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1.	Aiempanakit, Montri, 2000-, et al. (författare) Effects on deposition rate when varying the magnetic field strength in magnetron sputtering 2008 Ingår i: 14th International Congress on Thin Films,2008. Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract Poster
2.	Ameur, Adam, et al. (författare) SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population 2017 Ingår i: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260 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.
3.	Churakova, Yelena, et al. (författare) Biogenic silica accumulation in picoeukaryotes : Novel players in the marine silica cycle 2023 Ingår i: Environmental Microbiology Reports. - : John Wiley & Sons. - 1758-2229. ; 15:4, s. 282-290 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.
4.	Du, Hao, et al. (författare) 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.
5.	Dupont, Chris L., et al. (författare) 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- 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.
6.	Eisfeldt, Jesper, et al. (författare) Whole genome characterization of array defined clustered CNVs reveals two distinct complex rearrangement subclasses generated through either non homologous repair or template switching 2017 Ingår i: Molecular Cytogenetics. - : BIOMED CENTRAL LTD. - 1755-8166. ; 10 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
7.	Hasan, Mohammad I., et al. (författare) Modeling the extraction of sputtered metal from high power impulse hollow cathode discharges 2013 Ingår i: Plasma sources science & technology. - : IOP Publishing. - 0963-0252 .- 1361-6595. ; 22:3, s. 035006- 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.
8.	Herlemann, Daniel P. R., et al. (författare) Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria 2013 Ingår i: mBio. - 2161-2129 .- 2150-7511. ; 4:3, s. e00569-12- 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.
9.	Herlemann, Daniel P. R., et al. (författare) Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea 2016 Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7 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.
10.	Lundin, Daniel, et al. (författare) Transition between the discharge regimes of high power impulse magnetron sputtering and conventional direct current magnetron sputtering 2009 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.
11.	Magnfält, Daniel, et al. (författare) Origin of energetic Ar+ ions in high power impulse magnetron sputtering discharges Annan publikation (övrigt vetenskapligt/konstnärligt)
12.	Niiranen, Pentti, et al. (författare) Biased quartz crystal microbalance method for studies of chemical vapor deposition surface chemistry induced by plasma electrons 2023 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.
13.	Rehling, Daniel, et al. (författare) Structural and biochemical investigation of class I ribonucleotide reductase from the hyperthermophile Aquifex aeolicus 2022 Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 61:2, s. 92-106 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.
14.	Shu, Rui, 1990-, et al. (författare) 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 Ingår i: ACS APPLIED ELECTRONIC MATERIALS. - : American Chemical Society (ACS). - 2637-6113. ; 3:6, s. 2748-2756 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.
15.	Shu, Rui, et al. (författare) Multicomponent TixNbCrAl nitride films deposited by dc and high-power impulse magnetron sputtering 2021 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.
16.	Aguilera, Anabella, et al. (författare) Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria 2023 Ingår i: Environmental Microbiology. - Chichester : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 25:9, s. 1674-1695 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.
17.	Aiempanakit, Montri, 1977-, et al. (författare) Understanding the discharge current behavior in reactive high power impulse magnetron sputtering of oxides 2013 Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 113:13, s. 133302- 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.
18.	Aijaz, Asim, et al. (författare) A strategy for increased carbon ionization in magnetron sputtering discharges 2012 Ingår i: Diamond and related materials. - : Elsevier BV. - 0925-9635 .- 1879-0062. ; 23, s. 1-4 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.
19.	Aijaz, Asim, et al. (författare) Dual-magnetron open field sputtering system for sideways deposition of thin films 2010 Ingår i: SURFACE and COATINGS TECHNOLOGY. - : Elsevier BV. - 0257-8972. ; 204:14, s. 2165-2169 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.
20.	Aijaz, Asim, et al. (författare) Synthesis of hydrogenated diamondlike carbon thin films using neon-acetylene based high power impulse magnetron sputtering discharges 2016 Ingår i: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : American Vacuum Society. - 0734-2101 .- 1520-8559. ; 34:6 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.
21.	Al-Minawi, Ali Z., et al. (författare) The ERCC1/XPF endonuclease is required for completion of homologous recombination at DNA replication forks stalled by inter-strand cross-links 2009 Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 37:19, s. 6400-6413 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.
22.	Alneberg, Johannes, et al. (författare) 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.
23.	Alneberg, Johannes, et al. (författare) 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] .
24.	Amnebrink, Dennis, et al. (författare) Genome-resolved analysis reveals transcriptional transitions across seasons in Baltic Sea prokaryotes 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.
25.	Amnebrink, Dennis, et al. (författare) Seasonal dynamics and life cycle strategies of the cyanobacterium Aphanizomenon in the Baltic proper 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.
26.	Amnebrink, Dennis (författare) Seasonality influences gene expression in Baltic Sea microbial communities 2024 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Prokaryotes are the most abundant living organisms in the marine environment. They contribute to primary production and the recycling of its products. Collectively they influence the marine element cycles of carbon along with elements like nitrogen and sulfur. However, much remains to learn of the functional characteristics of microbial communities carrying out these processes, and how different communities respond to changing environmental conditions in space and time.The composition of marine prokaryotic communities is known to change in a seasonal manner, but how seasonality influences their gene expression or “activity” remains largely unknown. In this thesis I investigate the relationship between prokaryotic activity, relative gene expression, and seasonality using time series field data on gene expression combined with reference genomes of prokaryotic populations (metagenome assembled genomes, MAGs). This revealed pronounced seasonal succession in overall transcriptional dynamics. Importantly, roughly half of the 50 populations with highest relative abundance in transcription altered their transcriptional profiles across seasons. Thus, changes in relative gene expression on the annual scale is explained by community turnover and modulation of activity within populations. Characterization of a MAG representative of the filamentous cyanobacterial genus Aphanizomenon that forms summer blooms in the Baltic Proper, highlighted seasonal patterns in transcription of genes underlying key prokaryotic activities. This included genes related to photosynthesis (different genes expressed in different seasons), nitrogen- fixation (expression peaking in summer) and oxidative stress (peaking in winter). A mesocosm study in the Bothnian Sea using temperature and nutrient manipulations simulating the winter to summer transition showed lower growth efficiency and higher maintenance respiration in winter conditions, implying larger relative losses of CO2 through respiration in winter. Additionally, temperature, nutrients, and their combination, caused separation in both prokaryotic taxonomy and transcription of metabolic pathways. Key features included archaeal transcription of ammonium oxidation in winter conditions, and Oceanospirillales central metabolisms in summer. Taken together, these results highlight the pronounced effect of seasonality on prokaryotic community gene expression and the capability of prokaryotic populations to alter their expressed genetic repertoire. This emphasizes the importance of the temporal perspective when considering how prokaryotic communities will respond to changes in environmental conditions.
27.	Amnebrink, Dennis, et al. (författare) Structuring of marine prokaryotic gene expression by temperature and dissolved organic matter Annan publikation (övrigt vetenskapligt/konstnärligt)abstract Temperature and dissolved organic matter (DOM) are important drivers of marine microbial activity, but their effects, alone or in combination, on the physiological responses of sub-arctic prokaryotic assemblages remain poorly understood. In a one-month mesocosm experiment initiated in early March in the northern Baltic Sea, we thus exposed a coastal microbial community to temperature and nutrient regimes representative of winter and early summer (i.e., 1°C and 10°C, with and without DOM additions) in a 2x2 factorial design. Prokaryotic abundance and heterotrophic production increased until around day 17 in the 10°C mesocosms. Yet, mid through the experiment (days 10 and 17, when samples for metatranscriptomics analyses were analyzed), estimates of growth rates were highest for the 10°C plus DOM treatment (TN; ~2.5 day-1), comparable for the 1°C plus DOM (N) and the 10°C treatments (T; ~1.0 day-1), and low for the control (C; 0.2 day-1). PCA analysis showed that samples for prokaryotic transcription in the 1°C plus DOM and the 10°C treatments clustered in different directions from the control, and the combined 10°C plus DOM treatment triggered even further changes. Taxonomic analysis of the transcripts uncovered broad treatment specific responses. This included a dominance of Nitrosopumilus (Archaea) in the 1°C mesocosms (with and without DOM), an increase in the relative expression of Alphaproteobacteria (both Rhodobacterales and SAR11) in the 10°C mesocosms without DOM addition, and an increase in Oceanospirillales in the 10°C plus DOM treatment. Burkholderiales (Betaproteobacteria) maintained a high relative expression (up to 25%) in all mesocosms. A PERMANOVA on the total of 182,618 transcribed genes revealed statistically significant effects of both temperature and DOM, and also a significant interaction effect between the two factors. EdgeR analysis identified significant differential transcription for up to 10% of the genes in each of the tested contrasts. Prominent features among the significant genes included Nitrosopumilus genes for ammonium uptake and ammonia oxidation in the 1°C mesocosms (C, N), membrane transporters for small organic acids in the N-treatment, genes for N and P assimilation along with molecular chaperones in the T-treatment, and dominance of Oceanospirillales genes for energy and growth metabolism in the TN treatment. These metatranscriptomics responses were associated with changes in ecologically important characteristics of the prokaryotic communities, such as growth rates and growth efficiency, providing clues to how successional changes in community composition and metabolism are induced by environmental conditions linked with seasonality.
28.	Antunes, V. G., et al. (författare) Influence of the magnetic field on the extension of the ionization region in high power impulse magnetron sputtering discharges 2023 Ingår i: Plasma sources science & technology. - : IOP Publishing. - 0963-0252 .- 1361-6595. ; 32:7 Tidskriftsartikel (refereegranskat)abstract The high power impulse magnetron sputtering (HiPIMS) discharge brings about increased ionization of the sputtered atoms due to an increased electron density and efficient electron energization during the active period of the pulse. The ionization is effective mainly within the electron trapping zone, an ionization region (IR), defined by the magnet configuration. Here, the average extension and the volume of the IR are determined based on measuring the optical emission from an excited level of the argon working gas atoms. For particular HiPIMS conditions, argon species ionization and excitation processes are assumed to be proportional. Hence, the light emission from certain excited atoms is assumed to reflect the IR extension. The light emission was recorded above a 100 mm diameter titanium target through a 763 nm bandpass filter using a gated camera. The recorded images directly indicate the effect of the magnet configuration on the average IR size. It is observed that the shape of the IR matches the shape of the magnetic field lines rather well. The IR is found to expand from 10 and 17 mm from the target surface when the parallel magnetic field strength 11 mm above the racetrack is lowered from 24 to 12 mT at a constant peak discharge current.
29.	Arkani, Samara, et al. (författare) Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort 2018 Ingår i: Human genome variation. - : Springer Nature. - 2054-345X. ; 5:1 Tidskriftsartikel (refereegranskat)abstract Bladder exstrophy is a congenital closure defect of the urinary bladder with a profound effect on morbidity. Although the malformation is usually sporadic, a genetic background is supported by an increased recurrence risk in relatives, higher concordance rates in monozygotic twins and several associated chromosomal aberrations. Recently, the ISL1 gene was presented as a candidate gene for bladder exstrophy and epispadias complex (BEEC) development in two different studies. In our study, we screened for genetic variants in the ISL1 gene in DNA from 125 Swedish patients using Sanger sequencing and array-CGH analysis. In addition, we evaluated ISL1 expression in RNA of human bladder during embryonic and fetal weeks 5–10 relative to that in lung tissue (week 9). In total, 21 single-nucleotide variants were identified, including a potentially novel missense variant, c.137C>G p.(Ala46Gly), substituting a conserved amino acid. This variant was inherited from an unaffected mother. No structural variants were identified. RNA sequencing revealed ISL1 mRNA expression during the critical time frame of human bladder development. In conclusion, we did not detect any known or likely pathogenic variants in the ISL1 gene in 125 Swedish BEEC patients, indicating that variation in the ISL1 gene is not a common genetic mechanism of BEEC development in the Swedish population.
30.	Aurelius, Oskar, et al. (författare) The Crystal Structure of Thermotoga maritima Class III Ribonucleotide Reductase Lacks a Radical Cysteine Pre-Positioned in the Active Site 2015 Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:7 Tidskriftsartikel (refereegranskat)abstract Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to deoxyribonucleotides, the building blocks for DNA synthesis, and are found in all but a few organisms. RNRs use radical chemistry to catalyze the reduction reaction. Despite RNR having evolved several mechanisms for generation of different kinds of essential radicals across a large evolutionary time frame, this initial radical is normally always channelled to a strictly conserved cysteine residue directly adjacent to the substrate for initiation of substrate reduction, and this cysteine has been found in the structures of all RNRs solved to date. We present the crystal structure of an anaerobic RNR from the extreme thermophile Thermotoga maritima (tmNrdD), alone and in several complexes, including with the allosteric effector dATP and its cognate substrate CTP. In the crystal structure of the enzyme as purified, tmNrdD lacks a cysteine for radical transfer to the substrate pre-positioned in the active site. Nevertheless activity assays using anaerobic cell extracts from T. maritima demonstrate that the class III RNR is enzymatically active. Other genetic and microbiological evidence is summarized indicating that the enzyme is important for T. maritima. Mutation of either of two cysteine residues in a disordered loop far from the active site results in inactive enzyme. We discuss the possible mechanisms for radical initiation of substrate reduction given the collected evidence from the crystal structure, our activity assays and other published work. Taken together, the results suggest either that initiation of substrate reduction may involve unprecedented conformational changes in the enzyme to bring one of these cysteine residues to the expected position, or that alternative routes for initiation of the RNR reduction reaction may exist. Finally, we present a phylogenetic analysis showing that the structure of tmNrdD is representative of a new RNR subclass IIIh, present in all Thermotoga species plus a wider group of bacteria from the distantly related phyla Firmicutes, Bacteroidetes and Proteobacteria.
31.	Babu, Swetha Suresh, et al. (författare) High power impulse magnetron sputtering of tungsten : a comparison of experimental and modelling results 2023 Ingår i: Plasma sources science & technology. - : IOP Publishing. - 0963-0252 .- 1361-6595. ; 32:3, s. 034003- Tidskriftsartikel (refereegranskat)abstract Here, we compare the ionization region model (IRM) against experimental measurements of particle densities and electron temperature in a high power impulse magnetron sputtering discharge with a tungsten target. The semi-empirical model provides volume-averaged temporal variations of the various species densities as well as the electron energy for a particular cathode target material, when given the measured discharge current and voltage waveforms. The model results are compared to the temporal evolution of the electron density and the electron temperature determined by Thomson scattering measurements and the temporal evolution of the relative neutral and ion densities determined by optical emission spectrometry. While the model underestimates the electron density and overestimates the electron temperature, the temporal trends of the species densities and the electron temperature are well captured by the IRM.
32.	Babu, Swetha Suresh, et al. (författare) Modeling of high power impulse magnetron sputtering discharges with tungsten target 2022 Ingår i: Plasma sources science & technology. - : IOP Publishing. - 0963-0252 .- 1361-6595. ; 31:6, s. 065009- Tidskriftsartikel (refereegranskat)abstract The ionization region model (IRM) is applied to model a high power impulse magnetron sputtering discharge with a tungsten target. The IRM gives the temporal variation of the various species and the average electron energy, as well as internal discharge parameters such as the ionization probability and the back-attraction probability of the sputtered species. It is shown that an initial peak in the discharge current is due to argon ions bombarding the cathode target. After the initial peak, the W+ ions become the dominating ions and remain as such to the end of the pulse. We demonstrate how the contribution of the W+ ions to the total discharge current at the target surface increases with increased discharge voltage for peak discharge current densities J (D,peak) in the range 0.33-0.73 A cm(-2). For the sputtered tungsten the ionization probability increases, while the back-attraction probability decreases with increasing discharge voltage. Furthermore, we discuss the findings in terms of the generalized recycling model and compare to experimentally determined deposition rates and find good agreement.
33.	Baichoo, Shakuntala, et al. (författare) H3ABioNet computational metagenomics workshop in Mauritius : training to analyse microbial diversity for Africa 2015 Ingår i: Standards in Genomic Sciences. - : Springer Science and Business Media LLC. - 1944-3277. ; 10 Tidskriftsartikel (refereegranskat)abstract In the context of recent international initiatives to bolster genomics research for Africa, and more specifically to develop bioinformatics expertise and networks across the continent, a workshop on computational metagenomics was organized during the end of 2014 at the University of Mauritius. The workshop offered background on various aspects of computational biology, including databases and algorithms, sequence analysis fundamentals, metagenomics concepts and tools, practical exercises, journal club activities and research seminars. We have discovered a strong interest in metagenomics research across Africa, to advance practical applications both for human health and the environment. We have also realized the great potential to develop genomics and bioinformatics through collaborative efforts across the continent, and the need for further reinforcing the untapped human potential and exploring the natural resources for stronger engagement of local scientific communities, with a view to contributing towards the improvement of human health and well-being for the citizens of Africa.
34.	Baltar, Federico, et al. (författare) Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic 2016 Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7 Tidskriftsartikel (refereegranskat)abstract To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.
35.	Barynova, Kateryna, et al. (författare) On working gas rarefaction in high power impulse magnetron sputtering 2024 Ingår i: Plasma sources science & technology. - : IOP Publishing. - 0963-0252 .- 1361-6595. ; 33:6 Tidskriftsartikel (refereegranskat)abstract The ionization region model (IRM) is applied to explore working gas rarefaction in high power impulse magnetron sputtering discharges operated with graphite, aluminum, copper, titanium, zirconium, and tungsten targets. For all cases the working gas rarefaction is found to be significant, the degree of working gas rarefaction reaches values of up to 83%. The various contributions to working gas rarefaction, including electron impact ionization, kick-out by the sputtered species or hot argon atoms, and diffusion, are evaluated and compared for the different target materials, and over a range of discharge current densities. The relative importance of the various processes varies between different target materials. In the case of a graphite target with argon as the working gas at 1 Pa, electron impact ionization (by both primary and secondary electrons) is the dominating contributor to working gas rarefaction, with over 90% contribution, while the contribution of sputter wind kick-out is small < 10 %. In the case of copper and tungsten targets, the kick-out dominates, with up to ∼60% contribution at 1 Pa. For metallic targets the kick-out is mainly due to metal atoms sputtered from the target, while for the graphite target the small kick-out contribution is mainly due to kick-out by hot argon atoms and to a smaller extent by carbon atoms. The main factors determining the relative contribution of the kick-out by the sputtered species to working gas rarefaction appear to be the sputter yield and the working gas pressure.
36.	Bensch, Hanna, et al. (författare) Bacteroidetes to Firmicutes : captivity changes the gut microbiota composition and diversity in a social subterranean rodent 2023 Ingår i: Animal Microbiome. - : BioMed Central (BMC). - 2524-4671. ; 5:1 Tidskriftsartikel (refereegranskat)abstract BackgroundIn mammals, the gut microbiota has important effects on the health of their hosts. Recent research highlights that animal populations that live in captivity often differ in microbiota diversity and composition from wild populations. However, the changes that may occur when animals move to captivity remain difficult to predict and factors generating such differences are poorly understood. Here we compare the bacterial gut microbiota of wild and captive Damaraland mole-rats (Fukomys damarensis) originating from a population in the southern Kalahari Desert to characterise the changes of the gut microbiota that occur from one generation to the next generation in a long-lived, social rodent species.ResultsWe found a clear divergence in the composition of the gut microbiota of captive and wild Damaraland mole-rats. Although the dominating higher-rank bacterial taxa were the same in the two groups, captive animals had an increased ratio of relative abundance of Firmicutes to Bacteroidetes compared to wild animals. The Amplicon Sequence Variants (ASVs) that were strongly associated with wild animals were commonly members of the same bacterial families as those strongly associated with captive animals. Captive animals had much higher ASV richness compared to wild-caught animals, explained by an increased richness within the Firmicutes.ConclusionWe found that the gut microbiota of captive hosts differs substantially from the gut microbiota composition of wild hosts. The largest differences between the two groups were found in shifts in relative abundances and diversity of Firmicutes and Bacteroidetes.
37.	Bensch, Hanna, et al. (författare) Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal 2023 Ingår i: Journal of Evolutionary Biology. - : John Wiley & Sons. - 1010-061X .- 1420-9101. ; 36:12, s. 1753-1760 Tidskriftsartikel (refereegranskat)abstract In social species, group members commonly show substantial similarity in gut microbiome composition. Such similarities have been hypothesized to arise either by shared environmental effects or by host relatedness. However, disentangling these factors is difficult, because group members are often related, and social groups typically share similar environmental conditions. In this study, we conducted a cross-foster experiment under controlled laboratory conditions in group-living Damaraland mole-rats (Fukomys damarensis) and used 16S amplicon sequencing to disentangle the effects of the environment and relatedness on gut microbiome similarity and diversity. Our results show that a shared environment is the main factor explaining gut microbiome similarity, overshadowing any effect of host relatedness. Together with studies in wild animal populations, our results suggest that among conspecifics environmental factors are more powerful drivers of gut microbiome composition similarity than host genetics.
38.	Bensch, Hanna, et al. (författare) Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples 2022 Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 10 Tidskriftsartikel (refereegranskat)abstract Background: The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows transport and storage at ambient temperature.Methods: In this study we compare alpha diversity and 16S microbiome composition of 20 fecal sample replicates from Damaraland mole-rats (Fukomys damarensis) preserved in a minus 80 °C freezer and transported on dry ice to freeze-dried samples that were stored and transported in ambient temperature until DNA extraction.Results: We found strong correlations between relative abundances of Amplicon Sequence Variants (ASVs) between preservation treatments of the sample, no differences in alpha diversity measures between the two preservation treatments and minor effects of the preservation treatment on beta diversity measures. Our results show that freeze-drying samples can be a useful method for cost-effective transportation and storage of microbiome samples that yields quantitatively almost indistinguishable results in 16S microbiome analyses as those stored in minus 80 °C.
39.	Bensch, Hanna, et al. (författare) Gut microbiome similarity in wild mole-rats : The effects of shared common descent Annan publikation (övrigt vetenskapligt/konstnärligt)abstract Group members often show high similarity in their gut microbiomes. This is typically attributed to increased social transmission of microbes within social groups and the shared environment. However, despite extensive research on within-group variation in gut microbiomes of wild hosts, between-group variation has remained less explored. Here, we use faecal samples collected from a long-term study population of wild Damaraland mole-rats (Fukomys damarensis) to study within- and between group variation in gut microbiome similarity. We show that overall, group members have more similar gut microbiomes than those of individuals from separate groups. For individuals who had dispersed to become breeders in separate groups, dispersal from the same birth group predicted more similar microbiomes. The birth group affiliation therefore has long lasting effects on the microbiome, which individuals bring with them as they disperse to establish their own groups. Our results also suggest that when these individuals start to breed, their gut microbiome is transferred to their offspring, who show higher microbiome similarity if their parents shared birth groups. Together, we show that the gut microbiome can be transferred over generations and variation between groups can be predicted by the dispersal histories of individuals. Although we also identify some environmental effects on the gut microbiome within the population, our study shows that the gut microbiome can be inherited through shared common descent of the parental generation. Our results help to explain similarities in gut microbiomes within and between groups of social mammals.
40.	Bensch, Hanna (författare) Social below ground : Life-history and gut microbiome of Damaraland mole-rats 2023 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Studying the consequences of variation in individual life-histories is vital for our understanding of the evolution of animal societies. In this thesis, I study the ecology and consequences of group living on growth, survival, reproduction, and the gut microbiome of the Damaraland mole-rat (Fukomys damarensis), a subterranean cooperatively breeding mammal. For this, I used data and faecal samples collected from a long-term study population in the Kalahari Desert, South Africa.I explored the effects of group size and group composition on individuals’ growth and survival. While large group size had no clear advantages for either growth or survival, individuals within groups biased to their own sex grew more slowly. The number of recruits increased modestly with group size, but experimentally created pairs showed the same reproductive success as established groups. Further, single individuals exhibited high survival rates and good body condition. Combined, these results suggest that mole-rats delay dispersal to maximise their own fitness, and that group living has costs and benefits for all group members.I also investigated the effects of individual life-histories and group affiliation on the gut microbiome. This work shows that individuals bring the gut microbiome from their birth group when they disperse, and that group members have more similar gut microbiomes. When dispersed individuals start to reproduce in their new groups, they subsequently transfer this microbiome to their offspring, resulting in higher similarity between offspring with common descent of breeders. This pattern could arise from shared early life environment of breeders or through genetic relatedness of breeders. To separate the effects of these factors, I used a cross-foster experiment of captive animals, which showed that group members have more similar gut microbiomes, regardless of host relatedness.My thesis gives deepened insights into the ecology of the Damaraland mole-rat. It shows how variation in the social environment of group living species affects their life-histories, their fitness, and beyond that extended phenotypic traits such as the gut microbiome composition.
41.	Berggren, Gustav, et al. (författare) Assembly of Dimanganese and Heterometallic Manganese Proteins 2017 Ingår i: Encyclopedia of Inorganic and Bioinorganic Chemistry. - Chichester, UK : John Wiley & Sons. - 9781119951438 Bokkapitel (refereegranskat)
42.	Berggren, Gustav, et al. (författare) Homo- and Heterometallic Dinuclear Manganese Proteins : Active Site Assembly 2017 Ingår i: Metalloprotein Active Site Assembly. - : John Wiley & Sons. - 9781119159834 ; , s. 215-233 Bokkapitel (refereegranskat)
43.	Berggren, Hanna, et al. (författare) Fish skin microbiomes are highly variable among individuals and populations but not within individuals 2022 Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 12 Tidskriftsartikel (refereegranskat)abstract Fish skin-associated microbial communities are highly variable among populations and species and can impact host fitness. Still, the sources of variation in microbiome composition, and particularly how they vary among and within host individuals, have rarely been investigated. To tackle this issue, we explored patterns of variation in fish skin microbiomes across different spatial scales. We conducted replicate sampling of dorsal and ventral body sites of perch (Perca fluviatilis) from two populations and characterized the variation of fish skin-associated microbial communities with 16S rRNA gene metabarcoding. Results showed a high similarity of microbiome samples taken from the left and right side of the same fish individuals, suggesting that fish skin microbiomes can be reliably assessed and characterized even using a single sample from a specific body site. The microbiome composition of fish skin differed markedly from the bacterioplankton communities in the surrounding water and was highly variable among individuals. No ASV was present in all samples, and the most prevalent phyla, Actinobacteria, Bacteroidetes, and Proteobacteria, varied in relative abundance among fish hosts. Microbiome composition was both individual- and population specific, with most of the variation explained by individual host. At the individual level, we found no diversification in microbiome composition between dorsal and ventral body sites, but the degree of intra-individual heterogeneity varied among individuals. To identify how genetic and phenotypic characteristics of fish hosts impact the rate and nature of intra-individual temporal dynamics of the skin microbiome, and thereby contribute to the host-specific patterns documented here, remains an important task for future research.
44.	Björk Grimberg, Kristian, et al. (författare) Basic Leucine Zipper Protein Cnc-C is a Substrate and Transcriptional Regulator of the Drosophila 26S Proteasome 2011 Ingår i: Molecular and Cellular Biology. - 0270-7306 .- 1098-5549. ; 31:4, s. 897-909 Tidskriftsartikel (refereegranskat)abstract While the 26S proteasome is a key proteolytic complex, little is known about how proteasome levels are maintained in higher eukaryotic cells. Here we describe an RNA interference (RNAi) screen of Drosophila melanogaster that was used to identify transcription factors that may play a role in maintaining levels of the 26S proteasome. We used an RNAi library against 993 Drosophila transcription factor genes to identify genes whose suppression in Schneider 2 cells stabilized a ubiquitin-green fluorescent protein reporter protein. This screen identified Cnc (cap 'n' collar [CNC]; basic region leucine zipper) as a candidate transcriptional regulator of proteasome component expression. In fact, 20S proteasome activity was reduced in cells depleted of cnc. Immunoblot assays against proteasome components revealed a general decline in both 19S regulatory complex and 20S proteasome subunits after RNAi depletion of this transcription factor. Transcript-specific silencing revealed that the longest of the seven transcripts for the cnc gene, cnc-C, was needed for proteasome and p97 ATPase production. Quantitative reverse transcription-PCR confirmed the role of Cnc-C in activation of transcription of genes encoding proteasome components. Expression of a V5-His-tagged form of Cnc-C revealed that the transcription factor is itself a proteasome substrate that is stabilized when the proteasome is inhibited. We propose that this single cnc gene in Drosophila resembles the ancestral gene family of mammalian nuclear factor erythroid-derived 2-related transcription factors, which are essential in regulating oxidative stress and proteolysis.
45.	Borgmästars, Emmy, et al. (författare) Circulating tissue polypeptide-specific antigen in pre-diagnostic pancreatic cancer samples 2021 Ingår i: Cancers. - : MDPI. - 2072-6694. ; 13:21 Tidskriftsartikel (refereegranskat)abstract Early detection of pancreatic ductal adenocarcinoma (PDAC) is challenging, and late diagnosis partly explains the low 5-year survival. Novel and sensitive biomarkers are needed to enable early PDAC detection and improve patient outcomes. Tissue polypeptide specific antigen (TPS) has been studied as a biomarker in PDAC diagnostics, and it has previously been shown to reflect clinical status better than the ‘golden standard’ biomarker carbohydrate antigen 19-9 (CA 19-9) that is most widely used in the clinical setting. In this cross-sectional case-control study using pre-diagnostic plasma samples, we aim to evaluate the potential of TPS as a biomarker for early PDAC detection. Furthermore, in a subset of individuals with multiple samples available at different time points before diagnosis, a longitudinal analysis was used. We assessed plasma TPS levels using enzyme-linked immunosorbent assay (ELISA) in 267 pre-diagnostic PDAC plasma samples taken up to 18.8 years before clinical PDAC diagnosis and in 320 matched healthy controls. TPS levels were also assessed in 25 samples at PDAC diagnosis. Circulating TPS levels were low both in pre-diagnostic samples of future PDAC patients and in healthy controls, whereas TPS levels at PDAC diagnosis were significantly increased (odds ratio 1.03; 95% confidence interval: 1.01–1.05) in a logistic regression model adjusted for age. In conclusion, TPS levels increase late in PDAC progression and hold no potential as a biomarker for early detection.
46.	Borgmästars, Emmy, et al. (författare) Metabolomics for early pancreatic cancer detection in plasma samples from a Swedish prospective population-based biobank Annan publikation (övrigt vetenskapligt/konstnärligt)
47.	Borgmästars, Emmy, et al. (författare) Metabolomics for early pancreatic cancer detection in plasma samples from a Swedish prospective population-based biobank 2024 Ingår i: Journal of Gastrointestinal Oncology. - : AME Publishing Company. - 2078-6891 .- 2219-679X. ; 15:2, s. 755-767 Tidskriftsartikel (refereegranskat)abstract Background: Pancreatic ductal adenocarcinoma (pancreatic cancer) is often detected at late stages resulting in poor overall survival. To improve survival, more patients need to be diagnosed early when curative surgery is feasible. We aimed to identify circulating metabolites that could be used as early pancreatic cancer biomarkers.Methods: We performed metabolomics by liquid and gas chromatography-mass spectrometry in plasma samples from 82 future pancreatic cancer patients and 82 matched healthy controls within the Northern Sweden Health and Disease Study (NSHDS). Logistic regression was used to assess univariate associations between metabolites and pancreatic cancer risk. Least absolute shrinkage and selection operator (LASSO) logistic regression was used to design a metabolite-based risk score. We used receiver operating characteristic (ROC) analyses to assess the discriminative performance of the metabolite-based risk score.Results: Among twelve risk-associated metabolites with a nominal P value <0.05, we defined a risk score of three metabolites [indoleacetate, 3-hydroxydecanoate (10:0-OH), and retention index (RI): 2,745.4] using LASSO. A logistic regression model containing these three metabolites, age, sex, body mass index (BMI), smoking status, sample date, fasting status, and carbohydrate antigen 19-9 (CA 19-9) yielded an internal area under curve (AUC) of 0.784 [95% confidence interval (CI): 0.714–0.854] compared to 0.681 (95% CI: 0.597–0.764) for a model without these metabolites (P value =0.007). Seventeen metabolites were significantly associated with pancreatic cancer survival [false discovery rate (FDR) <0.1].Conclusions: Indoleacetate, 3-hydroxydecanoate (10:0-OH), and RI: 2,745.4 were identified as the top candidate biomarkers for early detection. However, continued efforts are warranted to determine the usefulness of these metabolites as early pancreatic cancer biomarkers.
48.	Borgmästars, Emmy, et al. (författare) Metabolomics for early pancreatic cancer detection in plasma samples from a Swedish prospective population-based biobank 2024 Ingår i: Journal of Gastrointestinal Oncology. - : AME Publishing Company. - 2078-6891 .- 2219-679X. ; 15:2, s. 755-767 Tidskriftsartikel (refereegranskat)abstract Background: Pancreatic ductal adenocarcinoma (pancreatic cancer) is often detected at late stages resulting in poor overall survival. To improve survival, more patients need to be diagnosed early when curative surgery is feasible. We aimed to identify circulating metabolites that could be used as early pancreatic cancer biomarkers.Methods: We performed metabolomics by liquid and gas chromatography-mass spectrometry in plasma samples from 82 future pancreatic cancer patients and 82 matched healthy controls within the Northern Sweden Health and Disease Study (NSHDS). Logistic regression was used to assess univariate associations between metabolites and pancreatic cancer risk. Least absolute shrinkage and selection operator (LASSO) logistic regression was used to design a metabolite-based risk score. We used receiver operating characteristic (ROC) analyses to assess the discriminative performance of the metabolite-based risk score.Results: Among twelve risk-associated metabolites with a nominal P value <0.05, we defined a risk score of three metabolites [indoleacetate, 3-hydroxydecanoate (10:0-OH), and retention index (RI): 2,745.4] using LASSO. A logistic regression model containing these three metabolites, age, sex, body mass index (BMI), smoking status, sample date, fasting status, and carbohydrate antigen 19-9 (CA 19-9) yielded an internal area under curve (AUC) of 0.784 [95% confidence interval (CI): 0.714–0.854] compared to 0.681 (95% CI: 0.597–0.764) for a model without these metabolites (P value =0.007). Seventeen metabolites were significantly associated with pancreatic cancer survival [false discovery rate (FDR) <0.1].Conclusions: Indoleacetate, 3-hydroxydecanoate (10:0-OH), and RI: 2,745.4 were identified as the top candidate biomarkers for early detection. However, continued efforts are warranted to determine the usefulness of these metabolites as early pancreatic cancer biomarkers.
49.	Brege, Harald, 1988-, et al. (författare) Multiactor touchpoints in the customer journey 2022 Konferensbidrag (refereegranskat)abstract This paper explores how B2B firms can manage the value creation process at multi-actor touchpoints in the customer journey. We argue that B2B firms can benefit from opening up their touchpoints to multi-actor interactions between the customer, firm, partners and other customers, answering recent calls for broadening the scope of customer journeys to also include such multi-actor touchpoints. In our research we perceive the value creating process as the actors, activities and resources involved in the emergence of value through the customer journey. An ecosystem perspective is adopted to increase understanding of how firms can enhance the value creating process through the B2B customer journey. By empirically examining an industrial ecosystem, our tentative findings point towards the importance of balancing the number of touchpoints as well as designing touchpoints depending on the customer’s needs and requirements to manage the value creation process.
50.	Brenning, Nils, et al. (författare) A bulk plasma model for dc and HiPIMS magnetrons 2008 Ingår i: PLASMA SOURCES SCIENCE and TECHNOLOGY. - : IOP Publishing. - 0963-0252 .- 1361-6595. ; 17:4, s. 045009- Tidskriftsartikel (refereegranskat)abstract A plasma discharge model has been developed for the bulk plasma (also called the extended presheath) in sputtering magnetrons. It can be used both for high power impulse magnetron sputtering (HiPIMS) and conventional dc sputtering magnetrons. Demonstration calculations are made for the parameters of the HiPIMS sputtering magnetron at Link "oping University, and also benchmarked against results in the literature on dc magnetrons. New insight is obtained regarding the structure and time development of the currents, the electric fields and the potential profiles. The transverse resistivity eta(perpendicular to) has been identified as having fundamental importance both for the potential profiles and for the motion of ionized target material through the bulk plasma. New findings are that in the HiPIMS mode, as a consequence of a high value of eta(perpendicular to), (1) there can be an electric field reversal that in our case extends 0.01-0.04m from the target, (2) the electric field in the bulk plasma is typically an order of magnitude weaker than in dc magnetrons, (3) in the region of electric field reversal the azimuthal current is diamagnetic in nature, i.e. mainly driven by the electron pressure gradient, and actually somewhat reduced by the electron Hall current which here has a reversed direction and (4) the azimuthal current above the racetrack can, through resistive friction, significantly influence the motion of the ionized fraction of the sputtered material and deflect it sideways, away from the target and towards the walls of the magnetron.

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