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Sökning: WFRF:(Lim J) > Sveriges Lantbruksuniversitet

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2.
  • Hyde, K. D., et al. (författare)
  • Global consortium for the classification of fungi and fungus-like taxa
  • 2023
  • Ingår i: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
  • 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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3.
  • Klionsky, Daniel J., et al. (författare)
  • Guidelines for the use and interpretation of assays for monitoring autophagy
  • 2012
  • Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
  • Forskningsöversikt (refereegranskat)abstract
    • In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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  • Tedersoo, L., et al. (författare)
  • The Global Soil Mycobiome consortium dataset for boosting fungal diversity research
  • 2021
  • Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 111
  • Tidskriftsartikel (refereegranskat)abstract
    • Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The dataset comprises 722,682 fungal operational taxonomic units (OTUs) derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents. The plots are supplied with geographical and edaphic metadata. The OTUs are taxonomically and functionally assigned to guilds and other functional groups. The entire dataset has been corrected by excluding chimeras, index-switch artefacts and potential contamination. The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data. The GSMc dataset is available over the PlutoF repository.
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  • Kattge, Jens, et al. (författare)
  • TRY plant trait database - enhanced coverage and open access
  • 2020
  • Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
  • Tidskriftsartikel (refereegranskat)abstract
    • Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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6.
  • Bogota-Angel, G., et al. (författare)
  • Climate and geological change as drivers of Mauritiinae palm biogeography
  • 2021
  • Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 48:5, s. 1001-1022
  • Tidskriftsartikel (refereegranskat)abstract
    • Aim Forest composition and distribution are determined by a myriad of factors, including climate. As models of tropical rain forest, palms are often used as indicator taxa, particularly the Mauritiinae. We question, what characterizes the Mauritiinae pollen in the global fossil record? And when did the Mauritiinae become endemic to South America? Location Global tropics. Taxon Mauritiinae palms (Arecaceae: Lepidocaryeae). Methods Pollen trait data from extinct and extant Mauritiinae pollen were generated from light-, scanning-, and transmission electron microscopy. Statistical morphometric analysis was used to define species and their relationships to other Mauritiinae. We also compiled a comprehensive pollen database for extinct and extant Mauritiinae and mapped their global geographical distribution from Late Cretaceous to present, using GBIF and fossil data. Results Our morphometric analysis identified 18 species (11 extinct and seven extant), all exhibiting exine indentations, a synapomorphy of the subtribe. The fossil taxa and early divergent extant Lepidocaryum are all monosulcate, whereas the extant Mauritia and Mauritiella species are all monoulcerate. Paleobiogeographical maps of fossil Mauritiinae pollen occurrences suggest the taxon originated in equatorial Africa during the Cretaceous, and expanded their range to South America, and to India in the Paleocene. Range retraction started in the early Eocene with extirpation from India, and reduction in diversity in Africa culminating at the Eocene-Oligocene Transition (EOT). In contrast, in South America, the distribution is maintained, and since the Neogene Mauritiinae palms are mostly restricted to swampy, lowland habitats. Main conclusions Morphometric analysis shows that since their origin Mauritiinae pollen are relatively species poor, and Mauritiidites resembles Lepidocaryum. We also conclude that the biogeographical history of the Mauriitinae and, by extension, tropical forests was strongly affected by global climatic cooling events. In particular, the climate change at the EOT was a fundamental determinant of current tropical forest distribution.
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  • Serikova, Svetlana, et al. (författare)
  • High carbon emissions from thermokarst lakes of Western Siberia
  • 2019
  • Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • The Western Siberia Lowland (WSL), the world's largest permafrost peatland, is of importance for understanding the high-latitude carbon (C) cycle and its response to climate change. Warming temperatures increase permafrost thaw and production of greenhouse gases. Also, permafrost thaw leads to the formation of lakes which are hotspots for atmospheric C emissions. Although lakes occupy similar to 6% of WSL, lake C emissions from WSL remain poorly quantified. Here we show high C emissions from lakes across all permafrost zones of WSL. The C emissions were especially high in shoulder seasons and in colder permafrost-rich regions. The total C emission from permafrost-affected lakes of WSL equals similar to 12 +/- 2.6 Tg C yr(-1) and is 2-times greater than region's C export to the Arctic coast. The results show that C emission from WSL lakes is a significant component in the high-latitude C cycle, but also suggest that C emission may decrease with warming.
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9.
  • Tedersoo, Leho, et al. (författare)
  • Global patterns in endemicity and vulnerability of soil fungi.
  • 2022
  • Ingår i: Global change biology. - : Wiley. - 1365-2486 .- 1354-1013. ; 28:22, s. 6696-6710
  • Tidskriftsartikel (refereegranskat)abstract
    • Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
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