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- 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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| 4. |
- Frago, Enric, et al.
(författare)
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Common pheromone use among host-associated populations of the browntail moth, euproctis chrysorrhoea, displaying different adult phenologies
- 2019
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Ingår i: Entomologia Generalis. - : Schweizerbart. - 0171-8177. ; 39:3-4, s. 295-306
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Tidskriftsartikel (refereegranskat)abstract
- The diversity of herbivorous insects may arise from colonization and subsequent specialization on different host plants. Such specialization requires changes in several insect traits, which may lead to host race formation if they reduce gene flow among populations that feed on different plants. Behavioural changes may play a relevant role in host race formation, for example if different races evolve distinct sexual communication signals or adult phenology. Previous research has revealed differences in larval phenology in different host-associated populations of the browntail moth, Euproctis chrysorrhoea (Lepidoptera: Erebidae). Here, sex pheromones among populations of this species are compared, and pheromone trapping data obtained is used in the field to build a phenological model that tests whether populations that feed on different plants differ in their adult flight period. The chemical and electrophysiological analyses revealed that two E. chrysorrhoea populations (on Prunus and on Arbutus unedo) use the same sex pheromone component for mate finding. Our trapping data, however, showed that males fly on average 25 days earlier in populations whose larvae feed on A. unedo compared to those whose larvae feed on Quercus species. Although the shifted phenology described here may underlie host-plant specialization in E. chrysorrhoea, and adults of this species are short-lived, the use of a common sexual pheromone and a large overlap in flight periods suggest that host race formation via allochronic isolation is unlikely in this moth.
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| 5. |
- Ahola, T, et al.
(författare)
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Therapeutics and vaccines against chikungunya virus
- 2015
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Ingår i: Vector borne and zoonotic diseases (Larchmont, N.Y.). - : Mary Ann Liebert Inc. - 1557-7759 .- 1530-3667. ; 15:4, s. 250-257
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Tidskriftsartikel (refereegranskat)
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| 6. |
- Green, L, et al.
(författare)
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Data supporting: Invader at the edge - genomic origins and physiological differences of round gobies across a steep urban salinity gradient
- 2022
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Annan publikationabstract
- Species invasions are a global problem of increasing concern, especially in highly connected aquatic environments. Despite this, salinity conditions can pose physiological barriers to their spread and understanding them is important for management. In Scandinavia’s largest cargo port, the invasive round goby (Neogobius melanostomus), is established across a steep salinity gradient. We used 12 937 SNPs to identify the genetic origin and diversity of three sites along the salinity gradient and round goby from western, central and northern Baltic Sea, as well as north European rivers. Fish from two sites from the extreme ends of the gradient were also acclimated to freshwater and seawater, and tested for respiratory and osmoregulatory physiology. Fish from the high salinity environment in the outer port showed higher genetic diversity, and closer relatedness to the other regions, compared to fish from lower salinity upstream the river. Fish from the high salinity site also had higher maximum metabolic rate, fewer blood cells and lower blood Ca2+. Despite these genotypic and phenotypic differences, salinity acclimation affected fish from both sites in the same way: seawater increased the blood osmolality and Na+ levels, and freshwater increased the levels of the stress hormone cortisol. Our results show genotypic and phenotypic differences over short spatial scales across this steep salinity gradient. These patterns of the physiologically robust round goby are likely driven by multiple introductions into the high salinity site, and a process of sorting, likely based on behaviour or selection, along the gradient. Since this euryhaline fish risks spreading from this area, seascape genomics and phenotypic characterisation can inform management strategies even within an area as small as a coastal harbour inlet.
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| 10. |
- Zdziarski, Andrzej A., et al.
(författare)
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Hybrid Comptonization and Electron-Positron Pair Production in the Black-hole X-Ray Binary MAXI J1820+070
- 2021
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Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 914:1
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Tidskriftsartikel (refereegranskat)abstract
- We study X-ray and soft gamma-ray spectra from the hard state of the accreting black-hole binary MAXI J1820+070. We perform an analysis of two joint spectra from NuSTAR and INTEGRAL, covering the range of 3-650 keV, and of an average joint spectrum over the rise of the hard state, covering the 3-2200 keV range. The spectra are well modeled by Comptonization of soft seed photons. However, the distributions of the scattering electrons are not purely thermal; we find they have substantial high-energy tails, well modeled as power laws. The photon tail in the average spectrum is detected well beyond the threshold for electron-positron pair production, 511 keV. This allows us to calculate the rate of the electron-positron pair production and put a lower limit on the size of the source from pair equilibrium. At the fitted Thomson optical depth of the Comptonizing plasma, the limit is about 4 gravitational radii. If we adopt the sizes estimated by us from the reflection spectroscopy of >20 gravitational radii, the fractional pair abundance becomes much less than unity. The low pair abundance is confirmed by the lack of both an annihilation feature and of a pair absorption cutoff above 511 keV in the average spectrum.
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