| 1. |
- Fredriksson, Åsa, 1968, et al.
(författare)
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Effects of aging and reproduction on protein quality control in soma and gametes of Drosophila melanogaster
- 2012
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Ingår i: Aging Cell. - : Wiley. - 1474-9718. ; 11:4, s. 634-643
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Tidskriftsartikel (refereegranskat)abstract
- In organisms with a somagerm demarcation, the germline must be preserved such that harmful damage is not transmitted to the offspring. Keeping the progeny free of damage may be achieved by gametes enjoying elevated, and/or more functional, homeostatic maintenance systems. This possibility was approached here by testing whether the soma and maturating oocytes (eggs) dissected from female Drosophila melanogaster in reproductive ages display differential capacities for protein quality control and whether these capacities change during aging and mating. Eggs exhibited a high capacity to prevent protein aggregation, strong capacity for 26S proteasome-dependent degradation and reduced levels of oxidatively damaged (carbonylated) proteins compared to the soma. The capacity to prevent protein aggregation was not affected in either soma or eggs by age and/or mating, while the 26S proteasome capacity declined in the soma but was maintained in the eggs of aged females. However, the levels of carbonylated proteins increased with age in both soma and eggs, and this increase was more pronounced in females allowed to mate continuously. Furthermore, the levels of carbonylated proteins in the eggs of mated flies correlated negatively with the propensity of the eggs to develop into an adult fly. In young flies, mating caused a decrease in 26S proteasome capacity and an increase in protein carbonylation in the soma, but not in the eggs. These results are in line with trade-off theories of aging where aging is considered a consequence of investment in reproduction over somatic maintenance.
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| 2. |
- Pinder, Matthew I. M., 1990, et al.
(författare)
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Genome Sequence of Kordia sp. Strain SMS9 Identified in a Non-Axenic Culture of the Diatom Skeletonema marinoi.
- 2019
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Ingår i: Journal of genomics. - : Ivyspring International Publisher. - 1839-9940. ; 7, s. 46-49
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Tidskriftsartikel (refereegranskat)abstract
- Initial efforts to sequence the genome of the marine diatom Skeletonema marinoi were hampered by the presence of genetic material from bacteria, and there was sufficient material from some of these bacteria to enable the assembly of full chromosomes. Here, we report the genome of strain SMS9, one such bacterial species identified in a non-axenic culture of S. marinoi strain ST54. Its 5,482,391 bp circular chromosome contains 4,641 CDSs, and has a G+C content of 35.6%. Based on 16S rRNA comparison, phylotaxonomic analysis, and the genome similarity metrics dDDH and OrthoANI, we place this strain in the genus Kordia, and to the best of our knowledge, this is the first Kordia species to be initially described from European waters. As attempts to culture this strain have failed, however, the specifics of its relationship with S. marinoi are still uncertain.
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| 3. |
- Smeds, Patrik, et al.
(författare)
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Hydra-genetics, a modular framework for bioinformatics pipeline development
- 2024
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Ingår i: European Journal of Human Genetics. - : Nature Portfolio. - 1018-4813 .- 1476-5438. ; 32:Suppl. 1, s. 675-676
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Background: Processing information from massively parallel sequencing/next-generation sequencing (NGS) data involves several steps that transform millions of rows of input data into more accessible genetic information. The combination of bioinformatics tools that extract all requested information for a particular clinical/research application, how they are tuned and the order in which they are executed constitute a bioinformatics pipeline. Software is often reused in several pipelines and regularly updated. For clinically validated NGS pipelines it may be challenging when individual components of several pipelines needs updating or when tools are replaced with new applications.Methods: The Hydra-genetics framework takes advantage of version controlled Snakemake modules. Pipeline steps are split into modules that can be configured and tested individually. The modules can be combined to build complete bioinformatics analyses, or be added to existing pipelines. All modules are subjected to extensive testing to ensure that new releases do not unexpectedly break existing pipelines or deviate from guidelines and best practices on how to write code.Results: Bioinformaticians from five Genomics Medicine Sweden centers used Hydra-genetics to develop the bioinformatics pipeline for the comprehensive solid tumor panel, GMS560. The pipeline analyses tumor DNA and/or RNA data and generates information on genetic variation including complex biomarkers such as tumor mutation burden and microsatellite instability. It is validated and in clinical use.Conclusions: The Hydra-genetics framework provides a platform for structured bioinformatics pipeline development and facilitates joint development projects involving multiple partners. It makes clinical pipeline development easier, faster and more structured.
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| 4. |
- Töpel, Mats H., 1973, et al.
(författare)
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The Skeletonema marinoi genome project
- 2015
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Ingår i: EMBO: Molecular life of Diatoms. 7-10 July, Seattle, USA.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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