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- Duchemin, Wandrille, et al.
(författare)
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RecPhyloXML : a format for reconciled gene trees
- 2018
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 34:21, s. 3646-3652
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc. -along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Results: Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities.
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| 2. |
- Suljevic, Damir, et al.
(författare)
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Assessing hexavalent chromium tissue-specific accumulation patterns and induced physiological responses to probe chromium toxicity in Coturnix japonica quail
- 2021
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Ingår i: Chemosphere. - Oxford : Pergamon Press. - 0045-6535 .- 1879-1298. ; 266
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Tidskriftsartikel (refereegranskat)abstract
- Hexavalent chromium (Cr(VI)) is an environmental pollutant with vast mutagenic and carcinogenic potential. Various past and recent studies confirm the deleterious effects of Cr(VI) in different models, from invertebrates to mammalians. However, there is a lack of studies that comprehensively assess and correlate Cr(VI) accumulation patterns and the resulting physiological responses. Here we used an attractive toxicological model, male Japanese quail (Coturnix japonica), as an alternative probing system to evaluate Cr(VI) accumulation in the vital organs, including the brain, heart, kidneys, liver, and testes after 20 days of exposure to 1.2 μg/mL and 2.4 μg/mL potassium dichromate-K2Cr2O7 ingested in the form of drinking water. The observed effects were correlated with the shift in immune system readiness, hematological indices, serum biochemistry and enzyme activity. Regardless of the exposure dose, the Cr(VI) distribution and accumulation pattern in terms of relative Cr(VI) concentration in tissues was: testes > kidneys > liver > heart > brain. Moreover, Cr(VI) triggered the development of microcytic and hypochromic anemia and reduced the immune system’s readiness to cope with challenges. Besides, serum biochemistry presented significant shifts, including reduction of serum electrolytes and proteins and an increase in creatine kinase (CK) and lactate dehydrogenase (LDH) activity. Our study provides novel toxicological data that can be translated to higher animal models to help in the extrapolation of Cr(VI) toxicity in humans.
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