Project description:The Afrikaner population of South Africa are the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the “Coloured" populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5%-7.2%. NB two individuals withdrew consent so this data contains only 75 individuals as compared to the 77 cited in the article.
Project description:True cobras of the genus Naja are venomous snakes with particular medical importance in Africa and Asia. The Cape cobra Naja nivea is one of the most toxic of the African true cobras, but the composition of its venom has rarely been investigated using proteomics methods.
Project description:Purpose: This study aimed to explore the mechanism of SBM to promote hair regeneration through single-cell transcriptomics Methods: Supplementation with intragastric administration or smear administration of SBM in artificially shaved C57BL/6 mice to observe its hair growth. Single-cell RNA sequencing were performed to explore the role of SBM for hair regeneration. Results: SBM significantly induced hair growth compared with control treatment.The results of single-cell sequencing revealed that after SBM treatment, the number of hair follicle stem cells (HFSCs) and dermal papilla cells (DPCs) increased significantly. Cell interactions and volcano maps show that interaction of FGF signaling pathway was significantly enhanced, in which FGF7 expression was especially upregulated in DPCs. In addition, Wnt signaling pathway also had a partially enhanced effect on the interactions between various cells in the skin. Network pharmacology study showed that the promotion of FGF and Wnt pathways by SBM was also enriched in alopecia diseases. Conclusion: We report that SBM has a potential effect on the promotion of hair growth by mainly activating FGF signaling pathway. The use of SBM may be a novel therapeutic option for hair loss.
Project description:Caffeic acid phenethyl ester (CAPE), derived from various plant sources, has been shown to ameliorate ischemia/reperfusion (I/R) injury in vivo, and this has been attributed to its ability to reduce the oxidative stress. Here we investigated the cytoprotection of CAPE against menadione (MD)-induced oxidative stress in human umbilical vein endothelial cells (HUVEC) to evaluate potential gene expression involvement. CAPE exhibited dose-dependent cytoprotection of HUVEC that required preincubation. A gene screen with microarrays was performed to identify the potential cytoprotective gene(s) induced by CAPE. Heme oxygenase-1 (HO-1) was highly upregulated by CAPE and this was confirmed with reverse transcriptase polymerase chain reaction (RT-PCR) and western blotting. Keywords: gene expression in HUVEC, CAPE cytoprotective dose response Confluent HUVEC were incubated with cytoprotective dose of CAPE at 5 µg/ml or 0.1% DMSO as vehicle control for 6 hrs. Both treatments were done in triplicates. Total RNA was isolated at the end of the treatment and applied to microarray experiments in order to identify transcriptional response of HUVEC to CAPE. Microarray experiments were based on a two-color reference design using human universal reference RNA to compare results bwtween CAPE treatment and vehicle control groups.
Project description:Caffeic acid phenethyl ester (CAPE), derived from various plant sources, has been shown to ameliorate ischemia/reperfusion (I/R) injury in vivo, and this has been attributed to its ability to reduce the oxidative stress. Here we investigated the cytoprotection of CAPE against menadione (MD)-induced oxidative stress in human umbilical vein endothelial cells (HUVEC) to evaluate potential gene expression involvement. CAPE exhibited dose-dependent cytoprotection of HUVEC that required preincubation. A gene screen with microarrays was performed to identify the potential cytoprotective gene(s) induced by CAPE. Heme oxygenase-1 (HO-1) was highly upregulated by CAPE and this was confirmed with reverse transcriptase polymerase chain reaction (RT-PCR) and western blotting. Keywords: Gene expression in HUVEC, CAPE cytoprotective dose response Confluent HUVEC were incubated with cytoprotective dose of CAPE at 5 µg/ml or 0.1% DMSO as vehicle control for 6 hrs. Both treatments were done in triplicates. Total RNA was isolated at the end of the treatment and applied to microarray experiments in order to identify transcriptional response of HUVEC to CAPE. Microarray experiments were based on a two-color reference design using human universal reference RNA to compare results bwtween CAPE treatment and vehicle control groups.
Project description:We used in vivo biotin labeling of a nuclear envelope protein in individual cell types followed by affinity isolation of labeled nuclei to measure gene expression and chromatin features of the hair and non-hair cell types of the Arabidopsis root epidermis. Keywords: Chromatin affinity-purification on microarray
Project description:Small-cell lung cancer H446 cells were treated with CAPE. The regulation mediated by miR-3960 after CAPE treatment was explored and the altered signaling pathways were predicted in a bioinformatics analysis.CAPE decreased the expression of yes-associated protein 1 (YAP1) and cellular myelocytomatosis oncogene (c-MYC) protein. Moreover, the upregulation of miR-3960 by CAPE contributed to CAPE-induced apoptosis. The knockdown of miR-3960 decreased the CAPE-induced apoptosis.
Project description:Esophageal squamous cell carcinoma (ESCC) is an aggressive cancer with one of the highest world incidences in the Eastern Cape region of South Africa. Several genome wide studies have been performed on ESCC cohorts from Asian countries, North America, Malawi and other parts of the world but none has been conducted on ESCC tumors from South Africa to date, where the molecular pathology and etiology of this disease remains unclear. We report here tumor associated copy number changes observed in 51 ESCC patients’ samples from the Eastern Cape province of South Africa. We extracted tumor DNA from 51 archived ESCC specimens and interrogated tumor associated DNA copy number changes using Affymetrix® 500K SNP array technology. The Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm was applied to identify significant focal regions of gains and losses. Gains of the top recurrent cancer genes were validated by fluorescence in situ hybridization and their protein expression assessed by immunohistochemistry. Twenty-three significant focal gains were identified across samples. Gains involving the CCND1, MYC, EGFR and JAG1 loci recapitulated those described in studies on Asian and Malawian cohorts. The two most significant gains involved the chromosomal sub-bands 3q28, encompassing the TPRG1 gene and 11q13.3 including the CTTN, PPFIA1and SHANK2 genes. There was no significant homozygous loss and the most recurrent hemizygous deletion involved the B3GAT1 gene on chromosome11q25. Focal gains on 11q13.3 in 37% of cases (19/51), consistently involved CTTN and SHANK2 genes. Twelve of these cases (23,5%), had a broader region of gain that also included the CCND1, FGF19, FGF4 and FGF3 genes. SHANK2 and CTTN are co-amplified in several cancers, these proteins interact functionally together and are involved in cell motility. Immunohistochemistry confirmed both Shank2 (79%) and cortactin (69%) protein overexpression in samples with gains of these genes. In contrast, cyclin D1 (65%) was moderately expressed in samples with CCND1 DNA gain. This study reports copy number changes in a South African ESCC cohort and highlights similarities and differences with cohorts from Asia and Malawi. Our results strongly suggest a role for CTTN and SHANK2 in the pathogenesis of ESCC in South Africa.
Project description:These data were generated in May of 2016 on a Thermo Q-Exactive at the University of Cape Town in South Africa. Samples were drawn from 48 cases of malignant medulloblastoma that were added to the FFPE archive between 1988 and 2014 under approval from the University of Cape Town Faculty of Health Sciences Human Research Ethics Committee (HREC 149/2014). Assignment to Group 3 or Group 4 categories was performed via Nanostring analysis and IHC (other subtypes were also analyzed in the larger study). Five distinct samples from each of the two Groups were subjected to LC-MS/MS. After conversion to mzML, a total of 245,589 tandem mass spectra were available, of which 36% corresponded to doubly-charged precursor ions. Over all ten experiments, tandem mass spectra were acquired at a rate of 4.55 Hz. MS/MS scans averaged a peak density average of 148 peaks per spectrum.
More complete information is available in Omesan Nair's Ph.D. Dissertation: http://hdl.handle.net/11427/26896.