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- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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- Bidartondo, Martin, et al.
(författare)
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Preserving accuracy in GenBank
- 2008
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Ingår i: Science. ; 319:5870
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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- Floriddia, Elisa M., et al.
(författare)
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Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Mature oligodendrocytes (MOLs) show transcriptional heterogeneity, the functional consequences of which are unclear. MOL heterogeneity might correlate with the local environment or their interactions with different neuron types. Here, we show that distinct MOL populations have spatial preference in the mammalian central nervous system (CNS). We found that MOL type 2 (MOL2) is enriched in the spinal cord when compared to the brain, while MOL types 5 and 6 (MOL5/6) increase their contribution to the OL lineage with age in all analyzed regions. MOL2 and MOL5/6 also have distinct spatial preference in the spinal cord regions where motor and sensory tracts run. OL progenitor cells (OPCs) are not specified into distinct MOL populations during development, excluding a major contribution of OPC intrinsic mechanisms determining MOL heterogeneity. In disease, MOL2 and MOL5/6 present different susceptibility during the chronic phase following traumatic spinal cord injury. Our results demonstrate that the distinct MOL populations have different spatial preference and different responses to disease.
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- Gluck-Thaler, Emile, et al.
(författare)
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Giant mobile elements : Agents of multivariate phenotypic evolution in fungi
- 2022
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Ingår i: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 32:5, s. R234-R236
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Fungal mobile genetic elements are typically small, vertically inherited, and are not known to encode adaptive traits. A new study documents HEPHAESTUS - a large, horizontally transferred, cargo-carrying mobile element that confers tolerance to several metals in fungi.
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- Jung, Christian, et al.
(författare)
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A comparison of very old patients admitted to intensive care unit after acute versus elective surgery or intervention
- 2019
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Ingår i: Journal of critical care. - : W B SAUNDERS CO-ELSEVIER INC. - 0883-9441 .- 1557-8615. ; 52, s. 141-148
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Tidskriftsartikel (refereegranskat)abstract
- Background: We aimed to evaluate differences in outcome between patients admitted to intensive care unit (ICU) after elective versus acute surgery in a multinational cohort of very old patients (80 years; VIP). Predictors of mortality, with special emphasis on frailty, were assessed.Methods: In total, 5063 VIPs were induded in this analysis, 922 were admitted after elective surgery or intervention, 4141 acutely, with 402 after acute surgery. Differences were calculated using Mann-Whitney-U test and Wilcoxon test. Univariate and multivariable logistic regression were used to assess associations with mortality.Results: Compared patients admitted after acute surgery, patients admitted after elective surgery suffered less often from frailty as defined as CFS (28% vs 46%; p < 0.001), evidenced lower SOFA scores (4 +/- 5 vs 7 +/- 7; p < 0.001). Presence of frailty (CFS >4) was associated with significantly increased mortality both in elective surgery patients (7% vs 12%; p = 0.01), in acute surgery (7% vs 12%; p = 0.02).Conclusions: VIPs admitted to ICU after elective surgery evidenced favorable outcome over patients after acute surgery even after correction for relevant confounders. Frailty might be used to guide clinicians in risk stratification in both patients admitted after elective and acute surgery.
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- Karamacoska, Diana, et al.
(författare)
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How are early‐career dementia researchers considered and supported on a national level by dementia plans and organizations? An overview of global policy approaches
- 2024
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Ingår i: Alzheimer's & Dementia. - 1552-5260 .- 1552-5279.
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTIONDespite representing an essential workforce, it is unclear how global policy efforts target early-career dementia researchers (ECDRs). Thus, this study aimed to provide an overview of policies through which ECDRs are considered and supported by dementia plans and organizations.METHODSG20 member states were evaluated for their national dementia plan alongside policies of leading dementia organizations. Data targeting support for ECDRs were extracted and subject to content analysis using inductive coding. Findings were categorized and narratively synthesized.RESULTSOnly China, Denmark, England, Greece, Northern Ireland, Scotland, Spain, and the United States mentioned ECDRs in their national plan. Additionally, 17 countries formalized ECDR support via dementia organizations. Support efforts included research funding, dissemination and networking, career development, and research advice.DISCUSSIONFew nations formally recognized ECDRs in dementia plans or through dementia organizations. To facilitate equal prospects for ECDRs, top-down approaches are urged to enhance and align their efforts.
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- Kluting, Kerri
(författare)
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Fungal molecular ecology in boreal forests and challenges associated with unidentified environmental DNA sequences
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Many fungi are characteristically difficult to observe and collect, making the process of documenting the world’s fungal diversity challenging. The vast majority of fungal species are undescribed. The use of DNA sequencing technologies has revolutionized the study of fungal diversity by facilitating the detection of new species, the investigation of community structure and dynamics, and the elucidation of evolutionary relationships. In this dissertation, I focus on filling in some of the many gaps in our understanding of fungal diversity and community ecology in boreal pine forests through the use of DNA sequence data. In the first half of this thesis, a metabarcoding approach is used to study the composition of fungal communities found in the soil of a Lithuanian coastal pine forest and in association with the bark beetle Tomicus piniperda in Swedish pine forests. In the second half, two different approaches are taken to describe taxa detected in environmental DNA. In paper I, I demonstrate how soil microhabitats, defined based on mineral vs organic soil type and root presence or absence, vary with respect to a suite of abiotic factors and shape fungal community composition belowground. These microhabitats support functionally and taxonomically distinct fungal communities and support the overall fungal diversity of the site through niche variation. In paper II, the relationships between a) the fungal communities found on and in bark beetles from forests that have been affected by forest fire and forests that have not, b) pine phloem that has been colonized by bark beetles and phloem that has not at two different post-colonization time points, and c) phloem chemical nutrients are described. In paper III, the diversity of species within the fungal class Archaeorhizomycetes in the soil of a Swedish pine forest was studied, and two new species are described using an integrative taxonomic approach that relies on environmental DNA sequence data as taxonomical evidence. Finally, in paper IV, a new class is described to accommodate a lineage previously detected in environmental DNA, and its first known species is described based on isolates collected during the study of paper III, one of which serves as the type specimen.
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