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| 2. |
- Leong, Su-lin L., et al.
(författare)
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Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date
- 2015
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Ingår i: Environmental Microbiology. - Hoboken, USA : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 17:2, s. 496-513
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Tidskriftsartikel (refereegranskat)abstract
- Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its dry' but nutrient-rich environment, X.bisporus appears to have relinquished abilities for combative interactions. Elements to sense/signal osmotic stress, e.g. HogA pathway, were present in X.bisporus. However, transcriptomes at optimal (approximate to 0.89) versus low a(w) (0.68) revealed differential expression of only a few stress-related genes; among these, certain (not all) steps for glycerol synthesis were upregulated. Xeromyces bisporus increased glycerol production during hypo- and hyper-osmotic stress, and much of its wet weight comprised water and rinsable solutes; leaked solutes may form a protective slime. Xeromyces bisporus and other food-borne moulds increased membrane fatty acid saturation as water activity decreased. Such modifications did not appear to be transcriptionally regulated in X.bisporus; however, genes modulating sterols, phospholipids and the cell wall were differentially expressed. Xeromyces bisporus was previously proposed to be a chaophile', preferring solutes that disorder biomolecular structures. Both X.bisporus and the closely related xerophile, Xerochrysium xerophilum, with low membrane unsaturation indices, could represent a phylogenetic cluster of chaophiles'.
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| 3. |
- Thrane, Kim, 1984-
(författare)
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Exploring Biological Systems using Spatial Transcriptomic Technologies
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The transcriptome and the cells’ spatial organization are important determinants for the functions of biological systems, such as a tumor, brain, or skin tissue. Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for profiling the transcriptome of individual cells. The nuanced characterization of cell types and states enabled by scRNA-seq has revolutionized our understanding of biological systems. However, these methods rely on the dissociation of tissues into single cells whereby spatial context is lost. Recent advancements have resulted in technologies that retain and associate spatial information with the gene expression of tissues, which has permitted the delineation of biological systems at an unprecedented level. The Spatial Transcriptomics (ST) technology offers transcriptome profiling across thousands of subareas of a tissue section by capturing mRNA in situ and sequencing ex situ.In Paper I, ST was used to explore heterogeneity in lymph node metastases of human cutaneous malignant melanoma. A data-driven analysis approach revealed inter- and intratumor heterogeneity in the examined tumor tissue, whereas the stromal tissue exhibited similar gene expression across patients. Paper II presents an integration of ST, scRNA-seq, and spatial protein analysis to characterize human cutaneous squamous cell carcinoma. The spatial resolution of ST is not at the single-cell level; however, this multimodal approach allowed for the identification of tumor subpopulations and revealed the niches in which they reside. In Paper III, ST and scRNA-seq data were generated to build an atlas of human skin. The combined data was used to map cell-type abundance and intercellular communications in homeostasis. Moreover, cell-of-origin analysis allowed for the identification of candidate cell types accountable for human genetic skin diseases. Paper IV introduces Spatial VDJ, a technique for spatial analysis of B and T cell antigen receptor transcripts, hence determining the position of lymphocyte clones. The spatial VDJ technique was applied to human tonsil and human breast cancer tissues, and this revealed enrichment of immunoglobulin clones in distinct spatial regions. Finally, Paper V explores an alternative protocol for ST that uses long-read sequencing to enable spatial isoform profiling in tissue sections. The protocol was applied to mouse brain and identified genes with spatially distinct alternative isoform expression. Additionally, the full-length transcript information was used to explore RNA editing events across different anatomical regions of the mouse brain.
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| 4. |
- Thrane, M., et al.
(författare)
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Eco-labelling of wild-caught seafood products
- 2009
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Ingår i: Journal of Cleaner Production. - : Elsevier BV. - 0959-6526 .- 1879-1786. ; 17:3, s. 416-423
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Tidskriftsartikel (refereegranskat)abstract
- Several eco-labels for wild-caught seafood have been developed during the last decade. This article describes and analyses the criteria applied by four different eco-labelling schemes for seafood products from capture fisheries, and discusses the criteria in terms of environmental impacts, based on the ISO 14040 standard for life cycle assessment. It is concluded that the most widespread eco-label, the Marine Stewardship Council (MSC), mainly addresses the fishing stage, in particular the overexploitation of marine resources. LCA studies confirm that the fishing stage represents the most significant environmental burden, but energy consumption and emissions of anti-fouling agents at the fishing or harvesting stage contribute with significant impacts that are not being addressed by international labelling initiatives for wild-caught seafood. LCA studies show that significant environmental impacts are related to the life cycle stages after landing. This includes fish processing, transport, cooling and packaging (especially for highly processed seafood products). Hence, another challenge would be to include criteria related to the post-landing consumption of energy, certain materials and chemicals, waste handling and wastewater emissions. Minimizing product losses throughout the product chain would also be an important area for future criteria in order to avoid fishing at high environmental costs only to produce something that is later wasted. The analysis shows that the Swedish KRAV is the only one that currently addresses a range of issues that include energy and chemicals in the whole life cycle of the products. International initiatives such as MSC cover fish products from many parts of the world emphasizing 'overexploitation of fish resources'. It is recommended, however, that international initiatives such as MSC develop criteria related to energy use and chemicals - at least at the fishing stage. Over time, other life cycle stages could be addressed as well to the extent that this is manageable. © 2008 Elsevier Ltd. All rights reserved.
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