Comprehensive Analysis of YTH Domain-Containing Genes, Encoding m6A Reader and Their Response to Temperature Stresses and Yersinia ruckeri Infection in Rainbow Trout (Oncorhynchus mykiss).

YTH domain-containing genes are important readers of N6-methyladenosine (m6A) modifications with ability to directly affect the fates of distinct RNAs in organisms. Despite their importance, little is known about YTH domain-containing genes in teleosts until now. In the present study, a total of 10 YTH domain-containing genes have been systematically identified and functionally characterized in rainbow trout (Oncorhynchus mykiss). According to the phylogenetic tree, gene structure and syntenic analysis, these YTH domain-containing genes could be classified into three evolutionary subclades, including YTHDF, YTHDC1 and YTHDC2. Of them, the copy number of OmDF1, OmDF2, OmDF3, and OmDC1 were duplicated or even triplicated in rainbow trout due to the salmonid-specific whole-genome duplication event. The three-dimensional protein structure analysis revealed that there were similar structures and the same amino acid residues that were associated with cage formation between humans and rainbow trout, implying their similar manners in binding to m6A modification. Additionally, the results of qPCR experiment indicated that the expression patterns of a few YTH domain-containing genes, especially OmDF1b, OmDF3a and OmDF3b, were significantly different in liver tissue of rainbow trout under four different temperatures (7 °C, 11 °C, 15 °C, and 19 °C). The expression levels of OmDF1a, OmDF1b and OmDC1a were obviously repressed in spleen tissue of rainbow trout at 24 h after Yersinia ruckeri infection, while increased expression was detected in OmDF3b. This study provides a systemic overview of YTH domain-containing genes in rainbow trout and reveals their biological roles in responses to temperature stress and bacterial infection.

The Relationship and Changes of Liver Blood Supply, Portal Pressure Gradient, and Liver Volume following TIPS in Cirrhosis.

Aim: Transjugular intrahepatic portosystemic shunt (TIPS) alters the liver blood supply and reduces portal pressure. This study was to investigate the changes and associations of the hepatic blood flow, liver volume, and portal pressure gradient (PPG) after TIPS in liver cirrhosis. Methods: Twenty-one patients with liver cirrhosis who received TIPS were recruited. The contrast CT images were used to assess the iodine density (ID) of liver parenchymal and liver volume. The ID of the liver parenchyma was used to reflect hepatic blood flow. We used a paired t-test and regression analysis to investigate the effect of TIPS on hepatic blood flow, liver volume, and PPG in individuals with cirrhosis and the factors that affect changes in liver volume. Results: After TIPS, there was a significant improvement in the ID of liver parenchyma at arterial phase (AP) and PPG in individuals with cirrhosis (P < 0.05). Each 1 unit increase in the ID change of whole liver parenchyma at the venous phase (VP) was significantly associated with a 269.44 cm3 increase in the liver volume after TIPS (b = 269.44, P = 0.012). With an increasing ID change of whole liver parenchyma at VP, the change in liver volume followed an increasing trend (P for overall association = 0.005). Conclusions: Our data indicate that there was a significant improvement in hepatic blood flow, especially at AP, after TIPS and the change in hepatic blood supply from the portal vein is positively associated with the change in liver volume after TIPS. Increasing the blood supply to the liver from the portal vein may improve the reduction of liver volume.

Completely mitochondrial genome of Neolissochilus heterostomus.

In this study, we determined the complete mitochondrial genome of Neolissochilus heterostomus. The genome is 16,585 bp in length, including 2 ribosomal RNA genes, 13 proteins-coding genes, 22 transfer RNA genes, and two non-coding control regions. Sequence analysis showed that the overall base composition of N. heterostomus is T 24.8%, C 27.7%, A 31.7%, and G 15.8%. The sequence is a slight A + T bias of 56.5%, which is similar to other fishes. We describe a phylogenetic analysis of 16 species of Cypriniformes based on the complete mitochondrial genome, and the result showed that N. stracheyi is most closely related to N. heterostomus. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship of the Cyprinidae.

Induction of T helper 17 cell response by interleukin-7 in patients with primary cutaneous melanoma.

Interleukin (IL)-7 plays a vital role in proliferation and activation of T cells, however, its signaling through CD127 is impaired in T cells in cancers and chronic infections. The mechanisms underlying T helper 17 (Th17) cell responses by IL-7 in melanoma remain not fully understood. The aim of this study was to assess the effect of IL-7 signaling on Th17 responses in patients with primary cutaneous melanoma. Healthy and primary cutaneous melanoma donors were selected for this study of Th17 cell function. IL-17+CD4+ Th17 cells and CD127 expression on Th17 cells were determined by flow cytometry. Cytokine level was measured by ELISA. Peripheral and tissue-infiltrating CD4+ T cells were isolated using magnetic beads, and then stimulated with IL-7 and/or signal transducer and activator of transcription 5 inhibitor. Activated signaling molecules were analyzed by flow cytometry. Peripheral and tumor-infiltrating Th17 cells percentage was decreased, while peripheral IL-7 level was also reduced in melanoma patients. There was no significant difference of CD127 expression on Th17 cells between melanoma patients and controls. Antiapoptotic protein Bcl-2 was downregulated, whereas proapoptotic protein-activated caspase-3 was upregulated in peripheral and tissue-infiltrating Th17 cells in melanoma patients. Higher concentration of IL-7 (10 ng/mL), but not lower IL-7 concentration (1 ng/mL), promoted Bcl-2 expression and decreased caspase-3 expression in Th17 cells in melanoma patients. Inhibition of signal transducer and activator of transcription 5 resulted in the downregulation of Bcl-2 while upregulation of caspase-3 in Th17 cells. The present data suggested that reduced IL-7 responsiveness might be insufficient for Th17 activation in patients with primary cutaneous melanoma.

Complete mitochondrial genome of Geoemyda spengleri.

In this study, we determined the complete mitochondrial genome of Geoemyda spengleri. The genome was 17,448bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 main non-coding regions. The overall base composition of G. spengleri is A 33.67%, T 27.64%, C 25.56%, and G 13.14%, with a highly A + T bias of 61.31%. Here, we describe a phylogenetic analysis of 16 species of Tesudines based on the complete mitochondrial genome, the result showed that G. japonica is most closely related to G. spengleri. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Tesudines.

Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication.

Genomic regions that are unusually divergent between closely related species or racial groups can be particularly informative about the process of speciation or the operation of natural selection. The two sequenced genomes of cultivated Asian rice, Oryza sativa, reveal that at least 6% of the genomes are unusually divergent. Sequencing of ten unlinked loci from the highly divergent regions consistently identified two highly divergent haplotypes with each locus in nearly complete linkage disequilibrium among 25 O. sativa cultivars and 35 lines from six wild species. The existence of two highly divergent haplotypes in high divergence regions in species from all geographical areas (Africa, Asia, and Oceania) was in contrast to the low polymorphism and low linkage disequilibrium that were observed in other parts of the genome, represented by ten reference loci. While several natural processes are likely to contribute to this pattern of genomic variation, domestication may have greatly exaggerated the trend. In this hypothesis, divergent haplotypes that were adapted to different geographical and ecological environments migrated along with humans during the development of domesticated varieties. If true, these high divergence regions of the genome would be enriched for loci that contribute to the enormous range of phenotypic variation observed among domesticated breeds.