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- Bastard, P, et al.
(författare)
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Preexisting autoantibodies to type I IFNs underlie critical COVID-19 pneumonia in patients with APS-1
- 2021
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Ingår i: The Journal of experimental medicine. - : Rockefeller University Press. - 1540-9538 .- 0022-1007. ; 218:7
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Tidskriftsartikel (refereegranskat)abstract
- Patients with biallelic loss-of-function variants of AIRE suffer from autoimmune polyendocrine syndrome type-1 (APS-1) and produce a broad range of autoantibodies (auto-Abs), including circulating auto-Abs neutralizing most type I interferons (IFNs). These auto-Abs were recently reported to account for at least 10% of cases of life-threatening COVID-19 pneumonia in the general population. We report 22 APS-1 patients from 21 kindreds in seven countries, aged between 8 and 48 yr and infected with SARS-CoV-2 since February 2020. The 21 patients tested had auto-Abs neutralizing IFN-α subtypes and/or IFN-ω; one had anti–IFN-β and another anti–IFN-ε, but none had anti–IFN-κ. Strikingly, 19 patients (86%) were hospitalized for COVID-19 pneumonia, including 15 (68%) admitted to an intensive care unit, 11 (50%) who required mechanical ventilation, and four (18%) who died. Ambulatory disease in three patients (14%) was possibly accounted for by prior or early specific interventions. Preexisting auto-Abs neutralizing type I IFNs in APS-1 patients confer a very high risk of life-threatening COVID-19 pneumonia at any age.
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| 2. |
- Bruhn, Anders Dalhoff, et al.
(författare)
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Terrestrial Dissolved Organic Matter Mobilized From Eroding Permafrost Controls Microbial Community Composition and Growth in Arctic Coastal Zones
- 2021
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Ingår i: Frontiers in Earth Science. - : Frontiers Media SA. - 2296-6463. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Climate warming is accelerating erosion along permafrost-dominated Arctic coasts. This results in the additional supply of organic matter (OM) and nutrients into the coastal zone. In this study we investigate the impact of coastal erosion on the marine microbial community composition and growth rates in the coastal Beaufort Sea. Dissolved organic matter (DOM) derived from three representative glacial deposit types (fluvial, lacustrine, and moraine) along the Yukon coastal plain, Canada, were used as substrate to cultivate marine bacteria using a chemostat setup. Our results show that DOM composition (inferred from UV-Visible spectroscopy) and biodegradability (inferred from DOC concentration, bacterial production and respiration) significantly differ between the three glacial deposit types. DOM derived from fluvial and moraine types show clear terrestrial characteristics with low aromaticity (Sr: 0.63 ± 0.02 and SUVA254: 1.65 ± 0.06 L mg C−1 m−1 & Sr: 0.68 ± 0.01 and SUVA254: 1.17 ± 0.06 L mg C−1 m−1, respectively) compared to the lacustrine soil type (Sr: 0.71 ± 0.02 and SUVA254: 2.15 ± 0.05 L mg C−1 m−1). The difference in composition of DOM leads to the development of three different microbial communities. Whereas Alphaproteobacteria dominate in fluvial and lacustrine deposit types (67 and 87% relative abundance, respectively), Gammaproteobacteria is the most abundant class for moraine deposit type (88% relative abundance). Bacterial growth efficiency (BGE) is 66% for DOM from moraine deposit type, while 13 and 28% for DOM from fluvial and lacustrine deposit types, respectively. The three microbial communities therefore differ strongly in their net effect on DOM utilization depending on the eroded landscape type. The high BGE value for moraine-derived DOM is probably caused by a larger proportion of labile colorless DOM. These results indicate that the substrate controls marine microbial community composition and activities in coastal waters. This suggests that biogeochemical changes in the Arctic coastal zone will depend on the DOM character of adjacent deposit types, which determine the speed and extent of DOM mineralization and thereby carbon channeling into the microbial food web. We conclude that marine microbes strongly respond to the input of terrestrial DOM released by coastal erosion and that the landscape type differently influence marine microbes.
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| 3. |
- Duchemin, Wandrille, et al.
(författare)
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RecPhyloXML : a format for reconciled gene trees
- 2018
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 34:21, s. 3646-3652
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc. -along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Results: Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities.
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