Project description:Background biology: Global warming has accelerated in recent decades, with the Arctic warming 2–3 times faster than the global average. As a result boreal species are expanding into the Arctic, at a pace reflecting environmental warming. Nevertheless, the poleward expansion of boreal marine species is restricted by their ability to tolerate low water temperatures, and in the case of intertidal species, sub-zero air temperatures during winter. In Greenland, however, the number of days with extreme sub-zero air temperatures has decreased by more than 50% since the 1950’s, suggesting that the low air temperature constraint is weakening. Although boreal intertidal species could potentially benefit from this warmer climate to establish populations in the Arctic, recent work has shown that local intertidal summer air temperatures in Greenland can exceed 36°C. This temperature is above the thermoregulatory capacity of many boreal intertidal species, including the highly abundant blue mussel Mytilus edulis. Therefore will further colonisation of M. edulis in Greenland be inhibited by the increasingly warm summer temperatures. Aim of experiment: Intertidal animals (Greenland blue mussel M. edulis) were sampled in situ on the first warm days of the year from the inner (warmer) and outer (cooler) regions of the Godthåbsfjorden around Nuuk (64°N) to examine the fjord temperature gradient effect. In addition, subtidal M. edulis were also collected and subjected to two acute temperature shocks of 22 and 32°C, which represented common and extreme summer air temperatures for intertidal habitats near Nuuk.

2020-11-25 | E-MTAB-9786 | biostudies-arrayexpress

Total and mitochondrial transcriptomic and proteomic insights into energy regulation mechanism for shoot fast growth initiation in Moso bamboo(Phyllostachys edulis)

Project description:Moso bamboo (Phyllostachys edulis) is one of the fast-growing plant species and has high comprehensive utilization value. However, how Moso bamboo realize the transition from initial growth of winter shoot to fast growth of spring shoot is still unknown. Large increase of biomass in spring shoot suggests that alterations in bioenergetic processes may contribute to fast growth initiation. In this study, we successfully isolated mitochondria from winter shoots and spring shoots of Moso bamboo, and performed a total and mitochondrial transcriptomic and proteomic analysis using RNA sequencing and Label-free quantitative proteomics technology. The main objective of the study was to augment the genomic and proteomic data available for Moso bamboo, identify key genes/proteins involved in energy metabolism, and systematically understand the energy metabolism mechanism of shoots growth during the transitory stage from initial growth to rapid growth.

2021-08-30 | PXD028178 |

Tropheryma whipplei proteome - Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme

Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.

2017-12-18 | PXD006238 | Pride

tfGorAlbo

Project description:Gordius_albopunctatus, genomic and transcriptomic data

| PRJEB78907 | ENA

ilEutHype

Project description:Eutresis hypereia, genomic and transcriptomic data

| PRJEB74517 | ENA

idNemNiti

Project description:Nemopoda nitidula, genomic and transcriptomic data

| PRJEB74592 | ENA

ilTheFirm

Project description:Thera firmata, genomic and transcriptomic data