| 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. |
- Gomez-Gener, L., et al.
(författare)
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Global carbon dioxide efflux from rivers enhanced by high nocturnal emissions
- 2021
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Ingår i: Nature Geoscience. - : Springer Science and Business Media LLC. - 1752-0894 .- 1752-0908. ; 14, s. 289-294
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Tidskriftsartikel (refereegranskat)abstract
- Carbon dioxide (CO2) emissions to the atmosphere from running waters are estimated to be four times greater than the total carbon (C) flux to the oceans. However, these fluxes remain poorly constrained because of substantial spatial and temporal variability in dissolved CO2 concentrations. Using a global compilation of high-frequency CO2 measurements, we demonstrate that nocturnal CO2 emissions are on average 27% (0.9 gC m(-2) d(-1)) greater than those estimated from diurnal concentrations alone. Constraints on light availability due to canopy shading or water colour are the principal controls on observed diel (24 hour) variation, suggesting this nocturnal increase arises from daytime fixation of CO2 by photosynthesis. Because current global estimates of CO2 emissions to the atmosphere from running waters (0.65-1.8 PgC yr(-1)) rely primarily on discrete measurements of dissolved CO2 obtained during the day, they substantially underestimate the magnitude of this flux. Accounting for night-time CO2 emissions may elevate global estimates from running waters to the atmosphere by 0.20-0.55 PgC yr(-1). Failing to account for emission differences between day and night will lead to an underestimate of global CO2 emissions from rivers by up to 0.55 PgC yr(-1), according to analyses of high-frequency CO2 measurements.
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| 3. |
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| 4. |
- Mann, P. J., et al.
(författare)
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The biogeochemistry of carbon across a gradient of streams and rivers within the Congo Basin
- 2014
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Ingår i: Journal of Geophysical Research: Biogeosciences. - 2169-8953. ; 119:4, s. 687-702
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Tidskriftsartikel (refereegranskat)abstract
- Dissolved organic carbon (DOC) and inorganic carbon (DIC, pCO(2)), lignin biomarkers, and theoptical properties of dissolved organic matter (DOM) were measured in a gradient of streams and rivers within the Congo Basin, with the aim of examining how vegetation cover and hydrology influences the composition and concentration of fluvial carbon (C). Three sampling campaigns (February 2010, November 2010, and August 2011) spanning 56 sites are compared by subbasin watershed land cover type (savannah, tropical forest, and swamp) and hydrologic regime (high, intermediate, and low). Land cover properties predominately controlled the amount and quality of DOC, chromophoric DOM (CDOM) and lignin phenol concentrations (Sigma(8)) exported in streams and rivers throughout the Congo Basin. Higher DIC concentrations and changing DOM composition (lower molecular weight, less aromatic C) during periods of low hydrologic flow indicated shifting rapid overland supply pathways in wet conditions to deeper groundwater inputs during drier periods. Lower DOC concentrations in forest and swamp subbasins were apparent with increasing catchment area, indicating enhanced DOC loss with extended water residence time. Surface water pCO(2) in savannah and tropical forest catchments ranged between 2,600 and 11,922 mu atm, with swamp regions exhibiting extremely high pCO(2) (10,598-15,802 mu atm), highlighting their potential as significant pathways for water-air efflux. Our data suggest that the quantity and quality of DOM exported to streams and rivers are largely driven by terrestrial ecosystem structure and that anthropogenic land use or climate change may impact fluvial C composition and reactivity, with ramifications for regional C budgets and future climate scenarios.
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| 5. |
- Gerstung, M, et al.
(författare)
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The evolutionary history of 2,658 cancers
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 122-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes3. Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)4, we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection.
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| 6. |
- Six, A., et al.
(författare)
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Red light induces starch accumulation in Chlorella vulgaris without affecting photosynthesis efficiency, unlike abiotic stress
- 2024
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Ingår i: Algal Research. - : Elsevier. - 2211-9264. ; 80
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Tidskriftsartikel (refereegranskat)abstract
- Microalgae show great promise as sources of starch, one of the most widely consumed macromolecules. In this study, we evaluated the impact of three starch-inducing factors, namely nitrogen deprivation, supra-optimal temperature, and red light, on the physiology and starch accumulation capacity of Chlorella vulgaris. This starch accumulation was monitored by measuring the total carbohydrate content and transmission electron microscopy (TEM) imaging. Nitrogen deprivation and a supra-optimal temperature of 39 °C resulted in carbohydrate contents of 69.7 and 64.3 % of dry weight (DW) respectively. This constituted a 5.3- and 3.3-fold increase in carbohydrate productivity compared to the control, after 4 days of cultivation. During this period, carbohydrates represented over 80 % of the produced material (DW basis). However, nitrogen deprivation and supra-optimal temperature were accompanied by extensive stress, leading to lower cell division rates and damage to the photosynthetic apparatus. Red light illumination resulted in a more moderate production of carbohydrates. After 4 days of cultivation, the carbohydrate content reached 46.8 %, representing a 3.0-fold increase in productivity compared to control. The composition of the starch formed under red light was surprisingly poor in amylose, similar to transitory-type starch rather than storage starch. Most notably, the starch accumulation under red light was sustained over 7 days without affecting the rate of cell division and quantum yield efficiency. To the best of our knowledge, red light is the only factor reported so far to induce a significant starch accumulation without hindering cell division and photosynthesis efficiency, even after long-term exposure (7 days). Furthermore, all three conditions induced a cell wall thickening, albeit without affecting the recovery of accumulated starch by high-pressure homogenization. These results highlight the potential of red light as a starch inducer in Chlorella vulgaris and open up perspectives for the production of starch-based bioplastics from microalgae.
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| 7. |
- Makelele, I. A., et al.
(författare)
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Conservative N cycling despite high atmospheric deposition in early successional African tropical lowland forests
- 2022
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Ingår i: Plant and Soil. - : Springer Science and Business Media LLC. - 0032-079X .- 1573-5036. ; 477, s. 743-758
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Tidskriftsartikel (refereegranskat)abstract
- Background Across the tropics, the share of secondary versus primary forests is strongly increasing. The high rate of biomass accumulation during this secondary succession relies on the availability of essential nutrients, such as nitrogen (N). Nitrogen primarily limits many young secondary forests in the tropics. However, recent studies have shown that forests of the Congo basin are subject to high inputs of atmospheric N deposition, potentially alleviating this N limitation in early succession. Methods To address this hypothesis, we assessed the N status along a successional gradient of secondary forests in the Congo basin. In a set-up of 18 plots implemented along six successional stages, we quantified year-round N deposition, N leaching, N2O emission and the N flux of litterfall and fine root assimilation. Additionally, we determined the N content and C:N stoichiometry for canopy leaves, fine roots, and litter, as well as delta N-15 of canopy leaves. Results We confirmed that these forests receive high amounts of atmospheric N deposition, with an increasing deposition as forest succession proceeds. Additionally, we noted lower C:N ratios, and higher N leaching losses, N2O emission, and foliar delta N-15 in older secondary forest (60 years). In contrast, higher foliar, litter and root C:N ratios, and lower foliar delta N-15, N leaching, and N2O emission in young (< 20 years) secondary forest were observed. Conclusions Altogether, we show that despite high N deposition, this early forest succession still shows conservative N cycling characteristics, which are likely indicating N limitation early on in secondary forest succession. As secondary succession advances, the N cycle gradually becomes more open.
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| 8. |
- Penzenstadler, Birgit, et al.
(författare)
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ICT4S 2029 : What will be the Systems Supporting Sustainability in 15 Years?
- 2014
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Ingår i: Proceedings of the 2014 conference ict for sustainability. - Paris, France : Atlantis Press. ; , s. 30-39
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Konferensbidrag (refereegranskat)abstract
- Research is often inspired by visions of the future. These visions can take on various narrative forms, and can fall anywhere along the spectrum from utopian to dystopian. Even though we recognize the importance of such visions to help us shape research questions and inspire rich design spaces to be explored, the opportunity to discuss them is rarely given in a research context. Imagine how civilization will have changed in 15 years. What is your vision for systems that will be supporting sustainability in that time? Which transformational changes will have occurred in the mean time that allow for these systems? Is ICT even the right tool or does it contradict sustainability by making our world ever more complex? How can we make systems and our societies more sustainable and resilient by ICT4S? This paper presents a compilation of fictional abstracts for inspiration and discussion, and provides means to stimulate discussion on future research and contributes to ICT4S community building.
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| 9. |
- Yu, Longfei, et al.
(författare)
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What can we learn from N2O isotope data? - Analytics, processes and modelling
- 2020
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Ingår i: Rapid Communications in Mass Spectrometry. - : Wiley. - 0951-4198 .- 1097-0231. ; 34:20
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Tidskriftsartikel (refereegranskat)abstract
- The isotopic composition of nitrous oxide (N2O) provides useful information for evaluating N2O sources and budgets. Due to the co-occurrence of multiple N2O transformation pathways, it is, however, challenging to use isotopic information to quantify the contribution of distinct processes across variable spatiotemporal scales. Here, we present an overview of recent progress in N2O isotopic studies and provide suggestions for future research, mainly focusing on: analytical techniques; production and consumption processes; and interpretation and modelling approaches. Comparing isotope-ratio mass spectrometry (IRMS) with laser absorption spectroscopy (LAS), we conclude that IRMS is a precise technique for laboratory analysis of N2O isotopes, while LAS is more suitable forin situ/inline studies and offers advantages for site-specific analyses. When reviewing the link between the N2O isotopic composition and underlying mechanisms/processes, we find that, at the molecular scale, the specific enzymes and mechanisms involved determine isotopic fractionation effects. In contrast, at plot-to-global scales, mixing of N2O derived from different processes and their isotopic variability must be considered. We also find that dual isotope plots are effective for semi-quantitative attribution of co-occurring N2O production and reduction processes. More recently, process-based N2O isotopic models have been developed for natural abundance and(15)N-tracing studies, and have been shown to be effective, particularly for data with adequate temporal resolution. Despite the significant progress made over the last decade, there is still great need and potential for future work, including development of analytical techniques, reference materials and inter-laboratory comparisons, further exploration of N2O formation and destruction mechanisms, more observations across scales, and design and validation of interpretation and modelling approaches. Synthesizing all these efforts, we are confident that the N2O isotope community will continue to advance our understanding of N2O transformation processes in all spheres of the Earth, and in turn to gain improved constraints on regional and global budgets.
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