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- Martijn, Joran, et al.
(författare)
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Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution
- 2015
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 9:11, s. 2373-2385
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Tidskriftsartikel (refereegranskat)abstract
- The bacterial family Rickettsiaceae includes a group of well-known etiological agents of many human and vertebrate diseases, including epidemic typhus-causing pathogen Rickettsia prowazekii. Owing to their medical relevance, rickettsiae have attracted a great deal of attention and their host-pathogen interactions have been thoroughly investigated. All known members display obligate intracellular lifestyles, and the best-studied genera, Rickettsia and Orientia, include species that are hosted by terrestrial arthropods. Their obligate intracellular lifestyle and host adaptation is reflected in the small size of their genomes, a general feature shared with all other families of the Rickettsiales. Yet, despite that the Rickettsiaceae and other Rickettsiales families have been extensively studied for decades, many details of the origin and evolution of their obligate host-association remain elusive. Here we report the discovery and single-cell sequencing of 'Candidatus Arcanobacter lacustris', a rare environmental alphaproteobacterium that was sampled from Damariscotta Lake that represents a deeply rooting sister lineage of the Rickettsiaceae. Intriguingly, phylogenomic and comparative analysis of the partial 'Candidatus Arcanobacter lacustris' genome revealed the presence chemotaxis genes and vertically inherited flagellar genes, a novelty in sequenced Rickettsiaceae, as well as several host-associated features. This finding suggests that the ancestor of the Rickettsiaceae might have had a facultative intracellular lifestyle. Our study underlines the efficacy of single-cell genomics for studying microbial diversity and evolution in general, and for rare microbial cells in particular.
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- Sole, Marina, et al.
(författare)
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Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds
- 2019
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Ingår i: BMC Genomics. - : BMC. - 1471-2164. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses. Results We investigated the patterns, population variation and gene annotation of CNV using the Axiom (R) Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (similar to 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs. Conclusions This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.
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- Toor, Salman, et al.
(författare)
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SNIC Science Cloud (SSC): A national-scale cloud infrastructure for Swedish academia
- 2017
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Ingår i: Proceedings - 13th IEEE International Conference on eScience, eScience 2017. - Los Alamitos, CA : IEEE Computer Society. ; , s. 219-227, s. 219-227
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Konferensbidrag (refereegranskat)abstract
- The cloud computing paradigm have fundamentally changed the way computational resources are being offered. Although the number of large-scale providers in academia is still relatively small, there is a rapidly increasing interest and adoption of cloud Infrastructure-as-a-Service in the scientific community. The added flexibility in how applications can be implemented compared to traditional batch computing systems is one of the key success factors for the paradigm, and scientific cloud computing promises to increase adoption of simulation and data analysis in scientific communities not traditionally users of large scale e-Infrastructure, the so called long tail of science. In 2014, the Swedish National Infrastructure for Computing (SNIC) initiated a project to investigate the cost and constraints of offering cloud infrastructure for Swedish academia. The aim was to build a platform where academics could evaluate cloud computing for their use-cases. SNIC Science Cloud (SSC) has since then evolved into a national-scale cloud infrastructure based on three geographically distributed regions. In this article we present the SSC vision, architectural details and user stories. We summarize the experiences gained from running a nationalscale cloud facility into ten simple rules for starting up a science cloud project based on OpenStack. We also highlight some key areas that require careful attention in order to offer cloud infrastructure for ubiquitous academic needs and in particular scientific workloads.
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