Project description:Microbiome sequencing model is a Named Entity Recognition (NER) model that identifies and annotates microbiome nucleic acid sequencing method or platform in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with sequencing metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications
Project description:NGPS is a method for de-novo, full-length protein sequencing in high throughput. The method is based on cleavage of the protein at semi-random sites by microwave-assisted acid hydrolysis (MAAH), enrichment of LC-MS/MS amenable peptides from the hydrolysate by solid-phase-extraction, LC-MS/MS analysis, de-novo long peptide tag sequencing of resulting peptides and assembly of peptide tags into consensus contigs.
Project description:Parasite proteins secreted at the interface of nematode and host are believed to play an essential role in parasitism. Here, we present an efficient pipeline of bio-informatic algorithms and laboratory experiments to identify candidate parasitism genes within nematode secretomes, i.e. the repertoire of secreted proteins in an organism. We performed our approach on 12 218 expressed sequence tags (ESTs) originating from three life stages of the plant parasitic nematode Meloidogyne chitwoodi--a molecularly unexplored root-knot nematode species. The ESTs from M. chitwoodi were assembled into 5880 contigs and open reading frames translated from the consensus sequences were searched for features of putative signal peptides for protein secretion and trans-membrane regions, resulting in the identification of 398 secretome members. The products of parasitism genes are secreted by a range of organs, including the oesophageal, amphidial and rectal glands, the intestine, and the hypodermis. To localize the site of expression in M. chitwoodi, we subjected the most abundant secretome members to in situ hybridization microscopy. We found hybridization of one tag in the dorsal oesophageal gland, seven in the two subventral oesophageal glands, two in the intestine and one tag hybridized to the tail tip in the proximity of the phasmids. Four sequences showed similarity to putative parasitism genes from other nematode species, whereas seven represented pioneering sequences. Our approach presents an efficient method to identify candidate parasitism genes, which does not require sophisticated cDNA isolation and selection protocols, and can therefore be used as a powerful starting point for the molecular investigation of parasites.
Project description:Root-knot nematodes (RKN), Meloidogyne spp., are important crop pests that cause severe losses in crop production worldwide, reducing both productivity and crop quality. Meloidogyne chitwoodi Golden, O'Bannon, Santo & Finley, 1980 is considered a quarantine organism by the European and Mediterranean Plant Protection Organization (EPPO) causing damage in tomato and potato crops. The development of nonchemical and sustainable management strategies to reduce nematode damage is crucial. The resistance of Solanum linnaeanum Hepper & P.-M.L. Jaeger and S. sisymbriifolium Lamarck cv. Sis 6001 to M. chitwoodi was evaluated based on gall index (GI), the Bridge & Page (1980) rating chart and reproduction factor (RF). Both plant species were resistant to M. chitwoodi. Solanum linnaeanum had an average of 519 small root swellings/plant, with 45% adult nematodes inside the roots, all males. Solanum sisymbriifolium had GI ≤ 2 and RF ≤ 1 with a high percentage (69%) of nematodes inside the roots that did not develop beyond the sexually undifferentiated second-stage. The use of S. linnaeanum as a new source of resistance is a good alternative for the control of RKN in the quest to develop nonchemical and sustainable management strategies to protect crops.