Extraction of high quality DNA from polysaccharides-secreting xanthomonads

A DNA extraction method using CTAB was used for the isolation of genomic DNA from ten Xanthomonas  campestris pathovars, ten isolates of Xanthomonas albilineans and one isolate of Pseudomonas  rubrisubalbicans. High quality DNA was obtained that was ideal for molecular analyses. Extracellular polysaccharides were effectively removed thus resulting in DNA that dissolved easily and was well digested by restriction enzymes. All of the other methods tested resulted in the coprecipitation of the polysaccharides together with the nucleic acids upon addition of alcohol so that even high yields could not compensate for this contamination. DNA obtained by the CTAB method was used for cloning, Southern hybridizations and PCR for up to three years after the extraction.Keywords: Polysaccharides, CTAB, polymerase chain reaction, DNA

Genetic diversity in Anthurium andraeanum cultivars in Mauritius

Anthurium andraeanum is an important ornamental in the flower industry in Mauritius. Classical phenotype methods of identification, although still very useful, are difficult to use between very closely related Anthurium cultivars. The objectives of this study were to assess the genetic diversity of 12 A. andraeanum cultivars in Mauritius using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers and identify cultivar specific markers for the genetic profiling of A. andraeanum cultivars. Polymorphism among the 12 cultivars was assessed using RAPD and ISSR primers. Reproducible results were used for statistical analysis. The presence and absence of bands were scored as 1 and 0, respectively to form a matrix from which a dendrogram was obtained using NTSYS. Dendrograms were obtained from matrices derived from RAPD and ISSR analyses to give an estimate of the genetic distance between the tested cultivars. Both ISSR and RAPD were found to be useful tools in differentiating locally grown A. andraeanum.Key words: Anthurium andraeanum, RAPD, ISSR, genetic diversity, cluster analysis

Prevalence of Shiga-toxigenic <em>Escherichia coli</em> in Mauritian dairy cattle

Shiga-toxigenic Escherichia coli (STEC) are important human pathogens (1). They are characterized by their ability to pro­duce Shiga toxins (stx1 and stx2). Seven STEC have been shown to withstand food processing procedures that are expected to ensure food safety. Clinical symptoms associated with STEC infection can vary from abdominal cramps and acute bloody diarrhea to more severe aftereffects including hemorrhagic coli­tis, hemolytic uremic syndrome and thrombocytopenic purpura, which can lead to kidney failure and death. Dairy cattle, which excrete STEC in their feces, are a major source of STEC infection (2). Humans become infected with STEC through direct contact with infected animals or by inges­tion of contaminated water, raw and unpasteurized milk, meat products, and/or plant-derived products (4–6). The objectives of this study were to estimate both cow-level and farm-level point prevalence estimates of STEC fecal shedding in Mauritian dairy cattle and to characterize putative STEC isolates based on their virulence factors. A cross-sectional study was conducted to investigate the preva­lence of STEC in the dairy cattle population of Mauritius. Fecal samples were collected from 150 individual dairy cattle from 38 dairy farms located throughout the nine district regions of the island. Collected samples were enriched in modified Tryptic Soy broth followed by isolation on CHROMagarTM STEC (3). Suspected isolates were streaked onto EMB agar, further puri­fied on nutrient agar and subsequently cryopreserved in glyc­erol until further investigation. Putative isolates were charac­terized using molecular techniques (7, 8) for the presence of chromosomal sequences encoding Shiga toxin genes (stx1 and stx2), the intimin protein (eaeA) and the plasmid-encoded hemo­lysin (hlyA). Out of the 38 farm samples, 29 farms (76%) were found to be positive for presumptive STEC isolates. From the 150 fecal samples collected, 111 (74%) were found to harbor presump­tive STEC isolates (Table I). Polymerase-chain-reaction- (PCR-) based characterization has confirmed the presence of STEC in a number of fecal samples. Results obtained so far indicate that STEC are common members of the gut microbiome of dairy cattle in Mauritius. Presumptive STEC isolates are currently being screened with PCR targeting stx1, stx2, eaeA and hlyA genes. This epidemiological study on STEC is the first of its kind in Mauritius and in the Indian Ocean region. It aims at providing new information concerning the presence of STEC in Mauritian dairy cattle. It involves the use of the latest chromogenic agar (CHROMagarTM STEC) available on the market. This culture medium has been designed for the detection of a wide range of STEC from different sources. The study highlights the importance of implementing proper sanitary measures at the dairy farm level to prevent cross contamination of milk and the surrounding environment

H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet