| 62851. |
- Kõljalg, Urmas, et al.
(författare)
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Digital identifiers for fungal species
- 2016
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 352:6290, s. 1182-1183
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Tidskriftsartikel (refereegranskat)
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| 62852. |
- Kõljalg, U., et al.
(författare)
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The taxon hypothesis paradigm—On the unambiguous detection and communication of taxa
- 2020
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Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:12
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Tidskriftsartikel (refereegranskat)abstract
- Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
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| 62853. |
- Kõljalg, Urmas, et al.
(författare)
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Towards a unified paradigm for sequence-based identification of fungi.
- 2013
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Ingår i: Molecular ecology. - : Wiley. - 1365-294X .- 0962-1083. ; 22:21, s. 5271-7
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
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| 62854. |
- Kõljalg, Urmas, et al.
(författare)
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UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi
- 2005
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 166:3, s. 1063-1068
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Tidskriftsartikel (refereegranskat)abstract
- Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using BLAST n, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a BLAST search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URLhttp://unite.zbi.ee.
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| 62855. |
- Koljonen, Tuula, et al.
(författare)
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Evaluating the enactment of a scripted teaching model
- 2023
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Ingår i: Proceedings of the Thirteenth Congress of the European Society for Research in Mathematics Education (CERME13). - Budapest : Eötvös Loránd University and ERME.
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Konferensbidrag (refereegranskat)
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| 62856. |
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| 62857. |
- Kollander, B., et al.
(författare)
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Inorganic arsenic in food products on the Swedish market and a risk-based intake assessment
- 2019
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697. ; 672, s. 525-535
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Tidskriftsartikel (refereegranskat)abstract
- Inorganic arsenic (iAs) and total arsenic (tAs) were determined in common food from the Swedish market. Special focus was on rice, fish and shellfish products. For the speciation of iAs the European standard EN:16802 based on anion exchange chromatography coupled to ICP-MS was used. The two market basket food groups cereals (including rice), and sweets and condiments (a mixed group of sugar, sweets, tomato ketchup and dressings), contained the highest iAs levels (means 9 and 7 mu g iAs/kg), whereas other food groups, including fish, did not exceed 2 mu g iAs/kg. Varying levels of iAs were found in separate samples of tomato ketchup, 2.4-26 mu g/kg, and is suggested to be one reason of the rather high average level of iAs in the food group sweets and condiments. Some specific food products revealed iAs levels much higher, i.e. lice crackers 152 and Norway lobster 89 mu g iAs/kg. The intake of iAs via food was estimated by data from two national consumption surveys, performed in 2010-11 (1797 adults) and 2003 (2259 children). The estimated median iAs intakes in adults and children were 0.047 and 0.095 mu g/kg body weight and day, respectively. The iAs intake for rice eaters was about 1.4 times higher than for non-rice eaters. Validation of the consumption survey-based iAs intake, using food purchase and market basket data mainly from 2015, resulted in a per capita intake of a similar magnitude, i.e. 0.056 mu g/kg body weight and day. The estimated cancer risk for adults using low-dose linear extrapolation is <1 per 100,000 per year. (C) 2019 Elsevier B.V. All rights reserved.
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| 62858. |
- Kollberg, Gittan, 1963, et al.
(författare)
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A novel homozygous RRM2B missense mutation in association with severe mtDNA depletion.
- 2009
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Ingår i: Neuromuscular disorders : NMD. - : Elsevier BV. - 0960-8966. ; 19:2, s. 147-50
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Tidskriftsartikel (refereegranskat)abstract
- This report describes two brothers, both deceased in infancy, with severe depletion of mitochondrial DNA (mtDNA) in muscle tissue. Both had feeding difficulties, failure to thrive, severe muscular hypotonia and lactic acidosis. One of the boys developed a renal proximal tubulopathy. A novel homozygous c.686 G-->T missense mutation in the RRM2B gene, encoding the p53-inducible ribonucleotide reductase subunit (p53R2), was identified. This is the third report on mutations in RRM2B associated with severe mtDNA depletion, which further highlights the importance of de novo synthesis of deoxyribonucleotides (dNTPs) for mtDNA maintenance.
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| 62859. |
- Kollberg, Gittan, 1963, et al.
(författare)
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Antisense oligonucleotide therapeutics for iron-sulphur cluster deficiency myopathy.
- 2009
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Ingår i: Neuromuscular disorders : NMD. - : Elsevier BV. - 1873-2364 .- 0960-8966. ; 19:12, s. 833-6
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Tidskriftsartikel (refereegranskat)abstract
- Iron-sulphur cluster deficiency myopathy is caused by a deep intronic mutation in ISCU resulting in inclusion of a cryptic exon in the mature mRNA. ISCU encodes the iron-sulphur cluster assembly protein IscU. Iron-sulphur clusters are essential for most basic redox transformations including the respiratory-chain function. Most patients are homozygous for the mutation with a phenotype characterized by a non-progressive myopathy with childhood onset of early fatigue, dyspnoea and palpitation on trivial exercise. A more severe phenotype with early onset of a slowly progressive severe muscle weakness, severe exercise intolerance and cardiomyopathy is caused by a missense mutation in compound with the intronic mutation. Treatment of cultured fibroblasts derived from three homozygous patients with an antisense phosphorodiamidate morpholino oligonucleotide for 48 h resulted in 100% restoration of the normal splicing pattern. The restoration was stable and after 21 days the correctly spliced mRNA still was the dominating RNA species.
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| 62860. |
- Kollberg, Gittan, 1963, et al.
(författare)
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Cardiomyopathy and exercise intolerance in muscle glycogen storage disease 0.
- 2007
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Ingår i: The New England journal of medicine. - 1533-4406. ; 357:15, s. 1507-14
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Tidskriftsartikel (refereegranskat)abstract
- Storage of glycogen is essential for glucose homeostasis and for energy supply during bursts of activity and sustained muscle work. We describe three siblings with profound muscle and heart glycogen deficiency caused by a homozygous stop mutation (R462-->ter) in the muscle glycogen synthase gene. The oldest brother died from sudden cardiac arrest at the age of 10.5 years. Two years later, an 11-year-old brother showed muscle fatigability, hypertrophic cardiomyopathy, and an abnormal heart rate and blood pressure while exercising; a 2-year-old sister had no symptoms. In muscle-biopsy specimens obtained from the two younger siblings, there was lack of glycogen, predominance of oxidative fibers, and mitochondrial proliferation. Glucose tolerance was normal.
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