| 1. |
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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
-
Ingår i: Scripta Materialia. - : Elsevier. - 1359-6462 .- 1872-8456. ; 234
-
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
-
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
-
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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| 11. |
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| 12. |
- Niiranen, Pentti, et al.
(författare)
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Biased quartz crystal microbalance method for studies of chemical vapor deposition surface chemistry induced by plasma electrons
- 2023
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 94:2
-
Tidskriftsartikel (refereegranskat)abstract
- A recently presented chemical vapor deposition (CVD) method involves using plasma electrons as reducing agents for deposition of metals. The plasma electrons are attracted to the substrate surface by a positive substrate bias. Here, we present how a standard quartz crystal microbalance (QCM) system can be modified to allow applying a DC bias to the QCM sensor to attract plasma electrons to it and thereby also enable in situ growth monitoring during the electron-assisted CVD method. We show initial results from mass gain evolution over time during deposition of iron films using the biased QCM and how the biased QCM can be used for process development and provide insight into the surface chemistry by time-resolving the CVD method. Post-deposition analyses of the QCM crystals by cross-section electron microscopy and high-resolution x-ray photoelectron spectroscopy show that the QCM crystals are coated by an iron-containing film and thus function as substrates in the CVD process. A comparison of the areal mass density given by the QCM crystal and the areal mass density from elastic recoil detection analysis and Rutherford backscattering spectrometry was done to verify the function of the QCM setup. Time-resolved CVD experiments show that this biased QCM method holds great promise as one of the tools for understanding the surface chemistry of the newly developed CVD method.
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| 13. |
- Rehling, Daniel, et al.
(författare)
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Structural and biochemical investigation of class I ribonucleotide reductase from the hyperthermophile Aquifex aeolicus
- 2022
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 61:2, s. 92-106
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Tidskriftsartikel (refereegranskat)abstract
- Ribonucleotide reductase (RNR) is an essential enzyme with a complex mechanism of allosteric regulation found innearly all living organisms. Class I RNRs are composed of two proteins, a large α-subunit (R1) and a smaller β-subunit (R2) that exist as homodimers, that combine to form an active heterotetramer. Aquifex aeolicus is a hyperthermophilic bacterium with an unusual RNR encoding a 346-residue intein in the DNA sequence encoding its R2 subunit. We present the first structures of the A. aeolicus R1 and R2 (AaR1 and AaR2, respectively) proteins as well as the biophysical and biochemical characterization of active and inactive A. aeolicus RNR. While the active oligomeric state and activity regulation of A. aeolicus RNR are similar to those of other characterized RNRs, the X-ray crystal structures also reveal distinct features and adaptations. Specifically, AaR1 contains a β-hairpin hook structure at the dimer interface, which has an interesting π stacking interaction absent in other members of the NrdAh subclass, and its ATP cone houses two ATP molecules. We determined structures of two AaR2 proteins: one purified from a construct lacking the intein (AaR2) and a second purified from a construct including the intein sequence (AaR2_genomic). These structures in the context of metal content analysis and activity data indicate that AaR2_genomic displays much higher iron occupancy and activity compared to AaR2, suggesting that the intein is important for facilitating complete iron incorporation, particularly in the Fe2 site of the mature R2 protein, which may be important for the survival of A. aeolicus in low-oxygen environments.
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| 14. |
- Shu, Rui, 1990-, et al.
(författare)
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Influence of Metal Substitution and Ion Energy on Microstructure Evolution of High-Entropy Nitride (TiZrTaMe)N1-x (Me = Hf, Nb, Mo, or Cr) Films
- 2021
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Ingår i: ACS APPLIED ELECTRONIC MATERIALS. - : American Chemical Society (ACS). - 2637-6113. ; 3:6, s. 2748-2756
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Tidskriftsartikel (refereegranskat)abstract
- Multicomponent or high-entropy ceramics show unique combinations of mechanical, electrical, and chemical properties of importance in coating applications. However, generalizing controllable thin-film processes for these complex materials remains a challenge. Here, understoichiometric (TiZrTaMe)N1-x (Me = Hf, Nb, Mo, or Cr, 0.12 <= x <= 0.30) films were deposited on Si(100) substrates at 400 degrees C by reactive magnetron sputtering using single elemental targets. The influence of ion energy during film growth was investigated by varying the negative substrate bias voltage from similar to 10 V (floating potential) to 130 V. The nitrogen content for the samples determined by elastic recoil detection analysis varied from 34.9 to 43.8 at. % (0.12 <= x <= 0.30), and the metal components were near-equimolar and not affected by the bias voltage. On increasing the substrate bias, the phase structures of (TiZrTaMe)N1-x (Me = Hf, Nb, or Mo) films evolved from a polycrystalline fcc phase to a (002) preferred orientation along with a change in surface morphology from faceted triangular features to a dense and smooth structure with nodular mounds. All the four series of (TiZrTaMe)N1-x (Me = Hf, Nb, Mo, or Cr) films exhibited increasing intrinsic stress with increasing negative bias. The maximum compressive stress reached similar to 3.1 GPa in Hf- and Cr-containing films deposited at -130 V. The hardness reached a maximum value of 28.0 +/- 1.0 GPa at a negative bias >= 100 V for all the four series of films. The effect of bias on the mechanical properties of (TiNbZrMe)N1-x films can thus guide the design of protective high-entropy nitride films.
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| 15. |
- Shu, Rui, et al.
(författare)
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Multicomponent TixNbCrAl nitride films deposited by dc and high-power impulse magnetron sputtering
- 2021
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Ingår i: Surface & Coatings Technology. - : Elsevier. - 0257-8972 .- 1879-3347. ; 426
-
Tidskriftsartikel (refereegranskat)abstract
- Multicomponent TixNbCrAl nitride films were deposited on Si(100) substrates by reactive direct current magnetron sputtering (dcMS) and high power impulse magnetron sputtering (HiPIMS) in the absence of substrate heating and bias. Three single Ti, Nb, and Cr50Al50 targets were either driven by three de or three HiPIMS power supplies. The Ti content in the films was varied by tuning the power applied to the Ti target. The composition was determined by ion beam analysis. The nitrogen content is nearly stoichiometric (48-50 at.%) in the HiPIMS series, while the dcMS are understoichiometric (39-45 at.%). The crystal structure, stress and density of the studied film were investigated by X-ray techniques and the microstructure was examined by scanning electron microscopy. All the Ti-containing films for both series exhibit an fcc NaCl-type phase structure. In particular, the dcMS series shows a (111) preferred orientation, resulting in a faceted surface morphology compared to a dense and smooth microstructure of the HiPIMS films. The compressive stress of the HiPIMS series (> 2.0 GPa) is significantly larger than the values of the dcMS series (<0.5 GPa). Nanoindentation measurements show a maximum hardness of 29.9 GPa and Young's modulus of 304 GPa were obtained in the HiPIMS series. The results may promote HiPIMS techniques for the synthesis of complex multicomponent films for the application aspect to protective and hard coatings.
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| 16. |
- Aguilera, Anabella, et al.
(författare)
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Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria
- 2023
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Ingår i: Environmental Microbiology. - Chichester : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 25:9, s. 1674-1695
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Tidskriftsartikel (refereegranskat)abstract
- Cluster 5 picocyanobacteria significantly contribute to primary productivity in aquatic ecosystems. Estuarine populations are highly diverse and consist of many co-occurring strains, but their physiology remains largely understudied. In this study, we characterized 17 novel estuarine picocyanobacterial strains. Phylogenetic analysis of the 16S rRNA and pigment genes (cpcBandcpeBA) uncovered multiple estuarine and freshwater-related clusters and pigment types. Assays with five representative strains (three phycocyanin rich and two phycoerythrin rich) under temperature (10–30°C), light(10–190 μmol photons m-2s-1), and salinity (2–14 PSU) gradients revealed distinct growth optima and tolerance, indicating that genetic variability was accompanied by physiological diversity. Adaptability to environmental conditions was associated with differential pigment content and photosynthetic performance. Amplicon sequence variants at a coastal and an offshore station linked population dynamics with phylogenetic clusters, supporting that strains isolated in this study represent key ecotypes within the Baltic Sea picocyanobacterial community. The functional diversity found within strains with the same pigment type suggests that understanding estuarine picocyanobacterial ecology requires analysis beyond the phycocyanin and phycoerythrin divide. This new knowledge of the environmental preferences in estuarine picocyanobacteria is important for understanding and evaluating productivity in current and future ecosystems.
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| 17. |
- Aiempanakit, Montri, 1977-, et al.
(författare)
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Understanding the discharge current behavior in reactive high power impulse magnetron sputtering of oxides
- 2013
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 113:13, s. 133302-
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Tidskriftsartikel (refereegranskat)abstract
- The discharge current behavior in reactive high power impulse magnetron sputtering (HiPIMS) of Ti-O and Al-O is investigated. It is found that for both metals, the discharge peak current significantly increases in the oxide mode in contrast to the behavior in reactive direct current magnetron sputtering where the discharge current increases for Al but decreases for Ti when oxygen is introduced. In order to investigate the increase in the discharge current in HiPIMS-mode, the ionic contribution of the discharge in the oxide and metal mode is measured using time-resolved mass spectrometry. The energy distributions and time evolution are investigated during the pulse-on time as well as in the post-discharge. In the oxide mode, the discharge is dominated by ionized oxygen, which has been preferentially sputtered from the target surface. The ionized oxygen determines the discharge behavior in reactive HiPIMS.
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| 18. |
- Aijaz, Asim, et al.
(författare)
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A strategy for increased carbon ionization in magnetron sputtering discharges
- 2012
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Ingår i: Diamond and related materials. - : Elsevier BV. - 0925-9635 .- 1879-0062. ; 23, s. 1-4
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Tidskriftsartikel (refereegranskat)abstract
- A strategy that facilitates a substantial increase of carbon ionization in magnetron sputtering discharges is presented in this work. The strategy is based on increasing the electron temperature in a high power impulse magnetron sputtering discharge by using Ne as the sputtering gas. This allows for the generation of an energetic C+ ion population and a substantial increase in the C+ ion flux as compared to a conventional Ar-HiPIMS process. A direct consequence of the ionization enhancement is demonstrated by an increase in the mass density of the grown films up to 2.8 g/cm(3); the density values achieved are substantially higher than those obtained from conventional magnetron sputtering methods.
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| 19. |
- Aijaz, Asim, et al.
(författare)
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Dual-magnetron open field sputtering system for sideways deposition of thin films
- 2010
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Ingår i: SURFACE and COATINGS TECHNOLOGY. - : Elsevier BV. - 0257-8972. ; 204:14, s. 2165-2169
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Tidskriftsartikel (refereegranskat)abstract
- A dual-magnetron system for deposition inside tubular substrates has been developed. The two magnetrons are facing each other and have opposing magnetic fields forcing electrons and thereby also ionized material to be transported radially towards the substrate. The depositions were made employing direct current magnetron sputtering (DCMS) and high power impulse magnetron sputtering (HiPIMS). To optimize the deposition rate, the system was characterized at different separation distances between the magnetrons under the same sputtering conditions. The deposition rate is found to increase with increasing separation distance independent of discharge technique. The emission spectrum from the HiPIMS plasma shows a highly ionized fraction of the sputtered material. The electron densities of the order of 10(16) m(-3) and 10(18) m(-3) have been determined in the DCMS and the HiPIMS plasma discharges respectively. The results demonstrate a successful implementation of the concept of sideways deposition of thin films providing a solution for coating complex shaped surfaces.
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| 20. |
- Aijaz, Asim, et al.
(författare)
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Synthesis of hydrogenated diamondlike carbon thin films using neon-acetylene based high power impulse magnetron sputtering discharges
- 2016
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Ingår i: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : American Vacuum Society. - 0734-2101 .- 1520-8559. ; 34:6
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Tidskriftsartikel (refereegranskat)abstract
- Hydrogenated diamondlike carbon (DLC:H) thin films exhibit many interesting properties that can be tailored by controlling the composition and energy of the vapor fluxes used for their synthesis. This control can be facilitated by high electron density and/or high electron temperature plasmas that allow one to effectively tune the gas and surface chemistry during film growth, as well as the degree of ionization of the film forming species. The authors have recently demonstrated by adding Ne in an Ar-C high power impulse magnetron sputtering (HiPIMS) discharge that electron temperatures can be effectively increased to substantially ionize C species [Aijaz et al., Diamond Relat. Mater. 23, 1 (2012)]. The authors also developed an Ar-C2H2 HiPIMS process in which the high electron densities provided by the HiPIMS operation mode enhance gas phase dissociation reactions enabling control of the plasma and growth chemistry [Aijaz et al., Diamond Relat. Mater. 44, 117 (2014)]. Seeking to further enhance electron temperature and thereby promote electron impact induced interactions, control plasma chemical reaction pathways, and tune the resulting film properties, in this work, the authors synthesize DLC: H thin films by admixing Ne in a HiPIMS based Ar/C2H2 discharge. The authors investigate the plasma properties and discharge characteristics by measuring electron energy distributions as well as by studying discharge current characteristics showing an electron temperature enhancement in C2H2 based discharges and the role of ionic contribution to the film growth. These discharge conditions allow for the growth of thick (>1 mu m) DLC: H thin films exhibiting low compressive stresses (similar to 0.5 GPa), high hardness (similar to 25 GPa), low H content (similar to 11%), and density in the order of 2.2 g/cm(3). The authors also show that film densification and change of mechanical properties are related to H removal by ion bombardment rather than subplantation.
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| 21. |
- Al-Minawi, Ali Z., et al.
(författare)
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The ERCC1/XPF endonuclease is required for completion of homologous recombination at DNA replication forks stalled by inter-strand cross-links
- 2009
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 37:19, s. 6400-6413
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Tidskriftsartikel (refereegranskat)abstract
- Both the ERCC1-XPF complex and the proteins involved in homoIogous recombination (HR) have critical roles in inter-strand cross-link (ICL) repair. Here, we report that mitomycin C-induced lesions inhibit replication fork elongation. Furthermore, mitomycin C-induced DNA double-strand breaks (DSBs) are the result of the collapse of ICL-stalled replication forks. These are not formed through replication run off, as we show that mitomycin C or cisplatin-induced DNA lesions are not incised by global genome nucleotide excision repair (GGR). We also suggest that ICL-lesion repair is initiated either by replication or transcription, as the GGR does not incise ICL-lesions. Furthermore, we report that RAD51 foci are induced by cisplatin or mitomycin C independently of ERCC1, but that mitomycin C-induced HR measured in a reporter construct is impaired in ERCC1-defective cells. These data suggest that ERCC1-XPF plays a role in completion of HR in ICL repair. We also find no additional sensitivity to cisplatin by siRNA co-depletion of XRCC3 and ERCC1, showing that the two proteins act on the same pathway to promote survival.
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| 22. |
- Alneberg, Johannes, et al.
(författare)
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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within microbial ecosystems, but are computationally heavy to perform. We here present the BAltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.
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| 23. |
- Alneberg, Johannes, et al.
(författare)
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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
- 2018
-
Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .
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| 24. |
- Amnebrink, Dennis, et al.
(författare)
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Genome-resolved analysis reveals transcriptional transitions across seasons in Baltic Sea prokaryotes
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Microbial communities in surface waters of temperate seas are exposed to recurring annual seasonal variation in temperature and nutrient concentrations. To what extent bacterioplankton populations in natural communities alter their functional repertoire as a result of seasonal succession has not been thoroughly investigated. Here we use metatranscriptomics and leverage a comprehensive catalogue of metagenome-assembled genomes (MAGs) to follow gene expression in individual populations over a two-year time period at an offshore station in the Baltic Sea. We show that the collective expression of the MAGs changed in a consistent manner across seasons in the two years, forming clusters representing the four seasons, and that more than 80% of these displayed a recurring seasonal pattern. Furthermore, we found that the changes in expression could partly be explained by modulation of expression within the prokaryotic populations, since intra-population expression patterns also changed with season. Taken together, our results demonstrate how natural microbial populations alter their expression on the gene level, and how these changes drive large scale changes on both population and community level. This work aims to broaden the understanding of how microbes respond and adapt to their environment by preferentially altering their expressed genetic repertoire, and how microbial community dynamics can be explained through the gene expression of various populations constituting the community.
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| 25. |
- Amnebrink, Dennis, et al.
(författare)
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Seasonal dynamics and life cycle strategies of the cyanobacterium Aphanizomenon in the Baltic proper
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Aphanizomenon, together with Dolichospermum and Nodularia, constitute the major genera of bloom forming filamentous nitrogen fixing cyanobacteria in the Baltic Sea. Like the other genera, Aphanizomenon displays summer blooms that are highly variable in magnitude and duration but unlike the others it is considered a holoplanktonic species. Still, the molecular mechanisms enabling Aphanizomenon year-round presence in surface waters are currently unknown. Here we combine analysis of Aphanizomenon population dynamics at the Linnaeus Microbial Observatory (LMO) station in the Baltic Proper over nine years (2011-2019) with associated gene expression patterns during 2016-2017 to identify annual abundance, and metabolic and life cycle strategies. Aphanizomenon biomass showed large annual variability and a consistent biovolume peak in summer, with bloom intensity ranging from 78-1334 mm3 m-3. 16S rRNA gene amplicon sequence data showed that one Aphanizomenon amplicon sequence variant (ASV) dominated, and its relative abundance correlated with biovolume measurements. Metatranscriptomic reads that mapped to an Aphanizomenon metagenome- assembled genome (MAG) revealed annually repeating gene expression patterns, resulting in distinct gene expression profiles during different meteorological seasons. Genes encoding proteins involved in several important functional classes, e.g. carbon fixation, photosynthesis, and associated photopigments showed seasonal variation, but were detected year round. Other genes, particularly those involved in nitrogen fixation, were highly expressed in summer, while absent in winter. Vitamin metabolism and phosphorus scavenging genes were preferentially expressed during the colder periods of the annual cycle. Together, these data show that Aphanizomenon regulates the molecular machinery on the seasonal scale, providing context to the observed dynamics of Aphanizomenon in the Baltic Proper and a foundation for understanding the ecology of these cyanobacteria.
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