| 1. |
- Delgado, Luis Fernando, et al.
(författare)
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Phylogeny-based comparative genomics of Vibrio vulnificus links genetic traits to pathogenicity
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Vibrio vulnificus is a natural part of the microbiome of brackish waters worldwide. It is also an opportunistic pathogen that can cause severe infections and septicemia via consumption of seafood or through wound infections. The species possess diverse virulence factors, yet its precise disease mechanism remains undefined. Comparative genomics between clinical and environmental isolates offers a means to identify key virulence genes, but the scarcity of environmental isolates for V. vulnificus has constituted a significant limitation. Here we sequenced genomes of 82 V. vulnificus isolates from water, sediment and seagrass surface from stations along the Baltic Sea coast and complemented these with 208 and 117 previously sequenced clinical and environmental genomes, respectively, in a comparative analysis. Phylogenetic reconstruction corroborated earlier analysis with four main lineages forming within the species. Strains from the Baltic Sea region were confined to certain phylogenetic lineages (L4 and sublineages L2c and L2e) whereas clinical and environmental strains were found in all lineages, indicting that the phylogenetic structure of V. vulnificus reflects adaptations to specific environmental conditions rather than pathogenicity. Employing orthologue enrichment analysis in a phylogenetic framework using the PhyloBOTL pipeline developed in this work revealed 58 significantly enriched orthologs in clinical compared to environmental isolates. These orthologs were grouped into 18 co-localisation clusters based on the corresponding genes’ proximity in the genomes. The co-localisation clusters entailed clusters with 1 genes previously linked with pathogenicity in V. vulnificus, such as genes for capsular polysaccharide (CPS) synthesis and biofilm formation, but also clusters with genes not previously associated with virulence in the species. Examples of the latter were genes for pilus biosynthesis of the usher-chaperone (CU) pathway, for spermidine synthesis, and for effector proteins of the Type VI secretion system. Finally we leveraged on the clinically enriched genes to design PCR primers for detection and surveillance of pathogenic V. vulnificus strains.
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| 2. |
- Finoguenov, A., et al.
(författare)
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CODEX clusters : Survey, catalog, and cosmology of the X-ray luminosity function
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 638
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Tidskriftsartikel (refereegranskat)abstract
- Context. Large area catalogs of galaxy clusters constructed from ROSAT All-Sky Survey provide the basis for our knowledge of the population of clusters thanks to long-term multiwavelength efforts to follow up observations of these clusters.Aims. The advent of large area photometric surveys superseding previous, in-depth all-sky data allows us to revisit the construction of X-ray cluster catalogs, extending the study to lower cluster masses and higher redshifts and providing modeling of the selection function.Methods. We performed a wavelet detection of X-ray sources and made extensive simulations of the detection of clusters in the RASS data. We assigned an optical richness to each of the 24 788 detected X-ray sources in the 10 382 square degrees of the Baryon Oscillation Spectroscopic Survey area using red sequence cluster finder redMaPPer version 5.2 run on Sloan Digital Sky Survey photometry. We named this survey COnstrain Dark Energy with X-ray (CODEX) clusters.Results. We show that there is no obvious separation of sources on galaxy clusters and active galactic nuclei (AGN) based on the distribution of systems on their richness. This is a combination of an increasing number of galaxy groups and their selection via the identification of X-ray sources either by chance or by groups hosting an AGN. To clean the sample, we use a cut on the optical richness at the level corresponding to the 10% completeness of the survey and include it in the modeling of the cluster selection function. We present the X-ray catalog extending to a redshift of 0.6.Conclusions. The CODEX suvey is the first large area X-ray selected catalog of northern clusters reaching fluxes of 10−13 ergs s−1 cm−2. We provide modeling of the sample selection and discuss the redshift evolution of the high end of the X-ray luminosity function (XLF). Our results on z < 0.3 XLF agree with previous studies, while we provide new constraints on the 0.3 < z < 0.6 XLF. We find a lack of strong redshift evolution of the XLF, provide exact modeling of the effect of low number statistics and AGN contamination, and present the resulting constraints on the flat ΛCDM.
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| 3. |
- Kiiveri, K., et al.
(författare)
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CODEX weak lensing mass catalogue and implications on the mass-richness relation
- 2021
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 502:1, s. 1494-1526
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Tidskriftsartikel (refereegranskat)abstract
- The COnstrain Dark Energy with X-ray clusters (CODEX) sample contains the largest flux limited sample of X-ray clusters at 0.35 < z < 0.65. It was selected from ROSAT data in the 10 000 square degrees of overlap with BOSS, mapping a total number of 2770 high-z galaxy clusters. We present here the full results of the CFHT CODEX programme on cluster mass measurement, including a reanalysis of CFHTLS Wide data, with 25 individual lensing-constrained cluster masses. We employ LENSFIT shape measurement and perform a conservative colour–space selection and weighting of background galaxies. Using the combination of shape noise and an analytic covariance for intrinsic variations of cluster profiles at fixed mass due to large-scale structure, miscentring, and variations in concentration and ellipticity, we determine the likelihood of the observed shear signal as a function of true mass for each cluster. We combine 25 individual cluster mass likelihoods in a Bayesian hierarchical scheme with the inclusion of optical and X-ray selection functions to derive constraints on the slope α, normalization β, and scatter σln λ|μ of our richness–mass scaling relation model in log-space: |${\langle {\rm In}\,\, \lambda\!\!\mid\!\!\mu\rangle = \alpha\mu + \beta,} $| with μ = ln (M200c/Mpiv), and Mpiv = 1014.81M⊙. We find a slope |$\alpha = 0.49^{+0.20}_{-0.15}$|, normalization |$\exp (\beta) = 84.0^{+9.2}_{-14.8}$|, and |$\sigma _{\ln \lambda | \mu } = 0.17^{+0.13}_{-0.09}$| using CFHT richness estimates. In comparison to other weak lensing richness–mass relations, we find the normalization of the richness statistically agreeing with the normalization of other scaling relations from a broad redshift range (0.0 < z < 0.65) and with different cluster selection (X-ray, Sunyaev–Zeldovich, and optical).
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| 4. |
- Riedinger, David J., et al.
(författare)
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Control of Vibrio vulnificus proliferation in the Baltic Sea through eutrophication and algal bloom management
- 2024
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Ingår i: Communications Earth & Environment. - : Springer Nature. - 2662-4435. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Due to climate change the pathogenic bacterium Vibrio vulnificus proliferates along brackish coastlines, posing risks to public health, tourism, and aquaculture. Here we investigated previously suggested regulation measures to reduce the prevalence of V. vulnificus, locally through seagrass and regionally through the reduction of eutrophication and consequential formation of algal blooms. Field samples collected in the summer of 2021 covered the salinity and eutrophication gradients of the Baltic Sea, one of the largest brackish areas worldwide. Physico-, biological- and hydrochemical parameters were measured and variables explaining V. vulnificus occurrence were identified by machine learning. The best V. vulnificus predictors were eutrophication-related features, such as particulate organic carbon and nitrogen, as well as occurrence of potential phytoplankton blooms and associated species. V. vulnificus abundance did not vary significantly between vegetated and non-vegetated areas. Thus, reducing nutrient inputs could be an effective method to control V. vulnificus populations in eutrophied brackish coasts.
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