Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1100461 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28676058_1.fastq.gz | Fastqsanger.gz | |||
| SRR28676058_2.fastq.gz | Fastqsanger.gz | |||
| SRR28676059_1.fastq.gz | Fastqsanger.gz | |||
| SRR28676059_2.fastq.gz | Fastqsanger.gz | |||
| SRR28676060_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The investigation of archaeological samples, which are of inestimable value, requires minimally destructive or non-destructive sampling techniques. One of the most promising and recent non-invasive techniques is known under the acronym EVA, an ethylene vinyl acetate film which avoids contamination and proteins damages. The present work reports the results of the metaproteomic analysis performed on the middle part of a trunk, and on the portion of a trunk tip tissue of two different woolly mammoths some 40000 years’ old. In particular, proteins were extracted by applying EVA (Ethylene-Vinyl Acetate) films to the surface of these tissues belonging to two Mammuthus primigenus specimens, discovered in two regions located in the Russian Far East, and then investigated via a shotgun MS-based approach. This approach allowed to obtain two interesting results: i) an indirect description of the habitat of these two mammoths, and ii) an improved sequence characterization of the alpha-1 type I collagen (col1a1), the major component of type I collagen. Sequence characterization of the col1a1 highlighted some differences between M. primigenius and other Proboscidea together with the identification of two potentially diagnostic amino acidic mutations that could be used to reliably distinguish the Mammuthus primigenius respect to the other two genera of elephantids (i.e. Elephas and Loxodonta), and the extinct American mastodon (i.e. Mammut americanum). The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the “original” endogenous peptides from contaminant ones.
2022-05-19 | PXD029558 | Pride
Project description:Palaeoproteomic study of mummified human skin using a non-destructive sampling technique, based on mixed-bed chromatographic media stabilised on ethylene vinyl acetate membranes (“EVA”), which had previously been used exclusively on historical material, was successful in extracting ancient proteins from the surface of Ancient Egyptian mummies. We tested the method on a decontextualised fragment of skin and assessed the endogeneity of its metaproteome by comparison with a procedural blank. Furthermore, we retrieved and authenticated sequences of collagen and keratin from the mummy of a young woman (Supp. 16747 of the Museum of Anthropology and Ethnography of the University of Turin) who lived and died between 2400 and 2200 BC, during the Old Kingdom of Egypt.
2020-06-10 | PXD015572 | Pride
Project description:The marine bacterium Rhodococcus erythropolis PR4 was demonstrated to be able for assimilation/biodegradation of hydrocarbons. Not just the chromosome but two large plasmids provide versatile enzyme sets involved in many metabolic pathways. In order to identify the key elements involved in biodegradation of the model compound, hexadecane, and diesel oil, we performed whole transcriptome analysis on cells grown in the presence of n-hexadecane and diesel oil. Sodium acetate grown cells were used as control. The final goal of the project is a comparative transcriptomic analysis of Rhodococcus erythropolis PR4 cells grown on acetate, on the model compound: hexadecane and the real substrate: diesel oil. Comparative transcriptomics of Rhodococcus erythropolis PR4 grown on n-hexadecane, diesel oil, and sodium acetate.
2014-04-21 | E-GEOD-56474 | biostudies-arrayexpress
Project description:The marine bacterium Rhodococcus erythropolis PR4 was demonstrated to be able for assimilation/biodegradation of hydrocarbons. Not just the chromosome but two large plasmids provide versatile enzyme sets involved in many metabolic pathways. In order to identify the key elements involved in biodegradation of the model compound, hexadecane, and diesel oil, we performed whole transcriptome analysis on cells grown in the presence of n-hexadecane and diesel oil. Sodium acetate grown cells were used as control. The final goal of the project is a comparative transcriptomic analysis of Rhodococcus erythropolis PR4 cells grown on acetate, on the model compound: hexadecane and the real substrate: diesel oil.
2014-04-21 | GSE56474 | GEO
Project description:Although the biodegradation of biodegradable plastics in soil and compost is well-studied, there is little knowledge on the metabolic mechanisms of synthetic polymers degradation by marine microorganisms. Here, we present a multiomics study to elucidate the biodegradation mechanism of a commercial aromatic-aliphatic copolyester film by a marine microbial enrichment culture. The plastic film and each monomer can be used as sole carbon source. Our analysis showed that the consortium synergistically degrades the polymer, different degradation steps being performed by different members of the community. Analysis of gene expression and translation profiles revealed that the relevant degradation processes in the marine consortium are closely related to poly(ethylene terephthalate) biodegradation from terrestrial microbes. Although there are multiple genes and organisms with the potential to perform a degradation step, only a few of these are active during biodegradation. Our results elucidate the potential of marine microorganisms to mineralize biodegradable plastic polymers and describe the mechanisms of labor division within the community to get maximum energetic yield from a complex synthetic substrate.
2020-09-25 | PXD018391 | Pride
Project description:The investigation about archaeological samples, which are of inestimable value, requires minimally destructive or nondestructive sampling techniques. One of the most promising and recent non-invasive techniques is known under the acronym EVA, an ethylene vinyl acetate film which avoids contamination and proteins damages. This paper reports the results of the first-ever analysis of proteins extracted from the EVA film applied to a tissue sample some 40000 years old. In particular, the gut sample of a woolly mammoth (Mammuthus primigenus), discovered in 1972 close to the Shandrin River (Yakutia, Russia), via a shotgun MS-based approach was investigated. Proteomic and peptidomic analysis allowed the exploration of the mammoth dietary plants and its gut bacteria. The results were validated through the level of deamidation and other post-translational modifications of the peptides of the samples, which were used to discrimitate the “original” endogenous peptides from contaminant ones. Overall, the results of the metaproteomic analysis here reported are in accordance with the previous paleobotanical studies and with the reconstructed habitat of the Shandrin mammoth.
2021-11-03 | PXD025518 | Pride
Project description:Understanding the bacterial community structure, and their functional analysis for active bioremediation process is essential to design better and cost effective strategies. Microarray analysis enables us to simultaneously study the functional and phylogenetic markers of hundreds of microorganisms which are involved in active bioremediation process in an environment. We have previously described development of a hybrid 60-mer multibacterial microarray platform (BiodegPhyloChip) for profiling the bacterial communities and functional genes simultaneously in environments undergoing active bioremediation process (Pathak et al; Appl Microbiol Biotechnol,Vol. 90, 1739-1754). The present study involved profiling the status of bacterial communities and functional (biodegradation) genes using the developed 60-mer oligonucleotide microarray BiodegPhyloChip at five contaminated hotspots in the state of Gujarat, in western India. The expression pattern of functional genes (coding for key enzymes in active bioremediation process) at these sites was studied to understand the dynamics of biodegradation in the presence of diverse group of chemicals. The results indicated that the nature of pollutants and their abundance greatly influence the structure of bacterial communities and the extent of expression of genes involved in various biodegradation pathways. In addition, site specific factors also play a pivotal role to affect the microbial community structure as was evident from results of 16S rRNA gene profiling of the five contaminated sites, where the community structure varied from one site to another drastically.
2012-12-01 | GSE38004 | GEO
Project description:We have used genome-wide proteomic profiling to examine leaves of hybrids for molecular phenotypes. Profiles of the proteome of maize leaves revealed hybrid-specific differences in the chloroplast and mitochondria; levels of their energy transduction complexes and ribosomes were selectively elevated 10-20% above mid-parent levels. Each of these protein machines is comprised of nuclear-encoded and organelle-encoded subunits and we refer to them as digenomic protein complexes. Expression heterosis of the organelle ribosome proteins was quantitatively predictive of growth heterosis in a set of hybrids. Ethylene biosynthetic enzyme levels were reduced in hybrids and an ethylene biosynthesis mutant in an inbred background partially phenocopied the molecular differences seen in hybrids indicating that reduced ethylene levels may play a role in maize heterosis.
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