Historical Manihot glaziovii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA698751 | ENA |
REPOSITORIES: ENA
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Project description:Clonal emergence is a major driver for changes in bacterial disease epidemiology. Recently, it has been proposed that episodic emergence of novel, hypervirulent clones of group A Streptococcus (GAS) results from horizontal gene transfer (HGT) and recombination events leading to increased expression of the cytotoxins Nga (NADase) and SLO (streptolysin O). We previously described a gene fusion event involving the gene encoding the GAS M protein (emm) and an adjacent M-like protein (enn) in the emm4 GAS population, a GAS emm type that lacks the hyaluronic acid capsule. Using whole genome sequencing of a temporally and geographically diverse set of 1,127 isolates, we discovered that the North American emm4 GAS population has undergone clonal replacement with emergent GAS strains completely replacing historical isolates by 2017. Emergent emm4 GAS strains were defined by a handful of small genetic variations, including the emm-enn gene fusion, and showed a marked in vitro growth defect compared to historical strains. In contrast to other previously described GAS clonal emergence events, emergent emm4 GAS lacked significant HGT events and showed no significant increase in transcript levels of nga/slo toxin gene via RNA sequencing and quantitative real-time PCR analysis relative to historic strains. Despite the in vitro growth differences, emergent emm4 GAS strains demonstrated hypervirulence in mouse and ex vivo growth in human blood compared to historical strains. Thus, these data detail the emergence and dissemination of a hypervirulent acapsular GAS clone defined by small genetic variation thereby defining a novel model for GAS strain replacement.
2021-05-05 | GSE160737 | GEO
Project description:Despite high vaccination coverage, pertussis is on the rise in many countries including Czech Republic. To better understand B. pertussis resurgence we compared the changes in genome structures between Czech vaccine and circulating strains and subsequently, we determined how these changes translated into global transcriptomic and proteomic profiles. The whole-genome sequencing revealed that both historical and recent isolates of B. pertussis display substantial variation in genome organization and cluster separately. The RNA-seq and LC-MS/MS analyses indicate that these variations translated into discretely separated transcriptomic and proteomic profiles. Compared to vaccine strains, recent isolates displayed increased expression of flagellar genes and decreased expression of polysaccharide capsule operon. Czech strains (Bp46, K10, Bp155, Bp318 and Bp6242)exhibited increased expression of T3SS and sulphate metabolism genes when compared to Tohama I. In spite of 50 years of vaccination the Czech vaccine strains (VS67, VS393 and VS401) differ from recent isolates to a lesser extent than from another vaccine strain Tohama I.
2021-09-08 | PXD015184 | Pride
Project description:<p>The living and dried specimens in botanical collections play an important role in society for scientific and recreational purposes, offering the opportunity to obtain both macroscopic and molecular information for individual plants, ecosystems, and environmental studies. Untargeted metabolomics is an analytical approach that permits the simultaneous study of multiple small molecules present in an organism, which allows us to statistically compare different conditions of interest. Metabolomic approaches have been used on living specimens in botanical collections, but, until now, not on historical dried material. Using the Nicotiana genus herbaceous plant (tobacco) as a case study, we propose an untargeted metabolomic study to evaluate the potential of dried historical specimens as a source of metabolomic information on the past. The metabolomic profile from polar and less-polar/apolar aqueous extracts of four modern handmade tobacco cigars (split into wrapper, binder, and filler leaves), and a set of eight late-19th to early-20th century tobacco specimens (seven tobacco leaves and one snuff powder) from the collection of the Royal Botanical Gardens at Kew (London, UK) were analysed by liquid chromatography coupled to high resolution mass spectrometry. Results showed a wide range of polar and less-polar/apolar molecules which are preserved in dried botanical material, providing information optimal for metabolomic studies. The metabolomic profiles of historical dried samples were distinct enough to classify as Nicotiana tabacum or Nicotiana rustica, and showed differences based on geographic provenance or product transformation/processing. Statistical models based on the molecular data from the historical material permitted us to validate the labelling of the historical collection, which identified one possible mislabelled specimen and offered some clues as to the species of one unknown Nicotiana sample. Finally, metabolomic differences in profiles between Nicotiana tabacum and modern cigars showed that both share a large proportion of their metabolomic profile, where molecular differences could be possibly associated with both location of growth and anthropogenic transformation suffered by the plant in the last two centuries. This study demonstrates that dry botanical collections are a feasible source of information, and, if applied to a large set of individuals, conclusions may be drawn about the possible evolution and anthropogenic modification over time in plant material. The results are significant for disciplines interested in the history of plants, such as botany, history and archaeology.</p>
2024-03-06 | MTBLS4564 | MetaboLights
Project description:Whole genome sequencing of eastern gorilla historical museum samples
| PRJEB29503 | ENA
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:An historical collection of UK C. difficile strains from 1980-1986.
| PRJEB39589 | ENA
Project description:VARIOLA VIRUS IN HISTORICAL SAMPLES FROM THE NATIONAL MUSEUM OF PRAGUE
| PRJEB18730 | ENA
Project description:Natural history museum specimens of historical honeybees have been successfully used to explore the genomic past of the honeybee, indicating fast and rapid changes between historical and modern specimens, possibly as a response to current challenges. In our study we explore a potential untapped archive from natural history collections - specimens of beeswax. We examine an Apis mellifera mellifera queen cell specimen from the 19th century. The intact and closed cell was analysed by X-ray Computed Tomography (CT) to reveal a perfectly preserved queen bee inside her cell. Subsequently, a micro-destructive approach was used to evaluate the possibility of protein extraction from the cell. Our results show that studies on specimens such as these provide valuable information about the past rearing of queens, their diet and development, which is relevant for understanding current honeybee behaviour. In addition we evaluate the feasibility of using historical beeswax as a biomolecular archive for ancient proteins to study honeybees.
2024-09-05 | PXD034106 | Pride
Project description:Mitogenomics of historical type specimens of Australasian turtles
| PRJEB31010 | ENA