| 1. |
- Suh, Alexander, et al.
(författare)
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Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes
- 2015
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653 .- 1759-6653. ; 7:1, s. 205-217
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Tidskriftsartikel (refereegranskat)abstract
- Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians.
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| 2. |
- Suh, Alexander, et al.
(författare)
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The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses
- 2013
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 1791-
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Tidskriftsartikel (refereegranskat)abstract
- Paleovirology involves the identification of ancient endogenous viral elements within eukaryotic genomes. The evolutionary origins of the reverse-transcribing hepatitis B viruses, however, remain elusive, due to the small number of endogenized sequences present in host genomes. Here we report a comprehensively dated genomic record of hepatitis B virus endogenizations that spans bird evolution from > 82 to < 12.1 million years ago. The oldest virus relic extends over a 99% complete hepatitis B virus genome sequence and constitutes the first discovery of a Mesozoic paleovirus genome. We show that Hepadnaviridae are 463 million years older than previously known and provide direct evidence for coexistence of hepatitis B viruses and birds during the Mesozoic and Cenozoic Eras. Finally, phylogenetic analyses and distribution of hepatitis B virus relics suggest that birds potentially are the ancestral hosts of Hepadnaviridae and mammalian hepatitis B viruses probably emerged after a bird-mammal host switch. Our study reveals previously undiscovered and multi-faceted insights into prehistoric hepatitis B virus evolution and provides valuable resources for future studies, such as in-vitro resurrection of Mesozoic hepadnaviruses.
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| 3. |
- Green, Richard E., et al.
(författare)
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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1335-
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Tidskriftsartikel (refereegranskat)abstract
- To provide context for the diversification of archosaurs-the group that includes crocodilians, dinosaurs, and birds-we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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| 4. |
- La Torre, Enrico, et al.
(författare)
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Local probe of irradiation-induced structural changes and orbital magnetism in Fe60Al40 thin films via an order-disorder phase transition
- 2018
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Ingår i: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 98:2
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Tidskriftsartikel (refereegranskat)abstract
- Hard x-ray absorption and magnetic circular dichroism spectroscopy have been applied to study the consequential changes of the local environment around Fe atoms and their orbital polarizations in 40 nm thick Fe60Al40 thin films along the order-disorder (B2 -> A2) phase transition initiated by 20-keV Ne+ ion irradiation with fluences of (0.75-6) x 10(14) ions cm(-2). The analysis of the extended x-ray absorption fine structure spectra measured at the Fe K edge at room temperature revealed an increased number of Fe-Fe nearest neighbors from 3.47(7) to 5.0(1) and similar to 1% of volume expansion through the transition. The visualization of the Fe and Al nearest-neighbor rearrangement in the first coordination shell of Fe absorbers via the transition was carried out by wavelet transformations. The obtained changes in Fe coordination are evidently reflected in the x-ray magnetic circular dichroism spectra which show an increased orbital magnetic moment of Fe atoms and a pronounced magnetic multielectronic excitations peak at similar to 60 eV above the edge. The amplitudes of both peaks demonstrated similar dependencies on the irradiation fluence. The results of self-consistent density functional calculations on relaxed Fe60Al40 model structures for the ordered (B2) and the disordered (A2) phases are consistent with the experimental findings and point to the formation of Fe-rich regions in the films studied.
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| 5. |
- Lindblad, Peter, et al.
(författare)
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CyanoFactory, a European consortium to develop technologies needed to advance cyanobacteria as chassis for production of chemicals and fuels
- 2019
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Ingår i: Algal Research. - : Elsevier. - 2211-9264. ; 41
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Forskningsöversikt (refereegranskat)abstract
- CyanoFactory, Design, construction and demonstration of solar biofuel production using novel (photo) synthetic cell factories, was an R&D project developed in response to the European Commission FP7-ENERGY-2012-1 call "Future Emerging Technologies" and the need for significant advances in both new science and technologies to convert solar energy into a fuel. CyanoFactory was an example of "purpose driven" research and development with identified scientific goals and creation of new technologies. The present overview highlights significant outcomes of the project, three years after its successful completion. The scientific progress of CyanoFactory involved: (i) development of a ToolBox for cyanobacterial synthetic biology; (ii) construction of DataWarehouse/Bioinformatics web-based capacities and functions; (iii) improvement of chassis growth, functionality and robustness; (iv) introduction of custom designed genetic constructs into cyanobacteria, (v) improvement of photosynthetic efficiency towards hydrogen production; (vi) biosafety mechanisms; (vii) analyses of the designed cyanobacterial cells to identify bottlenecks with suggestions on further improvements; (viii) metabolic modelling of engineered cells; (ix) development of an efficient laboratory scale photobioreactor unit; and (x) the assembly and experimental performance assessment of a larger (1350 L) outdoor flat panel photobioreactor system during two seasons. CyanoFactory - Custom design and purpose construction of microbial cells for the production of desired products using synthetic biology - aimed to go beyond conventional paths to pursue innovative and high impact goals. CyanoFactory brought together ten leading European partners (universities, research organizations and enterprises) with a common goal - to develop the future technologies in Synthetic biology and Advanced photobioreactors.
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| 6. |
- Singh, B., et al.
(författare)
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Study of doubly strange systems using stored antiprotons
- 2016
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Ingår i: Nuclear Physics A. - : Elsevier. - 0375-9474 .- 1873-1554. ; 954, s. 323-340
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Tidskriftsartikel (refereegranskat)abstract
- Bound nuclear systems with two units of strangeness are still poorly known despite their importance for many strong interaction phenomena. Stored antiprotons beams in the GeV range represent an unparalleled factory for various hyperon-antihyperon pairs. Their outstanding large production probability in antiproton collisions will open the floodgates for a series of new studies of systems which contain two or even more units of strangeness at the PANDA experiment at FAIR. For the first time, high resolution gamma-spectroscopy of doubly strange Lambda Lambda-hypernuclei will be performed, thus complementing measurements of ground state decays of Lambda Lambda-hypernuclei at J-PARC or possible decays of particle unstable hypernuclei in heavy ion reactions. High resolution spectroscopy of multistrange Xi(-) -atoms will be feasible and even the production of Omega(-) -atoms will be within reach. The latter might open the door to the vertical bar S vertical bar = 3 world in strangeness nuclear physics, by the study of the hadronic Omega(-) -nucleus interaction. For the first time it will be possible to study the behavior of Xi(+) in nuclear systems under well controlled conditions.
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| 7. |
- Szabo, Paul S., et al.
(författare)
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Dynamic Potential Sputtering of Lunar Analog Material by Solar Wind Ions
- 2020
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Ingår i: Astrophysical Journal. - : IOP PUBLISHING LTD. - 0004-637X .- 1538-4357. ; 891:1
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Tidskriftsartikel (refereegranskat)abstract
- Pyroxenes ((Ca, Mg, Fe, Mn)(2)Si2O6) belong to the most abundant rock forming minerals that make up the surface of rocky planets and moons. Therefore, sputtering of pyroxenes by solar wind ions has to be considered as a very important process for modifying the surface of planetary bodies. This is increased due to potential sputtering by multiply charged ions; to quantify this effect, sputtering of wollastonite (CaSiO3) by He2+ ions was investigated. Thin films of CaSiO3 deposited on a quartz crystal microbalance were irradiated, allowing precise, in situ, real time sputtering yield measurements. Experimental results were compared with SDTrimSP simulations, which were improved by adapting the used input parameters. On freshly prepared surfaces, He2+ ions show a significant increase in sputtering, as compared to equally fast He+ ions. However, the yield decreases exponentially with fluence, reaching a lower steady state after sputtering of the first few monolayers. Experiments using Ar8+ ions show a similar behavior, which is qualitatively explained by a preferential depletion of surface oxygen due to potential sputtering. A corresponding quantitative model is applied, and the observed potential sputtering behaviors of both He and Ar are reproduced very well. The results of these calculations support the assumption that mainly O atoms are affected by potential sputtering. Based on our findings, we discuss the importance of potential sputtering for the solar wind eroding the lunar surface. Estimated concentration changes and sputtering yields are both in line with previous modeling for other materials, allowing a consistent perspective on the effects of solar wind potential sputtering.
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