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- Feng, Shaohong, et al.
(author)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Journal article (peer-reviewed)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 4. |
- Helander, Björn, 1946-, et al.
(author)
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Major lead exposure from hunting ammunition in eagles from Sweden
- 2021
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; , s. 1-16
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Journal article (peer-reviewed)abstract
- Exposure to lead (Pb) from ammunition in scavenging and raptorial birds has achieved worldwide recognition based on incidences of lethal poisoning, but exposure implies also sublethal levels with potential harmful effects.Background and elevated Pb levels in liver from 116 golden eagles (GE, Aquila chrysaetos) and 200 white-tailed sea eagles (WTSE, Haliaeetus albicilla) from Sweden 2003–2011 are here examined, with supporting data from a previous WTSE report and eagle owl (EO, Bubu bubo) report. GE and WTSE display seasonal patterns, with no Pb level exceeding a generally accepted threshold for subclinical effects during summer but strongly elevated levels from October. Fledged juveniles show significantly lower levels than all other age classes, but reach levels found in older birds in autumn after the start of hunting seasons. Pb levels in EO (non-scavenger) show no seasonal changes and indicate no influence from ammunition, and are close to levels observed in juvenile eagles before October. In all, 15% WTSE and 7% GE were lethally poisoned. In areas with high-exposure to hunting ammunition, 24% of WTSE showed lethal Pb levels, compared to 7% in both eagle species from low-exposure areas. Lethal poisoning of WTSE remained as frequent after (15%) as before (13%) a partial ban on use of Pb-based shotgun ammunition over shallow waters (2002). Pb levels increased significantly in WTSE 1981–2011,in contrast to other biota from the same period. A significant decrease of Pb in WTSE liver occurred below a threshold at 0.25 μg/g (dry weight), exceeded by 81% of the birds. Trend patterns in Pb isotope ratios lend further support to this estimated cut-off level for environmental background concentrations. Pb from spent ammunition affects a range of scavenging and predatory species. A shift to Pb-free ammunition to save wildlife from unnecessary harm is an important environmental and ethical issue.
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| 5. |
- Hummel, Thomas, et al.
(author)
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Androstadienone odor thresholds in adolescents.
- 2005
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In: Horm Behav. - 0018-506X. ; 47:3, s. 306-10
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Journal article (peer-reviewed)abstract
- A sex-related difference in olfactory sensitivity to androstenone has been reported to occur during adolescence. More males than females exhibited anosmia to androstenone, or an increase in androstenone threshold with age. The current study addressed the question whether similar, sexually dimorphic effects of aging over puberty can also be found for androstadienone. A total of 102 subjects participated (36 females, 66 males). Similar to previous investigations, subjects were divided into a group of 47 individuals with a mean age of 13.3 years, defined as pre/peri-pubertal, and a group of 55 subjects with a mean age of 17.1 years, defined as post-pubertal. All subjects underwent tests for verbal abilities, general olfactory function, and measurements of androstadienone thresholds. The study provided the following major results: (1) Male subjects exhibited higher androstadienone sensitivity in the pre/peri-pubertal group as compared to the post-pubertal group. This difference was not observed in female subjects. Correspondingly, a negative correlation between age and androstadienone sensitivity was found for male subjects, but not for female subjects. (2) In contrast to this sex-specific change of the androstadienone odor threshold, verbal skills and odor identification abilities increased with age in all subjects regardless of their sex. In conclusion, the present observations confirm previous research on sex-differentiated effects of aging during puberty on sensitivity towards odorous steroids. While the underlying causes are unknown, it may be hypothesized that the decreased sensitivity could result from the increased endogenous levels of androstadienone in male subjects. Future studies should include both steroid and non-steroid odorants to futher explore these age-related changes.
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| 7. |
- Kruse, Bastian, et al.
(author)
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CD4+ T cell-induced inflammatory cell death controls immune-evasive tumours
- 2023
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In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 618:7967, s. 1033-1040
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Journal article (peer-reviewed)abstract
- Most clinically applied cancer immunotherapies rely on the ability of CD8+ cytolytic T cells to directly recognize and kill tumour cells1,2,3. These strategies are limited by the emergence of major histocompatibility complex (MHC)-deficient tumour cells and the formation of an immunosuppressive tumour microenvironment4,5,6. The ability of CD4+ effector cells to contribute to antitumour immunity independently of CD8+ T cells is increasingly recognized, but strategies to unleash their full potential remain to be identified7,8,9,10. Here, we describe a mechanism whereby a small number of CD4+ T cells is sufficient to eradicate MHC-deficient tumours that escape direct CD8+ T cell targeting. The CD4+ effector T cells preferentially cluster at tumour invasive margins where they interact with MHC-II+CD11c+ antigen-presenting cells. We show that T helper type 1 cell-directed CD4+ T cells and innate immune stimulation reprogramme the tumour-associated myeloid cell network towards interferon-activated antigen-presenting and iNOS-expressing tumouricidal effector phenotypes. Together, CD4+ T cells and tumouricidal myeloid cells orchestrate the induction of remote inflammatory cell death that indirectly eradicates interferon-unresponsive and MHC-deficient tumours. These results warrant the clinical exploitation of this ability of CD4+ T cells and innate immune stimulators in a strategy to complement the direct cytolytic activity of CD8+ T cells and natural killer cells and advance cancer immunotherapies.
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