Identification of Genes Related to White and Black Plumage Formation by RNA-Seq from White and Black Feather Bulbs in Ducks

To elucidate the genes involved in the formation of white and black plumage in ducks, RNA from white and black feather bulbs of an F2 population were analyzed using RNA-Seq. A total of 2,642 expressed sequence tags showed significant differential expression between white and black feather bulbs. Among these tags, 186 matched 133 annotated genes that grouped into 94 pathways. A number of genes controlling melanogenesis showed differential expression between the two types of feather bulbs. This differential expression was confirmed by qPCR analysis and demonstrated that Tyr (Tyrosinase) and Tyrp1 (Tyrosinase-related protein-1) were expressed not in W-W (white feather bulb from white dorsal plumage) and W-WB (white feather bulb from white-black dorsal plumage) but in B-B (black feather bulb from black dorsal plumage) and B-WB (black feather bulb from white-black dorsal plumage) feather bulbs. Tyrp2 (Tyrosinase-related protein-2) gene did not show expression in the four types of feather bulbs but expressed in retina. C-kit (The tyrosine kinase receptor) expressed in all of the samples but the relative mRNA expression in B-B or B-WB was approximately 10 fold higher than that in W-W or W-WB. Additionally, only one of the two Mitf isoforms was associated with plumage color determination. Downregulation of c-Kit and Mitf in feather bulbs may be the cause of white plumage in the duck

Vector Magnetic Fields and Current Helicities in Coronal Holes and Quiet Regions

In the solar photosphere, many properties of coronal holes (CHs) are not known, especially vector magnetic fields. Using observations from \emph{Hinode}, we investigate vector magnetic fields, current densities and current helicities in two CHs and compare them with two normal quiet regions (QRs) for the first time. We find that, in the CHs and QRs, the areas where large current helicities are located are mainly co-spatial with strong vertical and horizontal field elements both in shape and location. In the CHs, horizontal magnetic fields, inclination angles, current densities and current helicities are larger than those in the QRs. The mean vertical current density and current helicity, averaged over all the observed areas including the CHs and QRs, are approximately 0.008 A m$^{-2}$ and 0.005 G$^{2}$ m$^{-1}$, respectively. The mean current density in magnetic flux concentrations where the vertical fields are stronger than 100 G is as large as 0.012 $\pm$ 0.001 A m$^{-2}$, consistent with that in the flare productive active regions. Our results imply that the magnetic fields, especially the strong fields, both in the CHs and QRs are nonpotential.Comment: 21 pages, 1 table, 9 figures, ApJ (accepted for publication

The DNA Methylation Status of Wnt and Tgfβ Signals Is a Key Factor on Functional Regulation of Skeletal Muscle Satellite Cell Development

DNA methylation is an important form of epigenetic regulation that can regulate the expression of genes and the development of tissues. Muscle satellite cells play an important role in skeletal muscle development and regeneration. Therefore, the DNA methylation status of genes in satellite cells is important in the regulation of the development of skeletal muscle. This study systematically investigated the changes of genome-wide DNA methylation in satellite cells during skeletal muscle development. According to the MeDIP-Seq data, 52,809–123,317 peaks were obtained for each sample, covering 0.70–1.79% of the genome. The number of reads and peaks was highest in the intron regions followed by the CDS regions. A total of 96,609 DMRs were identified between any two time points. Among them 6198 DMRs were annotated into the gene promoter regions, corresponding to 4726 DMGs. By combining the MeDIP-Seq and RNA-Seq data, a total of 202 overlap genes were obtained between DMGs and DEGs. GO and Pathway analysis revealed that the overlap genes were mainly involved in 128 biological processes and 23 pathways. Among the biological processes, terms related to regulation of cell proliferation and Wnt signaling pathway were significantly different. Gene–gene interaction analysis showed that Wnt5a, Wnt9a, and Tgfβ1 were the key nodes in the network. Furthermore, the expression level of Wnt5a, Wnt9a, and Tgfβ1 genes could be influenced by the methylation status of promoter region during skeletal muscle development. These results indicated that the Wnt and Tgfβ signaling pathways may play an important role in functional regulation of satellite cells, and the DNA methylation status of Wnt and Tgfβ signals is a key regulatory factor during skeletal muscle development. This study provided new insights into the effects of genome-wide methylation on the function of satellite cells

Understanding Haemophilus parasuis infection in porcine spleen through a transcriptomics approach

<p>Abstract</p> <p>Background</p> <p><it>Haemophilus parasuis </it>(HPS) is an important swine pathogen that causes Glässer's disease, which is characterized by fibrinous polyserositis, meningitis and arthritis. The molecular mechanisms that underlie the pathogenesis of the disease remain poorly understood, particularly the resistance of porcine immune system to HPS invasion. In this study, we investigated the global changes in gene expression in the spleen following HPS infection using the Affymetrix Porcine Genechip™.</p> <p>Results</p> <p>A total of 931 differentially expressed (DE) transcripts were identified in the porcine spleen 7 days after HPS infection; of these, 92 unique genes showed differential expression patterns based on analysis using BLASTX and Gene Ontology. The DE genes involved in the immune response included genes for inflammasomes (<it>RETN</it>, <it>S100A8</it>, <it>S100A9</it>, <it>S100A12</it>), adhesion molecules (<it>CLDN3</it>, <it>CSPG2</it>, <it>CD44</it>, <it>LGALS8</it>), transcription factors (<it>ZBTB16</it>, <it>SLC39A14</it>, <it>CEBPD</it>, <it>CEBPB</it>), acute-phase proteins and complement (<it>SAA1</it>, <it>LTF</it>, <it>HP</it>, <it>C3</it>), differentiation genes for epithelial cells and keratinocytes (<it>TGM1</it>, <it>MS4A8B</it>, <it>CSTA</it>), and genes related to antigen processing and presentation (<it>HLA-B</it>, <it>HLA-DRB1</it>). Further immunostimulation analyses indicated that mRNA levels of <it>S100A8</it>, <it>S100A9</it>, and <it>S100A12 </it>in porcine PK-15 cells increased within 48 h and were sustained after administration of lipopolysaccharide (LPS) and Poly(I:C) respectively. In addition, mapping of DE genes to porcine health traits QTL regions showed that 70 genes were distributed in 7 different known porcine QTL regions. Finally, 10 DE genes were validated by quantitative PCR.</p> <p>Conclusion</p> <p>Our findings demonstrate previously unrecognized changes in gene transcription that are associated with HPS infection <it>in vivo</it>, and many potential cascades identified in the study clearly merit further investigation. Our data provide new clues to the nature of the immune response in mammals, and we have identified candidate genes that are related to resistance to HPS.</p

Genome-Wide Identification of Histone Modifications Involved in Placental Development in Pigs

Development of placental folds is a critical event affecting placental function in pigs because it can increase surface area for improvement in capillary density as gestation advances. However, the molecular mechanisms of the event are not well defined. Histone modifications have important roles in gene regulation. To investigate their effects on regulation of genes controlling porcine placental development, RNA-seq and ChIP-seq of porcine placental tissues from gestational days 50 (establishment stage of placental folds) and 95 (expanding stage of placental folds) were carried out in this study. The differentially expressed genes were identified and of which the down- and up-regulated genes are related to endoplasmic reticulum (ER) stress and angiogenesis, respectively. In addition, we mapped the genome-wide profiles of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac), which are associated with transcriptional activation. A number of differential modification regions between the 2 gestational stages were identified and majority of them are those with increased signals of H3K4me3 (14,576 out of 16,931). Furthermore, we observed that the increase of H3K4me3 is significantly correlated with the elevated expression levels of the neighboring genes, and notably, these genes were enriched in pathways related to blood vessel formation and microvascular permeability. Taken together, the findings suggest important roles of histone modifications on placental remolding in response to developmental changes

LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs

Transcriptional profiling of Tongcheng and Landrace pigs using long serial analysis of gene expression provides insight into the molecular mechanism underlying differences in muscle growth