Project description:In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from sediments adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut and oral microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material usually discarded, as it is sediments adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual.

2025-09-15 | PXD057056 | Pride

Gene expression profiling as a tool for sediment risk assessment: a pilot study using Caenorhabditis elegans whole genome microarrays

Project description:Toxicity of river sediments are assessed using whole sediment toxicity tests with benthic organisms. The challenge, however, is the differentiation between multiple effects caused by complex contaminant mixtures and the unspecific toxicity endpoints such as survival, growth or reproduction. Moreover, natural sediment properties, such as grain size distribution and organic carbon content, can influence the test parameters by masking pollutant toxicity. The use of gene expression profiling facilitates the identification of transcriptional changes at the molecular level that are specific to the bioavailable fraction of pollutants. The nematode Caenorhabditis elegans is ideally suited for these purposes, as (i) it can be exposed to whole sediments, and (ii) its genome is fully sequenced and widely annotated. In this pilot study we exposed C. elegans for 48 h to three sediments varying in degree of contamination with e.g. heavy metals and organic pollutants. Following the exposure period, gene expression was profiled using a whole genome DNA-microarray approach.

2008-06-25 | GSE11837 | GEO

SWATH-MS data of Multi Drug Resistant and drug sensitive Escherichia coli isolated from anthropogenic river Yamuna, Delhi, India

Project description:Integrative proteo-trnascriptomics analysis of MDR abd drug sensitive E. coli strains isolated from river Yamuna, Delhi, India to identify novel drug targets against Multi drug Resistant E. coli

2025-02-10 | PXD048998 | Pride

Gene expression profiling as a tool for sediment risk assessment: a pilot study using Caenorhabditis elegans whole genome microarrays

2008-06-25 | E-GEOD-11837 | biostudies-arrayexpress