Ontology highlight
ABSTRACT:
PROVIDER: PRJNA422624 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6381510.fastq.gz | Fastqsanger.gz | |||
| SRR6381520.fastq.gz | Fastqsanger.gz | |||
| SRR6381530.fastq.gz | Fastqsanger.gz | |||
| SRR6381540.fastq.gz | Fastqsanger.gz | |||
| SRR6381511.fastq.gz | Fastqsanger.gz |
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Project description:Sequencing of ancient DNA of Mycobacterium tuberculosis from archaeological specimens
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Project description:Palaeoproteomics analysis of archaeological bird eggshells from archaeological Çatalhöyük site. This project aimed to taxonomically identify fragments of eggshells from the site, using a combination of morphological observations (by light microscopy) and protein analyses (MALDI-MS and LC-MS/MS).
2020-06-10 | PXD014558 | Pride
Project description:Metabolomic approaches, such as in clinical applications of living individuals, have shown potential use for solving questions regarding the past when applied to archaeological material. Here, we study for the first time the potential of this Omic approach as applied to metabolites extracted from archaeological human dentin. Dentin obtained from micro sampling the dental pulp of teeth of victims and non-victims of <i>Yersinia pestis</i> (plague) from a 6th century Cambridgeshire site are used to evaluate the potential use of such unique material for untargeted metabolomic studies on disease state through liquid chromatography hyphenated to high-resolution mass spectrometry (LC-HRMS). Results show that small molecules of both likely endogenous and exogenous sources are preserved for a range of polar and less polar/apolar metabolites in archaeological dentin; however, untargeted metabolomic profiles show no clear differentiation between healthy and infected individuals in the small sample analysed (<i>n</i> = 20). This study discusses the potential of dentin as a source of small molecules for metabolomic assays and highlights: (1) the need for follow up research to optimise sampling protocols, (2) the requirements of studies with larger sample numbers and (3) the necessity of more databases to amplify the positive results achievable with this Omic technique in the archaeological sciences.
2024-03-15 | MTBLS7394 | MetaboLights
Project description:Background: Respiratory allergy triggered by pollen allergens is increasing at an alarming rate worldwide. Sunflower pollen is thought to be an important source of inhalant allergens. Present study aims to identify the prevalence of sunflower pollinosis among the Indian allergic population and characterizes the pollen allergens using immuno-proteomic tools. Methodology: Clinico-immunological tests were performed to understand the prevalence of sensitivity towards sunflower pollen among the atopic population. Sera from selected sunflower positive patients were used as probe to detect the IgE-reactive proteins from the one and two dimensionally separated proteome of sunflower pollen. The antigenic nature of the sugar moiety of the glycoprotein allergens was studied by meta-periodate modification of IgE-immunoblot. Finally, these allergens were identified by mass-spectrometry (MALDI TOF/TOF and LC ESI qTOF). MASCOT searching was performed against NCBInr database. However, Helianthus annuus genome is not fully sequenced and partially annotated. So in case of low confidence (p> 0.05) protein identification, searching was performed against EST library of Helianthus annuus. Results: Prevalence of sunflower pollen allergy was observed among 21% of the atopic population and associated with elevated level of specific IgE and histamine in the sera of these patients. Immunoscreening of sunflower pollen proteome with patient serum detected seven IgE-reactive proteins with varying molecular weight and pI. Hierarchical clustering of 2D-immunoblot data highlighted three allergens characterized by a more frequent immuno-reactivity and increased levels of IgE antibodies in the sera of susceptible patients. These allergens were considered as the major allergens of sunflower pollen and were found to have their glycan moiety critical for inducing IgE response. Homology driven search of MS/MS data of these IgE-reactive proteins identified seven previously unreported allergens from sunflower pollen. Three major allergenic proteins were identified as two non-isoformic pectate lyases and a cystein protease. Conclusion: Novelty of the present report is the identification of a panel of seven sunflower pollen allergens for the first time at immuno-biochemical and proteomic level, which substantiated the clinical evidence of sunflower allergy. Further purification and recombinant expression of these allergens will improve component-resolved diagnosis and therapy of pollen allergy.
2015-10-05 | PXD002397 | Pride
Project description:Proteomics is continually being applied to a wider range of applications, now including the analysis of archaeological samples and anatomical specimens, in particular, collagen-containing tissues such as bones and teeth. Here we present the application of a chemi-cal digestion-based proteomics sample preparation protocol to the analysis of fresh, anatomical and archaeological samples. We are describing and discussing two protocols, one using hydroxylamine as an additional step of the proteomic workflow, applied to the insoluble fraction, and another focusing directly on demineralized bones and teeth. We demonstrate the additional information that can be extracted using both protocols, including increasing the sequence coverage and number of peptides detected in modern and archaeological samples, and increasing the number of proteins identified in archaeological samples. Targeting research related to collagens or extracellular matrix proteins, the use of this protocol will open new insights considering both fresh and ancient mineral-ized samples.
2024-03-28 | PXD046969 | Pride
Project description:HaHB11 is a divergent member of the sunflower homeodomain-leucine zipper I subfamily of transcription factors. A sunflower microarray was hybridized with RNA from HaHB11-transformed leaf-disks and its analysis indicated the regulation of many genes encoding enzymes from fermentative pathways. A 1300 bp sequence exhibiting flooding-responsive cis-acting elements, upstream the transcription initiation site, was isolated and Arabidopsis plants transformed with a construct in which this promoter directs GUS expression. GUS expression was induced after flooding treatments and, in the same sense, HaHB11 expression was induced by flooding stress in sunflower. Furthermore, Arabidopsis plants were transformed with different constructs, varying in the promoter used, able to express HaHB11 cDNA. These transgenic plants exhibited differential phenotypes which the more remarkable traits were a significant increase in the rosette biomass and seeds yield. Moreover these plants exhibited an enhanced tolerance to flooding stress, both to submergence and waterlogging. Starch, sucrose and glucose contents were higher in the transgenics compared to WT and decreased less after submergence treatments. Finally, transcript levels of selected genes, involved in fermentative pathways, and the corresponding enzymatic activities were assessed both in sunflower and transgenic Arabidopsis plants after submergence indicating a general repression of the fermentative pathway which suggested that tolerance occurs via the quiescent strategy. Altogether the results indicated a role for HaHB11 in the flooding response and allowed us to propose this gene as a biotechnological tool to improve crops for increased yield and biomass and flooding tolerance.
2015-08-03 | GSE71654 | GEO
Project description:Characterisation of ancient proteomes from avian eggshell, archaeological site of Shubayqa
2024-05-25 | PXD047233 | Pride
Project description:Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. We studied in parallel microRNA profiles on the same samples and we will try to identify sunflower microRNA regulated genes in response to ABA. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.-The experiment consisted of 3 repeats of four 12-day-old-plantlets of sunflower genotype SF193 (INRA code: XRQ) grown in growth chamber conditions and submitted to a 6-hour-treatment of 10 µM absissic acid or not. Growth conditions were 14h light at 23°C and 10h night at 20°C under fluorescent bulbs. Plants were grown in 6 hydroponic boxes containing 20 litres of aerated liquid culture medium (as described in Massonneau et al., 2001 Planta). Leaves (not cotyledons) 1 to 4 were harvested 4 hours after light onset and frozen immediately in liquid nitrogen.
2012-12-09 | GSE22519 | GEO