Comparative Blood Transcriptome Analysis of Semi-Natural and Controlled Environment Populations of Yangtze Finless Porpoise.

The Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis) living in different environments display significant differences in behavior and physiology. To compare and analyze gene expression differences between an ex situ population and a controlled environment population of the Yangtze finless porpoise, we sequenced the transcriptome of blood tissues living in a semi-natural reserve and an artificial facility, respectively. We identified 6860 differentially expressed genes (DEGs), of which 6603 were up-regulated and 257 were down-regulated in the controlled environment vs ex situ comparison. GO and KEGG enrichment analysis showed that the up-regulated genes in the controlled environment population were significantly associated with glucose metabolism, amino acid metabolism, and the nervous system, while those up-regulated in the ex situ population were significantly associated with energy supply and biosynthesis. Further analysis showed that metabolic and hearing-related genes were significantly affected by changes in the environment, and key metabolic genes such as HK, PFK, IDH, and GLS and key hearing-related genes such as OTOA, OTOF, SLC38A1, and GABBR2 were identified. These results suggest that the controlled environment population may have enhanced glucose metabolic ability via activation of glycolysis/gluconeogenesis, the TCA cycle, and inositol phosphate metabolism, while the ex situ population may meet higher energy requirements via enhancement of the amino acid metabolism of the liver and muscle and oxidative phosphorylation. Additionally, the acoustic behavior and auditory-related genes of Yangtze finless porpoise may show responsive changes and differential expression under different environment conditions, and thus the auditory sensitivity may also show corresponding adaptive characteristics. This study provides a new perspective for further exploration of the responsive changes of the two populations to various environments and provides a theoretical reference for further improvements in conservation practices for the Yangtze finless porpoise.

Gapless genome assembly of East Asian finless porpoise.

In recent years, conservation efforts have increased for rare and endangered aquatic wildlife, especially cetaceans. However, the East Asian finless porpoise (Neophocaena asiaeorientalis sunameri), which has a wide distribution in China, has received far less attention and protection. As an endangered small cetacean, the lack of a chromosomal-level reference for the East Asian finless porpoise limits our understanding of its population genetics and conservation biology. To address this issue, we combined PacBio HiFi long reads and Hi-C sequencing data to generate a gapless genome of the East Asian finless porpoise that is approximately 2.5 Gb in size over its 21 autosomes and two sex chromosomes (X and Y). A total of 22,814 protein-coding genes were predicted where ~97.31% were functionally annotated. This high-quality genome assembly of East Asian finless porpoise will not only provide new resources for the comparative genomics of cetaceans and conservation biology of threatened species, but also lay a foundation for more speciation, ecology, and evolutionary studies. Measurement(s) Neophocaena asiaeorientalis sunameri • Gapless genome assembly • sequence annotation Technology Type(s) MGISEQ. 2000 • PacBio HiFi Sequencing • Hi-C Sample Characteristic - Organism Neophocaena asiaeorientalis sunameri Sample Characteristic - Environment seawater Sample Characteristic - Location Yellow Sea near Lianyungang City, Jiangsu Province, China.

Interaction of Microbiota between Fish and the Environment of an In-Pond Raceway System in a Lake.

Due to its ability to collect and remove aquaculture waste, an in-pond raceway system (IPRS) has been used to decrease the uncontrolled waste discharge in the traditional cage aquaculture method in large water bodies. However, when applied to large water bodies, its environmental performance is still lacking. This study focused on analyzing the microbial characteristics and the interaction between largemouth bass (gill and gut) microbiota and the environment (water and sediment) microbiota of an IPRS. Further, it revealed the primary relationship from the perspective of microbiota in the IPRS. The results show that (1) the alpha diversity of microbiota in the water is significantly lower than that of fish and sediment. The relationship between water microbiota and fish microbiota is limited. (2) The water microbiota inside and outside the tank showed high similarity and were not significantly affected by environmental factors. (3) The SourceTrack analysis showed that fish microbiota is one of the primary sources of sediment microbiota, and more than 15% of the sediment microbiota come from fish. Microbes such as Faecalibacterium, Escherichia-Shigella, and Bacteroides can significantly enrich the sediment. Our study revealed the characteristics and preliminary interaction of fish and environmental microbiota in the IPRS. It provided a reference for evaluating microbial health status in the application of IPRS in large water bodies' aquaculture.

Effects of washing step and salt-addition levels on textural and quality properties in the chicken-surimi products.

The massive wastewater from surimi manufacture and salt addition is controversial. In our previous study, a chicken-surimi (CS) product can be successfully developed from the spent-hen breast via 3 times of washing steps and 2.5% salt addition in the recipe. Due to the characteristics of broiler breast (higher protein contents in muscle), this study was to optimize the washing step for CS batter recovered from broiler breast and the salt-addition level in the CS-product recipe. The step of washing once with 0.1% salt solution showed no (P > 0.05) differences in the texture profile and color parameters (expect a* value) in CS batters compared to initial washing steps (a 3-step washing procedure). The CS batter obtained by this washing step had higher amino-acid contents than boiler breast and large Grade A egg and even fit adults' daily essential amino-acid requirement. Besides, the lower (P < 0.05) water loss of cooked CS products during the storage (4°C) was shown beyond 2.0% salt addition in CS products. For efficient/ecofriendly extraction and sodium-content reduction, the washing once with a 0.1% salt solution and 2% salt addition in the recipe is recommended in the CS batter recovered from broiler breast and its products, respectively.

The bacteria of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) are site-specific and distinct from freshwater environment.

Bacteria play an essential role in the health of marine mammals, and the bacteria of marine mammals are widely concerned, but less is known about freshwater mammals. In this study, we investigated the bacteria of various body sites of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) and analyzed their association with freshwater environmental bacteria. The bacterial community and function of Yangtze finless porpoise showed apparent site-specificity. Various body sites have distinct differences in bacteria and have their dominant bacteria. Romboutsia, Plesiomonas, Actinobacillus, Candidatus Arthromitus dominated in the intestine (fecal and rectal samples). Fusobacterium, Streptococcus, and Acinetobacter dominated in the oral. The dominant genera in the blowhole include Suttonella, Psychrobacter, and two uncultured genera. Psychrobacter, Flavobacterium, and Acinetobacter were dominant in the skin. The alpha diversity of intestinal (fecal and rectal) bacteria was the lowest, while that of skin was the highest. The oral and skin bacteria of Yangtze finless porpoise significantly differed between the natural and semi-natural conditions, but no sex difference was observed. A clear boundary was found between the animal and the freshwater environmental bacteria. Even the skin bacteria, which are more affected by the environment, are significantly different from the environmental bacteria and harbor indigenous bacteria. Our results provide a comprehensive preliminary exploration of the bacteria of Yangtze finless porpoise and its association with bacteria in the freshwater environment.

Integrated analysis of blood mRNAs and microRNAs reveals immune changes with age in the Yangtze finless porpoise (Neophocaena asiaeorientalis).

Populations of Yangtze finless porpoises (YFPs) have rapidly declined in recent decades, raising the specter of extinction. In order to protect YFPs, a greater understanding of their biology is needed, including studying how their immune functioning changes with age. Here, we systematically studied the hematologic and biochemical parameters, as well as mRNAs and miRNAs profiles of old, adult, and young YFPs. The lymphocyte (LYMPH), neutrophils (NEUT) and eosinophils (EOS) counts in old YFPs were lower than those in young or adult YFPs. When comparing old to adult YFPs, the latter showed higher expression of genes associated with the innate and adaptive immune systems, including complement components, major histocompatibility complex, interleukins, TNF receptors, and chemokines/cytokines. When comparing old to young YFPs, the most striking difference was in higher toll-like receptor signaling in the latter. When comparing adult to young YFPs, the former exhibited higher expression of genes related to adaptive immunity and the FoxO signaling pathway, but lower expression of genes associated with the PI3K-Akt signaling pathway. Negative miRNA-mRNA interactions were predicted in comparisons of the old and adult (326), old and young (316), adult and young (211) groups. Overall, these results delineate a progression from early innate immune function dominance to adaptive immune function enhancement (young to adult) and deterioration (adult to old), and the changes in miRNAs profile correlate with the effects of age on immune functions. This study is the first to observe the changes of immune function of Yangtze finless porpoise with age using transcriptome method, and the study's findings are of great significance for protecting this endangered species.

Metabolic mechanisms of Coilia nasus in the natural food intake state during migration.

As a prominent member of freshwater and coastal fish faunas, Coilia nasus migrates annually from the sea up the Yangtze River in China to spawn. It is traditionally believed that C. nasus generally do not feed during their spawning migration. However, we recently documented the occurrence of food intake phenomenon in C. nasus following voluntary fasting. The purpose of the current study is to explore the metabolic mechanisms on C. nasus in response to food intake during migration. A total of 23,159 differentially expressed mRNA molecules and 204 metabolites were identified in transcriptome and metabolome analyses. Our results provide insights into the activation of energy consumption and reinforcement of energy storage during migration, and also identify key genes involved in food intake regulation. Our findings will be useful for future research on population recruitment and energy utilization in wild C. nasus.

Exopolysaccharide from Cryptococcus heimaeyensis S20 induces autophagic cell death in non-small cell lung cancer cells via ROS/p38 and ROS/ERK signalling.

OBJECTIVES: Cryptococcus heimaeyensis S20 is found in Antarctica and can produce exopolysaccharides (CHEPS). Here, we explore the anti-tumour effects of CHEPS on non-small cell lung cancer (NSCLC). MATERIALS AND METHODS: Cell viability was assessed by CCK8 and colony formation assays. Flow cytometry was used to analyse the cell cycle, cell apoptosis and reactive oxygen species (ROS). Cell autophagy was detected by EGFP-LC3 puncta assay, Lyso-Tracker Red staining and transmission electron microscopy. mRNA and protein levels were analysed by qRT-PCR and Western blot. Related mechanisms were confirmed using appropriate inhibitors or shRNA. In vitro results were further confirmed by a tumour xenograft study. RESULTS: CHEPS inhibited the proliferation of NSCLC cells by inducing S- and G2/M-phase arrest and autophagic cell death, but not apoptosis. CHEPS was less toxic to normal human embryonic lung fibroblasts. CHEPS activated the MAPK pathway in NSCLC cells, and p38 and ERK promoted CHEPS-induced cell death. Further studies showed that p38 and ERK promoted CHEPS-induced NSCLC cell autophagy and ERK promoted CHEPS-induced S- and G2/M-phase arrest. ROS were induced by CHEPS. A ROS scavenger attenuated CHEPS-induced p38 and ERK activation, autophagy and cell death. Finally, CHEPS reduced orthotopic lung tumour growth without organ-related toxicity. CHEPS also induced ROS, activated p38 and ERK, and triggered autophagy in vivo. CONCLUSIONS: CHEPS induces autophagic cell death and S- and G2/M-phase arrest in NSCLC cells via ROS/p38 and ROS/ERK signalling.

Changes in the fecal microbiome of the Yangtze finless porpoise during a short-term therapeutic treatment.

The fecal microbiome is an integral part of aquatic mammals, like an inner organ. But we know very little about this inner organ of the threatened aquatic species, Yangtze finless porpoise (YFP). Four YFPs were placed into a purse seine for skin ulceration treatment, and this opportunity was taken to nurse the animals closer. In particular, we collected the feces of the YFPs before and after the paired healing and therapeutic treatment, along with samples of their fish diet and water habitat, to explore the changes in their fecal microbiome. Firmicutes (20.9-96.1%), Proteobacteria (3.8-78.7%), Actinobacteria (0.1-35.0%) and Tenericutes (0.8-17.1%) were the most dominant phyla present in the feces. The proportion of Proteobacteria and Actinobacteria increased after the treatment. Firmicutes showed a significant decrease, and most potential pathogens were absent, which reflected the administration of ciprofloxacin hydrochloride. Moreover, environmental shifts can also contribute to changes in the fecal microbiome. These results indicate that certain microbial interactions can be affected by environmental shifts, dietary changes and health-care treatments, which can also help maintain the internal environment of YFPs. These findings will inform the future enhanced protection and management of endangered YFPs and other vulnerable aquatic animals.

Spatiotemporal Distribution and Assemblages of Fishes below the Lowermost Dam in Protected Reach in the Yangtze River Main Stream: Implications for River Management.

Now more and more ecologists concern about the impacts of dam construction on fish. However, studies of fishes downstream Gezhouba Dam were rarely reported except Chinese sturgeon (Acipenser sinensis Gray). In this study, catch investigations and five hydroacoustic detections were completed from 2015 to 2016 to understand the distribution, size, and categories of fishes and their relationship with the environmental factors below Gezhouba Dam in protected reach in the Yangtze River main stream. Results showed significant differences in fish distribution and TS (target strength) between wet and flood seasons. Mean TS in five hydroacoustic detections were -59.98 dB, -54.70 dB, -56.16 dB, -57.90 dB, and -59.17 dB, respectively, and dominant fish species are Coreius guichenoti (Bleeker), Siniperca chuatsi (Basilewsky), and Pelteobagrus vachelli (Richardson). In the longitudinal direction, fish preferred to stay in some specific sections like reaches 2, 4, 7, 8, 11, and 16. Since hydrology factors change greatly in different seasons, environmental characteristics vary along the reaches, and human activities play an important role in the fish behavior, it is concluded that great cross-season changes in hydrology lead to the differences in TS and fish assemblages and that geography characteristics, especially channel geography, together with human activities influence fish longitudinal distribution. This finding provides basic knowledge of spatiotemporal distribution and assemblages of fishes in the extended reaches downstream Gezhouba Dam. In addition, it offers implications for river management. It could also serve as reference of future research on fish habitat.

[Interspecies diet relationship of Coreius from Yinbin reach of Yangtze River, China].

This study investigated the diet compositions of Coreius heterodon and C. guichenoti in Yibin reach of Yangtze River from April to May, 2012 by carbon and nitrogen stable isotopes technique, and analyzed their diet relationship by the multivariate statistical technique, which covered the diet similarity index, overlap coefficient, and the influence of morphological differences in feeding organ between the two species on diet compositions. The results showed that, 1) the δ13C and δ15N of C. heterodon was from -21.15 per thousand to -20.31 per thousand and 9.67 per thousand to 10.21 per thousand, respectively, which indicated that the fish had an omnivorous possessing carnivorous preference. The δ13C and δ15N of C. guichenoti was from -23.30 per thousand to -21.18 per thousand and 7.40 per thousand to 9.21 per thousand, respectively, which had an omnivorous possessing phytophagous preference. There were some differences in the results between the stable isotopes and the traditional intestinal contents analysis. 2) The diet similarity index and the overlap coefficient was 78.7% and 55.6%, respectively. 3) The principal component analysis (PCA) result showed that the morphological characters of the feeding organs in the two fishes were different. In conclusion, the interspecies competition was not intense between the C. heterodon and C. guichenoti, and as the last investigation of the diet composition and food relationship of the two species before the impoundment of the Xiangjiaba Reservoir, the results could provide reference for analyzing the influence of impoundment on the fish trophic structure in Yibin reach of Yangtze River.