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Sökning: WFRF:(Tellgren R.)

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1.
  • Zhu, Y., et al. (författare)
  • Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis
  • 2017
  • Ingår i: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 45:5, s. 2629-2643
  • Tidskriftsartikel (refereegranskat)abstract
    • Complete and accurate genome assembly and annotation is a crucial foundation for comparative and functional genomics. Despite this, few complete eukaryotic genomes are available, and genome annotation remains a major challenge. Here, we present a complete genome assembly of the skin commensal yeast Malassezia sympodialis and demonstrate how proteogenomics can substantially improve gene annotation. Through long-read DNA sequencing, we obtained a gap-free genome assembly for M. sympodialis (ATCC 42132), comprising eight nuclear and one mitochondrial chromosome. We also sequenced and assembled four M. sympodialis clinical isolates, and showed their value for understanding Malassezia reproduction by confirming four alternative allele combinations at the two mating-type loci. Importantly, we demonstrated how proteomics data could be readily integrated with transcriptomics data in standard annotation tools. This increased the number of annotated protein-coding genes by 14% (from 3612 to 4113), compared to using transcriptomics evidence alone. Manual curation further increased the number of protein-coding genes by 9% (to 4493). All of these genes have RNA-seq evidence and 87% were confirmed by proteomics. The M. sympodialis genome assembly and annotation presented here is at a quality yet achieved only for a few eukaryotic organisms, and constitutes an important reference for future host-microbe interaction studies.
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2.
  • Berger, R, et al. (författare)
  • Structure refinements of LiCu2O2 and LiCu3O3 from neutron powder diffraction data
  • 1992
  • Ingår i: Journal of Alloys and Compounds. ; 184, s. 315-322
  • Tidskriftsartikel (refereegranskat)abstract
    • In its inherent ability to discern light elements in a heavy-atom matrix, neutron powder diffraction has been used at room temperature to confirm structure hypotheses of LiCu2O2 and LiCu3O3, inferred from previous X-ray diffraction studies.
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5.
  • Maletka, K, et al. (författare)
  • Phase transitions in the ionic conductor Li2UBr6 studied by neutron diffraction
  • 1998
  • Ingår i: SOLID STATE IONICS. - : ELSEVIER SCIENCE BV. ; 106:1-2
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • The crystal structure of the Li2UBr6 ionic conductor has been studied as a function of the temperature by powder neutron diffraction. The room and high temperature structures have been determined. At 300 K the compound crystallises in a trigonal unit cel
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6.
  • Svedberg, Dennis, et al. (författare)
  • Functional annotation of a divergent genome using sequence and structure-based similarity
  • 2024
  • Ingår i: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 25:1
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundMicrosporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence similarity. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes.ResultsIn this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin named ANNOTEX (Annotation Extension for ChimeraX), allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome of Vairimorpha necatrix. First, the 3080 predicted protein-coding DNA sequences, of which 89% were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of the V. necatrix genome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterized Encephalitozoon cuniculi genes.ConclusionWe provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.
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  • Aidas, Kestutis, et al. (författare)
  • The Dalton quantum chemistry program system
  • 2014
  • Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
  • Tidskriftsartikel (refereegranskat)abstract
    • Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
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9.
  • Andersson, AS, et al. (författare)
  • The magnetic structure and properties of rhombohedral Li3Fe2(PO4)(3)
  • 2000
  • Ingår i: JOURNAL OF MATERIALS CHEMISTRY. - : ROYAL SOC CHEMISTRY. - 0959-9428. ; 10:11, s. 2542-2547
  • Tidskriftsartikel (refereegranskat)abstract
    • Magnetic susceptibility measurements indicate that rhombohedral Li3Fe2(PO4)(3), obtained by ion exchange of monoclinic Na3Fe2(PO4)(3), exhibits a paramagnetic to antiferromagnetic transition at T-N approximate to 27 K. Curie-Weiss-like behaviour is observ
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10.
  • Andersson, Y, et al. (författare)
  • Neutron powder diffraction investigations of pure and deuterated Ti3PO0.58.
  • 1997
  • Ingår i: JOURNAL OF ALLOYS AND COMPOUNDS. - : ELSEVIER SCIENCE SA LAUSANNE. ; 253
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • The crystal structures of Ti3PO0.58 and Ti3PO0.58D0.37 have been refined from neutron powder diffraction room temperature data using the Rietveld method. Ti3PO0.58 crystallizes in the filled Re3B type structure, space group Cmcm, with the unit cell dimen
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14.
  • Baron, V, et al. (författare)
  • The influence of iron substitution on the magnetic properties of hausmannite, Mn2+(Fe,Mn)(2)(3+)O-4
  • 1998
  • Ingår i: AMERICAN MINERALOGIST. - : MINERALOGICAL SOC AMER. - 0003-004X. ; 83:7-8, s. 786-793
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • The occurrence of hausmannite with an apparent Curie temperature close to 750 K, instead of 41.8 K was recently described from hydrothermally altered manganese ore from the Kalahari manganese field, South Africa. The unusual magnetic properties were relat
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19.
  • Ivanov, SA, et al. (författare)
  • Structural and magnetic study of magnetoelectric perovskite Sr2CoMoO6
  • 2006
  • Ingår i: ZEITSCHRIFT FUR KRISTALLOGRAPHIE 537-542 Part 2 Suppl. 23, 2006. ; :2, s. 537-542
  • Tidskriftsartikel (refereegranskat)abstract
    • A study of the crystal and magnetic structure of the double perovskite Sr2CoMoO6 has been carried out on a polycrystalline sample using neutron diffraction (NPD) data between 10-700K. An analysis of NPD patterns at 295K has shown that this compound crystallizes in the tetragonal space group 14/m with a = 5.5616(l) and c = 7.9470(2) angstrom and has a 1:1 ordered arrangement of the B-sites. This compound undergoes a 14/m -> Fm3m improper ferroelectric phase transition near 563 K. A low-temperature antiferomagnetic ordering (below T-N = 37 K) has been followed from a sequence of low-temperature NPD data sets. The magnetic structure is defined by the propagation vector (k) over right arrow = (1/2,0,1/2). Alongside the obtained experimental results on magnetic and electric properties some aspects of magnetoelectricity in this perovskite is also discussed.
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21.
  • Kaufmann, Philipp, 1991-, et al. (författare)
  • Assembly of polymorphic Y chromosomes reveals molecular basis of variation in male body size
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • The Y chromosome of males is theorized to facilitate the evolution of sexual dimorphism by accumulating sexually antagonistic loci, but empirical support is limited. In the seed beetle Callosobruchus maculatus, variation in sexually antagonistic body size is linked to at least two segregating Y haplotypes in males that facilitated rapid laboratory evolution of sexual size dimorphism. Here we assemble previously uncharacterized C. maculatus sex chromosome sequences and identify molecular differences between the two predicted Y haplotypes. The Y chromosome of C. maculatus shows typical hallmarks of degeneration: it is ampliconic and approximately 80% smaller than the X. Nevertheless, the Y harbors over 400 genes with a mixed autosomal and X chromosome ancestry that are enriched with metabolic, developmental and gene regulatory functions. Crucially, we find that besides an autosomal copy of the gene target of rapamycin (TOR), males carry an additional TOR copy on the Y chromosome. TOR is a conserved regulator of growth across taxa, and a Y-linked copy of TOR thus provides a male specific opportunity to alter body size. The two identified Y haplotypes show fixed single nucleotide differences in or in close proximity to over 100 genes, but also copy number variation for TOR, where the more frequent (~95%) Y haplotype that causes increased sexual size dimorphism has two additional TOR copies. These results suggest that part of the sexual conflict over body size has been mitigated by autosome to Y translocation of TOR followed by gene duplications that further increased sexual dimorphism.
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22.
  • Kaufmann, Philipp, et al. (författare)
  • Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles
  • 2023
  • Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 40:8
  • Tidskriftsartikel (refereegranskat)abstract
    • The Y chromosome is theorized to facilitate evolution of sexual dimorphism by accumulating sexually antagonistic loci, but empirical support is scarce. Due to the lack of recombination, Y chromosomes are prone to degenerative processes, which poses a constraint on their adaptive potential. Yet, in the seed beetle, Callosobruchus maculatus segregating Y linked variation affects male body size and thereby sexual size dimorphism (SSD). Here, we assemble C. maculatus sex chromosome sequences and identify molecular differences associated with Y-linked SSD variation. The assembled Y chromosome is largely euchromatic and contains over 400 genes, many of which are ampliconic with a mixed autosomal and X chromosome ancestry. Functional annotation suggests that the Y chromosome plays important roles in males beyond primary reproductive functions. Crucially, we find that, besides an autosomal copy of the gene target of rapamycin (TOR), males carry an additional TOR copy on the Y chromosome. TOR is a conserved regulator of growth across taxa, and our results suggest that a Y-linked TOR provides a male specific opportunity to alter body size. A comparison of Y haplotypes associated with male size difference uncovers a copy number variation for TOR, where the haplotype associated with decreased male size, and thereby increased sexual dimorphism, has two additional TOR copies. This suggests that sexual conflict over growth has been mitigated by autosome to Y translocation of TOR followed by gene duplications. Our results reveal that despite of suppressed recombination, the Y chromosome can harbor adaptive potential as a male-limited supergene.
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23.
  • Larsson, T, et al. (författare)
  • The crystal structure of Ti3PD2.4
  • 1996
  • Ingår i: JOURNAL OF ALLOYS AND COMPOUNDS. - : ELSEVIER SCIENCE SA LAUSANNE. ; 236:1-2
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • The crystal structure of the deuteride phase of Ti3P has been refined from neutron powder diffraction data taken at 25 degrees C and 250 degrees C using the Rietveld method. The tetragonal beta-V3S-type structure, space group P4(2)/nbc, involves three cr
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24.
  • Lundgren, J. O., et al. (författare)
  • Neutron diffraction study of oxonium trifluoromethanesulphonate
  • 1978
  • Ingår i: Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry. - : International Union of Crystallography (IUCr). - 0567-7408. ; 34:9, s. 2945-2947
  • Tidskriftsartikel (refereegranskat)
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25.
  • Lundqvist, P, et al. (författare)
  • Neutron-diffraction studies and bond valence sums of charge neutrally doped Nd1-2xCaxThxBa2Cu3O7-delta
  • 1997
  • Ingår i: PHYSICAL REVIEW B-CONDENSED MATTER. - : AMER INST PHYSICS. - 0163-1829. ; 56:5, s. 2824-2830
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • Equal amounts of Ca and Th have been doped into the Nd1-2xCaxThxBa2Cu3O7-delta superconductor with x = 0. 0.015. 0.03, 0.05. and 0.10. This causes a fast and linear decrease of the superconducting transition temperature, T-c. A single orthorhombic phase w
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26.
  • Lundqvist, P, et al. (författare)
  • Neutron-diffraction studies and interatomic distances in Ca-Pr doped NdBa2Cu3O7-delta
  • 1996
  • Ingår i: PHYSICA C. - : ELSEVIER SCIENCE BV. ; 269:3-4
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Sintered samples of Nd1-2xCaxPrxBa2Cu3O7-delta with x = 0, 0.025, 0.050, and 0.10 have been studied by electrical-resistivity measurements, X-ray and neutron diffraction and from calculated bond-valence sums (BVS). Doping of equal amounts of Ca-Pr suppre
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27.
  • MALETKA, K, et al. (författare)
  • HIGH-TEMPERATURE PHASE-TRANSITION IN NA2UI6 BY NEUTRON POWDER DIFFRACTION
  • 1995
  • Ingår i: SOLID STATE IONICS. - : ELSEVIER SCIENCE BV. ; 76:1-2
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • The behaviour of Na2UI6 has been studied as a function of temperature by neutron powder diffraction. The neutron diffraction experiments carried out at 650 and 700 K, revealed a gradual rearrangement of the occupancy of the sodium atoms which tend - as t
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28.
  • Maletka, K, et al. (författare)
  • Neutron diffraction and electrical conductivity studies of Li2UI6 ionic conductor
  • 1996
  • Ingår i: SOLID STATE IONICS. - : ELSEVIER SCIENCE BV. ; 90:1-4
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • The room and high temperature structures of Li2UI6 have been determined using the neutron powder diffraction. It has been shown that at 300 K, the compound crystallizes in trigonal unit cell with a = b = 7.3927(8), c = 13.826(2) Angstrom with space group
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29.
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30.
  • ONNERUD, P, et al. (författare)
  • A MAGNETIC-STRUCTURE INVESTIGATION OF TETRAGONAL (FE1-XCOX)(2)AS
  • 1995
  • Ingår i: JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS. - : ELSEVIER SCIENCE BV. - 0304-8853. ; 147:3, s. 346-354
  • Tidskriftsartikel (refereegranskat)abstract
    • The crystal and magnetic structures of tetragonal (Fe1-xCox)(2) As have been investigated using magnetization measurements, Mossbauer spectroscopy and neutron powder diffraction. Mossbauer and magnetisation measurements were performed on compositions with
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31.
  • Onnerud, P, et al. (författare)
  • The crystal and magnetic structures of ordered cubic Pd3MnD0.7
  • 1997
  • Ingår i: SOLID STATE COMMUNICATIONS. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0038-1098. ; 101:6, s. 433-437
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • The crystal and magnetic structures of deuterated cubic Pd3Mn have been investigated by means of magnetisation and neutron powder diffraction measurements. The deuterium atoms were found to be situated in octahedral interstices surrounded by-six palladiu
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32.
  • Onnerud, P, et al. (författare)
  • The ferromagnetic structure of hexagonal (Fe1-xCo2)(2)As
  • 1997
  • Ingår i: SOLID STATE COMMUNICATIONS. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0038-1098. ; 101:4, s. 271-275
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • The magnetic structure of hexagonal (Fe1-xCox)(2)As has been studied by means of neutron powder diffraction and magnetisation measurements. The magnetic moments were found, by means of Rietveld refinements, to be aligned along the c-axis for x = 0.4 and
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33.
  • Onnerud, P, et al. (författare)
  • The magnetic structure of ordered cubic Pd3Mn
  • 1997
  • Ingår i: JOURNAL OF SOLID STATE CHEMISTRY. - : ACADEMIC PRESS INC JNL-COMP SUBSCRIPTIONS. - 0022-4596. ; 128:1, s. 109-114
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • Neutron powder diffraction and magnetization measurements have been carried out on ordered cubic Pd3Mn of the Cu3Au-type structure. The crystal and magnetic structures have been analyzed by means of the Rietveld method. The magnetic structure model was r
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35.
  • Tegenfeldt, J., et al. (författare)
  • Neutron diffraction study of sodium bromide dihydrate
  • 1979
  • Ingår i: Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry. - : International Union of Crystallography (IUCr). - 0567-7408. ; 35:7, s. 1679-1682
  • Tidskriftsartikel (refereegranskat)
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  • Tseggai, Mehreteab, et al. (författare)
  • Magnesium Substitution in Nd0.7Sr0.3MnO3
  • 2004
  • Ingår i: J. Solid State Chemistry. ; 177, s. 966-971
  • Tidskriftsartikel (refereegranskat)abstract
    • Magnesium substitution in Nd0.7Sr0.3MnO3 has been studied by neutron powder diffraction. Polycrystalline samples of nominal compositions Nd0.7Sr0.3Mn1−yMgyO3 with y=0.0, 0.1, 0.2 and 0.3 were synthesized by the standard solid-state reaction method. Rietveld refinements of the neutron powder diffraction data showed that all samples had distorted perovskite structure of orthorhombic symmetry. Mg initially preferred to substitute for Nd and only at Mg concentration greater than 0.1, a substantial substitution for Mn occurred. Our study also showed that Mg-substitution did not change the crystal structure of Nd0.7Sr0.3MnO3.
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42.
  • Tseggai, M., et al. (författare)
  • Synthesis, nuclear structure, and magnetic properties of LaCr1-yMnyO3 (y=0, 0.1, 0.2, and 0.3)
  • 2008
  • Ingår i: Journal of Alloys and Compounds. - : Elsevier BV. - 0925-8388 .- 1873-4669. ; 457:1-2, s. 532-540
  • Tidskriftsartikel (refereegranskat)abstract
    • The nuclear structure and magnetic properties of perovskite-type samples of compositions LaCr1-xMnyO3 (y=0, 0.1, 0.2, 0.3) have been studied using neutron powder diffraction technique and magnetization measurements. All samples have orthorhombic structure with space group Pnma (No. 62) in the temperature range 1.5-400 K. The pure lanthanum chromate LaCrO3 is a G-type antiferromagnet with a Neel temperature of 290 K. The Mn substituted samples also order antiferromagnetically at about 290 K, with canted magnetic moments yielding a ferromagnetic component.
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