| 1. |
- Barani-Beiranvand, Hossein, et al.
(författare)
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Phylogeny of penduline tits inferred from mitochondrial and microsatellite genotyping
- 2017
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Ingår i: Journal of Avian Biology. - : WILEY. - 0908-8857 .- 1600-048X. ; 48:7, s. 932-940
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Tidskriftsartikel (refereegranskat)abstract
- Penduline tits (Remiz spp.) are renowned for their diverse mating and parenting strategies, and are a well-studied system by behavioural ecologists. However, the phylogenetic relationships and species delimitations within this genus are poorly understood. Here, we investigate phylogenetic relationships within the genus Remiz by examining the genetic variation in the mitochondrial cytochrome-b gene of 64 individuals and in ten autosomal microsatellite markers from 44 individuals. The taxon sampling includes individuals from all currently recognized species (R. pendulinus, R. macronyx, R. coronatus, and R. consobrinus) and most subspecies in the Palearctic region. We showed that R. coronatus and R. consobrinus are genetically well differentiated and constitute independent evolutionary lineages, separated from each other and from R. pendulinus/macronyx. However, we found no evidence for significant differentiation among R. pendulinus/macronyx individuals in mtDNA haplotypes and only marginal differences between R. pendulinus and R. macronyx in microsatellite markers. Hence, based on present data our recommendation is to treat R. pendulinus and R. macronyx as conspecific and R. coronatus and R. consobrinus as separate species.
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| 2. |
- Bozóky, Benedek, et al.
(författare)
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Novel signatures of cancer-associated fibroblasts
- 2013
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 133:2, s. 286-293
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Tidskriftsartikel (refereegranskat)abstract
- Increasing evidence indicates the importance of the tumor microenvironment, in particular cancer-associated fibroblasts, in cancer development and progression. In our study, we developed a novel, visually based method to identify new immunohistochemical signatures of these fibroblasts. The method employed a protein list based on 759 protein products of genes identified by RNA profiling from our previous study, comparing fibroblasts with differential growth-modulating effect on human cancers cells, and their first neighbors in the human protein interactome. These 2,654 proteins were analyzed in the Human Protein Atlas online database by comparing their immunohistochemical expression patterns in normal versus tumor-associated fibroblasts. Twelve new proteins differentially expressed in cancer-associated fibroblasts were identified (DLG1, BHLHE40, ROCK2, RAB31, AZI2, PKM2, ARHGAP31, ARHGAP26, ITCH, EGLN1, RNF19A and PLOD2), four of them can be connected to the Rho kinase signaling pathway. They were further analyzed in several additional tumor stromata and revealed that the majority showed congruence among the different tumors. Many of them were also positive in normal myofibroblast-like cells. The new signatures can be useful in immunohistochemical analysis of different tumor stromata and may also give us an insight into the pathways activated in them in their true in vivo context. The method itself could be used for other similar analysis to identify proteins expressed in other cell types in tumors and their surrounding microenvironment.
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| 3. |
- Csitári, Bianka, et al.
(författare)
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Anion-type modulates the effect of salt stress on saline lake bacteria
- 2022
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Ingår i: Extremophiles. - : Springer Nature. - 1431-0651 .- 1433-4909. ; 26
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Tidskriftsartikel (refereegranskat)abstract
- Beside sodium chloride, inland saline aquatic systems often contain other anions than chloride such as hydrogen carbonate and sulfate. Our understanding of the biological effects of salt composition diversity is limited; therefore, the aim of this study was to examine the effect of different anions on the growth of halophilic bacteria. Accordingly, the salt composition and concentration preference of 172 strains isolated from saline and soda lakes that differed in ionic composition was tested using media containing either carbonate, chloride or sulfate as anion in concentration values ranging from 0 to 0.40 mol/L. Differences in salt-type preference among bacterial strains were observed in relationship to the salt composition of the natural habitat they were isolated from indicating specific salt-type adaptation. Sodium carbonate represented the strongest selective force, while majority of strains was well-adapted to growth even at high concentrations of sodium sulfate. Salt preference was to some extent associated with taxonomy, although variations even within the same bacterial species were also identified. Our results suggest that the extent of the effect of dissolved salts in saline lakes is not limited to their concentration but the type of anion also substantially impacts the growth and survival of individual microorganisms.
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| 4. |
- Felfoldi, Tamas, et al.
(författare)
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Biological treatment of coke plant effluents : from a microbiological perspective
- 2020
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Ingår i: BIOLOGIA FUTURA. - : SPRINGER HEIDELBERG. - 2676-8615 .- 2676-8607. ; 71:4, s. 359-370
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Forskningsöversikt (refereegranskat)abstract
- During coke production, large volume of effluent is generated, which has a very complex chemical composition and contains several toxic and carcinogenic substances, mainly aromatic compounds, cyanide, thiocyanate and ammonium. The composition of these high-strength effluents is very diverse and depends on the quality of coals used and the operating and technological parameters of coke ovens. In general, after initial physicochemical treatment, biological purification steps are applied in activated sludge bioreactors. This review summarizes the current knowledge on the anaerobic and aerobic transformation processes and describes key microorganisms, such as phenol- and thiocyanate-degrading, floc-forming, nitrifying and denitrifying bacteria, which contribute to the removal of pollutants from coke plant effluents. Providing the theoretical basis for technical issues (in this case the microbiology of coke plant effluent treatment) aids the optimization of existing technologies and the design of new management techniques.
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| 5. |
- Felföldi, Tamás, et al.
(författare)
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Polyphasic bacterial community analysis of an aerobic activated sludge removing phenols and thiocyanate from coke plant effluent
- 2010
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Ingår i: Bioresource Technology. - : Elsevier BV. - 0960-8524 .- 1873-2976. ; 101:10, s. 3406-3414
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Tidskriftsartikel (refereegranskat)abstract
- Biological purification processes are effective tools in the treatment of hazardous wastes such as toxic compounds produced in coal coking. In this study, the microbial community of a lab-scale activated sludge system treating coking effluent was assessed by cultivation-based (strain isolation and identification, biodegradation tests) and culture-independent techniques (sequence-aided T-RFLP, taxon-specific PCR). The results of the applied polyphasic approach showed a simple microbial community dominated by easily culturable heterotrophic bacteria. Comamonas badia was identified as the key microbe of the system, since it was the predominant member of the bacterial community, and its phenol degradation capacity was also proved. Metabolism of phenol, even at elevated concentrations (up to 1500 mg/L), was also presented for many other dominant (Pseudomonas, Rhodanobacter, Oligella) and minor (Alcaligenes, Castellaniella, Microbacterium) groups, while some activated sludge bacteria (Sphingomonas, Rhodopseudomonas) did not tolerate it even in lower concentrations (250 mg/L). In some cases, closely related strains showed different tolerance and degradation properties. Members of the genus Thiobacillus were detected in the activated sludge, and were supposedly responsible for the intensive thiocyanate biodegradation observed in the system. Additionally, some identified bacteria (e.g. C. badia and the Ottowia-related strains) might also have had a significant impact on the structure of the activated sludge due to their floc-forming abilities. © 2009 Elsevier Ltd. All rights reserved.
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| 6. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)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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| 7. |
- Küpper, Clemens, et al.
(författare)
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Heterozygosity-fitness correlations of conserved microsatellite markers in Kentish plovers Charadrius alexandrinus
- 2010
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Ingår i: Molecular Ecology. - 1365-294X. ; 19:23, s. 5172-5185
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Tidskriftsartikel (refereegranskat)abstract
- Abstract Heterozygosity-fitness correlations (HFCs) are frequently used to examine the relationship between genetic diversity and fitness. Most studies have reported positive HFCs, although there is a strong bias towards investigating HFCs in genetically impoverished populations. We investigated HFCs in a large genetically diverse breeding population of Kentish plovers Charadrius alexandrinus in southern Turkey. This small shorebird exhibits highly variable mating and care systems, and it is becoming an ecological model species to understand breeding system evolution. Using 11 conserved and six anonymous microsatellite markers, we tested whether and how heterozygosity was associated with chick survival, tarsus and body mass growth controlling for nongenetic effects (chick sex, hatching date, length of biparental care and site quality) that influence survival and growth. There was no genome-wide effect of heterozygosity on fitness, and we did not find any significant effects of heterozygosity on growth rates. However, two of the 11 conserved markers displayed an association with offspring survival: one marker showed a positive HFC, whereas the other marker showed a negative HFC. Heterozygosity at three further conserved loci showed significant interaction with nongenetic variables. In contrast, heterozygosity based on anonymous microsatellite loci was not associated with fitness or growth. Markers that were correlated with chick survival were not more likely to be located in exons or introns than other markers that lacked this association.
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| 8. |
- Küpper, Clemens, et al.
(författare)
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Kentish versus Snowy Plover: Phenotypic and Genetic Analyses of Charadrius alexandrinus Reveal Divergence of Eurasian and American Subspecies
- 2009
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Ingår i: Auk. - 0004-8038. ; 126:4, s. 839-852
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Tidskriftsartikel (refereegranskat)abstract
- Abstract.—Many shorebird species have widespread geographic distributions comprising several continents. Because shorebirds are excellent flyers and can migrate large distances, it is often unclear whether reproductive barriers between subspecies and populations from different continents exist. Kentish–Snowy Plovers (Charadrius alexandrinus) are cosmopolitan shorebirds. Whether the American and Eurasian subspecies—Snowy Plover and Kentish Plover, respectively—constitute a single species is the subject of a longstanding debate. We examined the divergence between American and Eurasian populations to reassess the current taxonomy by comparing genetic and phenotypic characters of the American subspecies C. a. nivosus and the Eurasian subspecies C. a. alexandrinus from seven populations. Genetic analyses revealed that American and Eurasian populations have strongly diverged, the Kentish Plover being more closely related to the White-fronted Plover (C. marginatus) than to the Snowy Plover. These results were consistent across all assessed nuclear markers (26 microsatellites and a partial CHD sequence) and two mitochondrial markers (ND3 and ATPase 6/8). Within subspecies, populations sampled across large geographic distances were not genetically differentiated (all Fst ≤ 0.01 and all Φst ≤ 0.06), which suggests panmixia. Snowy Plovers differed morphologically from Kentish Plovers, having significantly shorter tarsi and wings. Chick plumage and calls also may serve as diagnostic characters to distinguish Snowy and Kentish plovers, although more data are needed to quantify these differences. Our combined results suggest that the taxonomic status of C. alexandrinus needs to be revised, and we propose that Kentish Plover and Snowy Plover be recognized as separate species: C. alexandrinus and C. nivosus, respectively.
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| 9. |
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| 10. |
- Lindenfors, Patrik, 1964-, et al.
(författare)
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Directional changes in sexual size dimorphism in shorebirds, gulls and alcids
- 2003
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Ingår i: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 16, s. 930-938
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Tidskriftsartikel (refereegranskat)abstract
- The Charadrii (shorebirds, gulls and alcids) are one of the most diverse avian groups from the point of view of sexual size dimorphism, exhibiting extremes in both male-biased and female-biased dimorphism, as well as monomorphism. In this study we use phylogenetic comparative analyses to investigate how size dimorphism has changed over evolutionary time, distinguishing between changes that have occurred in females and in males. Independent contrasts analyses show that both body mass and wing length have been more variable in males than in females. Directional analyses show that male-biased dimorphism has increased after inferred transitions towards more polygynous mating systems. There have been analogous increases in female-biased dimorphism after transitions towards more socially polyandrous mating systems. Changes in dimorphism in both directions are attributable to male body size changing more than female body size. We suggest that this might be because females are under stronger natural selection constraints related to fecundity. Taken together, our results suggest that the observed variation in dimorphism of Charadrii can be best explained by male body size responding more sensitively to variable sexual selection than female body size
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