Ontology highlight
ABSTRACT:
PROVIDER: PRJNA412577 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6123580.fastq.gz | Fastqsanger.gz |
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Project description:Phytophthora cinnamomi Rands is a cosmopolite and phyllophagous pathogen of woody plants which during the last couple of centuries has spread all over the world from its center of origin in Southeast Asia. Despite Chinese cork tree (Quercus variabilis Blume) forests native to Asia being generally healthy, the populations of cork trees (Quercus suber L.) in Europe have been decimated by P. cinnamomi. The present study tries to identify the differences in the early proteomic and metabolomic response of these two tree species that lead to their contrasting susceptibility to P. cinnamomi attack. By using micropropagated clonal plants, we tried to minimize the plant-to-plant differences in the defense response that is maximized by the high intraspecific genetic variability inherent to the Quercus genus. The evolution on the content of Phytophthora proteins in the roots during the first 36 hours after inoculation suggest a slower infection process in Q. variabilis plants. These plants displayed a significant decrease in sugars in the roots, together with a downregulation of proteins related to carbon metabolism. In the leaves, the biggest changes in proteomic profiling were observed 16 hours after inoculation. and included increased abundance of peroxidases, superoxidedismutases and gluthatione S-transferases in Q. variabilis plants, which probably aided its resistance against P. cinnamomi attack.
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2018-08-07 | MSV000082753 | MassIVE
Project description:The evolutionary relationships among extinct African hominin species are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. For Paranthropus robustus, a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa, and the nature of intraspecific variation are still debated. Here we report the first successful mass spectrometric sequencing of enamel proteomes from four ca. 2 million years old dental specimens morphologically identified as P. robustus from the site of Swartkrans.
2025-06-09 | PXD040221 | Pride
Project description:The emergence and fast global spread of COVID-19 has presented one of the greatest public health challenges in modern times with no proven cure or vaccine. Africa is still early in this epidemic, therefore the extent of disease severity is not yet clear. We used a mathematical model to fit to the observed cases of COVID-19 in South Africa to estimate the basic reproductive number and critical vaccination coverage to control the disease for different hypothetical vaccine efficacy scenarios. We also estimated the percentage reduction in effective contacts due to the social distancing measures implemented. Early model estimates show that COVID-19 outbreak in South Africa had a basic reproductive number of 2.95 (95% credible interval [CrI] 2.83–3.33). A vaccine with 70% efficacy had the capacity to contain COVID-19 outbreak but at very higher vaccination coverage 94.44% (95% Crl 92.44–99.92%) with a vaccine of 100% efficacy requiring 66.10% (95% Crl 64.72–69.95%) coverage. Social distancing measures put in place have so far reduced the number of social contacts by 80.31% (95% Crl 79.76–80.85%). These findings suggest that a highly efficacious vaccine would have been required to contain COVID-19 in South Africa. Therefore, the current social distancing measures to reduce contacts will remain key in controlling the infection in the absence of vaccines and other therapeutics.
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2020-01-28 | E-MTAB-8757 | biostudies-arrayexpress
Project description:Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. It is essential to maximize the effectiveness of these plantations by increasing their productivity, the quality and value of their products. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven individual E. grandis trees. A 1532-probe cDNA microarray was constructed by arraying 768 cDNA-AFLP fragments and 810 cDNA library clones from seven individual E. grandis trees onto silanised slides. The results revealed that 32% of the spotted fragments showed distinct expression patterns (with a fold change of at least 1.4 or -1.4 and a p value of 0.01) and could be grouped into clusters representing co-expressed genes. Evaluation of the binary distribution of cDNA-AFLP fragments on the array showed that the individual genotypes could be discriminated. A simple, yet general method was developed for genotyping and expression profiling of wood-forming tissue of E. grandis trees differing in their splitting characteristics and in their lignin contents. Evaluation of gene expression profiles and the binary distribution of cDNA-AFLP fragments on the chip suggest that the prototype chip developed could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programmes.
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