Publications by authors named "Fourie Joubert"

37 Publications

Single-Cell Transcriptome Analysis of Human Adipose-Derived Stromal Cells Identifies a Contractile Cell Subpopulation.

Stem Cells Int 2021 28;2021:5595172. Epub 2021 Apr 28.

Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa.

The potential for human adipose-derived stromal cells (hASCs) to be used as a therapeutic product is being assessed in multiple clinical trials. However, much is still to be learned about these cells before they can be used with confidence in the clinical setting. An inherent characteristic of hASCs that is not well understood is their heterogeneity. The aim of this exploratory study was to characterize the heterogeneity of freshly isolated hASCs after two population doublings (P2) using single-cell transcriptome analysis. A minimum of two subpopulations were identified at P2. A major subpopulation was identified as contractile cells which, based on gene expression patterns, are likely to be pericytes and/or vascular smooth muscle cells (vSMCs).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1155/2021/5595172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8102097PMC
April 2021

Limited diversity in the CD8+ antigen-coding loci in Theileria parva parasites from cattle from southern and eastern Africa.

Vet Parasitol 2021 Mar 5;291:109371. Epub 2021 Feb 5.

Vectors and Vector-borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, South Africa.

Theileria parva infections in cattle causes huge economic losses in the affected African countries, directly impacting the livelihood of the poor small-holder farmers. The current immunization protocol using live sporozoites in eastern Africa, is among the control measures designed to limit T. parva infections in cattle. However, the ability of the immune protection induced by this immunization to protect against field parasites has been compromised by the diversity of the parasite involving the schizont antigen genes. Previous studies have reported on the antigenic diversity of T. parva parasites from southern and eastern Africa, however, similar reports on T. parva parasites particularly from cattle from southern Africa remains scanty, due to the self-limiting nature of Corridor disease. Thus, we evaluated the diversity of CD8+ T-cell regions of ten schizont antigen genes in T. parva parasites associated with Corridor disease and East Coast fever (ECF) from southern and eastern Africa respectively. Regions of schizont antigen (TpAg) genes containing the CD8+ T-cell epitopes (CTL determinants) were amplified from genomic DNA extracted from blood of T. parva positive samples, cloned and sequenced. The results revealed limited diversity between the two parasite groups from cattle from southern and eastern Africa, defying the widely accepted notion that antigen-encoding loci in cattle-derived parasites are conserved, while in buffalo-derived parasites, they are extensively variable. This suggests that only a sub-population of parasites is successfully transmitted from buffalo to cattle, resulting in the limited antigenic diversity in Corridor disease parasites. Tp4, Tp5, Tp7 and Tp8 showed limited to absence of diversity in both parasite groups, suggesting the need to further investigate their immunogenic properties for consideration as candidates for a subunit vaccine. Distinct and common variants of Tp2 were detected among the ECF parasites from eastern Africa indicating evidence of parasite mixing following immunization. This study provides additional information on the comparative diversity of TpAg genes in buffalo- and cattle-derived T. parva parasites from cattle from southern and eastern Africa.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.vetpar.2021.109371DOI Listing
March 2021

The immuno-oncological implications of insulin.

Life Sci 2021 Jan 4;264:118716. Epub 2020 Nov 4.

Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa.

Emerging evidence has implicated insulin in regulating the phenotypes of various immune cells through canonical downstream signalling effectors of insulin, namely, the PI3K/Akt/mTOR pathway. Notably, these signalling components also exhibit crosstalk with other immune signalling pathways, such as the JAK/STAT pathway (activated by cytokines and growth factors), and, importantly, are also negatively regulated by the immune checkpoint blockers (ICBs), PD-1 and CTLA-4. Here, we point out recent findings, suggesting that insulin may promote a pro-inflammatory phenotype with potential implications on ICB therapy. As an example, the contemporary paradigm holds that, while T cell receptor recognition of distinct MHC-expressed epitopes ensures specificity, co-activation of CD28 along with signal inputs form various cytokines and insulin operates to 'fine-tune' the immune response via PI3K and other downstream signalling molecules. These considerations highlight the urgent need for focused investigations into the role of insulin in regulating immune cell function in the context of ICB therapies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.lfs.2020.118716DOI Listing
January 2021

Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.

AAS Open Res 2018 7;1. Epub 2019 Aug 7.

Computational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.

The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Building on the network's Standard Operating Procedures (SOPs) for common genomic analyses, H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon in 2016, with the purpose of translating those SOPs into analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on Quay.io.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.12688/aasopenres.12847.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194140PMC
August 2019

The Draft Genome of .

J Nematol 2019 29;51. Epub 2019 Jul 29.

Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.

The nematode is used as biological control agent against the invasive woodwasp , a serious invasive pest of plantations globally. The draft genome of this ecologically and economically important entomoparasitic nematode was determined.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.21307/jofnem-2019-036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6916137PMC
July 2019

Functional annotation of putative QTL associated with black tea quality and drought tolerance traits.

Sci Rep 2019 02 6;9(1):1465. Epub 2019 Feb 6.

Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.

The understanding of black tea quality and percent relative water content (%RWC) traits in tea (Camellia sinensis) by a quantitative trait loci (QTL) approach can be useful in elucidation and identification of candidate genes underlying the QTL which has remained to be difficult. The objective of the study was to identify putative QTL controlling black tea quality and percent relative water traits in two tea populations and their F1 progeny. A total of 1,421 DArTseq markers derived from the linkage map identified 53 DArTseq markers to be linked to black tea quality and %RWC. All 53 DArTseq markers with unique best hits were identified in the tea genome. A total of 5,592 unigenes were assigned gene ontology (GO) terms, 56% comprised biological processes, cellular component (29%) and molecular functions (15%), respectively. A total of 84 unigenes in 15 LGs were assigned to 25 different Kyoto Encyclopedia of Genes and Genomes (KEGG) database pathways based on categories of secondary metabolite biosynthesis. The three major enzymes identified were transferases (38.9%), hydrolases (29%) and oxidoreductases (18.3%). The putative candidate proteins identified were involved in flavonoid biosynthesis, alkaloid biosynthesis, ATPase family proteins related to abiotic/biotic stress response. The functional annotation of putative QTL identified in this current study will shed more light on the proteins associated with caffeine and catechins biosynthesis and % RWC. This study may help breeders in selection of parents with desirable DArTseq markers for development of new tea cultivars with desirable traits.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-37688-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365519PMC
February 2019

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics.

BMC Bioinformatics 2018 Nov 29;19(1):457. Epub 2018 Nov 29.

Computational Biology Division, Department of Integrative Medical Biosciences, IDM, University of Cape Town, Cape Town, South Africa.

Background: The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led research consortium funded by the US National Institutes of Health and the UK Wellcome Trust, aimed at using genomics to study and improve the health of Africans. A key role of H3ABioNet is to support H3Africa projects by building bioinformatics infrastructure such as portable and reproducible bioinformatics workflows for use on heterogeneous African computing environments. Processing and analysis of genomic data is an example of a big data application requiring complex interdependent data analysis workflows. Such bioinformatics workflows take the primary and secondary input data through several computationally-intensive processing steps using different software packages, where some of the outputs form inputs for other steps. Implementing scalable, reproducible, portable and easy-to-use workflows is particularly challenging.

Results: H3ABioNet has built four workflows to support (1) the calling of variants from high-throughput sequencing data; (2) the analysis of microbial populations from 16S rDNA sequence data; (3) genotyping and genome-wide association studies; and (4) single nucleotide polymorphism imputation. A week-long hackathon was organized in August 2016 with participants from six African bioinformatics groups, and US and European collaborators. Two of the workflows are built using the Common Workflow Language framework (CWL) and two using Nextflow. All the workflows are containerized for improved portability and reproducibility using Docker, and are publicly available for use by members of the H3Africa consortium and the international research community.

Conclusion: The H3ABioNet workflows have been implemented in view of offering ease of use for the end user and high levels of reproducibility and portability, all while following modern state of the art bioinformatics data processing protocols. The H3ABioNet workflows will service the H3Africa consortium projects and are currently in use. All four workflows are also publicly available for research scientists worldwide to use and adapt for their respective needs. The H3ABioNet workflows will help develop bioinformatics capacity and assist genomics research within Africa and serve to increase the scientific output of H3Africa and its Pan-African Bioinformatics Network.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-018-2446-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6264621PMC
November 2018

IMA Genome-F 8: Draft genome of , , and .

IMA Fungus 2017 Dec 21;8(2):385-396. Epub 2017 Nov 21.

Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.

The genomes of , , and are presented in this genome announcement. Three of these genomes are from plant pathogens and otherwise economically important fungal species. and are not known to cause significant disease but are closely related to species of economic importance. The genome sizes range from 25.99 Mb in the case of to 4.82 Mb for . These genomes include the first reports of a genome from the genus . The availability of these genome data will allow the resolution of longstanding questions regarding the taxonomy of these species. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these species or close relatives cause disease.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5598/imafungus.2017.08.02.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729718PMC
December 2017

Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans.

Nat Commun 2017 12 12;8(1):2062. Epub 2017 Dec 12.

Institute for Cellular and Molecular Medicine, Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, 0084, South Africa.

The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern African populations for a better understanding of human genetic diversity. In this pilot study the Southern African Human Genome Programme characterizes the genomes of 24 individuals (8 Coloured and 16 black southeastern Bantu-speakers) using deep whole-genome sequencing. A total of ~16 million unique variants are identified. Despite the shallow time depth since divergence between the two main southeastern Bantu-speaking groups (Nguni and Sotho-Tswana), principal component analysis and structure analysis reveal significant (p < 10) differentiation, and F analysis identifies regions with high divergence. The Coloured individuals show evidence of varying proportions of admixture with Khoesan, Bantu-speakers, Europeans, and populations from the Indian sub-continent. Whole-genome sequencing data reveal extensive genomic diversity, increasing our understanding of the complex and region-specific history of African populations and highlighting its potential impact on biomedical research and genetic susceptibility to disease.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-017-00663-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5727231PMC
December 2017

Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem.

Plant J 2017 Feb 13;89(4):746-763. Epub 2017 Feb 13.

Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.

We used a systems genetics approach to elucidate the molecular mechanisms of the responses of maize to grey leaf spot (GLS) disease caused by Cercospora zeina, a threat to maize production globally. Expression analysis of earleaf samples in a subtropical maize recombinant inbred line population (CML444 × SC Malawi) subjected in the field to C. zeina infection allowed detection of 20 206 expression quantitative trait loci (eQTLs). 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 susceptibility to GLS. 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 defence 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 COI1 and enrichment of genes with the Gene Ontology term 'cullin-RING ubiquitin ligase complex' in the TQ-r module. Consistent with this, JAZ repressor expression was highly correlated with the severity of GLS disease in the GY-s susceptibility network.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.13419DOI Listing
February 2017

IMA Genome-F 6: Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723.

IMA Fungus 2016 Jun 21;7(1):217-27. Epub 2016 Jun 21.

Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada; Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada.

The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 21 Mb in the case of Ceratocystiopsis minuta to 58 Mb for the basidiomycete Armillaria fuscipes. These genomes include the first reports of genomes for the genus Endoconidiophora. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5598/imafungus.2016.07.01.11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941685PMC
June 2016

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt.

PLoS Comput Biol 2016 Feb 4;12(2):e1004395. Epub 2016 Feb 4.

South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742231PMC
February 2016

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

Genome Res 2016 Feb 1;26(2):271-7. Epub 2015 Dec 1.

University of the Free State, Bloemfontein, South Africa 9300;

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.196295.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728379PMC
February 2016

Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis.

BMC Genomics 2015 May 22;16:402. Epub 2015 May 22.

Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa.

Background: Carbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown. Since Carbohydrate Active enZymes (CAZymes) in plants are responsible for the synthesis, modification and degradation of carbohydrate biopolymers, the differences in gene copy number and regulation between woody and herbaceous species have been highlighted previously. There are still many unanswered questions about the role of CAZymes in land plant evolution and the formation of wood, a strong carbohydrate sink.

Results: Here, twenty-two publically available plant genomes were used to characterize the frequency, diversity and complexity of CAZymes in plants. We find that a conserved suite of CAZymes is a feature of land plant evolution, with similar diversity and complexity regardless of growth habit and form. In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species Eucalyptus grandis and Populus trichocarpa, highlighting the major CAZyme classes involved in xylogenesis and lignocellulosic biomass production.

Conclusions: CAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit. The stoichiometric conservation of gene expression in woody and non-woody tissues of Eucalyptus and Populus are indicative of gene balance preservation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-015-1571-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440533PMC
May 2015

Virus genome dynamics under different propagation pressures: reconstruction of whole genome haplotypes of West Nile viruses from NGS data.

BMC Genomics 2015 Feb 22;16:118. Epub 2015 Feb 22.

Poultry Section, Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, 0110, South Africa.

Background: Extensive focus is placed on the comparative analyses of consensus genotypes in the study of West Nile virus (WNV) emergence. Few studies account for genetic change in the underlying WNV quasispecies population variants. These variants are not discernable in the consensus genome at the time of emergence, and the maintenance of mutation-selection equilibria of population variants is greatly underestimated. The emergence of lineage 1 WNV strains has been studied extensively, but recent epidemics caused by lineage 2 WNV strains in Hungary, Austria, Greece and Italy emphasizes the increasing importance of this lineage to public health. In this study we explored the quasispecies dynamics of minority variants that contribute to cell-tropism and host determination, i.e. the ability to infect different cell types or cells from different species from Next Generation Sequencing (NGS) data of a historic lineage 2 WNV strain.

Results: Minority variants contributing to host cell membrane association persist in the viral population without contributing to the genetic change in the consensus genome. Minority variants are shown to maintain a stable mutation-selection equilibrium under positive selection, particularly in the capsid gene region.

Conclusions: This study is the first to infer positive selection and the persistence of WNV haplotype variants that contribute to viral fitness without accompanying genetic change in the consensus genotype, documented solely from NGS sequence data. The approach used in this study streamlines the experimental design seeking viral minority variants accurately from NGS data whilst minimizing the influence of associated sequence error.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-015-1340-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338619PMC
February 2015

A novel inhibitor of Plasmodium falciparum spermidine synthase: a twist in the tail.

Malar J 2015 Feb 5;14:54. Epub 2015 Feb 5.

Department of Biochemistry, UP Centre for Sustainable Malaria Control, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.

Background: Plasmodium falciparum is the most pathogenic of the human malaria parasite species and a major cause of death in Africa. It's resistance to most of the current drugs accentuates the pressing need for new chemotherapies. Polyamine metabolism of the parasite is distinct from the human pathway making it an attractive target for chemotherapeutic development. Plasmodium falciparum spermidine synthase (PfSpdS) catalyzes the synthesis of spermidine and spermine. It is a major polyamine flux-determining enzyme and spermidine is a prerequisite for the post-translational activation of P. falciparum eukaryotic translation initiation factor 5A (elF5A). The most potent inhibitors of eukaryotic SpdS's are not specific for PfSpdS.

Methods: 'Dynamic' receptor-based pharmacophore models were generated from published crystal structures of SpdS with different ligands. This approach takes into account the inherent flexibility of the active site, which reduces the entropic penalties associated with ligand binding. Four dynamic pharmacophore models were developed and two inhibitors, (1R,4R)-(N1-(3-aminopropyl)-trans-cyclohexane-1,4-diamine (compound 8) and an analogue, N-(3-aminopropyl)-cyclohexylamine (compound 9), were identified.

Results: A crystal structure containing compound 8 was solved and confirmed the in silico prediction that its aminopropyl chain traverses the catalytic centre in the presence of the byproduct of catalysis, 5'-methylthioadenosine. The IC50 value of compound 9 is in the same range as that of the most potent inhibitors of PfSpdS, S-adenosyl-1,8-diamino-3-thio-octane (AdoDATO) and 4MCHA and 100-fold lower than that of compound 8. Compound 9 was originally identified as a mammalian spermine synthase inhibitor and does not inhibit mammalian SpdS. This implied that these two compounds bind in an orientation where their aminopropyl chains face the putrescine binding site in the presence of the substrate, decarboxylated S-adenosylmethionine. The higher binding affinity and lower receptor strain energy of compound 9 compared to compound 8 in the reversed orientation explained their different IC50 values.

Conclusion: The specific inhibition of PfSpdS by compound 9 is enabled by its binding in the additional cavity normally occupied by spermidine when spermine is synthesized. This is the first time that a spermine synthase inhibitor is shown to inhibit PfSpdS, which provides new avenues to explore for the development of novel inhibitors of PfSpdS.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12936-015-0572-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342090PMC
February 2015

The genome of Eucalyptus grandis.

Nature 2014 Jun 11;510(7505):356-62. Epub 2014 Jun 11.

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.

Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature13308DOI Listing
June 2014

Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria.

Malar J 2013 Mar 28;12:116. Epub 2013 Mar 28.

Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria 0001, South Africa.

Background: Drug resistance to anti-malarial compounds remains a serious problem, with resistance to newer pharmaceuticals developing at an alarming rate. The development of new anti-malarials remains a priority, and the rational selection of putative targets is a key element of this process. Discovery-2 is an update of the original Discovery in silico resource for the rational selection of putative drug target proteins, enabling researchers to obtain information for a protein which may be useful for the selection of putative drug targets, and to perform advanced filtering of proteins encoded by the malaria genome based on a series of molecular properties.

Methods: An updated in silico resource has been developed where researchers are able to mine information on malaria proteins and predicted ligands, as well as perform comparisons to the human and mosquito host characteristics. Protein properties used include: domains, motifs, EC numbers, GO terms, orthologs, protein-protein interactions, protein-ligand interactions. Newly added features include drugability measures from ChEMBL, automated literature relations and links to clinical trial information. Searching by chemical structure is also available.

Results: The updated functionality of the Discovery-2 resource is presented, together with a detailed case study of the Plasmodium falciparum S-adenosyl-L-homocysteine hydrolase (PfSAHH) protein. A short example of a chemical search with pyrimethamine is also illustrated.

Conclusion: The updated Discovery-2 resource allows researchers to obtain detailed properties of proteins from the malaria genome, which may be of interest in the target selection process, and to perform advanced filtering and selection of proteins based on a relevant range of molecular characteristics.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1475-2875-12-116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637051PMC
March 2013

Signaling pathways of ESE-16, an antimitotic and anticarbonic anhydrase estradiol analog, in breast cancer cells.

PLoS One 2013 31;8(1):e53853. Epub 2013 Jan 31.

Department of Physiology, University of Pretoria, Pretoria, Gauteng, South Africa.

Unlabelled: The aim of this study was to characterize the in vitro action of 2-ethyl-3-O-sulphamoyl-estra-1,3,5(10)16-tetraene (ESE-16) on non-tumorigenic MCF-12A, tumorigenic MCF-7 and metastatic MDA-MB-231 breast cancer cells. ESE-16 is able to inhibit the activity of a carbonic anhydrase II and a mimic of carbonic anhydrase IX in the nanomolar range. Gene and protein expression studies using various techniques including gene and antibody microarrays and various flow cytometry assays yielded valuable information about the mechanism of action of ESE-16. The JNK pathway was identified as an important pathway mediating the effects of ESE-16 while the p38 stress-induced pathway is more important in MDA-MB-231 cells exposed to ESE-16. Lysosomal rupture and iron metabolism was identified as important mediators of mitochondrial membrane depolarization. Abrogation of Bcl-2 phosphorylation status as a result of ESE-16 also plays a role in inducing mitochondrial membrane depolarization. The study provides a basis for future research projects to develop the newly synthesized compound into a clinically usable anticancer agent either alone or in combination with other agents.

Keywords: Antimitotic, anticarbonic anhydrase IX, apoptosis, autophagy, cell cycle arrest, Bcl-2, JNK, p38, mitochondrial membrane depolarization, flow cytometry, gene expression and protein microarray, anticancer.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0053853PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561402PMC
September 2013

In vitro evaluation of ESE-15-ol, an estradiol analogue with nanomolar antimitotic and carbonic anhydrase inhibitory activity.

PLoS One 2012 27;7(12):e52205. Epub 2012 Dec 27.

Department of Physiology, University of Pretoria, Pretoria, Gauteng, South Africa.

Antimitotic compounds are still one of the most widely used chemotherapeutic anticancer drugs in the clinic today. Given their effectiveness against cancer it is beneficial to continue enhancing these drugs. One way is to improve the bioavailability and efficacy by synthesizing derivatives that reversibly bind to carbonic anhydrase II (CAII) in red blood cells followed by a slow release into the blood circulation system. In the present study we describe the in vitro biological activity of a reduced derivative of 2-ethyl-3-O-sulphamoyl-estradiol (2EE), 2-ethyl-3-O-sulphamoyl-estra-1,3,5(10),15-tetraen-17-ol (ESE-15-ol). ESE-15-ol is capable of inhibiting carbonic anhydrase activity in the nanomolar range and is selective towards a mimic of carbonic anhydrase IX when compared to the CAII isoform. Docking studies using Autodock Vina suggest that the dehydration of the D-ring plays a role towards the selectivity of ESE-15-ol to CAIX and that the binding mode of ESE-15-ol is substantially different when compared to 2EE. ESE-15-ol is able to reduce cell growth to 50% after 48 h at 50-75 nM in MCF-7, MDA-MB-231, and MCF-12A cells. The compound is the least potent against the non-tumorigenic MCF-12A cells. In vitro mechanistic studies demonstrate that the newly synthesized compound induces mitochondrial membrane depolarization, abrogates the phosphorylation status of Bcl-2 and affects gene expression of genes associated with cell death and mitosis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052205PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531393PMC
July 2013

Docking, synthesis, and in vitro evaluation of antimitotic estrone analogs.

Chem Biol Drug Des 2011 Mar 19;77(3):173-81. Epub 2011 Jan 19.

Department of Physiology, University of Pretoria, Pretoria, South Africa.

In the present study, Autodock 4.0 was employed to discover potential carbonic anhydrase IX inhibitors that are able to interfere with microtubule dynamics by binding to the Colchicine binding site of tubulin. Modifications at position 2' of estrone were made to include moieties that are known to improve the antimitotic activity of estradiol analogs. 2-ethyl-3-O-sulphamoyl-estra-1,3,5(10),15-tetraen-3-ol-17-one estronem (C9) and 2-ethyl-3-O-sulphamoyl-estra-1,3,5(10)16-tetraene (C12) were synthesized and tested in vitro. Growth studies were conducted utilizing spectrophotometrical analysis with crystal violet as DNA stain. Compounds C9 and C12 were cytotoxic in MCF-7 and MDA-MB-231 tumorigenic and metastatic breast cancer cells, SNO non-keratinizing squamous epithelium cancer cells and HeLa cells after 48 h exposure. Compounds C9 inhibited cell proliferation to 50% of the vehicle-treated controls from 110 to 160 nm and C12 at concentrations ranging from 180 to 220 nm. Confocal microscopy revealed abnormal spindle morphology in mitotic cells. Cell cycle analysis showed an increase in the number of cells in the G(2) /M fraction after 24 h and an increase in the number of cell in the sub-G(1) fraction after 48 h, indicating that the compounds are antimitotic and able to induce apoptosis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1747-0285.2010.01064.xDOI Listing
March 2011

De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq.

BMC Genomics 2010 Dec 1;11:681. Epub 2010 Dec 1.

Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.

Background: De novo assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produced in 2010 for a Eucalyptus tree species (E. grandis) representing the most important hardwood fibre crop in the world. Genome annotation of this valuable woody plant and genetic dissection of its superior growth and productivity will be greatly facilitated by the availability of a comprehensive collection of expressed gene sequences from multiple tissues and organs.

Results: We present an extensive expressed gene catalog for a commercially grown E. grandis × E. urophylla hybrid clone constructed using only Illumina mRNA-Seq technology and de novo assembly. A total of 18,894 transcript-derived contigs, a large proportion of which represent full-length protein coding genes were assembled and annotated. Analysis of assembly quality, length and diversity show that this dataset represent the most comprehensive expressed gene catalog for any Eucalyptus tree. mRNA-Seq analysis furthermore allowed digital expression profiling of all of the assembled transcripts across diverse xylogenic and non-xylogenic tissues, which is invaluable for ascribing putative gene functions.

Conclusions: De novo assembly of Illumina mRNA-Seq reads is an efficient approach for transcriptome sequencing and profiling in Eucalyptus and other non-model organisms. The transcriptome resource (Eucspresso, http://eucspresso.bi.up.ac.za/) generated by this study will be of value for genomic analysis of woody biomass production in Eucalyptus and for comparative genomic analysis of growth and development in woody and herbaceous plants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-11-681DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053591PMC
December 2010

Genome sequence of Pantoea ananatis LMG20103, the causative agent of Eucalyptus blight and dieback.

J Bacteriol 2010 Jun 26;192(11):2936-7. Epub 2010 Mar 26.

Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa.

Pantoea ananatis is a Gram-negative plant pathogen that causes disease on a broad range of host plants, including pineapple, maize, rice, onion, melons, and Eucalyptus, and has been implicated in several cases of human disease. Here, we report the genome sequence of P. ananatis LMG20103 isolated from diseased Eucalyptus in South Africa.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JB.00060-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2876505PMC
June 2010

Discovery: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria.

Malar J 2009 Jul 30;8:178. Epub 2009 Jul 30.

Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, South Africa.

Background: Up to half a billion human clinical cases of malaria are reported each year, resulting in about 2.7 million deaths, most of which occur in sub-Saharan Africa. Due to the over-and misuse of anti-malarials, widespread resistance to all the known drugs is increasing at an alarming rate. Rational methods to select new drug target proteins and lead compounds are urgently needed. The Discovery system provides data mining functionality on extensive annotations of five malaria species together with the human and mosquito hosts, enabling the selection of new targets based on multiple protein and ligand properties.

Methods: A web-based system was developed where researchers are able to mine information on malaria proteins and predicted ligands, as well as perform comparisons to the human and mosquito host characteristics. Protein features used include: domains, motifs, EC numbers, GO terms, orthologs, protein-protein interactions, protein-ligand interactions and host-pathogen interactions among others. Searching by chemical structure is also available.

Results: An in silico system for the selection of putative drug targets and lead compounds is presented, together with an example study on the bifunctional DHFR-TS from Plasmodium falciparum.

Conclusion: The Discovery system allows for the identification of putative drug targets and lead compounds in Plasmodium species based on the filtering of protein and chemical properties.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1475-2875-8-178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2724543PMC
July 2009

A structural annotation resource for the selection of putative target proteins in the malaria parasite.

Malar J 2008 May 23;7:90. Epub 2008 May 23.

Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, 0002, South Africa.

Background: Protein structure plays a pivotal role in elucidating mechanisms of parasite functioning and drug resistance. Moreover, protein structure aids the determination of protein function, which can together with the structure be used to identify novel drug targets in the parasite. However, various structural features in Plasmodium falciparum proteins complicate the experimental determination of protein structures. Limited similarity to proteins in the Protein Data Bank and the shortage of solved protein structures in the malaria parasite necessitate genome-scale structural annotation of P. falciparum proteins. Additionally, the annotation of a range of structural features facilitates the identification of suitable targets for experimental and computational studies.

Methods: An integrated structural annotation system was developed and applied to P. falciparum, Plasmodium vivax and Plasmodium yoelii. The annotation included searches for sequence similarity, patterns and domains in addition to the following predictions: secondary structure, transmembrane helices, protein disorder, low complexity, coiled-coils and small molecule interactions. Subsequently, candidate proteins for further structural studies were identified based on the annotated structural features.

Results: The annotation results are accessible through a web interface, enabling users to select groups of proteins which fulfil multiple criteria pertaining to structural and functional features 1. Analysis of features in the P. falciparum proteome showed that protein-interacting proteins contained a higher percentage of predicted disordered residues than non-interacting proteins. Proteins interacting with 10 or more proteins have a disordered content concentrated in the range of 60-100%, while the disorder distribution for proteins having only one interacting partner, was more evenly spread.

Conclusion: A series of P. falciparum protein targets for experimental structure determination, comparative modelling and in silico docking studies were putatively identified. The system is available for public use, where researchers may identify proteins by querying with multiple physico-chemical, sequence similarity and interaction features.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1475-2875-7-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2413252PMC
May 2008

MADIBA: a web server toolkit for biological interpretation of Plasmodium and plant gene clusters.

BMC Genomics 2008 Feb 28;9:105. Epub 2008 Feb 28.

Bioinformatics and Computational Biology Unit, African Centre for Gene Technologies (ACGT), Department of Biochemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, 0002, South Africa.

Background: Microarray technology makes it possible to identify changes in gene expression of an organism, under various conditions. Data mining is thus essential for deducing significant biological information such as the identification of new biological mechanisms or putative drug targets. While many algorithms and software have been developed for analysing gene expression, the extraction of relevant information from experimental data is still a substantial challenge, requiring significant time and skill.

Description: MADIBA (MicroArray Data Interface for Biological Annotation) facilitates the assignment of biological meaning to gene expression clusters by automating the post-processing stage. A relational database has been designed to store the data from gene to pathway for Plasmodium, rice and Arabidopsis. Tools within the web interface allow rapid analyses for the identification of the Gene Ontology terms relevant to each cluster; visualising the metabolic pathways where the genes are implicated, their genomic localisations, putative common transcriptional regulatory elements in the upstream sequences, and an analysis specific to the organism being studied.

Conclusion: MADIBA is an integrated, online tool that will assist researchers in interpreting their results and understand the meaning of the co-expression of a cluster of genes. Functionality of MADIBA was validated by analysing a number of gene clusters from several published experiments - expression profiling of the Plasmodium life cycle, and salt stress treatments of Arabidopsis and rice. In most of the cases, the same conclusions found by the authors were quickly and easily obtained after analysing the gene clusters with MADIBA.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-9-105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2277412PMC
February 2008

Structural and mechanistic insights into the action of Plasmodium falciparum spermidine synthase.

Bioorg Med Chem 2007 Feb 13;15(4):1628-37. Epub 2006 Dec 13.

Bioinformatics and Computational Biology Unit, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa.

Spermidine synthase is currently considered as a promising drug target in the malaria parasite, Plasmodium falciparum, due to the vital role of spermidine in the activation of the eukaryotic translation initiation factor (eIF5A) and cell proliferation. However, very limited information was available regarding the structure and mechanism of action of the protein at the start of this study. Structural and mechanistic insights of the P. falciparum spermidine synthase (PfSpdSyn) were obtained utilizing molecular dynamics simulations of a homology model based on the crystal structures of the Arabidopsis thaliana and Thermotoga maritima homologues. Our data are supported by in vitro site-directed mutagenesis of essential residues as well as by a crystal structure of the protein that became available recently. We provide, for the first time, dynamic evidence for the mechanism of the aminopropyltransferase action of PfSpdSyn. This characterization of the structural and mechanistic properties of the PfSpdSyn as well as the elucidation of the active site residues involved in substrate, product, and inhibitor interactions paves the way toward inhibitor selection or design of parasite-specific inhibitors.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2006.12.017DOI Listing
February 2007

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

Malar J 2006 Nov 17;5:110. Epub 2006 Nov 17.

Department of Biochemistry and African Centre for Gene Technologies, Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002, Pretoria, South Africa.

The organization and mining of malaria genomic and post-genomic data is important to significantly increase the knowledge of the biology of its causative agents, and is motivated, on a longer term, by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should, therefore, be as reliable and versatile as possible. In this context, five aspects of the organization and mining of malaria genomic and post-genomic data were examined: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes, particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Recent progress towards a grid-enabled chemogenomic knowledge space is discussed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1475-2875-5-110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665468PMC
November 2006

Influence of prostaglandin A2 on Bax, Bcl-2 and PCNA expression in MCF-7 cells.

Biomed Res 2006 Aug;27(4):157-62

Department of Physiology, University of Pretoria, Pretoria, South Africa.

The effects of 20 microg/mL exogenous prostaglandin A(2) (PGA(2)) were determined on Bax, Bcl-2 and proliferating cell nuclear antigen (PCNA) expression levels in MCF-7 cells. Flow cytometric analysis indicated a pronounced increase in the S phase and a decrease in the G(1) phase, whereas a significant increase in the DNA content preceding the G(0)/G(1) peak was also observed after 48 h of exposure to PGA(2). Confirmation of apoptosis was determined after 12 h, 36 h and 48 h of PGA(2) exposure employing the mitosensor reagent that detects potential changes in the mitochondrial membrane. Twenty-eight percent of PGA(2)-exposed cells were in apoptosis when compared to the 7.1% vehicle-treated cells after 48 h. PGA(2) exposure led to statistically significant increase (1.25-fold) over vehicle-treated controls in Bax expression levels. Decreases in Bcl-2 (0.79-fold), as well as PCNA (0.69-fold) expression levels over vehicle-treated controls were observed. The Bax/Bcl-2 ratio for PGA(2)-exposed cells was 2.7. The present study suggests that an accumulation in the S phase, a decrease in expression levels of PCNA, as well as an altered ratio in favor of Bax, could lead to the induction of apoptosis in these cells.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2220/biomedres.27.157DOI Listing
August 2006
-->