| 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. |
- Spirin, Viacheslav, et al.
(författare)
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The genus Fomitopsis (Polyporales, Basidiomycota) reconsidered
- 2024
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Ingår i: STUDIES IN MYCOLOGY. - 0166-0616 .- 1872-9797. ; :107, s. 149-249
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Tidskriftsartikel (refereegranskat)abstract
- Based on seven- and three-gene datasets, we discuss four alternative approaches for a reclassification of Fomitopsidaceae (Polyporales, Basidiomycota). After taking into account morphological diversity in the family, we argue in favour of distinguishing three genera only, viz. Anthoporia, Antrodia and Fomitopsis. Fomitopsis becomes a large genus with 128 accepted species, containing almost all former Fomitopsis spp. and most species formerly placed in Antrodia, Daedalea and Laccocephalum. Genera Buglossoporus, Cartilosoma, Daedalea, Melanoporia, Neolentiporus, alongside twenty others, are treated as synonyms of Fomitopsis. This generic scheme allows for morphologically distinct genera in Fomitopsidaceae, unlike other schemes we considered. We provide arguments for retaining Fomitopsis and suppressing earlier (Daedalea, Caloporus) or simultaneously published generic names (Piptoporus) considered here as its synonyms. Taxonomy of nine species complexes in the genus is revised based on ITS, ITS + TEF1, ITS + TEF1 + RPB1 and ITS + TEF1 + RPB2 datasets. In total, 17 species are described as new to science, 26 older species are reinstated and 26 currently accepted species names are relegated to synonymy. A condensed identification key for all accepted species in the genus is provided.
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| 3. |
- Elands, B. H. M., et al.
(författare)
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Biocultural diversity : A novel concept to assess human-nature interrelations, nature conservation and stewardship in cities
- 2019
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Ingår i: Urban Forestry & Urban Greening. - : Elsevier BV. - 1618-8667 .- 1610-8167. ; 40, s. 29-34
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Forskningsöversikt (refereegranskat)abstract
- Biocultural diversity is an evolving perspective for studying the interrelatedness between people and their natural environment, not only in ecoregional hotspots and cultural landscapes, but also in urban green spaces. Developed in the 1990s in order to denote the diversity of life in all its manifestations. biological, cultural and linguistic. co-evolving within complex socio-ecological systems such as cities, biocultural diversity was identified in the GREEN SURGE project as a response to recent challenges cities face. Most important challenges are the loss of nature and degradation of ecosystems in and around cities as well as an alienation of urban residents from and loss of interaction with nature. The notion of biocultural diversity is dynamic in nature and takes local values and practices of relating to biodiversity of different cultural groups as a starting point for sustainable living with biodiversity. The issue is not only how to preserve or restore biocultural practices and values, but also how to modify, adapt and create biocultural diversity in ways that resonate with urban transformations. As future societies will largely diverge from today's societies, the cultural perspective on living with (urban) nature needs careful reconsideration. Biocultural diversity is not conceived as a definite concept providing prescriptions of what to see and study, but as a reflexive and sensitising concept that can be used to assess the different values and knowledge of people that reflect how they live with biodiversity. This short communication paper introduces a conceptual framework for studying the multi-dimensional features of biocultural diversity in cities along the three key dimensions of materialized, lived and stewardship, being departure points from which biocultural diversity can be studied.
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| 4. |
- Niemela, P, et al.
(författare)
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Sensitive and specific enzymatic assay for the determination of precursor forms of prostate-specific antigen after an activation step
- 2002
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Ingår i: Clinical Chemistry. - 0009-9147. ; 48:8, s. 1257-1264
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Tidskriftsartikel (refereegranskat)abstract
- Background: The proteome of the serine protease prostate-specific antigen (PSA) and its enzymatic properties have been clarified only recently. We have developed a specific and sensitive method for the measurement of active PSA and used it to measure proPSA in blood. Methods: We used the synthetic peptide KGISSQY, which possesses a PSA-specific cleavage site, as substrate. To ascertain the specificity of the assay, we used an anti-PSA monoclonal antibody that captures known forms of PSA. An activation step enabled us to measure proPSA by converting it to mature, active PSA. Results: The detection limit of the optimized assay was 0.5 mug/L. In blood samples from patients, the activation step substantially increased the concentration of active PSA, thus showing the presence of proPSA in the samples. ProPSA was 0-79% (median, 45%) of the amount of free PSA in 15 samples with total PSA concentrations of 5.3-423 mug/L. In samples obtained from three benign prostatic hyperplasia (BPH) patients after transurethal resection of the prostate, no significant increase in activity was detected after the activation step, thus showing that proPSA was not a portion of free PSA in plasma of BPH patients. Conclusions: Proforms of PSA are a considerable fraction of free PSA in the blood of patients with increased total PSA. The approach described can be used to study the diagnostic value of proPSA and active PSA in patients with BPH and prostate cancer.
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