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Mulder N.J.,University of Cape Town | Christoffels A.,University of the Western Cape | de Oliveira T.,University of KwaZulu - Natal | Gamieldien J.,University of the Western Cape | And 7 more authors.
PLoS Computational Biology | Year: 2016

Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt. © 2016 Mulder et al. Source


Meyer J.,Center for Proteomic and Genomic Research | Meyer J.,University of Pretoria | Murray S.L.,Center for Proteomic and Genomic Research | Murray S.L.,University of Cape Town | Berger D.K.,University of Pretoria
Physiological and Molecular Plant Pathology | Year: 2015

Plants accumulate a vast arsenal of chemically diverse secondary metabolites for defence against pathogens. This review will focus on the signal transduction and regulation of defence secondary metabolite production in five food security cereal crops: maize, rice, wheat, sorghum and oats. Recent research advances in this field have revealed novel processes and chemistry in these monocots that make this a rich field for future research. © 2015 Elsevier Ltd. Source


Solofoharivelo M.C.,Stellenbosch University | van der Walt A.P.,Center for Proteomic and Genomic Research | van der Walt A.P.,Stellenbosch University | Stephan D.,Stellenbosch University | And 3 more authors.
Plant Biology | Year: 2014

Since the first description of microRNAs (miRNAs) 20 years ago, the number of miRNAs identified in different eukaryotic organisms has exploded, largely due to the recent advances in DNA sequencing technologies. Functional studies, mostly from model species, have revealed that miRNAs are major post-transcriptional regulators of gene expression in eukaryotes. In plants, they are implicated in fundamental biological processes, from plant development and morphogenesis, to regulation of plant pathogen and abiotic stress responses. Although a substantial number of miRNAs have been identified in fruit trees to date, their functions remain largely uncharacterised. The present review aims to summarise the progress made in miRNA research in fruit trees, focusing specifically on the economically important species Prunus persica, Malus domestica, Citrus spp, and Vitis vinifera. We also discuss future miRNA research prospects in these plants and highlight potential applications of miRNAs in the on-going improvement of fruit trees. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands. Source


Chimusa E.R.,University of Cape Town | Mbiyavanga M.,Center for Proteomic and Genomic Research | Masilela V.,Center for Proteomic and Genomic Research | Kumuthini J.,Center for Proteomic and Genomic Research
PLoS Computational Biology | Year: 2015

A shortage of practical skills and relevant expertise is possibly the primary obstacle to social upliftment and sustainable development in Africa. The “omics” fields, especially genomics, are increasingly dependent on the effective interpretation of large and complex sets of data. Despite abundant natural resources and population sizes comparable with many first-world countries from which talent could be drawn, countries in Africa still lag far behind the rest of the world in terms of specialized skills development. Moreover, there are serious concerns about disparities between countries within the continent. The multidisciplinary nature of the bioinformatics field, coupled with rare and depleting expertise, is a critical problem for the advancement of bioinformatics in Africa. We propose a formalized matchmaking system, which is aimed at reversing this trend, by introducing the Knowledge Transfer Programme (KTP). Instead of individual researchers travelling to other labs to learn, researchers with desirable skills are invited to join African research groups for six weeks to six months. Visiting researchers or trainers will pass on their expertise to multiple people simultaneously in their local environments, thus increasing the efficiency of knowledge transference. In return, visiting researchers have the opportunity to develop professional contacts, gain industry work experience, work with novel datasets, and strengthen and support their ongoing research. The KTP develops a network with a centralized hub through which groups and individuals are put into contact with one another and exchanges are facilitated by connecting both parties with potential funding sources. This is part of the PLOS Computational Biology Education collection. © 2015 Chimusa et al. Source


Dimatelis J.J.,University of Cape Town | Hendricks S.,University of Cape Town | Hsieh J.,University of Cape Town | Vlok N.M.,Center for Proteomic and Genomic Research | And 3 more authors.
Experimental Physiology | Year: 2013

New Findings: • What is the central question of this study? Maternal separation exacerbates behavioural deficits induced by 6-hydroxydopamine lesioning in a rat model of Parkinson's disease. In contrast, voluntary exercise reduces these effects due to compensation in the non-lesioned hemisphere. We have asked how maternal separation and exercise affect protein expression in lesioned and non-lesioned hemispheres of the rat brain. • What is the main finding and its importance? Using isobaric tagging and quantification of peptides by matrix-assisted laser desorption/ionization tandem mass spectrometry, we show that exercise and maternal separation have opposing effects on the hippocampus in the non-lesioned hemisphere, with exercise partially reversing effects of maternal separation on the levels of energy metabolism and synaptic plasticity proteins. Animals subjected to maternal separation stress during the early stages of development display behavioural, endocrine and growth factor abnormalities that mirror the clinical findings in anxiety/depression. In addition, maternal separation has been shown to exacerbate the behavioural deficits induced by 6-hydroxydopamine (6-OHDA) in a rat model of Parkinson's disease. In contrast, voluntary exercise reduced the detrimental effects of 6-OHDA in the rat model. The beneficial effects of exercise appeared to be largely due to compensation in the non-lesioned hemisphere. The aim of the present study was to investigate whether voluntary exercise for 3 weeks could reverse the effects of maternal separation in rats challenged with the neurotoxin 6-OHDA infused into the medial forebrain bundle after 1 week of exercise, at postnatal day 60. The rats were killed 2 weeks later, at postnatal day 74. Their brains were dissected and the hippocampus rapidly removed for proteomic analysis by isobaric tagging (iTRAQ) and quantification of peptides by matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS). Maternal separation upregulated hippocampal proteins functionally involved in energy metabolism (nucleoside diphosphate kinase B, enolase and triosephosphate isomerase) and synaptic plasticity (α-synuclein, tenascin-R, Ba1-667, brevican and neurocan core protein) in the non-lesioned hemisphere. Exercise reversed many of these changes by downregulating the levels of hippocampal proteins functionally associated with energy metabolism (nucleoside diphosphate kinase B, enolase and triosephosphate isomerase) and synaptic plasticity (α-synuclein, tenascin-R, Ba1-667, brevican and neurocan core protein) in the non-lesioned hemisphere of rats subjected to maternal separation. Exercise and maternal separation therefore appeared to have opposing effects on the hippocampus in the non-lesioned hemisphere of the rat brain. Exercise seemed partly to reverse the effects of maternal separation stress on these proteins in the non-lesioned hemisphere. The partial reversal of maternal separation-induced proteins by exercise in the non-lesioned side sheds some insight into the mechanism by which exercise alters the molecular role players involved in determining the consequences of early life stress. © 2012 The Authors. Experimental Physiology © 2012 The Physiological Society. Source

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