Comparative genome analysis of trypanotolerance QTL

Joseph Nganga is ILRI authorCertain breeds of domestic ruminants show remarkable resistance to the effects of African trypano-somosis. Unlike susceptible animals, trypanotolerant animals control parasitemia and do not show severe anaemia or production loss. Identification of trypanotolerance genes in cattle is hampered by cost and breeding time. Marked differences between inbred strains of mice in their response to T. congolense infection can be exploited in the analysis of the genetic basis of the infection. Murine trypanotolerance QTLs have been identified on chromosome 17, 5 and 1, and designated as Tir1, 2 and 3, respectively. Tir1 and 2 have been fine mapped to a confidence interval of 1 cM. In order to find the mouse homologous region on the bovine genome, nucleotide sequence across 95% CI of Tir2 and 3 were used in the selection of candidate genes. Homologous sequences were used in the definition of synteny relationships and subsequent identification of the shared disease response genes. The homologous genes within the human genome were then identified and aligned to the bovine radiation hybrid map in order to identify the mouse/bovine homologous regions. This revealed homology between murine and bovine QTL on Tir3 while the region on Tir2 is linked to innate immune response

Antimicrobial acitivity of extracts from Tephrosia vogelii Hook F.

The dichloromethane extracts of the root and leaf of Tephrosia vogelii Hook F. (Family: Papilionaceae) grown in Kenya, were subjected to antimicrobial assays against Staphylococcus aureus, Escherichia coli and Fusarium phoseolida. The minimum inhibition concentrations (MIC) ranged between 0.25 to 6.4 μg/ml for all the microorganisms tested. The crude root and leaf extracts were also toxic to the brine shrimps, organisms used as indicators of toxicity (LC50: 0.960; 0.958 μg/ml, respectively). Chromatographic separation led to the identification of (6aß, 12aß, 5'ß)-6a, 12a, 4',5'-tetra hydro-2,3-dimethoxy 5'-ß- isopropenyl–furano (3',2': 8,9)-6H-rotoxen-12-one, (rotenone) in 9.75% yield, (roots), and 11.75% (leaves). Characterisation was achieved by use of spectroscopic techniques and comparison with rotenone standard and literature data. Novel HPLC conditions for purification of rotenoids were established. The MIC of rotenone against the tested microbes was found to be 5.2 and 1.0 μg/ml for Staphylococcus aureus and Escherichia coli respectively, while the LC50 against the brine shrimps was found to be 3.20 μg/ml. The findings indicate that the extracts of T. vogelii contain metabolites that have antimicrobial activity comparable to other medicinal plants.Keywords: Tephrosia vogelii, Rotenone, Staphylococcus aureus, Escherichiacoli, Fusarium phoseolida Journal of Agriculture, Science and Technology Vol. 8 (1) 2006: pp. 1-1

Profiling of RNA viruses in biting midges (Ceratopogonidae) and related Diptera from Kenya using metagenomics and metabarcoding analysis

Vector-borne diseases (VBDs) cause enormous health burden worldwide, as they account for more than 17% of all infectious diseases and over 700,000 deaths each year. A significant number of these VBDs are caused by RNA virus pathogens. Here, we used metagenomics and metabarcoding analysis to characterize RNA viruses and their insect hosts among biting midges from Kenya. We identified a total of 15 phylogenetically distinct insect-specific viruses. These viruses fall into six families, with one virus falling in the recently proposed negevirus taxon. The six virus families include Partitiviridae, Iflaviridae, Tombusviridae, Solemoviridae, Totiviridae, and Chuviridae. In addition, we identified many insect species that were possibly associated with the identified viruses. Ceratopogonidae was the most common family of midges identified. Others included Chironomidae and Cecidomyiidae. Our findings reveal a diverse RNA virome among Kenyan midges that includes previously unknown viruses. Further, metabarcoding analysis based on COI (cytochrome c oxidase subunit 1 mitochondrial gene) barcodes reveal a diverse array of midge species among the insects used in the study. Successful application of metagenomics and metabarcoding methods to characterize RNA viruses and their insect hosts in this study highlights a possible simultaneous application of these two methods as cost-effective approaches to virus surveillance and host characterization. IMPORTANCE The majority of the viruses that currently cause diseases in humans and animals are RNA viruses, and more specifically arthropod-transmitted viruses. They cause diseases such as dengue, West Nile infection, bluetongue disease, Schmallenberg disease, and yellow fever, among others. Several sequencing investigations have shown us that a diverse array of RNA viruses among insect vectors remain unknown. Some of these could be ancient lineages that could aid in comprehensive studies on RNA virus evolution. Such studies may provide us with insights into the evolution of the currently pathogenic viruses. Here, we applied metagenomics to field-collected midges and we managed to characterize several RNA viruses, where we recovered complete and nearly complete genomes of these viruses. We also characterized the insect host species that are associated with these viruses. These results add to the currently known diversity of RNA viruses among biting midges as well as their associated insect hosts

Genetically Determined Response to Artemisinin Treatment in Western Kenyan <i>Plasmodium falciparum</i> Parasites

<div><p>Genetically determined artemisinin resistance in <i>Plasmodium falciparum</i> has been described in Southeast Asia. The relevance of recently described Kelch 13-propeller mutations for artemisinin resistance in Sub-Saharan Africa parasites is still unknown. Southeast Asia parasites have low genetic diversity compared to Sub-Saharan Africa, where parasites are highly genetically diverse. This study attempted to elucidate whether genetics provides a basis for discovering molecular markers in response to artemisinin drug treatment in <i>P</i>. <i>falciparum</i> in Kenya. The genetic diversity of parasites collected pre- and post- introduction of artemisinin combination therapy (ACT) in western Kenya was determined. A panel of 12 microsatellites and 91 single nucleotide polymorphisms (SNPs) distributed across the <i>P</i>. <i>falciparum</i> genome were genotyped. Parasite clearance rates were obtained for the post-ACT parasites. The 12 microsatellites were highly polymorphic with post-ACT parasites being significantly more diverse compared to pre-ACT (p < 0.0001). The median clearance half-life was 2.55 hours for the post-ACT parasites. Based on SNP analysis, 15 of 90 post-ACT parasites were single-clone infections. Analysis revealed 3 SNPs that might have some causal association with parasite clearance rates. Further, genetic analysis using Bayesian tree revealed parasites with similar clearance phenotypes were more closely genetically related. With further studies, SNPs described here and genetically determined response to artemisinin treatment might be useful in tracking artemisinin resistance in Kenya.</p></div