Ontology highlight
ABSTRACT:
PROVIDER: PRJNA608840 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:An Escherichia coli strain, isolated from wild reindeer in a remote mountain area, contained a class 1 integron with two unusual features: a group II intron and a cassette with homology to a superintegron cassette. Alignments indicate that attC sites of gene cassettes may be insertion sites for introns.
| S-EPMC1140521 | BioStudies
Project description:The faecal microbiota of muskoxen (n=3) pasturing on Ryøya (69° 33' N 18° 43' E), Norway, in late September was characterized using high-throughput sequencing of partial 16S rRNA gene regions. A total of 16 209 high-quality sequence reads from bacterial domains and 19 462 from archaea were generated. Preliminary taxonomic classifications of 806 bacterial operational taxonomic units (OTUs) resulted in 53.7-59.3 % of the total sequences being without designations beyond the family level. Firmicutes (70.7-81.1 % of the total sequences) and Bacteroidetes (16.8-25.3 %) constituted the two major bacterial phyla, with uncharacterized members within the family Ruminococcaceae (28.9-40.9 %) as the major phylotype. Multiple-library comparisons between muskoxen and other ruminants indicated a higher similarity for muskoxen faeces and reindeer caecum (P>0.05) and some samples from cattle faeces. The archaeal sequences clustered into 37 OTUs, with dominating phylotypes affiliated to the methane-producing genus Methanobrevibacter (80-92 % of the total sequences). UniFrac analysis demonstrated heterogeneity between muskoxen archaeal libraries and those from reindeer and roe deer (P=1.0e-02, Bonferroni corrected), but not with foregut fermenters. The high proportion of cellulose-degrading Ruminococcus-affiliated bacteria agrees with the ingestion of a highly fibrous diet. Further experiments are required to elucidate the role played by these novel bacteria in the digestion of this fibrous Artic diet eaten by muskoxen.
| S-EPMC5343138 | BioStudies
Project description:Antimicrobial resistance E_coli in a high artic reindeer subspecies
| PRJEB40996 | ENA
Project description:High viral transmission in the COVID-19 pandemic has enabled SARS-CoV-2 to acquire new mutations that may impact genome sequencing methods. The ARTIC.v3 primer pool that amplifies short amplicons in a multiplex-PCR reaction is one of the most widely used methods for sequencing the SARS-CoV-2 genome. We observed that some genomic intervals are poorly captured with ARTIC primers. To improve the genomic coverage and variant detection across these intervals, we designed long amplicon primers and evaluated the performance of a short (ARTIC) plus long amplicon (MRL) sequencing approach. Sequencing assays were optimized on VR-1986D-ATCC RNA followed by sequencing of nasopharyngeal swab specimens from fifteen COVID-19 positive patients. ARTIC data covered 94.47% of the virus genome fraction in the positive control and patient samples. Variant analysis in the ARTIC data detected 217 mutations, including 209 single nucleotide variants (SNVs) and eight insertions & deletions. On the other hand, long-amplicon data detected 156 mutations, of which 80% were concordant with ARTIC data. Combined analysis of ARTIC + MRL data improved the genomic coverage to 97.03% and identified 214 high confidence mutations. The combined final set of 214 mutations included 203 SNVs, 8 deletions and 3 insertions. Analysis showed 26 SARS-CoV-2 lineage defining mutations including 4 known variants of concern K417N, E484K, N501Y, P618H in spike gene. Hybrid analysis identified 7 nonsynonymous and 5 synonymous mutations across the genome that were either ambiguous or not called in ARTIC data. For example, G172V mutation in the ORF3a protein and A2A mutation in Membrane protein were missed by the ARTIC assay. Thus, we show that while the short amplicon (ARTIC) assay provides good genomic coverage with high throughput, complementation of poorly captured intervals with long amplicon data can significantly improve SARS-CoV-2 genomic coverage and variant detection.
| S-EPMC8757904 | BioStudies
Project description:The most southern population of reindeer (Rangifer tarandus) inhabits northeastern China, but the migration route and origin of this population have not been confirmed. The sequences of mitochondrial DNA control regions from domestic and wild herds from Eurasia and China were analysed. The results showed that the Chinese reindeer population originated independently from north-central Russian domestic herds, belonging to a large reindeer population that was present across Beringia during the last glacial period. Some studies have reported that the Chinese reindeer population is closely related to wild forest reindeer herds in Russia. Our results, however, indicate that wild forest reindeer herds of southeastern Russia contributed little or nothing to the Chinese reindeer herd gene pool. Chinese reindeer herds have a much greater genetic similarity to more northerly distributed tundra-type herds that inhabit open areas. The present findings will be essential for future conservation planning for Chinese reindeer.
| S-EPMC6853604 | BioStudies
Project description:Reindeer (<i>Rangifer tarandus</i>) have shaped the cultures and provided livelihood to peoples of the Northern Hemisphere for thousands of years. They are still the socio-economic cornerstone of many northern cultures. Insight into reindeer mortality patterns is important for understanding past human-reindeer interactions and reindeer population fluctuations in relation to climatic and environmental change. Beyond archaeology, assessing the age structures of modern reindeer populations is important for developing wildlife management strategies. This paper presents a quick, non-destructive and cheap method to estimate age in reindeer in both modern and ancient populations based on tooth wear and eruption patterns of mandibular teeth. We devised the method using a large sample of Svalbard reindeer (<i>Rangifer tarandus platyrhynchus</i>) of known age. We blind-tested the method and tested its applicability on another known-age Svalbard reindeer mandible assemblage. The tests demonstrate our methods' user-friendliness and reliability to generate reproducible, reusable datasets and accuracy in estimating reindeer age-at-death.
| S-EPMC8248135 | BioStudies
Project description:The deer ked (Lipoptena cervi) is a harmful ectoparasite that emerged in the reindeer herding area of Finland in 2006. To understand the current range and the intensity of infestations on its novel reindeer host, we studied deer ked pupae collected from reindeer and moose bedding sites and conducted a questionnaire survey among the managers of 18 reindeer herding cooperatives in the southern part of the reindeer herding area. Our study confirmed that the deer ked can survive and successfully reproduce on reindeer through winter and that flying deer keds had been observed in reindeer wintering areas during several autumns in twelve cooperatives. The pupae originating from reindeer were smaller and showed lower hatching rates than the pupae from moose. The present results indicate that the range of the deer ked infestations on reindeer in Finland expanded during the recent 5 years, now reaching 14 cooperatives and bordering an area south of approximately 66° N 25° E in the west and 65° N 29° E east.
| S-EPMC7431400 | BioStudies
Project description:<h4>Purpose</h4>Most patients with early-stage breast cancer are treated with adjuvant radiotherapy (RT) after breast-conserving surgery (BCS) to prevent locoregional recurrence (LRR). However, no genomic tools are used currently to select the optimal RT strategy.<h4>Methods</h4>We profiled the transcriptome of primary tumors on a clinical grade assay from the SweBCG91-RT trial, in which patients with node-negative breast cancer were randomly assigned to either whole-breast RT after BCS or no RT. We derived a new classifier, Adjuvant Radiotherapy Intensification Classifier (ARTIC), comprising 27 genes and patient age, in three publicly available cohorts, then independently validated ARTIC for LRR in 748 patients in SweBCG91-RT. We also compared previously published genomic signatures for ability to predict benefit from RT in SweBCG91-RT.<h4>Results</h4>ARTIC was highly prognostic for LRR in patients treated with RT (hazard ratio [HR], 3.4; 95% CI, 2.0 to 5.9; <i>P</i> < .001) and predictive of RT benefit (<i>P</i><sub>interaction</sub> = .005). Patients with low ARTIC scores had a large benefit from RT (HR, 0.33 [95% CI, 0.21 to 0.52], <i>P</i> < .001; 10-year cumulative incidence of LRR, 6% <i>v</i> 21%), whereas those with high ARTIC scores benefited less from RT (HR, 0.73 [95% CI, 0.44 to 1.2], <i>P</i> = .23; 10-year cumulative incidence of LRR, 25% <i>v</i> 32%). In contrast, none of the eight previously published signatures were predictive of benefit from RT in SweBCG91-RT.<h4>Conclusion</h4>ARTIC identified women with a substantial benefit from RT as well as women with a particularly elevated LRR risk in whom whole-breast RT was not sufficiently effective and, thus, in whom intensified treatment strategies such as tumor-bed boost, and possibly regional nodal RT, should be considered. To our knowledge, ARTIC is the first classifier validated as predictive of benefit from RT in a phase III clinical trial with patients randomly assigned to receive or not receive RT.
| S-EPMC6901281 | BioStudies