| 1. |
- Aevarsson, Arnthór, et al.
(författare)
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Going to extremes - a metagenomic journey into the dark matter of life
- 2021
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 1574-6968. ; 368:12
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Forskningsöversikt (refereegranskat)abstract
- The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.
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| 2. |
- Arsın, Hasan, et al.
(författare)
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Exploring Codon Adjustment Strategies towards Escherichia coli-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium Hypnocyclicus thermotrophus
- 2021
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Ingår i: Viruses. - : MDPI AG. - 1999-4915. ; 13:7
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Tidskriftsartikel (refereegranskat)abstract
- Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production of proteins hinder access to downstream characterization, subsequently impeding the discovery process. While commonly utilized for the heterologous expression of prokaryotic genes, codon adjustment approaches have not been fully explored for viral genes. Herein, the sequence-based identification of a putative prophage is reported from within the genome of Hypnocyclicus thermotrophus, a Gram-negative, moderately thermophilic bacterium isolated from the Seven Sisters hydrothermal vent field. A prophage-associated gene cluster, consisting of 46 protein coding genes, was identified and given the proposed name Hypnocyclicus thermotrophus phage H1 (HTH1). HTH1 was taxonomically assigned to the viral family Siphoviridae, by lowest common ancestor analysis of its genome and phylogeny analyses based on proteins predicted as holin and DNA polymerase. The gene neighbourhood around the HTH1 lytic cassette was found most similar to viruses infecting Gram-positive bacteria. In the HTH1 lytic cassette, an N-acetylmuramoyl-L-alanine amidase (Amidase_2) with a peptidoglycan binding motif (LysM) was identified. A total of nine genes coding for enzymes putatively related to lysis, nucleic acid modification and of unknown function were subjected to heterologous expression in Escherichia coli. Codon optimization and codon harmonization approaches were applied in parallel to compare their effects on produced proteins. Comparison of protein yields and thermostability demonstrated that codon optimization yielded higher levels of soluble protein, but codon harmonization led to proteins with higher thermostability, implying a higher folding quality. Altogether, our study suggests that both codon optimization and codon harmonization are valuable approaches for successful heterologous expression of viral genes in E. coli, but codon harmonization may be preferable in obtaining recombinant viral proteins of higher folding quality.
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| 3. |
- Sharon, Keren, et al.
(författare)
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The Cosmic Telescope That Lenses the Sunburst Arc, PSZ1 G311.65-18.48 : Strong Gravitational Lensing Model and Source Plane Analysis
- 2022
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 941:2
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Tidskriftsartikel (refereegranskat)abstract
- We present a strong-lensing analysis of the cluster PSZ1 G311.65−18.48, based on Hubble Space Telescope imaging, archival VLT/MUSE spectroscopy, and Chandra X-ray data. This cool-core cluster (z = 0.443) lenses the brightest lensed galaxy known, dubbed the "Sunburst Arc" (z = 2.3703), a Lyman continuum (LyC) emitting galaxy multiply imaged 12 times. We identify in this field 14 additional strongly lensed galaxies to constrain a strong-lens model and report secure spectroscopic redshifts of four of them. We measure a projected cluster core mass of M(<250 kpc) = M⊙. The two least magnified but complete images of the Sunburst Arc's source galaxy are magnified by ∼13×, while the LyC clump is magnified by ∼4–80×. We present time delay predictions and conclusive evidence that a discrepant clump in the Sunburst Arc, previously claimed to be a transient, is not variable, thus strengthening the hypothesis that it results from an exceptionally high magnification. A source plane reconstruction and analysis of the Sunburst Arc finds its physical size to be 1 × 2 kpc and that it is resolved in three distinct directions in the source plane, 0°, 40°, and 75° (east of north). We place an upper limit of r ≲ 50 pc on the source plane size of unresolved clumps and r ≲ 32 pc for the LyC clump. Finally, we report that the Sunburst Arc is likely in a system of two or more galaxies separated by ≲6 kpc in projection. Their interaction may drive star formation and could play a role in the mechanism responsible for the leaking LyC radiation.
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