| 1. |
- Zhu, Y., et al.
(author)
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Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis
- 2017
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In: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 45:5, s. 2629-2643
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Journal article (peer-reviewed)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.
(author)
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Structure refinements of LiCu2O2 and LiCu3O3 from neutron powder diffraction data
- 1992
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In: Journal of Alloys and Compounds. ; 184, s. 315-322
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Journal article (peer-reviewed)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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| 4. |
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| 5. |
- Maletka, K, et al.
(author)
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Phase transitions in the ionic conductor Li2UBr6 studied by neutron diffraction
- 1998
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In: SOLID STATE IONICS. - : ELSEVIER SCIENCE BV. ; 106:1-2
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Other publication (other academic/artistic)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.
(author)
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Functional annotation of a divergent genome using sequence and structure-based similarity
- 2024
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In: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 25:1
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Journal article (peer-reviewed)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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| 7. |
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| 8. |
- Aidas, Kestutis, et al.
(author)
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The Dalton quantum chemistry program system
- 2014
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In: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
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Journal article (peer-reviewed)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.
(author)
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The magnetic structure and properties of rhombohedral Li3Fe2(PO4)(3)
- 2000
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In: JOURNAL OF MATERIALS CHEMISTRY. - : ROYAL SOC CHEMISTRY. - 0959-9428. ; 10:11, s. 2542-2547
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Journal article (peer-reviewed)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.
(author)
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Neutron powder diffraction investigations of pure and deuterated Ti3PO0.58.
- 1997
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In: JOURNAL OF ALLOYS AND COMPOUNDS. - : ELSEVIER SCIENCE SA LAUSANNE. ; 253
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Other publication (other academic/artistic)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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