BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize. RESULTS: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes. CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species.
- MeSH
- alely * MeSH
- Arabidopsis * genetika MeSH
- data mining * metody MeSH
- datové soubory jako téma * MeSH
- frekvence genu MeSH
- genotyp MeSH
- Glycine max * genetika MeSH
- internet * MeSH
- kukuřice setá * genetika MeSH
- metadata MeSH
- mutace MeSH
- pigmentace genetika MeSH
- rostlinné geny genetika MeSH
- software * MeSH
- substituce aminokyselin MeSH
- vegetační klid genetika MeSH
- vizualizace dat MeSH
- Publikační typ
- časopisecké články MeSH
- Klíčová slova
- retikulární lentigo,
- MeSH
- dospělí MeSH
- lentigo * diagnostické zobrazování MeSH
- lidé MeSH
- melanocyty MeSH
- pigmentace kůže MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- kazuistiky MeSH
- Klíčová slova
- Solidago virgaurea,
- MeSH
- homeopatie * metody MeSH
- infekce močového ústrojí * terapie MeSH
- inkontinence moči terapie MeSH
- komplementární terapie MeSH
- lidé MeSH
- materia medica terapeutické užití MeSH
- nemoci žlučníku terapie MeSH
- pigmentace kůže MeSH
- výsledek terapie MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- kazuistiky MeSH
- populární práce MeSH
Apart from morphological differences, male and female faces also vary in color, especially in overall lightness and facial contrast, i.e., the contrast between the luminance and color of facial features (eyes, lips, or brows) and luminance and color of the surrounding skin. In many populations, it has been demonstrated that women tend to be lighter than men. Other differences were found in facial contrast: women have a higher contrast between the lightness of their eyes and lips and the surrounding skin. Manipulation of this contrast in an artificial genderless face can result in a masculine or feminine appearance. So far, however, this phenomenon has been studied mostly in Euro-American and East Asian samples, with little evidence from populations with darker facial tone. We explored natural sexual dimorphism in both facial contrast and lightness in an African, namely Cameroonian, sample, and compared it with results for a European, in particular Czech, population. Our findings showed that sexual differences in luminance contrast of eyes and brows were in both studied populations similar but in the Cameroonian sample, significant difference in lips contrast was absent. These results indicate that sex differences in facial contrast are a side effect of the sex differences in skin color and can be used as a proxy for skin color perception.
- MeSH
- černoši MeSH
- lidé MeSH
- obličej * diagnostické zobrazování MeSH
- pigmentace kůže MeSH
- pohlavní dimorfismus * MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- střední Afrika MeSH
- MeSH
- černoši nebo Afroameričané * MeSH
- imunosupresivní léčba MeSH
- kvalita života MeSH
- lidé MeSH
- pigmentace kůže * MeSH
- rejekce štěpu diagnóza MeSH
- senioři MeSH
- transplantace obličeje * MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- Publikační typ
- dopisy MeSH
- kazuistiky MeSH
- Research Support, N.I.H., Extramural MeSH
Hormonal changes such as increased cortisol level in blood plasma in response to stress and social environmental stimuli are common among vertebrates including humans and typically accompanied by other physiological processes, such as changes in body pigmentation and/or pupil dilatation. The role of pupil size variation (PSV) as a response to stress have yet to be investigated in fish. We exposed albino and pigmented European catfish to short-term stress and measured changes in pupil size and cortisol level. Albinos showed lower pupil dilatation and higher cortisol levels than did pigmented conspecifics. A clear positive relationship between pupil dilatation and cortisol concentrations was observed for both pigmented and albino specimens, suggesting that PSV can be used as a stress indicator in fish, irrespective of albino's inability to express social communication by coloring. During the follow-up, we investigated whether a penultimate contest between albino individuals would impact contestants' social stress during subsequent contact. We observed PSV during the contact of unfamiliar albino catfish with different penultimate experiences (winner (W) and/or loser (L)). Then, the following treatment combinations were tested: WW, WL and LL. Twenty-four-hour contact of two unfamiliar catfish resulted in higher pupil dilatation among individuals with previous winner experience. Among treatment combinations, a WL contest displayed the highest pupil dilatation for winners. PSV reflected socially induced stress in individuals that was accompanied by the "winner" experience and dominancy in albinos. To conclude, the present study validates pupil dilatation as a non-invasive method to evaluate stress level in pigmented as well as albino fish in various contexts.
- MeSH
- hydrokortison krev MeSH
- komunikace zvířat * MeSH
- pigmentace kůže MeSH
- psychický stres krev patofyziologie MeSH
- pupila fyziologie MeSH
- sumci fyziologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
About 1-2% of European population are redheaded, meaning they synthesize more pheomelanin than eumelanin, the main melanin pigment in humans. Several mutations could be responsible for this phenotype. It has been suggested that corresponding mutations spread in Europe due to a founder effect shaped either by a relaxation of selection for dark, UV-protective phenotypes or by sexual selection in favour of rare phenotypes. In our study, we investigated the levels of vitamin D precursor 25(OH)D3 (calcidiol) and folic acid in the blood serum of 73 redheaded and 130 non-redheaded individuals. In redheaded individuals, we found higher 25(OH)D3 concentrations and approximately the same folic acid concentrations as in non-redheaded subjects. 25(OH)D3 concentrations correlated with the intensity of hair redness measured by two spectrophotometric methods and estimated by participants themselves and by independent observers. In non-redheaded individuals, 25(OH)D3 levels covaried with the amount of sun exposure and intensity of suntan while in redheaded individuals, this was not the case. It suggests that increased 25(OH)D3 levels in redheaded individuals are due to differences in physiology rather than in behaviour. We also found that folic acid levels increased with age and the intensity of baldness and decreased with the frequency of visiting tanning salons. Our results suggest that the redheaded phenotype could be an evolutionary adaptation for sufficient photosynthesis of provitamin D in conditions of low intensity of UVB radiation in central and northern parts of Europe.
- MeSH
- alopecie krev MeSH
- barva vlasů fyziologie MeSH
- dospělí MeSH
- fyziologická adaptace * MeSH
- kalcifediol krev MeSH
- kyselina listová krev MeSH
- lidé středního věku MeSH
- lidé MeSH
- molekulární evoluce MeSH
- opálení pleti fyziologie MeSH
- pigmentace kůže fyziologie MeSH
- podnebí MeSH
- sluneční záření MeSH
- stárnutí krev MeSH
- studie případů a kontrol MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- MeSH
- dermatologie * výchova MeSH
- kožní nemoci * MeSH
- kurzy a stáže v nemocnici * MeSH
- kůže MeSH
- lidé MeSH
- pigmentace kůže MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- dopisy MeSH
