Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1182973 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31259081_1.fastq.gz | Fastqsanger.gz | |||
| SRR31259081_2.fastq.gz | Fastqsanger.gz | |||
| SRR31259082_1.fastq.gz | Fastqsanger.gz | |||
| SRR31259082_2.fastq.gz | Fastqsanger.gz |
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Project description:Cultural heritage material Metagenome
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Project description:Paleofeces are an important source of information to study the evolution of dietary habits and human health. The UNESCO World Heritage region of Hallstatt-Dachstein/Salzkammergut is one of Europe’s oldest cultural and industrial landscapes; its underground salt mines dating back at least to the 14th century BC are one of the few archaeological sites where paleofeces are well preserved. The high salt concentrations and the constant annual temperature at around 8°C inside the isolated Hallstatt mines have perfectly preserved organic archaeological artefacts (e.g. paleofeces, clothing, mining tools) that provide unique insights into the daily life of a progressive community in Hallstatt. Here we subjected human paleofeces dated from the Bronze Age to early Modern Times to an in-depth microscopic, metagenomic and proteomic analysis. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as one of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food. Linked to these traditional dietary habits all ancient miners up to the early Modern times have gut microbiome structures akin to modern non-Westernized individuals which may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, we observed in one of the Iron Age samples a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provide the first molecular evidence for blue cheese and beer consumption during Iron Age Europe.
2021-11-02 | PXD027613 | Pride
Project description:Under hypoxic exposure in rats, activation of VEGF/Notch pathway may lead to pulmonary angiogenesis, and the expression of related proteins may be associated with down-regulation of miRNAs. We used microarrays to screen out miRNAs related to VEGF/Notch pathway in hypoxic exposure, and in this process, we found genes with a downregulation trend with prolonged exposure time.
2019-03-19 | GSE128451 | GEO
Project description:In this study we investigate the molecular physiology of the main S. cerevisiae commercial strain (PE-2) used on Brazilian bioethanol process under two distinct conditions: typical (TF) and flocculated (co-aggregated - FL) fermentation. Transcriptional machinery of PE-2 was assessed by high throughput sequencing-based methods (RNA-seq) during industrial fed-batch fermentations. Data from comparative analysis revealed distinct transcriptional profiles among conditions, characterized mainly by a deep gene repression on FL process. We investigated the transcriptional changes in S. cerevisiae PE-2 strain under industrial fermentation conditions using RNA-seq protocols. We analyzed 13 fermentation time-points where 6 time-points on typical fermentation conditions (TF) and 7 time-points on flocculate conditions(FL). The raw data have been submitted to SRA as SRP014755
2015-02-02 | E-GEOD-41834 | biostudies-arrayexpress
Project description:Undertaking the conservation of artworks informed by the results of molecular analyses has gained growing importance over the last decades, and today it can take advantage of state-of-the-art analytical techniques, such as mass spectrometry-based proteomics. Protein-based binders are among the most common organic materials used in artworks, having been used in their production for centuries. However, the applications of proteomics to these materials are still limited. In this work, a palaeoproteomic workflow was successfully tested on paint reconstructions, and subsequently applied to micro-samples from a 15th-century panel painting, attributed to the workshop of Sandro Botticelli. This method allowed the confident identification of the protein-based binders and their biological origin, as well as the discrimination of the binder used in the ground and paint layers of the painting. These results show that the approach is accurate, highly sensitive, and broadly applicable in the cultural heritage field, due to the limited amount of starting material required. Accordingly, a set of guidelines are suggested, covering the main steps of the data analysis and interpretation of protein sequencing results, optimised for artworks.
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Project description:The filamentous fungus Aspergillus oryzae is an important microbial cell factory for industrial production of useful enzymes, such as α-amylase. In order to optimize the industrial enzyme production process, there is a need to understand fundamental processes underlying protein production, here under how protein production links to metabolism through global regulatory structures. In this study, two α-amylase-producing strains of A. oryzae, a wild type strain and a transformant strain containing additional copies of the α-amylase gene, were characterized at a systematic level. Based on integrated analysis of ome-data together with genome-scale metabolic network and flux calculation, we identified key genes, key enzymes, key proteins, and key metabolites involved in the processes of protein synthesis and secretion, nucleotide metabolism, and amino acid metabolism that can be the potential targets for improving industrial protein production. Keywords: Two Aspergillus oryzae strains and two different carbon sources Two carbon sources (glucose, maltose) with three biological replicates for A. oryzae strain A1560 and strain CF1.1
2012-02-12 | E-GEOD-22566 | biostudies-arrayexpress
Project description:The interest of scientists in analysing items of World Cultural Heritage, has been exponentially increasing since the beginning of the new millennium. These studies have grown considerably in tandem with the development and the use of sophisticated and sensitive technologies such as the high-resolution mass spectrometry (MS) and the non-invasive and non-damaging technique, known under the acronym EVA. Here, we report the results about the MS-characterization of the peptides and proteins harvested by the EVA technology applied to three letters written in 1457 and 1475 by the voivode of Wallachia, Vlad III, also known as Vlad the Impaler, or Vlad Dracula. The discrimination of the “original” endogenous peptides from contaminant ones was obtained monitoring their different level of deamidation and of other diagenetic chemical modifica-tions. The characterization of the ancient proteins extracted from these documents allowed to explore the environmental conditions, in the second half of the 15th-century, of the Wallachia, a region considered as a meeting point for soldiers, mi-grants and travellers that probably carried not only trade goods and cultural traditions, but also diseases and epidemics. In addition, the identification of many human peptides and proteins harvested from the letters allowed to uncover more about Vlad Dracula the Impaler. Particularly, the experimental data show that he probably suffered of inflammatory processes of the respiratory tract and/or of the skin, and, according to some stories, he also suffered from a pathological condition called haemolacria, that is he could shed tears admixed with blood. It is worth to note that it cannot deny that more medieval peo-ple may have touched these documents, but it is also presumable that the most prominent ancient proteins should be related to the Prince Vlad the Impaler, who written and signed these letters.
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