| 1. |
- de Vries, Ronald P, et al.
(författare)
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Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
- 2017
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.ResultsWe have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli.ConclusionsMany aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
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| 2. |
- Floudas, Dimitrios, et al.
(författare)
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Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii
- 2015
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845. ; 76, s. 78-92
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Tidskriftsartikel (refereegranskat)abstract
- Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited. (C) 2015 Elsevier Inc. All rights reserved.
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| 3. |
- Grigoriev, Igor A., et al.
(författare)
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Capturing turbulent density flux effects in variable density flow by an explicit algebraic model
- 2015
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Ingår i: Physics of fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 27:4
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Tidskriftsartikel (refereegranskat)abstract
- The explicit algebraic Reynolds stress model of Grigoriev et al. ["A realizable explicit algebraic Reynolds stress model for compressible turbulent flow with significant mean dilatation," Phys. Fluids 25, 105112 (2013)] is extended to account for the turbulent density flux in variable density flows. The influence of the mean dilatation and the variation of mean density on the rapid pressure-strain correlation are properly accounted for introducing terms balancing a so-called "baroclinic" production in the Reynolds stress tensor equation. Applying the weak-equilibrium assumption leads to a self-consistent formulation of the model. The model together with a K - ω model is applied to a quasi-one-dimensional plane nozzle flow transcending from subsonic to supersonic regimes. The model remains realizable with constraints put on the model parameters. When density fluxes are taken into account, the model is less likely to become unrealizable. The density variance coupled with a "local mean acceleration" also can influence the model acting to increase anisotropy. The general trends of the behaviour of the anisotropy and production components under the variation of model parameters are assessed. We show how the explicit model can be applied to two- and three-dimensional mean flows without previous knowledge of a tensor basis to obtain the general solution. Approaches are proposed in order to achieve an approximate solution to the consistency equation in cases when analytic solution is missing. In summary, the proposed model has the potential to significantly improve simulations of variable-density flows.
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| 4. |
- Grigoriev, Igor, 1984-, et al.
(författare)
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Algebraic Reynolds stress modeling of turbulence subject to rapid homogeneous and non-homogeneous compression or expansion
- 2016
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Ingår i: Physics of fluids. - : American Institute of Physics (AIP). - 1070-6631 .- 1089-7666. ; 28:2, s. 026101-
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Tidskriftsartikel (refereegranskat)abstract
- A recently developed explicit algebraic Reynolds stress model (EARSM) by Grigoriev et al. ["A realizable explicit algebraic Reynolds stress model for compressible turbulent flow with significant mean dilatation," Phys. Fluids 25(10), 105112 (2013)] and the related differential Reynolds stress model (DRSM) are used to investigate the influence of homogeneous shear and compression on the evolution of turbulence in the limit of rapid distortion theory (RDT). The DRSM predictions of the turbulence kinetic energy evolution are in reasonable agreement with RDT while the evolution of diagonal components of anisotropy correctly captures the essential features, which is not the case for standard compressible extensions of DRSMs. The EARSM is shown to give a realizable anisotropy tensor and a correct trend of the growth of turbulence kinetic energy K, which saturates at a power law growth versus compression ratio, as well as retaining a normalized strain in the RDT regime. In contrast, an eddy-viscosity model results in a rapid exponential growth of K and excludes both realizability and high magnitude of the strain rate. We illustrate the importance of using a proper algebraic treatment of EARSM in systems with high values of dilatation and vorticity but low shear. A homogeneously compressed and rotating gas cloud with cylindrical symmetry, related to astrophysical flows and swirling supercritical flows, was investigated too. We also outline the extension of DRSM and EARSM to include the effect of non-homogeneous density coupled with "local mean acceleration" which can be important for, e.g., stratified flows or flows with heat release. A fixed-point analysis of direct numerical simulation data of combustion in a wall-jet flow demonstrates that our model gives quantitatively correct predictions of both streamwise and cross-stream components of turbulent density flux as well as their influence on the anisotropies. In summary, we believe that our approach, based on a proper formulation of the rapid pressure-strain correlation and accounting for the coupling with turbulent density flux, can be an important element in CFD tools for compressible flows.
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| 5. |
- Grigoriev, Igor, 1984-, et al.
(författare)
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Unified explicit algebraic Reynolds stress model for compressible, heat-releasing and supercritical flowswith large density variation
- 2016
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- An explicit algebraic model (EARSM) for variable denstiy turbulent flow developed by Grigoriev et al. [Phys. Fluids (2015)] is revisited here. We apply it to a quasi one-dimensional nozzle flow, a wall-jet flow with combustion and large density variation and a supercritical flow of carbon dioxide with heat transfer and buoyancy. It is confirmed that the coupling between strong mean density gradient due to high speed, heat release or thermodynamic variations and the 'local mean acceleration' of the flow produces strong turbulent density and heat fluxes, which strongly affect the turbulence. The possible calibration branches are identified and analyzed. We show that a simple and unified calibration of the model gives good predictions for all cases considered. Therefore, the model is a reliable tool for the computation of compressible flows with large density variation.
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| 6. |
- Kohler, Annegret, et al.
(författare)
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Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:4, s. 176-410
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Tidskriftsartikel (refereegranskat)abstract
- To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
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| 7. |
- Nagy, László G, et al.
(författare)
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Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities.
- 2015
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 33:4, s. 959-970
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Tidskriftsartikel (refereegranskat)abstract
- Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of 10 saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot.
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| 8. |
- Rineau, F., et al.
(författare)
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Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes
- 2017
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Ingår i: Mycorrhiza. - : Springer Science and Business Media LLC. - 0940-6360 .- 1432-1890. ; 27:4, s. 383-396
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Tidskriftsartikel (refereegranskat)abstract
- Hydrophobins are small secreted proteins that are present as several gene copies in most fungal genomes. Their properties are now well understood: they are amphiphilic and assemble at hydrophilic/hydrophobic interfaces. However, their physiological functions remain largely unexplored, especially within mycorrhizal fungi. In this study, we identified hydrophobin genes and analysed their distribution in eight mycorrhizal genomes. We then measured their expression levels in three different biological conditions (mycorrhizal tissue vs. free-living mycelium, organic vs. mineral growth medium and aerial vs. submerged growth). Results confirmed that the size of the hydrophobin repertoire increased in the terminal orders of the fungal evolutionary tree. Reconciliation analysis predicted that in 41% of the cases, hydrophobins evolved from duplication events. Whatever the treatment and the fungal species, the pattern of expression of hydrophobins followed a reciprocal function, with one gene much more expressed than others from the same repertoire. These most-expressed hydrophobin genes were also among the most expressed of the whole genome, which suggests that they play a role as structural proteins. The fine-tuning of the expression of hydrophobin genes in each condition appeared complex because it differed considerably between species, in a way that could not be explained by simple ecological traits. Hydrophobin gene regulation in mycorrhizal tissue as compared with free-living mycelium, however, was significantly associated with a calculated high exposure of hydrophilic residues.
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| 9. |
- Valiollahi Bisheh, Roudabeh, et al.
(författare)
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Electrochemical hydrogen production on a metal-free polymer
- 2019
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Ingår i: Sustainable Energy & Fuels. - : Royal Society of Chemistry. - 2398-4902. ; 3:12, s. 3387-3398
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Tidskriftsartikel (refereegranskat)abstract
- The exploration for true electrocatalytic reactions at organic conducting polymer electrodes, including chemisorption of a reactant and desorption of a product, is receiving renewed interest due to the profound implications it could have on low-cost large area electrochemical energy technology. Here, we finalize the debate about the ability of an organic electrode, more specifically poly(3,4-ethylenedioxythiophene) (PEDOT), to be an electrocatalyst for hydrogen production. This paper proves and covers fundamental studies of the hydrogen evolution reaction (HER) on PEDOT films. Both theory based on DFT (Density Functional Theory) and experimental studies using electrochemical techniques and operando mass spectrometry suggest a Volmer-Heyrovsky mechanism for the actual HER on PEDOT. It is shown that PEDOT reaches an exchange current density comparable to that of metals (i.e. Cu, Ni, and Au) and in addition does not form passivating oxide layers or suffer from chemical corrosion in acidic media. Finally, an electrolyzer stack using the organic polymer electrode demonstrates HER performance in real applications.
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| 10. |
- Vandaele, Ann Carine, et al.
(författare)
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Martian dust storm impact on atmospheric H2O and D/H observed by ExoMars Trace Gas Orbiter
- 2019
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Ingår i: Nature. - : Springer. - 1476-4687 .- 1476-4687 .- 0028-0836. ; 568:7753, s. 521-525
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Global dust storms on Mars are rare1,2 but can affect the Martian atmosphere for several months. They can cause changes in atmospheric dynamics and inflation of the atmosphere3, primarily owing to solar heating of the dust3. In turn, changes in atmospheric dynamics can affect the distribution of atmospheric water vapour, with potential implications for the atmospheric photochemistry and climate on Mars4. Recent observations of the water vapour abundance in the Martian atmosphere during dust storm conditions revealed a high-altitude increase in atmospheric water vapour that was more pronounced at high northern latitudes5,6, as well as a decrease in the water column at low latitudes7,8. Here we present concurrent, high-resolution measurements of dust, water and semiheavy water (HDO) at the onset of a global dust storm, obtained by the NOMAD and ACS instruments onboard the ExoMars Trace Gas Orbiter. We report the vertical distribution of the HDO/H2O ratio (D/H) from the planetary boundary layer up to an altitude of 80 kilometres. Our findings suggest that before the onset of the dust storm, HDO abundances were reduced to levels below detectability at altitudes above 40 kilometres. This decrease in HDO coincided with the presence of water-ice clouds. During the storm, an increase in the abundance of H2O and HDO was observed at altitudes between 40 and 80 kilometres. We propose that these increased abundances may be the result of warmer temperatures during the dust storm causing stronger atmospheric circulation and preventing ice cloud formation, which may confine water vapour to lower altitudes through gravitational fall and subsequent sublimation of ice crystals3. The observed changes in H2O and HDO abundance occurred within a few days during the development of the dust storm, suggesting a fast impact of dust storms on the Martian atmosphere.
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