| 1. |
- Abila, R., et al.
(författare)
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Oil extraction imperils Africa’s Great Lakes
- 2016
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 354:6312, s. 561-562
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- As the world's demands for hydrocarbons increase (1), remote areas previously made inaccessible by technological limitations are now being prospected for oil and gas deposits. Virtually unnoticed by the public, such activities are ongoing in the East African Great Lakes region, threatening these ecosystems famed for their hyper-diverse biota, including the unique adaptive radiations of cichlid fishes (2). Countries in the region see exploitation of hydrocarbon reserves as a vital economic opportunity. In the Lake Albert region of Uganda, for example, the government foresees a $3.6 billion oil profit per year starting in 2018—a sum almost as high as the country's current annual budget (3). However, oil extraction in the East African Great Lakes region poses grave risks to the environment and local communities.
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| 2. |
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| 3. |
- Dohle, G. R., et al.
(författare)
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Guidelines on testicular microlithiasis
- 2008
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Ingår i: Giornale Italiano di Medicina Sessuale e Riproduttiva. - 1592-2103. ; 51:2, s. 107-108
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Jungwirth, E., et al.
(författare)
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Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions
- 2021
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Ingår i: Hepatology Communications. - : Ovid Technologies (Wolters Kluwer Health). - 2471-254X. ; 5:10, s. 1721-1736
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Tidskriftsartikel (refereegranskat)abstract
- Farnesoid X receptor (FXR) is a nuclear receptor that controls gene regulation of different metabolic pathways and represents an upcoming drug target for various liver diseases. Several data sets on genome-wide FXR binding in different species and conditions exist. We have previously reported that these data sets are heterogeneous and do not cover the full spectrum of potential FXR binding sites. Here, we report the first meta-analysis of all publicly available FXR chromatin immunoprecipitation sequencing (ChIP-seq) data sets from mouse, rat, and human across different conditions using a newly generated analysis pipeline. All publicly available single data sets were biocurated in a standardized manner and compared on every relevant level from raw reads to affected functional pathways. Individual murine data sets were then virtually merged into a single unique "FXR binding atlas" spanning all potential binding sites across various conditions. Comparison of the single biocurated data sets showed that the overlap of FXR binding sites between different species is modest and ranges from 48% (mouse-human) to 55% (mouse-rat). Moreover, in vivo data among different species are more similar than human in vivo data compared to human in vitro data. The consolidated murine global FXR binding atlas virtually increases sequencing depth and allows recovering more and novel potential binding sites and signaling pathways that were missed in the individual data sets. The FXR binding atlas is publicly searchable (). Conclusion: Published single FXR ChIP-seq data sets and large-scale integrated omics data sets do not cover the full spectrum of FXR binding. Combining different individual data sets and creating an "FXR super-binding atlas" enhances understanding of FXR signaling capacities across different conditions. This is important when considering the potential wide spectrum for drugs targeting FXR in liver diseases.
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| 5. |
- Carmona-Gutierrez, D., et al.
(författare)
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Guidelines and recommendations on yeast cell death nomenclature
- 2018
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Ingår i: Microbial Cell. - : Shared Science Publishers OG. - 2311-2638. ; 5:1, s. 4-31
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Forskningsöversikt (refereegranskat)abstract
- Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research.
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| 6. |
- Jungwirth, Arne, et al.
(författare)
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Long-term individual marking of small freshwater fish : the utility of Visual Implant Elastomer tags
- 2019
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Ingår i: Behavioral Ecology and Sociobiology. - : Springer. - 0340-5443 .- 1432-0762. ; 73:4, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Tracking wild animals over long periods of time is a non-trivial challenge. This has caused a bias in the availability of individual-based long-term datasets with the majority including birds and mammals. Visual Implant Elastomer (VIE) tags are now a widely used technique that may facilitate the collection of such data for fish and amphibians. However, VIE tags might have important drawbacks. Overall, four potential issues with VIE tags have been proposed: tag loss or misidentification, limited number of individual identifiers, enhanced mortality risk, and effects on intra-specific interactions. Here, we present three experiments in which we investigated these potential problems with VIE tagging in small freshwater fish both in the laboratory and in the wild, using the cooperatively breeding Lake Tanganyika cichlid Neolamprologus pulcher. We find VIE tags to be generally suitable for work with these fish as they did not impair survival, were recognisable up to 2years after injection, and did not generally disturb group formation. Nevertheless, we identify specific issues of VIE tagging, including colour- and position-dependent variation in tag identification rates, and indications that specific colours may influence social behaviour. Our results demonstrate the suitability of VIE tags for long-term studies on small freshwater fish, while also highlighting the need of validating this method carefully for any species and study.Significance statementInformation on the survival, dispersal, and reproductive success of wild individuals across their lifespan is among the most valuable data in Behavioural Ecology. Because tracking of free-ranging individuals over extended periods of time is challenging, there exists a bias in the taxonomic distribution of such long-term datasets. Here, we investigate the suitability of visible implant elastomers (VIE) as a tracking technique to allow for the collection of such data also in small tropical freshwater fish. We show that VIE tags neither alter social behaviour in our study species, nor do they reduce survival, but they enable the tracking of wild individuals across years. We also identify colours and tag positions that are less suitable. We conclude that VIE tags can help produce long-term datasets also for small fish, provided certain precautions are met.
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| 7. |
- Jungwirth, Arne, et al.
(författare)
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Philopatry yields higher fitness than dispersal in a cooperative breeder with sex-specific life history trajectories
- 2023
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Ingår i: Science Advances. - : American Association for the Advancement of Science. - 2375-2548. ; 9:9
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Tidskriftsartikel (refereegranskat)abstract
- Social evolution is tightly linked to dispersal decisions, but the ecological and social factors selecting for philopatry or dispersal often remain obscure. Elucidating selection mechanisms underlying alternative life histories requires measurement of fitness effects in the wild. We report on a long-term field study of 496 individually marked cooperatively breeding fish, showing that philopatry is beneficial as it increases breeding tenure and lifetime reproductive success in both sexes. Dispersers predominantly join established groups and end up in smaller groups when they ascend to dominance. Life history trajectories are sex specific, with males growing faster, dying earlier, and dispersing more, whereas females more likely inherit a breeding position. Increased male dispersal does not seem to reflect an adaptive preference but rather sex-specific differences in intrasexual competition. Cooperative groups may thus be maintained because of inherent benefits of philopatry, of which females seem to get the greater share in social cichlids.
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| 8. |
- Jungwirth, Emilian, et al.
(författare)
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A Comprehensive FXR Signaling Atlas Derived from Pooled ChIP-seq Data.
- 2019
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Ingår i: Studies in health technology and informatics. - 1879-8365. ; 260, s. 105-112
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Tidskriftsartikel (refereegranskat)abstract
- ChIP-seq is a method to identify genome-wide transcription factor (TF) binding sites. The TF FXR is a nuclear receptor that controls gene regulation of different metabolic pathways in the liver.To re-analyze, standardize and combine all publicly available FXR ChIP-seq data sets to create a global FXR signaling atlas.All data sets were (re-)analyzed in a standardized manner and compared on every relevant level from raw reads to affected functional pathways.Public FXR data sets were available for mouse, rat and primary human hepatocytes in different treatment conditions. Standardized re-analysis shows that the data sets are surprisingly heterogeneous concerning baseline quality criteria. Combining different data sets increased the depth of analysis and allowed to recover more peaks and functional pathways.Published single FXR ChIP-seq data sets do not cover the full spectrum of FXR signaling. Combining different data sets and creating a "FXR super-signaling atlas" enhances understanding of FXR signaling capacities.
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| 9. |
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| 10. |
- Panzitt, Katrin, et al.
(författare)
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FXR-dependent Rubicon induction impairs autophagy in models of human cholestasis.
- 2020
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Ingår i: Journal of hepatology. - : Elsevier BV. - 1600-0641 .- 0168-8278. ; 72:6, s. 1122-1131
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Tidskriftsartikel (refereegranskat)abstract
- Cholestasis comprises a spectrum of liver diseases characterized by the accumulation of bile acids. Bile acids and activation of the farnesoid X receptor (FXR) can inhibit autophagy, a cellular self-digestion process necessary for cellular homeostasis and regeneration. In mice, autophagy appears to be impaired in cholestasis and induction of autophagy may reduce liver injury.Herein, we explored autophagy in human cholestasis invivo and investigated the underlying molecular mechanisms invitro. FXR chromatin immunoprecipitation-sequencing and qPCR were performed in combination with luciferase promoter studies to identify functional FXR binding targets in a human cholestatic liver sample.Autophagic processing appeared to be impaired in patients with cholestasis and in individuals treated with the FXR ligand obeticholic acid (OCA). Invitro, chenodeoxycholic acid and OCA inhibited autophagy at the level of autophagosome to lysosome fusion in an FXR-dependent manner. Rubicon, which inhibits autophago-lysosomal maturation, was identified as a direct FXR target that is induced in cholestasis and by FXR-agonistic bile acids. Genetic inhibition of Rubicon reversed the bile acid-induced impairment of autophagic flux. In contrast to OCA, ursodeoxycholic acid (UDCA), which is a non-FXR-agonistic bile acid, induced autophagolysosome formation independently of FXR, enhanced autophagic flux and was associated with reduced Rubicon levels.In models of human cholestasis, autophagic processing is impaired in an FXR-dependent manner, partly resulting from the induction of Rubicon. UDCA is a potent inducer of hepatic autophagy. Manipulating autophagy and Rubicon may represent a novel treatment concept for cholestatic liver diseases.Autophagy, a cellular self-cleansing process, is impaired in various forms of human cholestasis. Bile acids, which accumulate in cholestatic liver disease, induce Rubicon, a protein that inhibits proper execution of autophagy. Ursodeoxycholic acid, which is the first-line treatment option for many cholestatic liver diseases, induces hepatic autophagy along with reducing Rubicon.
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