| 1. |
- Brenninkmeijer, C. A. M., et al.
(författare)
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Civil Aircraft for the regular investigation of the atmosphere based on an instrumented container: The new CARIBIC system
- 2007
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Ingår i: Atmospheric Chemistry and Physics. - 1680-7324. ; 7:18, s. 4953-4976
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Tidskriftsartikel (refereegranskat)abstract
- An airfreight container with automated instruments for measurement of atmospheric gases and trace compounds was operated on a monthly basis onboard a Boeing 767-300 ER of LTU International Airways during long-distance flights from 1997 to 2002 (CARIBIC, Civil Aircraft for Regular Investigation of the Atmosphere Based on an Instrument Container, http://www.caribic-atmospheric.com). Subsequently a more advanced system has been developed, using a larger capacity container with additional equipment and an improved inlet system. CARIBIC phase #2 was implemented on a new long-range aircraft type Airbus A340-600 of the Lufthansa German Airlines (Star Alliance) in December 2004, creating a powerful flying observatory. The instrument package comprises detectors for the measurement of O-3, total and gaseous H2O, NO and NOy, CO, CO2, O-2, Hg, and number concentrations of sub-micrometer particles (>4 nm, >12 nm, and >18 nm diameter). Furthermore, an optical particle counter (OPC) and a proton transfer mass spectrometer (PTR-MS) are incorporated. Aerosol samples are collected for analysis of elemental composition and particle morphology after flight. Air samples are taken in glass containers for laboratory analyses of hydrocarbons, halocarbons and greenhouse gases (including isotopic composition of CO2) in several laboratories. Absorption tubes collect oxygenated volatile organic compounds. Three differential optical absorption spectrometers (DOAS) with their telescopes mounted in the inlet system measure atmospheric trace gases such as BrO, HONO, and NO2. A video camera mounted in the inlet provides information about clouds along the flight track. The flying observatory, its equipment and examples of measurement results are reported.
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| 2. |
- Schebb, N. H., et al.
(författare)
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Formation, Signaling and Occurrence of Specialized Pro-Resolving Lipid Mediators-What is the Evidence so far?
- 2022
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Ingår i: Frontiers in Pharmacology. - : Frontiers Media SA. - 1663-9812. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Formation of specialized pro-resolving lipid mediators (SPMs) such as lipoxins or resolvins usually involves arachidonic acid 5-lipoxygenase (5-LO, ALOX5) and different types of arachidonic acid 12- and 15-lipoxygenating paralogues (15-LO1, ALOX15; 15-LO2, ALOX15B; 12-LO, ALOX12). Typically, SPMs are thought to be formed via consecutive steps of oxidation of polyenoic fatty acids such as arachidonic acid, eicosapentaenoic acid or docosahexaenoic acid. One hallmark of SPM formation is that reported levels of these lipid mediators are much lower than typical pro-inflammatory mediators including the monohydroxylated fatty acid derivatives (e.g., 5-HETE), leukotrienes or certain cyclooxygenase-derived prostaglandins. Thus, reliable detection and quantification of these metabolites is challenging. This paper is aimed at critically evaluating i) the proposed biosynthetic pathways of SPM formation, ii) the current knowledge on SPM receptors and their signaling cascades and iii) the analytical methods used to quantify these pro-resolving mediators in the context of their instability and their low concentrations. Based on current literature it can be concluded that i) there is at most, a low biosynthetic capacity for SPMs in human leukocytes. ii) The identity and the signaling of the proposed G-protein-coupled SPM receptors have not been supported by studies in knock-out mice and remain to be validated. iii) In humans, SPM levels were neither related to dietary supplementation with their omega-3 polyunsaturated fatty acid precursors nor were they formed during the resolution phase of an evoked inflammatory response. iv) The reported low SPM levels cannot be reliably quantified by means of the most commonly reported methodology. Overall, these questions regarding formation, signaling and occurrence of SPMs challenge their role as endogenous mediators of the resolution of inflammation.
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| 3. |
- Janouskovec, Jan, et al.
(författare)
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A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction
- 2017
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 27:23, s. 3717-3724.e5
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Tidskriftsartikel (refereegranskat)abstract
- The origin of eukaryotic cells represents a key transition in cellular evolution and is closely tied to outstanding questions about mitochondrial endosymbiosis [1, 2]. For example, gene-rich mitochondrial genomes are thought to be indicative of an ancient divergence, but this relies on unexamined assumptions about endosymbiont-to-host gene transfer [3-5]. Here, we characterize Ancoracysta twista, a new predatory flagellate that is not closely related to any known lineage in 201-protein phylogenomic trees and has a unique morphology, including a novel type of extrusome (ancoracyst). The Ancoracysta mitochondrion has a gene-rich genome with a coding capacity exceeding that of all other eukaryotes except the distantly related jakobids and Diphylleia, and it uniquely possesses heterologous, nucleus-, and mitochondrion-encoded cytochrome c maturase systems. To comprehensively examine mitochondrial genome reduction, we also assembled mitochondrial genomes from picozoans and colponemids and re-annotated existing mitochondrial genomes using hidden Markov model gene profiles. This revealed over a dozen previously overlooked mitochondrial genes at the level of eukaryotic supergroups. Analysis of trends over evolutionary time demonstrates that gene transfer to the nucleus was non-linear, that it occurred in waves of exponential decrease, and that much of it took place comparatively early, massively independently, and with lineage-specific rates. This process has led to differential gene retention, suggesting that gene-rich mitochondrial genomes are not a product of their early divergence. Parallel transfer of mitochondrial genes and their functional replacement by new nuclear factors are important in models for the origin of eukaryotes, especially as major gaps in our knowl-edge of eukaryotic diversity at the deepest level remain unfilled.
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| 4. |
- Janouškovec, Jan, et al.
(författare)
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Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:2, s. E171-E180
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Tidskriftsartikel (refereegranskat)abstract
- Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an early-branching position of Noctiluca, monophyly of thecate (plate-bearing) dinoflagellates, and paraphyly of athecate ones. This represents unambiguous phylogenetic evidence for a single origin of the group's cellulosic theca, which we show coincided with a radiation of cellulases implicated in cell division. By integrating dinoflagellate molecular, fossil, and biogeochemical evidence, we propose a revised model for the evolution of thecal tabulations and suggest that the late acquisition of dinosterol in the group is inconsistent with dinoflagellates being the source of this biomarker in pre-Mesozoic strata. Three distantly related, fundamentally nonphotosynthetic dinoflagellates, Noctiluca, Oxyrrhis, and Dinophysis, contain cryptic plastidial metabolisms and lack alternative cytosolic pathways, suggesting that all free-living dinoflagellates are metabolically dependent on plastids. This finding led us to propose general mechanisms of dependency on plastid organelles in eukaryotes that have lost photosynthesis; it also suggests that the evolutionary origin of bioluminescence in nonphotosynthetic dinoflagellates may be linked to plastidic tetrapyrrole biosynthesis. Finally, we use our phylogenetic framework to show that dinoflagellate nuclei have recruited DNA-binding proteins in three distinct evolutionary waves, which included two independent acquisitions of bacterial histone-like proteins.
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| 5. |
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| 6. |
- Tubiana, Luca, et al.
(författare)
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Topology in soft and biological matter
- 2024
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Ingår i: Physics reports. - : Elsevier. - 0370-1573 .- 1873-6270. ; 1075, s. 1-137
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Forskningsöversikt (refereegranskat)abstract
- The last years have witnessed remarkable advances in our understanding of the emergence and consequences of topological constraints in biological and soft matter. Examples are abundant in relation to (bio)polymeric systems and range from the characterization of knots in single polymers and proteins to that of whole chromosomes and polymer melts. At the same time, considerable advances have been made in the description of the interplay between topological and physical properties in complex fluids, with the development of techniques that now allow researchers to control the formation of and interaction between defects in diverse classes of liquid crystals. Thanks to technological progress and the integration of experiments with increasingly sophisticated numerical simulations, topological biological and soft matter is a vibrant area of research attracting scientists from a broad range of disciplines. However, owing to the high degree of specialization of modern science, many results have remained confined to their own particular fields, with different jargon making it difficult for researchers to share ideas and work together towards a comprehensive view of the diverse phenomena at play. Compelled by these motivations, here we present a comprehensive overview of topological effects in systems ranging from DNA and genome organization to entangled proteins, polymeric materials, liquid crystals, and theoretical physics, with the intention of reducing the barriers between different fields of soft matter and biophysics. Particular care has been taken in providing a coherent formal introduction to the topological properties of polymers and of continuum materials and in highlighting the underlying common aspects concerning the emergence, characterization, and effects of topological objects in different systems. The second half of the review is dedicated to the presentation of the latest results in selected problems, specifically, the effects of topological constraints on the viscoelastic properties of polymeric materials; their relation with genome organization; a discussion on the emergence and possible effects of knots and other entanglements in proteins; the emergence and effects of topological defects and solitons in complex fluids. This review is dedicated to the memory of Marek Cieplak. (c) 2024 Published by Elsevier B.V.
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