| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
- Schneider, K. M., et al.
(författare)
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Gut microbiota depletion exacerbates cholestatic liver injury via loss of FXR signalling
- 2021
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Ingår i: Nature Metabolism. - : Springer Science and Business Media LLC. - 2522-5812. ; 3:9, s. 1228-1241
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Tidskriftsartikel (refereegranskat)abstract
- Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease of unknown aetiology for which there are no approved therapeutic options. Patients with PSC display changes in gut microbiota and in bile acid (BA) composition; however, the contribution of these alterations to disease pathogenesis remains controversial. Here we identify a role for microbiota-dependent changes in BA synthesis that modulates PSC pathophysiology. In a genetic mouse model of PSC, we show that loss of microbiota-mediated negative feedback control of BA synthesis results in increased hepatic BA concentrations, disruption of bile duct barrier function and, consequently, fatal liver injury. We further show that these changes are dependent on decreased BA signalling to the farnesoid X receptor, which modulates the activity of the rate-limiting enzyme in BA synthesis, CYP7A1. Moreover, patients with advanced stages of PSC show suppressed BA synthesis as measured by serum C4 levels, which is associated with poor disease prognosis. Our preclinical data highlight the microbiota-dependent dynamics of BA metabolism in cholestatic liver disease, which could be important for future therapies targeting BA and gut microbiome interactions, and identify C4 as a potential biomarker to functionally stratify patients with PSC and predict disease outcomes. Patients with primary sclerosing cholangitis (PSC), a chronic cholestatic liver disease, display changes in the gut microbiota and in bile acid composition. Schneider, Candels and colleagues identify a role for microbiota-dependent regulation of bile acid synthesis through farnesoid X receptor signalling, which is relevant for PSC disease progression.
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| 3. |
- Divakar, Pradeep K., et al.
(författare)
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Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi
- 2015
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 208:4, s. 1217-1226
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Tidskriftsartikel (refereegranskat)abstract
- We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.
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| 4. |
- Lakka, A., et al.
(författare)
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The Cross-Polar Cap Saturation in GUMICS-4 During High Solar Wind Driving
- 2018
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Ingår i: Journal of Geophysical Research - Space Physics. - 2169-9380 .- 2169-9402. ; 123:5, s. 3320-3332
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Tidskriftsartikel (refereegranskat)abstract
- It is well known that the Earth's ionospheric cross‐polar cap potential (CPCP) saturates as a response to the solar wind (SW) driver especially when the level of driving is high and the interplanetary magnetic field is oriented southward. Moreover, previous studies have shown that the upstream Alfvén Mach number may be an important factor in the saturation effect. While the CPCP is often viewed as a measure of the SW‐magnetosphere‐ionosphere coupling, the processes associated with the nonlinearity of the coupling remain an open issue. We use fourth edition of the Grand Unified Magnetosphere‐Ionosphere Coupling Simulation (GUMICS‐4) and artificial SW data to mimic weak and strong driving in order to study the CPCP response to a wide range of interplanetary magnetic field magnitudes (3.5–30 nT) and upstream Alfvén Mach number values (1.2–22). The results provide the first overview of the CPCP saturation in GUMICS‐4 and show that the onset of saturation is strongly dependent on the upstream Alfvén Mach number and the physical processes responsible for the saturation effect might take place both in the Earth's magnetosheath and in the upstream SW.
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| 5. |
- Myllys, M., et al.
(författare)
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Plasma properties of suprathermal electrons near comet 67P/Churyumov-Gerasimenko with Rosetta
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP SCIENCES S A. - 0004-6361 .- 1432-0746. ; 630
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Tidskriftsartikel (refereegranskat)abstract
- Context: The Rosetta spacecraft escorted comet 67P/Churyumov-Gerasimenko from 2014 to September 2016. The mission provided in situ observations of the cometary plasma during different phases of the cometary activity, which enabled us to better understand its evolution as a function of heliocentric distance.Aims: In this study, different electron populations, called warm and hot, observed by the Ion and Electron Sensor (IES) of the Rosetta Plasma Consortium (RPC) are investigated near the comet during the escorting phase of the Rosetta mission.Methods: The estimates for the suprathermal electron densities and temperatures were extracted using IES electron data by fitting a double-kappa function to the measured velocity distributions. The fitting results were validated using observations from other RPC instruments. We give upgraded estimates for the warm and hot population densities compared to values previously shown in literature.Results: The fitted density and temperature estimates for both electron populations seen by IES are expressed as a function of heliocentric distance to study their evolution with the cometary activity. In addition, we studied the dependence between the electron properties and cometocentric distance.Conclusions: We observed that when the neutral outgassing rate of the nucleus is high (i.e., near perihelion) the suprathermal electrons are well characterized by a double-kappa distribution. In addition, warm and hot populations show a significant dependence with the heliocentric distance. The populations become clearly denser near perihelion while their temperatures are observed to remain almost constant. Moreover, the warm electron population density is shown to be strongly dependent on the radial distance from the comet. Finally, based on our results we reject the hypothesis that hot electron population seen by IES consists of solely suprathermal (halo) solar wind electrons, while we suggest that the hot electron population mainly consists of solar wind thermal electrons that have undergone acceleration near the comet.
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| 6. |
- Krieger, Ulrich K., et al.
(författare)
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A reference data set for validating vapor pressure measurement techniques : homologous series of polyethylene glycols
- 2018
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 11:1, s. 49-63
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Tidskriftsartikel (refereegranskat)abstract
- To predict atmospheric partitioning of organic compounds between gas and aerosol particle phase based on explicit models for gas phase chemistry, saturation vapor pressures of the compounds need to be estimated. Estimation methods based on functional group contributions require training sets of compounds with well-established saturation vapor pressures. However, vapor pressures of semivolatile and low-volatility organic molecules at atmospheric temperatures reported in the literature often differ by several orders of magnitude between measurement techniques. These discrepancies exceed the stated uncertainty of each technique which is generally reported to be smaller than a factor of 2. At present, there is no general reference technique for measuring saturation vapor pressures of atmospherically relevant compounds with low vapor pressures at atmospheric temperatures. To address this problem, we measured vapor pressures with different techniques over a wide temperature range for intercomparison and to establish a reliable training set. We determined saturation vapor pressures for the homologous series of polyethylene glycols (H-(O-CH2-CH2)(n)-OH) for n = 3 to n = 8 ranging in vapor pressure at 298 K from 10(-7) to 5 x 10(-2) Pa and compare them with quantum chemistry calculations. Such a homologous series provides a reference set that covers several orders of magnitude in saturation vapor pressure, allowing a critical assessment of the lower limits of detection of vapor pressures for the different techniques as well as permitting the identification of potential sources of systematic error. Also, internal consistency within the series allows outlying data to be rejected more easily. Most of the measured vapor pressures agreed within the stated uncertainty range. Deviations mostly occurred for vapor pressure values approaching the lower detection limit of a technique. The good agreement between the measurement techniques (some of which are sensitive to the mass accommodation coefficient and some not) suggests that the mass accommodation coefficients of the studied compounds are close to unity. The quantum chemistry calculations were about 1 order of magnitude higher than the measurements. We find that extrapolation of vapor pressures from elevated to atmospheric temperatures is permissible over a range of about 100 K for these compounds, suggesting that measurements should be performed best at temperatures yielding the highest-accuracy data, allowing subsequent extrapolation to atmospheric temperatures.
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| 7. |
- Miadlikowska, Jolanta, et al.
(författare)
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A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.
- 2014
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1095-9513 .- 1055-7903. ; 79:Online 18 April 2014, s. 132-168
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Tidskriftsartikel (refereegranskat)abstract
- The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 635 newly generated and 3307 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.
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| 8. |
- Myllys, L, et al.
(författare)
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High cyanobiont selectivity of epiphytic lichens in old growth boreal forest of Finland
- 2007
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Ingår i: New Phytologist. - : Wiley. - 1469-8137 .- 0028-646X. ; 173:3, s. 621-629
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Tidskriftsartikel (refereegranskat)abstract
- • Here, cyanobiont selectivity of epiphytic lichen species was examined in an old growth forest area in Finland. • Samples of the eight lichen species were collected from the same aspen (Populus tremula) and adjacent aspens in the same stand. The cyanobionts of these samples were compared with free and symbiotic Nostoc obtained from other habitats and geographic regions. • Our results, based on the phylogenetic analysis of a partial small subunit of the ribosomal DNA (16S rDNA) and the rbcLX gene complex did not show any correlation with the geographic origin of the samples at any spatial scale. Instead, there was a correlation between the cyanobionts and the alleged taxonomy of their mycobionts. • The results indicate that the lichen species examined are highly selective towards their cyanobiont partners. Only Lobaria pulmonaria proved to be more flexible, being able to associate with a wide range of Nostoc. A same Nostoc strain was found to form associations with taxonomically unrelated lichens indicating that the cyanobiont–mycobiont associations as a whole were not highly specific in the examined species.
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| 9. |
- Wellbrock, A., et al.
(författare)
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Observations of a Solar Energetic Particle Event from Inside and Outside the Coma of Comet 67P
- 2022
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Ingår i: Journal of Geophysical Research - Space Physics. - : John Wiley & Sons. - 2169-9380 .- 2169-9402. ; 127:12
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Tidskriftsartikel (refereegranskat)abstract
- We analyze observations of an SEP event at Rosetta’s target comet 67P/Churyumov-Gerasimenko during March 6th-10th 2015. The comet was 2.15AU from the Sun, with the Rosetta spacecraft approximately 70km from the nucleus placing it deep inside the comet’s coma and allowing us to study its response. The Eastern flank of an ICME also encountered Rosetta on March 6th and 7th. Rosetta’s RPC data indicate increases in ionization rates, and cometary water group pickup ions exceeding 1keV. Increased charge exchange reactions between solar wind ions and cometary neutrals also indicate increased upstream neutral populations consistent with enhanced SEP induced surface activity. In addition, the most intense parts of the event coincide with observations interpreted as an infant cometary bow shock, indicating that the SEPs may have enhanced the formation and/or intensified the observations. These solar transient events may also have pushed the cometopause closer to the nucleus.We track and discuss characteristics of the SEP event using remote observations by SOHO, WIND and GOES at the Sun, in-situ measurements at STEREO A, Mars and Rosetta, and ENLIL modeling. Based on its relatively prolonged duration, gradual and anisotropic nature and broad angular spread in the heliosphere, we determine the main particle acceleration source to be a distant ICME which emerged from the Sun on March 6th 2015 and was detected locally in the Martian ionosphere but was never encountered by 67P directly. The ICME’s shock produced SEPs for several days which traveled to the in-situ observation sites via magnetic field line connections.
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