School of Molecular & Cell Biology (Journal Articles)

Permanent URI for this collectionhttps://hdl.handle.net/10539/38040

Browse

End date: 2018Subject: search.filters.subject.SDG-17: Partnerships for the goals

Search Results

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Dimethylformamide is a novel nitrilase inducer in Rhodococcus rhodochrous
    (Springer, 2018-09) Chhiba-Govindjee, V. P.; Brady, D.; Mathiba, K.; van der Westhuyzen, C. W.; Steenkamp, P.; Rashamuse, J. K.; Stoychev, S.
    Nitrilases are of commercial interest in the selective synthesis of carboxylic acids from nitriles. Nitrilase induction was achieved here in three bacterial strains through the incorporation of a previously unrecognised and inexpensive nitrilase inducer, dimethylformamide (DMF), during cultivation of two Rhodococcus rhodochrous strains (ATCC BAA-870 and PPPPB BD1780), as well as a closely related organism (Pimelobacter simplex PPPPB BD-1781). Benzonitrile, a known nitrilase inducer, was ineffective in these strains. Biocatalytic product profiling, enzyme inhibition studies and protein sequencing were performed to distinguish the nitrilase activity from that of sequential nitrile hydratase-amidase activity. The expressed enzyme, a 40-kDa protein with high sequence similarity to nitrilase protein Uniprot Q-03217, hydrolyzed 3-cyanopyridine to produce nicotinic acid exclusively in strains BD-1780 and BD-1781. These strains were capable of synthesising both the vitamin nicotinic acid as well as β-amino acids, a compound class of pharmaceutical interest. The induced nitrilase demonstrated high enantioselectivity (>99%) in the hydrolysis of 3-amino-3-phenylpropanenitrile to the corresponding carboxylic acid.
  • Thumbnail Image
    Item
    Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data
    (BMC, 2018) Ceballos, Francisco C.; Hazelhurst, Scott; Ramsay, Michèle
    Background: Runs of Homozygosity (ROH) are genomic regions where identical haplotypes are inherited from each parent. Since their first detection due to technological advances in the late 1990s, ROHs have been shedding light on human population history and deciphering the genetic basis of monogenic and complex traits and diseases. ROH studies have predominantly exploited SNP array data, but are gradually moving to whole genome sequence (WGS) data as it becomes available. WGS data, covering more genetic variability, can add value to ROH studies, but require additional considerations during analysis. Results: Using SNP array and low coverage WGS data from 1885 individuals from 20 world populations, our aims were to compare ROH from the two datasets and to establish software conditions to get comparable results, thus providing guidelines for combining disparate datasets in joint ROH analyses. By allowing heterozygous SNPs per window, using the PLINK homozygosity function and non-parametric analysis, we were able to obtain non-significant differences in number ROH, mean ROH size and total sum of ROH between data sets using the different technologies for almost all populations. Conclusions: By allowing 3 heterozygous SNPs per ROH when dealing with WGS low coverage data, it is possible to establish meaningful comparisons between data using SNP array and WGS low coverage technologies.