Center for Proteomic and Genomic Research

Cape Town, South Africa

Center for Proteomic and Genomic Research

Cape Town, South Africa
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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.

PubMed | University of Witwatersrand, University of Sheffield, Sanguine, Future University of Sudan and 27 more.
Type: Journal Article | Journal: Genome research | Year: 2016

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.

PubMed | University of Witwatersrand, University of Pretoria, University of KwaZulu - Natal, University of Cape Town and 4 more.
Type: Historical Article | Journal: 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.

Chimusa E.R.,University of Cape Town | Chimusa E.R.,Center for Proteomic and Genomic Research | Meintjies A.,University of Cape Town | Tchanga M.,University of Cape Town | And 4 more authors.
PLoS Genetics | Year: 2015

We report a study of genome-wide, dense SNP (∼900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region. © 2015 Chimusa et al.

Bishop O.T.,University of South Africa | Adebiyi E.F.,Covenant University | Alzohairy A.M.,Zagazig University | Ghouila A.,H3ABionet Tunisia node | And 3 more authors.
Briefings in Bioinformatics | Year: 2015

The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s.The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually every field in the life sciences. This has placed a scientific premium on the availability of skilled bioinformaticians, a qualification that is extremely scarce on the African continent. The reasons for this are numerous, although the absence of a skilled bioinformatician at academic institutions to initiate a training process and build sustained capacity seems to be a common African shortcoming.This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis of genomes from African populations, which are among the most genetically diverse anywhere on the planet. Recent funding initiatives from the National Institutes of Health and theWellcomeTrust are aimed at ameliorating this shortcoming. In this paper, we discuss the problems that have limited the establishment of the bioinformatics field in Africa, as well as propose specific actions that will help with the education and training of bioinformaticians on the continent. This is an absolute requirement in anticipation of a boom in high-throughput approaches to human health issues unique to data from African populations. © The Author 2014.

PubMed | Center for Medical, University of Pretoria, Center for Proteomic and Genomic Research, Vlaams Institute for Biotechnology and University of Cape Town
Type: | Journal: The Plant journal : for cell and molecular biology | Year: 2016

We used a systems genetics approach to elucidate molecular mechanisms of maize responses to gray leaf spot (GLS) disease, caused by Cercosporazeina, a threat to maize production globally. Expression analysis of earleaf samples in a sub-tropical maize RIL population (CML444 X SC Malawi) subjected in field to C. zeina infection allowed detection of 20,206 expression QTLs (eQTL). Four trans-eQTL hotspots coincided with GLS disease QTLs mapped in the same field experiment. Co-expression network analysis identified three expression modules correlated with GLS disease scores. The module (GY-s) most highly correlated with susceptibility (r = 0.71; 179 genes) was enriched for the glyoxylate pathway, lipid metabolism, diterpenoid biosynthesis and responses to pathogen molecules such as chitin. The GY-s module was enriched for genes with trans-eQTLs in hotspots on chromosomes 9 and 10, which also coincided with phenotypic QTLs for GLS susceptibility. This transcriptional network has significant overlap with the GLS susceptibility response of maize line B73, and may reflect pathogen manipulation for nutrient acquisition and/or unsuccessful defense responses, such as kauralexin production by the diterpenoid biosynthesis pathway. The co-expression module that correlated best with resistance (TQ-r; 1498 genes) was enriched for genes with trans-eQTLs in hotspots coinciding with GLS resistance QTLs on chromosome 9. Jasmonate responses were implicated in resistance to GLS through co-expression of COI-1 and enrichment of genes with the GO term cullin-RING ubiquitin ligase complex in the TQ-r module. Consistent with this, JAZ repressor expression was highly correlated with GLS disease severity in the GY-s susceptibility network. This article is protected by copyright. All rights reserved.

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.

Blackburn J.M.,University of Cape Town | Shoko A.,Center for Proteomic and Genomic Research | Beeton-Kempen N.,University of Cape Town
Methods in Molecular Biology | Year: 2012

Systematic analysis of protein and enzyme function typically requires scale-up of protein expression and purification prior to assay development; this can often be limiting. Miniaturization of assays provides an alternative approach, but simple, generic methods are in short supply. Here we show how custom microarrays can be adapted to this purpose. We discuss the different routes to array fabrication and describe in detail one facile approach in which the purification and immobilization procedures are combined into a single step, significantly simplifying the array fabrication process. We illustrate this approach by reference to the creation of arrays of human protein kinases and of human cytochrome P450s. We discuss methods for both ligand-binding and turnover-based assays, as well as data analysis on such arrays. © 2012 Springer Science+Business Media, LLC.

Dimatelis J.J.,University of Cape Town | Hsieh J.H.,University of Cape Town | Sterley T.-L.,University of Cape Town | Marais L.,University of Cape Town | And 3 more authors.
Journal of Molecular Neuroscience | Year: 2015

Attention deficit hyperactivity disorder (ADHD) is a heterogeneous behavioural disorder that affects 3–15 % of children worldwide. Spontaneously hypertensive rats (SHR) display the major symptoms of ADHD (hyperactivity, impulsivity and poor performance in tasks that require sustained attention) and are widely used to model the disorder. The present study aimed to test the hypothesis that SHR have a diminished capacity to generate ATP required for rapid synchronized neuronal firing, failure of which might lead to disturbances in neurotransmission that could contribute to their ADHD-like behaviour. Duplicate pooled (n = 5) samples of prefrontal cortex and striatum of prepubertal (35-day-old) SHR and Wistar Kyoto (WKY) rats were subjected to iTRAQ labeling and matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS). The MS/MS spectra were analyzed with ProteinPilot using the Ratus ratus database. Proteins detected with >95 % confidence were tested. SHR had decreased levels of several proteins involved in energy metabolism, cytoskeletal structure, myelination and neurotransmitter function when compared to WKY. Differences in protein levels between SHR and WKY were similar in prefrontal cortex and striatum, suggesting global changes in cortico-striato-thalamo-cortical circuits. © 2015, Springer Science+Business Media New York.

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.

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