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| 2. |
- Ameur, Adam, et al.
(författare)
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SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population
- 2017
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Ingår i: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260
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Tidskriftsartikel (refereegranskat)abstract
- Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.
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| 3. |
- Churakova, Yelena, et al.
(författare)
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Biogenic silica accumulation in picoeukaryotes : Novel players in the marine silica cycle
- 2023
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Ingår i: Environmental Microbiology Reports. - : John Wiley & Sons. - 1758-2229. ; 15:4, s. 282-290
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Tidskriftsartikel (refereegranskat)abstract
- It is well known that the biological control of oceanic silica cycling is dominated by diatoms, with sponges and radiolarians playing additional roles. Recent studies have revealed that some smaller marine organisms (e.g. the picocyanobacterium Synechococcus) also take up silicic acid (dissolved silica, dSi) and accumulate silica, despite not exhibiting silicon dependent cellular structures. Here, we show biogenic silica (bSi) accumulation in five strains of picoeukaryotes (<2-3 mu m), including three novel isolates from the Baltic Sea, and two marine species (Ostreococcus tauri and Micromonas commoda), in cultures grown with added dSi (100 mu M). Average bSi accumulation in these novel biosilicifiers was between 30 and 92 amol Si cell(-1). Growth rate and cell size of the picoeukaryotes were not affected by dSi addition. Still, the purpose of bSi accumulation in these smaller eukaryotic organisms lacking silicon dependent structures remains unclear. In line with the increasing recognition of picoeukaryotes in biogeochemical cycling, our findings suggest that they can also play a significant role in silica cycling.
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| 4. |
- Du, Hao, et al.
(författare)
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Corundum-structured AlCrNbTi oxide film grown using high-energy early-arriving ion irradiation in high-power impulse magnetron sputtering
- 2023
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Ingår i: Scripta Materialia. - : Elsevier. - 1359-6462 .- 1872-8456. ; 234
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Tidskriftsartikel (refereegranskat)abstract
- Multicomponent or high-entropy oxide films are of interest due to their remarkable structure and properties. Here, energetic ion irradiation is utilized for controlling the phase formation and structure of AlCrNbTi oxide at growth temperature of 500 degrees C. The ion acceleration is achieved by using a high-power impulse magnetron sputtering (HiPIMS) discharge, accompanied by a 10 & mu;s-long synchronized substrate bias (Usync), to minimize the surface charging effect and accelerate early-arriving ions, mainly Al+, O+, Ar2+, and Al2+. By increasing the magnitude of Usync from-100 V to-500 V, the film structure changes from amorphous to single-phase corundum, followed by the formation of high-number-density stacking faults (or nanotwins) at Usync =-500 V. This approach paves the way to tailor the high-temperature-phase and defect formation of oxide films at low growth temperature, with prospects for use in protective-coating and dielectric applications.
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| 5. |
- 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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| 6. |
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| 7. |
- Hasan, Mohammad I., et al.
(författare)
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Modeling the extraction of sputtered metal from high power impulse hollow cathode discharges
- 2013
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Ingår i: Plasma sources science & technology. - : IOP Publishing. - 0963-0252 .- 1361-6595. ; 22:3, s. 035006-
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Tidskriftsartikel (refereegranskat)abstract
- High power impulse hollow cathode sputtering is studied as a means to produce high fluxes of neutral and ionized sputtered metal species. A model is constructed for the understanding and optimization of such discharges. It relates input parameters such as the geometry of the cathode, the electric pulse form and frequency, and the feed gas flow rate and pressure, to the production, ionization, temperature and extraction of the sputtered species. Examples of processes that can be quantified by the use of the model are the internal production of sputtered metal and the degree of its ionization, the speed and efficiency of out-puffing from the hollow cathode associated with the pulses, and the gas back-flow into the hollow cathode between pulses. The use of the model is exemplified with a special case where the aim is the synthesis of nanoparticles in an expansion volume that lies outside the hollow cathode itself. The goals are here a maximum extraction efficiency, and a high degree of ionization of the sputtered metal. It is demonstrated that it is possible to reach a degree of ionization above 85%, and extraction efficiencies of 3% and 17% for the neutral and ionized sputtered components, respectively.
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| 8. |
- Herlemann, Daniel P. R., et al.
(författare)
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Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria
- 2013
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Ingår i: mBio. - 2161-2129 .- 2150-7511. ; 4:3, s. e00569-12-
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Tidskriftsartikel (refereegranskat)abstract
- The verrucomicrobial subdivision 2 class Spartobacteria is one of the most abundant bacterial lineages in soil and has recently also been found to be ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of the Spartobacteria is one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within the Spartobacteria exists. Since no aquatic representative from the Spartobacteria has been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic Sea Spartobacteria phylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near-complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates, like cellulose, mannan, xylan, chitin, and starch, as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype's distribution within the Baltic Sea indicate a connection to Cyanobacteria that may be the main source of the polysaccharide substrates. IMPORTANCE The ecosystem roles of many phylogenetic lineages are not yet well understood. One such lineage is the class Spartobacteria within the Verrucomicrobia that, despite being abundant in soil and aquatic systems, is relatively poorly studied. Here we circumvented the difficulties of growing aquatic Verrucomicrobia by applying shotgun metagenomic sequencing on a water sample from the Baltic Sea. By using a method based on sequence signatures, we were able to in silico isolate genome fragments belonging to a phylotype of the Spartobacteria. The genome, which represents the first aquatic representative of this clade, encodes a diversity of glycoside hydrolases that likely allow degradation of various complex carbohydrates. Since the phylotype cooccurs with Cyanobacteria, these may be the primary producers of the carbohydrate substrates. The phylotype, which is highly abundant in the Baltic Sea during summer, may thus play an important role in the carbon cycle of this ecosystem.
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| 9. |
- Herlemann, Daniel P. R., et al.
(författare)
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Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea
- 2016
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results suggest that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity.
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| 10. |
- Lundin, Daniel, et al.
(författare)
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Transition between the discharge regimes of high power impulse magnetron sputtering and conventional direct current magnetron sputtering
- 2009
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Ingår i: Plasma sources science & technology. - : IOP Publishing. - 0963-0252 .- 1361-6595. ; 18:4
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Tidskriftsartikel (refereegranskat)abstract
- Current and voltage have been measured in a pulsed high power impulse magnetron sputtering (HiPIMS) system for discharge pulses longer than 100 mu s. Two different current regimes could clearly be distinguished during the pulses: (1) a high-current transient followed by (2) a plateau at lower currents. These results provide a link between the HiPIMS and the direct current magnetron sputtering (DCMS) discharge regimes. At high applied negative voltages the high-current transient had the characteristics of HiPIMS pulses, while at lower voltages the plateau values agreed with currents in DCMS using the same applied voltage. The current behavior was found to be strongly correlated with the chamber gas pressure, where increasing gas pressure resulted in increasing peak current and plateau current. Based on these experiments it is suggested here that the high-current transients cause a depletion of the working gas in the area in front of the target, and thereby a transition to a DCMS-like high-voltage, lower current regime.
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