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- McIntosh, Angus R., et al.
(author)
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The impact of trout on galaxiid fishes in New Zealand
- 2010
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In: New Zealand Journal of Ecology. - 0110-6465. ; 34:1, s. 195-206
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Journal article (peer-reviewed)abstract
- Compared with the effect of invaders on the native terrestrial fauna of New Zealand, interactions between native fishes and introduced trout (sports fish in the genera Salmo, Oncorhynchus and Salvelinus) are less well known and there have been fewer efforts to remedy their effects. Trout have caused widespread reductions in the distribution and abundance of native galaxiid fishes, a family dominated by threatened species. The effects have been most severe on non-diadromous species (those lacking a marine migratory stage), which are commonly eliminated from streams by trout. Galaxiid populations in lakes, and those with migratory 'whitebait' stages, have also been affected, but the extent of the impacts are less understood. The mechanisms controlling negative interactions between trout and native fish, and how the environment modifies those interactions, will be important for future management. Experiments and field comparisons indicate size-specific predation by trout is the main driver of negative interactions. Large trout (> 150 mm long) do the greatest damage and small galaxiids (those with adult sizes < 150 mm long) are the most at risk. The fry stage of non-diadromous galaxiids is particularly vulnerable. Despite galaxiid fry production in some trout-invaded reaches, often no fry survive making them population 'sinks' that must be sustained by adult dispersal. Trout are also associated with changes in galaxiid behaviour and alterations to stream benthic communities. However, effects on galaxiid growth and fecundity have been little studied. Recent work also indicates that habitat conditions, especially floods, low flows and natural acidity, can mediate trout-galaxiid interactions. We argue that managers should be more proactive in their response to the plight of galaxiids, and we identify avenues of research that will benefit native fish conservation activities in the future.
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- Campbell, Brittany B., et al.
(author)
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Comprehensive Analysis of Hypermutation in Human Cancer
- 2017
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In: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 171:5
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Journal article (peer-reviewed)abstract
- © 2017 Elsevier Inc. We present an extensive assessment of mutation burden through sequencing analysis of > 81,000 tumors from pediatric and adult patients, including tumors with hypermutation caused by chemotherapy, carcinogens, or germline alterations. Hypermutation was detected in tumor types not previously associated with high mutation burden. Replication repair deficiency was a major contributing factor. We uncovered new driver mutations in the replication-repair-associated DNA polymerases and a distinct impact of microsatellite instability and replication repair deficiency on the scale of mutation load. Unbiased clustering, based on mutational context, revealed clinically relevant subgroups regardless of the tumors' tissue of origin, highlighting similarities in evolutionary dynamics leading to hypermutation. Mutagens, such as UV light, were implicated in unexpected cancers, including sarcomas and lung tumors. The order of mutational signatures identified previous treatment and germline replication repair deficiency, which improved management of patients and families. These data will inform tumor classification, genetic testing, and clinical trial design. A large-scale analysis of hypermutation in human cancers provides insights into tumor evolution dynamics and identifies clinically actionable mutation signatures.
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- van Rijswijk, Merlijn, et al.
(author)
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The future of metabolomics in ELIXIR.
- 2017
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In: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 6
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Journal article (peer-reviewed)abstract
- Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.
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