Project description:The genetic foundation of chicken tail feather color is not very well studied to date, though that of body feather color is extensively explored. In the present study, we used a synthetic chicken dwarf line (DW), which was originated from the hybrids between a black tail chicken breed, Rhode Island Red (RIR) and a white tail breed, Dwarf Layer (DL), to understand the genetic rules of the white/black tail color. The DW line still contain the individuals with black or white tails, even if the body feather are predominantly red, after more than ten generation of self-crossing and being selected for the body feather color. We firstly performed four crosses using the DW line chickens including black tail male to female, reciprocal crosses between the black and white, and white male to female to elucidate the inheritance pattern of the white/black tail. We found that (i) the white/black tail feather colors are independent of body feather color and (ii) the phenotype are autosomal simple trait and (iii) the white are dominant to the black in the DW lines. Furtherly, we performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color by using black tail chickens from the RIR and DW chickens and white individuals from DW lines.
Project description:For gene expression analysis, RNA-seq was performed in seeds of Dongjin (white rice), Heukseol (black rice) and Jeokjinju (red rice) at 20 days after heading
Project description:The distinctive and visually striking wooden masks associated with the Bwa culture in Burkina Faso, West Africa, are carved from a soft wood into different shapes and display various geometrical patterns and symbols according to the purpose. One of their characteristic features is the use of the colors black, red and white, which evoke the three major rivers crossing the country: the Black, Red and White Voltas. According to published accounts of scholars who have worked directly with the artists, the materials used to obtain these colors include reptile excrement for the white, iron-rich stones powdered and mixed with egg or plant gums for the red, and boiled Acacia seed pods for the black, as well as modern materials such as enamel paint in some cases. A group of four Bwa masks in the Arts of Africa collection of the Art Institute of Chicago was investigated using a complement of analytical techniques including Fourier transform infrared spectroscopy, pyrolysis gas chromatography mass spectrometry, and mass spectrometry based proteomics to characterize their painting materials. The results obtained corroborate the published accounts, while also providing new insights into the nature of the coloring materials and the selection and substitution of pigments and binders. These findings highlight the complementary value of scientific research, in combination with field work and artists’ accounts, to generate a fuller understanding and appreciation of this traditional artistic practice.
Project description:Rice is a major component of the human diet and feeds more than 50 million people across the globe. Therefore, efforts are being made to improve the nutritional quality of rice seeds in order to make a super-rice cultivar rich in antioxidants and vitamins. We previously developed two rice cultivars, Super-hongmi (red seeds) and Super-jami (black seeds), that were highly rich in antioxidants and exhibited high levels of radical scavenging activities. However, the molecular mechanism underlying the color development and accumulation of different antioxidants in these rice cultivars remains largely elusive. Here, we report the proteome profiles of mature Super-hongmi, and Super-jami seeds and compared with the Hopum (white seeds) using a label-free quantitative proteomics approach. This approach led to the identification of 5127 rice seed proteins of which 1628 showed significant changes (ANOVA, Benjamini-Hochberg FDR ≤ 0.01, fold change ≥ 1.5). Functional annotation of the differentially modulated proteins led to the identification of a phytoene desaturase (PDS3) that was highly enriched in the red seeds and was decreased in the black seeds as compared to the control white seeds. PDS3 is involved in the conversion of phytoene to ζ-carotene which may be responsible for the accumulation of red color in red seeds. Moreover, black seeds seem to accumulate higher levels of anthocyanins because of the higher abundance of dihydroflavonol 4-reductase. In addition, proteins associated with lignin and tocopherol biosynthesis were found to be highly increased in both red and black cultivars. Taken together, these data report the seed proteome of three different colored rice seeds and identify novel components associated with pigment accumulation.
Project description:Genome-wide analysis of skin color-related lncRNA and mRNA expression in Koi carp, Cyprinus carpio L. LncRNAs information linked to fish skin color regulation is over-limited. In this study, Illumina sequencing and bioinformatics were primarily conducted on black, white and red skin colors of Koi carp. A total of 590,415,050 clean reads, 446,614 putative transcripts, 4,252 known and 72,907 novel lncRNAs were simultaneously obtained, respectively. Out of these genes, 92 significant differentially expressed lncRNAs and 722 mRNAs were excavated. Ccr_lnc5622441, Ccr_lnc765201 were found up-regulated in black and red skins; Ccr_lnc14074601 were up-regulated in white skin; and premelanosome proteins a (Pmela), tyrosinase (Tyr) were up-regulated in black skin, etc. Quantitative real-time PCR (qRT-PCR) further validated 12 differentially expressed genes were consistent with RNA-seq. Moreover, 70 lncRNAs on 107 target mRNAs in cis and 79 lncRNAs on 41,625 target mRNAs in trans were investigated, the networks revealed one lncRNAs can connected with numerous mRNAs, vice versa. These findings broadened the lncRNAs landscape of skin colors and provided new insights into the mechanisms underlying lncRNAs mediated pigmentation and differentiation in Koi carp.
Project description:we compared the skin transcriptomes of the black- and white-coated region from the Boer and Macheng Black crossbred goat with black head and white body using the Illumina RNA-Seq method. Six cDNA libraries derived from skin samples of the white coat region (n = 3) and black coat region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for each skin sample of black coat and white coat, respectively, of which 75.39% and 76.05% reads were covered in the genome database. Our study provides insight into the transcriptional regulation of two distinct coat color that might serve as a key resource for understanding coat color pigmentation of goat.
Project description:Influence of copy number changes at several chromosomes to melanin production and virulence of Cryptococcus neoformans Black(B4) and white(W2) strains were compared to each other. Black variant from white strain (W2BA1) is also compared to the black strain(B4).
Project description:Hepatocellular carcinoma (HCC) is a highly fatal disease with mortality running parallel to its incidence. For HCC patients, there is a statistically significant increase in incidence and mortality and a decrease in 5-year survival rates in African American (AA)/Black patients compared to non-Hispanic (white) patients. There is a gap of knowledge in our understanding of the molecular mechanism underlying the HCC racial disparity between AA/Black and white patients. To address this issue, we analyzed existing RNA-sequencing (RNA-seq) data from HCC patients in the TCGA database, and performed RNA-seq in 14 white and 19 AA/Black HCC patients from Virginia Commonwealth University. In both analysis the only pathway which showed statistically significant activation in AA/Black patients, compared to white patients, was type I interferon (IFN-I) signaling. A four gene signature of IFN-I-stimulated genes (ISGs) showed increased expression in AA/Black HCC tumors compared to their white counterparts. HCC is a disease of chronic inflammation and IFN-I function as a pro-inflammatory and immunosuppressive cytokine. These findings suggest a potential role of IFN-I in conferring disparity in AA/Black HCC patients.
Project description:Transcriptional profiling of Ovine skin samples comparing pigmentation samples from piebald and normal Merino sheep All pair comparison of 5 pigmentation samples with dye swaps. Dye swaps were performed with different biological replicates (labelled 1 or 2) NOR - White sample from a normal, non-affected wild-type individual sheep PBB - Black sample from a piebald individual sheep PBW - White sample from a piebald individual sheep RSB - Black sample from a recessive black sheep RSW - White sample from a recissive black sheep taken from the inguinal, non-pigmented area.