Genome-wide analysis reveals the contributors to fast molecular evolution of the Chinese hook snout carp (Opsariichthys bidens).

Variations in molecular evolutionary rate have been widely investigated among lineages and genes. However, it remains an open question whether fast rate of molecular evolution is driven by natural selection or random drift, and how the fast rate is linked to metabolic rate. Additionally, previous studies on fast molecular evolution have been largely restricted to concatenated matrix of genes or a few specifically selected genes, but less is known for individual genes at the genome-wide level. Here we addressed these questions using more than 5000 single-copy orthologous (SCO) genes through comparative genomic and phylogenetic analyses among fishes, with a special focus on a newly-sequenced clupeocephalan fish the Chinese hook snout carp Opsariichthys bidens. We showed O. bidens displays significantly higher mean substitution rate and more fast-evolving SCO genes (2172 genes) than most fishes studied here. The rapidly evolving genes are enriched in highly conserved and very basic functions such as translation and ribosome that are critical for biological fitness. We further revealed that ∼25 % of these fast-evolving genes exhibit a constant increase of substitution rate from the common ancestor down to the present, suggesting a neglected but important contribution from ancestral states. Model fitting showed that ∼85 % of fast-evolving genes exclusive to O. bidens and related species follow the adaptive evolutionary model rather than random-drift model, and 7.6 % of fast-evolving genes identified in O. bidens have experienced positive selection, both indicating the reflection of adaptive selection. Finally, metabolic rate was observed to be linked with substitution rate in a gene-specific manner. Overall, our findings reveal fast molecular evolution of SCO genes at genome-wide level in O. bidens, and uncover the evolutionary and ecological contributors to it.

Regulation and Response Mechanism of Acute Low-Salinity Stress during Larval Stages in Macrobrachium rosenbergii Based on Multi-Omics Analysis.

Macrobrachium rosenbergii is an essential species for freshwater economic aquaculture in China, but in the larval process, their salinity requirement is high, which leads to salinity stress in the water. In order to elucidate the mechanisms regulating the response of M. rosenbergii to acute low-salinity exposure, we conducted a comprehensive study of the response of M. rosenbergii exposed to different salinities' (0‱, 6‱, and 12‱) data for 120 h. The activities of catalase, superoxide dismutase, and glutathione peroxidase were found to be significantly inhibited in the hepatopancreas and muscle following low-salinity exposure, resulting in oxidative damage and immune deficits in M. rosenbergii. Differential gene enrichment in transcriptomics indicated that low-salinity stress induced metabolic differences and immune and inflammatory dysfunction in M. rosenbergii. The differential expressions of MIH, JHEH, and EcR genes indicated the inhibition of growth, development, and molting ability of M. rosenbergii. At the proteomic level, low salinity induced metabolic differences and affected biological and cellular regulation, as well as the immune response. Tyramine, trans-1,2-Cyclohexanediol, sorbitol, acetylcholine chloride, and chloroquine were screened by metabolomics as differential metabolic markers. In addition, combined multi-omics analysis revealed that metabolite chloroquine was highly correlated with low-salt stress.

Research on the Artemia nauplii microorganism compositions based on metagenomics next-generation sequencing.

Vibrio species represent the predominant and significant pathogen in global marine fish and shellfish aquaculture. Vibrio species are ubiquitously presented in Artemia cyst hatcheries, and their notable colonization in live prey, particularly Artemia nauplii, leads to the transmission of these pathogens into the digestive system of larval organisms, causing serious problems in Vibriosis in marine aquaculture. To eliminate the Vibriospecies in Artemia nauplii, trichloroisocyanuric acid (TCCA) was used for sterilization of the nauplii. In this study, 3 different concentrations, including 0.5 ppm (FA group), 1.0 ppm (FB group) and 1.5 ppm (FC group) of TCCA were used to treat nauplii for 25 min, and then genomic DNA of the different groups were extracted followed by metagenomic next-generation sequencing (NGS). Bioinformatics analysis was applied and the results indicated that Proteobacter constituted the predominant component within each group at the phylum level, albeit accounting for only 58.68% in the FB group, which was significantly lower than in other groups (>86%). The relative abundance of Vibrio species at genus level showed that when compared with the control group, the FB group (15.8%) was reduced by 25.5%. Beta diversity showed differences between the FB group and the other groups, suggesting that treatment with 1.0ppm TCCA for 25 min would obviously reduce the Vibrio in Artemia nauplii. In conclusion, the Vibrio species were significantly reduced after treatment with TCCA, indicating that TCCA might be an alternative to antibiotics used for live food sterilization in marine aquaculture.

Fluorofenidone protects liver against inflammation and fibrosis by blocking the activation of NF-κB pathway.

Despite the increasing understanding of the pathophysiology of hepatic fibrosis, the therapies to combat it remain inadequate. Fluorofenidone (AKF-PD) is a novel pyridone agent able to ameliorate hepatic fibrosis in an experimental hepatic fibrosis model induced by dimethylnitrosamine. However, the underlying mechanism remains to be further elucidated. In light of the critical role of the NF-κB pathway in inflammation and hepatic fibrosis, together with the preliminary finding that AKF-PD decreases the release of proinflammatory cytokines in the endotoxemia and unilateral ureteral occlusion model, the aim of this study was to explore whether AKF-PD exerts an antifibrotic effect in hepatic fibrosis by inhibiting inflammation and suppressing the activation of the NF-κB pathway in vivo and in vitro. To test this possibility, the effect of AKF-PD on hepatic fibrosis models induced by both carbon tetrachloride (CCL4 ) and porcine serum (PS) was investigated. Our results showed that AKF-PD treatment ameliorated hepatic injury and fibrosis in both models. Furthermore, the administration of AKF-PD induced a robust anti-inflammatory reaction revealed by the downregulation of the proinflammatory cytokines as well as the suppression of the infiltration of inflammatory cells in the fibrotic liver. The analysis of the mechanism of action demonstrated that the attenuation of the production of proinflammatory cytokines and chemokines mediated by AKF-PD in vivo and in vitro were accompanied by the suppression in the activation of the NF-κB signaling pathway. In conclusion, AKF-PD might be considered as an antifibrotic agent attenuating hepatic inflammation and fibrosis potentially through the suppression of the NF-κB pathway.

[Isolation and identification of a photosynthetic bacteria producing coenzyme Q10].

13 isolates producing Coenzyme Q10 (CoQ10) of purple non sulfur photosynthetic bacteria were enriched out of pond sludge, one isolate named 2c was selected based on its high CoQ10 content and identified systematically. The gram-negative and short-rod shaped strain 2c is 0.6microm - 0.9microm x 1.2microm - 2.0 microm, has one long flagellum on one end of the cell and contains lamellar intracytoplasmic membrane(ICM) system parallel to cytoplasmic membrane. Cultures produce red pigments in the light. Live cells under phototrophic conditions contain bacteriochlorophyll a and carotenoids. 2c grows anaerobically in the light and aerobically in the dark. Optimal growth occurs at 30degreesC - 35degreesC and at pH7.0 -pH8.0. Various organic compounds are used as photosynthetic electron donors and carbon sources. Peptone and (NH4 )2SO4 are its better nitride source,yeast extracts stimulates its growth. A phylogenetic analysis based on 16S rDNA gene sequences reveales that strain 2c gathers a cluster with 3 strains of Rhodopseudomonas palustris whose accession number in GenBank are AY751758, DQ001155, DQ001158, respectively. 2c subcultures 15 generations stably at least. The results presented here demonstrated strain 2c is Rhodopseudomonas palustris.