| 1. |
- Brindefalk, Björn, et al.
(författare)
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Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters
- 2016
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 18:12, s. 4442-4455
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Tidskriftsartikel (refereegranskat)abstract
- Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from similar to 0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 mu m), relative to the medium (0.8-3.0 mu m) and large (> 3.0 mu m) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.
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| 2. |
- Martínez Barrio, Álvaro, et al.
(författare)
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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
- 2016
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Ingår i: eLIFE. - 2050-084X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.
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| 3. |
- Dupont, Chris L., et al.
(författare)
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Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:2, s. e89549-
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
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| 4. |
- Bohlin, Markus, et al.
(författare)
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Statistical Anomaly Detection for Train Fleets
- 2012. - 9
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Ingår i: Proceedings of the National Conference on Artificial Intelligence, vol. 3, 2012. - Toronto, Canada. - 9781577355687 ; , s. 2217-2223
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Konferensbidrag (refereegranskat)abstract
- We have developed a method for statistical anomaly detection which has been deployed in a tool for condition monitoring of train fleets. The tool is currently used by several railway operators over the world to inspect and visualize the occurrence of "event messages" generated on the trains. The anomaly detection component helps the operators to quickly find significant deviations from normal behavior and to detect early indications for possible problems. The savings in maintenance costs comes mainly from avoiding costly breakdowns, and have been estimated to several million Euros per year for the tool. In the long run, it is expected that maintenance costs can be reduced with between 5 and 10 % by using the tool.
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| 5. |
- Lapere, Rémy, et al.
(författare)
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The Representation of Sea Salt Aerosols and Their Role in Polar Climate Within CMIP6
- 2023
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Ingår i: Journal of Geophysical Research - Atmospheres. - 2169-897X .- 2169-8996. ; 128:6
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Tidskriftsartikel (refereegranskat)abstract
- Natural aerosols and their interactions with clouds remain an important uncertainty within climate models, especially at the poles. Here, we study the behavior of sea salt aerosols (SSaer) in the Arctic and Antarctic within 12 climate models from CMIP6. We investigate the driving factors that control SSaer abundances and show large differences based on the choice of the source function, and the representation of aerosol processes in the atmosphere. Close to the poles, the CMIP6 models do not match observed seasonal cycles of surface concentrations, likely due to the absence of wintertime SSaer sources such as blowing snow. Further away from the poles, simulated concentrations have the correct seasonality, but have a positive mean bias of up to one order of magnitude. SSaer optical depth is derived from the MODIS data and compared to modeled values, revealing good agreement, except for winter months. Better agreement for aerosol optical depth than surface concentration may indicate a need for improving the vertical distribution, the size distribution and/or hygroscopicity of modeled polar SSaer. Source functions used in CMIP6 emit very different numbers of small SSaer, potentially exacerbating cloud-aerosol interaction uncertainties in these remote regions. For future climate scenarios SSP126 and SSP585, we show that SSaer concentrations increase at both poles at the end of the 21st century, with more than two times mid-20th century values in the Arctic. The pre-industrial climate CMIP6 experiments suggest there is a large uncertainty in the polar radiative budget due to SSaer.Plain Language Summary Aerosols emitted from the ocean, such as sea salt particles (aerosols), are critical for the climate of polar regions. However, there is still uncertainty in their representation in climate models. The purpose of this work is to evaluate the representation of sea salt aerosols (SSaer) in the Arctic and Antarctic in a recent model inter-comparison initiative, and to assess the consequences for our understanding of present-day and future polar climate. We find that the models disagree between them and with observations from ground stations and from space. This suggests that the formulation of sea salt emissions in global models is not adapted for polar regions. With sea ice retreat, SSaer will most likely increase in the future, which makes addressing the current uncertainty an important next step for the scientific community.
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| 6. |
- Wilcox, Laura J., et al.
(författare)
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Accelerated increases in global and Asian summer monsoon precipitation from future aerosol reductions
- 2020
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 20:20, s. 11955-11977
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Tidskriftsartikel (refereegranskat)abstract
- There is a large range of future aerosol emissions scenarios explored in the Shared Socioeconomic Pathways (SSPs), with plausible pathways spanning a range of possibilities from large global reductions in emissions by 2050 to moderate global increases over the same period. Diversity in emissions across the pathways is particularly large over Asia. Rapid reductions in anthropogenic aerosol and precursor emissions between the present day and the 2050s lead to enhanced increases in global and Asian summer monsoon precipitation relative to scenarios with weak air quality policies. However, the effects of aerosol reductions do not persist to the end of the 21st century for precipitation, when instead the response to greenhouse gases dominates differences across the SSPs. The relative magnitude and spatial distribution of aerosol changes are particularly important for South Asian summer monsoon precipitation changes. Precipitation increases here are initially suppressed in SSPs 2-4.5, 3-7.0, and 5-8.5 relative to SSP1-1.9 when the impact of remote emission decreases is counteracted by continued increases in South Asian emissions.
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| 7. |
- Ekman Burgman, Linus, 1985-, et al.
(författare)
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Should the Sludge Hit the Farm? : – How Chemo-Social Relations Affect Policy Efforts to Circulate Phosphorus in Sweden
- 2021
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Ingår i: Sustainable Production and Consumption. - : Elsevier. - 2352-5509. ; 27, s. 1488-1497
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Tidskriftsartikel (refereegranskat)abstract
- This article discerns why the substantial political efforts to increase circulation of nutrients in sewage sludge, and phosphorus in particular, have shown such meager results over the last twenty years in Sweden. We have analyzed stakeholders’ statements of opinions to four government-initiated inquiries, to decipher the chemo-social relations between stakeholders and phosphorus, and how these relations have transformed over time and made a difference in the policy process. In our analysis, we found five different relations: 1) a metabolic, 2) a purity, 3) a nutritional, 4) a marketable, and 5) a geopolitical. These relations connect actors, phosphorus and politics in different ways, and obstruct policymaking by creating tensions between political objectives, values and stakeholder positions. We observe how the extraction of phosphorus as a singular, marketable element to be sold for profit reasons on a global market, is increasingly favored in comparison to local eco-cycling of nutrients between farmers and consumers. We see this as a consequence of that the circular economy as a concept has replaced eco-cycle efforts in the Swedish policy debate. We conclude that if circular economy-initiatives are to be successfully implemented, they need to be informed by the current configuration of material flows that they wish to transform as well as the political implications of their efforts. So far, this has not been the case regarding sewage sludge in Sweden.
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| 8. |
- Ekman, Carl, et al.
(författare)
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Plasma concentrations of Gas6 and soluble Axl correlate with disease and predict mortality in patients with critical limb ischemia.
- 2010
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Ingår i: Clinical Biochemistry. - : Elsevier BV. - 1873-2933 .- 0009-9120. ; May 4, s. 873-876
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: Critical limb ischemia (CLI) is a severe peripheral arterial disease, characterized by rest pain, ulcers and gangrene in the legs. Gas6 is a vitamin K-dependent protein, which binds and activates the tyrosine kinase receptor Axl. Gas6-mediated Axl-signaling influences endothelial activation, neointima formation and immune regulation. Axl can be cleaved and soluble Axl (sAxl) is detectable in circulation. DESIGN AND METHODS: We quantified plasma concentrations of Gas6 and sAxl in 189 CLI patients and 204 controls. RESULTS: Gas6 and sAxl concentrations were increased in the CLI patients (p<0.0001) and correlated to C-reactive protein, interleukin-6, tumor necrosis factor alpha and neopterin. Patients who died within three years of sampling (n=84) had increased concentrations of Gas6 and sAxl as compared to survivors (p=0.0009 and p=0.0011). CONCLUSIONS: Plasma concentrations of Gas6 and sAxl correlate to inflammation and predict survival. This indicates that Gas6 and sAxl have a role in CLI, presumably connected to the inflammatory process.
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| 9. |
- Ekman, Carl, et al.
(författare)
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Plasma concentrations of growth arrest specific protein 6 and the soluble form of its tyrosine kinase receptor Axl as markers of large abdominal aortic aneurysms.
- 2010
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Ingår i: Clinical Biochemistry. - : Elsevier BV. - 1873-2933 .- 0009-9120. ; 43, s. 110-114
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: The tyrosine kinase receptor Axl is expressed in the vasculature and Gas6 is the ligand. The extracellular part of Axl (sAxl) can be found in circulation. The aim of this study was to determine plasma concentrations of Gas6 and sAxl in patients with abdominal aortic aneurysms (AAA) and to evaluate if Gas6 and sAxl can be used as biomarkers. DESIGN AND METHODS: Immunoassays for sAxl and Gas6 were used to investigate plasma from AAA patients. Patients with large (n=123) or small AAA (n=122) were compared with healthy controls (n=141). RESULTS: Gas6 correlated positively and sAxl correlated negatively with AAA size. As a consequence, the calculated Gas6/sAxl ratios correlated even better to AAA size. Forty percent of all patients with a large AAA had higher Gas6/sAxl ratio than any in the control group. DISCUSSION: The Gas6/Axl system might be involved in AAA pathogenesis, and the Gas6/sAxl ratio may be useful as a biomarker.
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| 10. |
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