| 1. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 2. |
- Baudry, T., et al.
(författare)
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Invasion and distribution of the redclaw crayfish, Cherax quadricarinatus, in Martinique
- 2020
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Ingår i: Knowledge and Management of Aquatic Ecosystems. - : EDP Sciences. - 1961-9502. ; :421
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Tidskriftsartikel (refereegranskat)abstract
- The redclaw crayfish, Cherax quadricarinatus, was introduced to Martinique Island for aquaculture purposes in 2004, in an attempt to revitalize the freshwater crustacean aquaculture sector. In 2015, three wild populations were discovered during an electrofishing survey on fish diversity. In 2018, a specific crayfish survey was performed at night using spotlighting and baited traps at 34 sites throughout the island. The species was mostly found in the center and northern part of the island, specifically, a total of 105 specimens were captured in eight streams and five closed water bodies. We sequenced a 491 base-pair fragment of the COI gene to understand the invasion history and pathway from the presumed source population at the Mangatal hatchery. Among the eight haplotypes found, three were dominant, of which, two occurred in the Mangatal hatchery. As crayfish are sold alive, there is a high risk of further human-mediated introductions across the island hydrographic basins. Thus, the distribution of this species could rapidly expand throughout Martinique freshwater ecosystems, with ecological impacts on native communities yet to be determined and requiring urgent investigation.
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| 3. |
- Hjelmstedt, P., et al.
(författare)
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Continuous physiological welfare evaluation of European whitefish (Coregonus lavaretus) during common aquaculture practices leading up to slaughter
- 2021
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486 .- 1873-5622. ; 534
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Tidskriftsartikel (refereegranskat)abstract
- European whitefish (Coregonus lavaretus) is an aquaculture species with the potential for expanded cultivation in the fresh and brackish waters of Northern Europe. Yet, relatively little species-specific information is available regarding the stress responses and associated welfare implications for this species in captivity. We addressed this knowledge gap by using a combination of implantable heart rate bio-loggers and a range of traditional stress indicators (e.g. haematological parameters and plasma concentrations of cortisol, glucose and ions) to comprehensively evaluate the physiological responses of freely swimming whitefish in captivity, as well as when subjected to aquaculture practices and stressors that commonly occur prior to and during slaughter. Whitefish appeared to recover rapidly from surgery, as resting heart rate decreased within 36 h to stabilize at similar to 25 beats min(-1) for the next 18 days when fish were left relatively undisturbed (i.e. personnel were only present when feeding fish). In contrast with previous studies on farmed rainbow trout and Atlantic salmon, whitefish did not exhibit a clear circadian heart rate rhythm, which may be related to species-specific differences in diurnal locomotor activity. Whitefish also appear to have a well-developed capacity for thermal acclimation of heart rate, as daily resting heart rate did not change during the undisturbed period despite an increase in body temperature from similar to 6.8 to 11.2 degrees C. Following acute stressors such as crowding and transportation, the physiological response of whitefish typically involved transient elevations in heart rate, plasma cortisol and glucose, and red blood cell swelling, while plasma [K+] decreased. In contrast, the heart rate of whitefish plummeted following the combination of brailing (i.e. to haul in fish with a brail/net) and CO2 exposure prior to slaughter, while plasma cortisol, glucose and [Ca2+] significantly increased. An unforeseen finding concerns the substantial and long-lasting physiological stress response observed in whitefish when held in close proximity (i.e. within similar to 10 m) to a rainbow trout net pen, as the mean heart rate of whitefish increased from similar to 32 to 43 beats min(-1) (i.e. an increase of similar to 34%). This may represent an innate physiological response to the threat of predation, which consequently increases the allostatic load and energetic expenditure of whitefish when farmed alongside salmonids. To conclude, this study highlights the importance of performing long-term, species-specific evaluations of freely swimming fish in real aquaculture settings, and provides a platform for further research aiming to determine the welfare implications of simultaneously farming predatory and prey species in close proximity.
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