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- Hyde, K. D., et al.
(författare)
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Global consortium for the classification of fungi and fungus-like taxa
- 2023
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Ingår i: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Tidskriftsartikel (refereegranskat)abstract
- The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, 'to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation', or 'are there too many genera in the Boletales?' and even more importantly, 'what should be done with the tremendously diverse 'dark fungal taxa?' There are undeniable differences in mycologists' perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others' work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
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| 2. |
- Karlsson, A. M., et al.
(författare)
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Prosodic Phrasing in Tonal and Non-tonal Dialects of Kammu
- 2007
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Ingår i: Proceedings of the 16th International congress of phonetic sciences. ; , s. 1309-1312
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Konferensbidrag (refereegranskat)abstract
- Kammu, a Mon-Khmer language spoken in Northern Laos, is a language that has developed lexical tones rather recently, from the point of view of language history. One of the main dialects of this language is a tone language with high or low tone on each syllable, while the other main dialect lacks lexical tones. The dialects differ only marginally in other respects. This type of language material allows us to investigate how the existence of lexical tones in a language influences the use of intonation, especially as a signal for focus and phrasing. We performed an introductory study of tonal means of phrasing in the tonal and non-tonal dialects of Kammu. As expected, we do find differences in boundary signaling. In both dialects, we found differences between (pragmatically) marked and unmarked boundaries. At marked phrase boundaries we find signaling of focus and of some expressive meanings. The difference between the two dialects is in the functional load of the intonational gestures. Thus, pragmatically marked boundaries are assigned high pitch in the tonal dialect, while in the non-tonal dialect it is a pitch fall that has high pragmatic load.
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| 5. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK)
- 2018
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Ingår i: Mycokeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :28, s. 65-82
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Tidskriftsartikel (refereegranskat)abstract
- Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS bar-code sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.
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| 6. |
- Svantesson, Anna, et al.
(författare)
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A mathematical model of the Pyrosequencing reaction system
- 2004
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Ingår i: Biophysical Chemistry. - : Elsevier BV. - 0301-4622 .- 1873-4200. ; 110:02-jan, s. 129-145
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Tidskriftsartikel (refereegranskat)abstract
- The Pyrosequencing(TM) technology is a newly developed DNA sequencing method that monitors DNA nucleotide incorporation in real-time. A set of coupled enzymatic reactions, together with bioluminescence, detects incorporated nucleotides in the form of light pulses, yielding a characteristic light profile. In this study, a biochemical model of the Pyrosequencing reaction system is suggested and implemented. The model is constructed utilizing an assumption of irreversible Michaelis-Menten rate equations and a constant incorporation efficiency. The kinetic parameters are studied and values are chosen to obtain as reliable simulation results as possible. The results presented here show strong resemblance with real experiments. The model is able to capture the dynamics of a single light pulse with great accuracy, as well as the overall characteristics of a whole pyrogram(TM). The plus- and minus-shift effects observed in experiments are successfully reconstructed by two constant efficiency factors. Furthermore, pulse broadening can partly be explained by apyrase inhibition and successive dilution.
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