaria are associated with varying parasite compatibility, affecting local transmission. It is thought that two species, B. choanomphala and B. sudanica, inhabit Lake Victoria; despite their biomedical importance, the taxonomy of these species has not been thoroughly examined. This study combined analysis of morphological and molecular variables; the results demonstrated that molecular groupings were not consistent with morphological divisions. Habitat significantly predicted morphotype, suggesting that the different Lake Victorian forms of Biomphalaria are ecophentoypes of one species. The nomenclature should be revised accordingly; the names B. choanomphala choanomphala and B. c. sudanica are proposed. From a public health perspective, these findings can be utilised by policy-makers for better understanding of exposure risk, resulting in more effective and efficient control initiatives.
Comparing thousands of circular genomes using the CGView Comparison Tool
Jason R Grant, Adriano S Arantes, Paul Stothard
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-202
Abstract: The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG (Clusters of Orthologous Groups of proteins) category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation.CCT can be used to visually compare a reference sequence to thousands of existing genomes or sequence collections (next-generation sequencing reads for example) on a standard desktop computer. It provides analysis and visualization functionality not available in any existing circular genome visualization tool. By visually presenting sequence conservation information along with functional classifications and sequence composition characteristics, CCT can be a useful tool for identifying rapidly evolving or novel sequences, horizontally transferred sequences, or unusual functional properties in newly sequenced genomes. CCT is freely available for download at http://stothard.afns.ualberta.ca/downloads/CCT/ webcite.
Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex
Karlene H Lynch, Paul Stothard, Jonathan J Dennis
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-599
Abstract: KS5, KS14 and KL3 are myoviruses with the A1 morphotype. The genomes of these phages are between 32317 and 40555 base pairs in length and are predicted to encode between 44 and 52 proteins. These phages have over 50% of their proteins in common with enterobacteria phage P2 and so can be classified as members of the Peduovirinae subfamily and the "P2-like viruses" genus. The BCC phage proteins similar to those encoded by P2 are predominantly structural components involved in virion morphogenesis. As prophages, KS5 and KL3 integrate into an AMP nucleosidase gene and a threonine tRNA gene, respectively. Unlike other P2-like viruses, the KS14 prophage is maintained as a plasmid. The P2 E+E' translational frameshift site is conserved among these three phages and so they are predicted to use frameshifting for expression of two of their tail proteins. The lysBC genes of KS14 and KL3 are similar to those of P2, but in KS5 the organization of these genes suggests that they may have been acquired via horizontal transfer from a phage similar to λ. KS5 contains two sequence elements that are unique among these three phages: an ISBmu2-like insertion sequence and a reverse transcriptase gene. KL3 encodes an EcoRII-C endonuclease/methylase pair and Vsr endonuclease that are predicted to function during the lytic cycle to cleave non-self DNA, protect the phage genome and repair methylation-induced mutations.KS5, KS14 and KL3 are the first BCC-specific phages to be identified as P2-like. As KS14 has previously been shown to be active against Burkholderia cenocepacia in vivo, genomic characterization of these phages is a crucial first step in the development of these and similar phages for clinical use against the BCC.The Burkholderia cepacia complex (BCC) is a group of at least seventeen species of Gram-negative opportunistic pathogens. Although these organisms can infect patients with a broad range of chronic conditions, the majority of infections occur in those with cystic fibrosi
Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages
Karlene H Lynch, Paul Stothard, Jonathan J Dennis
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-223
Abstract: KL1 and AH2 exhibit several unique phenotypic similarities: they infect the same B. cenocepacia strains, they require prolonged incubation at 30°C for the formation of plaques at low titres, and they do not form plaques at similar titres following incubation at 37°C. However, despite these similarities, we have determined using whole-genome pyrosequencing that these phages show minimal relatedness to one another. The KL1 genome is 42,832 base pairs (bp) in length and is most closely related to Pseudomonas phage 73 (PA73). In contrast, the AH2 genome is 58,065 bp in length and is most closely related to Burkholderia phage BcepNazgul. Using both BLASTP and HHpred analysis, we have identified and analyzed the putative virion morphogenesis, lysis, DNA binding, and MazG proteins of these two phages. Notably, MazG homologs identified in cyanophages have been predicted to facilitate infection of stationary phase cells and may contribute to the unique plaque phenotype of KL1 and AH2.The nearly indistinguishable phenotypes but distinct genomes of KL1 and AH2 provide further evidence of both vast diversity and convergent evolution in the BCC-specific phage population.
Analysis of genetic diversity of Trypanosoma cruzi: an application of riboprinting and gradient gel electrophoresis methods
Stothard, JR;Frame, IA;Carrasco, HJ;Miles, MA;
Memórias do Instituto Oswaldo Cruz , 2000, DOI: 10.1590/S0074-02762000000400017
Abstract: analysis of restriction fragment length polymorphism (rflp) profiles derived from digestion of polymerase chain reaction (pcr) products of the ribosomal 18s from trypanosoma cruzi yields a typical `riboprint' profile that can vary intraspecifically. a selection of 21 stocks of t. cruzi and three outgroup taxa: t. rangeli, t. conorhini and leishmania braziliensis were analysed by riboprinting to assess divergence within and between taxa. t. rangeli, t. conorhini and l. braziliensis could be easily differentiated from each other and from t. cruzi. phenetic analysis of pcr-rflp profiles indicated that, with one or two exceptions, stocks of t. cruzi could be broadly partitioned into two groups that formally corresponded to t. cruzi i and t. cruzi ii respectively. to test if ribosomal 18s sequences were homogeneous within each taxon, gradient gel electrophoresis methods were employed utilising either chemical or temperature gradients. upon interpretation of the melting profiles of riboprints and a section of the 18s independently amplified by pcr, there would appear to be at least two divergent 18s types present within t. cruzi. heterogeneity within copies of the ribosomal 18s within a single genome has therefore been demonstrated and interestingly, this dimorphic arrangement was also present in the outgroup taxa. presumably the ancestral duplicative event that led to the divergent 18s types preceded that of speciation within this group. these divergent 18s paralogues may have, or had, different functional pressures or rates of molecular evolution. whether or not these divergent types are equally transcriptionally active throughout the life cycle, remain to be assessed.
Control of urinary schistosomiasis on Zanzibar (Unguja Island): a pilot evaluation of the educational impact of the Juma na Kichocho health booklet within primary schools
Stothard, JR;Mook, P;Mgeni, AF;Khamis, IS;Khamis, AN;Rollinson, D;
Memórias do Instituto Oswaldo Cruz , 2006, DOI: 10.1590/S0074-02762006000900019
Abstract: to improve health education within primary schools, the health education booklet juma na kichocho was evaluated during a study within 5 schools using key-informant questionnaires that recorded children's knowledge and attitude (ka) towards schistosomiasis before and after daily structured-use of booklets. a total of 229 schoolchildren (114 boys : 115 girls) of between 11 and 15 years of age were interviewed and re-assessed after a working school week. existing and putative booklet-induced changes in ka scores for schistosomiasis were compared directly against equivalent ka scores for malaria. in total 47.4% of children were already aware that schistosomiasis was a water-borne disease while only 10.5% knew of its exact aetiology; after booklet intervention these levels increased to 54.6 and 15.7%, respectively. the majority of children still failed, however, to realise that re-infection could take place soon after treatment. while a positive increase was observed for children's total ka questionnaire scores for both malaria and schistosomiasis after booklet intervention, these were not statistically significant. in the context of control, further educational efforts are needed to promote and guide behavioural change, especially in relation to reduction of environmental water contact.
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