Browsing by Author "Chen, Liangbiao"
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- Differential tissue immune stimulation through immersion in bacterial and viral agonists in the Antarctic Notothenia rossiiPublication . Sousa, Carmen; Peng, Maoxiao; Guerreiro, Pedro; Cardoso, João; Chen, Liangbiao; Canario, Adelino; Power, DeborahThe genome evolution of Antarctic notothenioids has been modulated by their extreme environment over millennia and more recently by human -caused constraints such as overfishing and climate change. Here we investigated the characteristics of the immune system in Notothenia rossii and how it responds to 8 h immersion in viral (Poly I:C, polyinosinic: polycytidylic acid) and bacterial (LPS, lipopolysaccharide) proxies. Blood plasma antiprotease activity and haematocrit were reduced in Poly I:C-treated fish only, while plasma protein, lysozyme activity and cortisol were unchanged with both treatments. The skin and duodenum transcriptomes responded strongly to the treatments, unlike the liver and spleen which had a mild response. Furthermore, the skin transcriptome responded most to the bacterial proxy (cell adhesion, metabolism and immune response processes) and the duodenum (metabolism, response to stress, regulation of intracellular signal transduction, and immune system responses) to the viral proxy. The differential tissue response to the two proxy challenges is indicative of immune specialisation of the duodenum and the skin towards pathogens. NOD -like and C -type lectin receptors may be central in recognising LPS and Poly I:C. Other antimicrobial compounds such as iron and seleniumrelated genes are essential defence mechanisms to protect the host from sepsis. In conclusion, our study revealed a specific response of two immune barrier tissue, the skin and duodenum, in Notothenia rossii when exposed to pathogen proxies by immersion, and this may represent an adaptation to pathogen infective strategies.
- Population genomics of an icefish reveals mechanisms of glacier-driven adaptive radiation in Antarctic notothenioidsPublication . Lu, Ying; Li, Wenhao; Li, Yalin; Zhai, Wanying; Zhou, Xuming; Wu, Zhichao; Jiang, Shouwen; Liu, Taigang; Wang, Huamin; Hu, Ruiqin; Zhou, Yan; Zou, Jun; Hu, Peng; Guan, Guijun; Xu, Qianghua; Canario, Adelino; Chen, LiangbiaoBackground Antarctica harbors the bulk of the species diversity of the dominant teleost fish suborder—Notothenioidei. However, the forces that shape their evolution are still under debate. Results We sequenced the genome of an icefish, Chionodraco hamatus, and used population genomics and demographic modelling of sequenced genomes of 52 C. hamatus individuals collected mainly from two East Antarctic regions to investigate the factors driving speciation. Results revealed four icefish populations with clear reproduction separation were established 15 to 50 kya (kilo years ago) during the last glacial maxima (LGM). Selection sweeps in genes involving immune responses, cardiovascular development, and photoperception occurred differentially among the populations and were correlated with population-specific microbial communities and acquisition of distinct morphological features in the icefish taxa. Population and species-specific antifreeze glycoprotein gene expansion and glacial cycle-paced duplication/degeneration of the zona pellucida protein gene families indicated fluctuating thermal environments and periodic influence of glacial cycles on notothenioid divergence. Conclusions We revealed a series of genomic evidence indicating differential adaptation of C. hamatus populations and notothenioid species divergence in the extreme and unique marine environment. We conclude that geographic separation and adaptation to heterogeneous pathogen, oxygen, and light conditions of local habitats, periodically shaped by the glacial cycles, were the key drivers propelling species diversity in Antarctica.
- Protocol for isolating nuclei from frozen fish heart tissue for single-cell genomic assaysPublication . Wei, Chaoguang; Jia, Ruonan; Canario, Adelino; Chen, Liangbiao; Xu, Qianghua; Hu, PengUnbiased isolation of intact single nuclei from complex tissues, such as cryopreserved hearts, for massively parallel single-cell genomic assays is particularly challenging. Here, we present a protocol for isolating high-quality nuclei from the heart tissue of Trematomus bernacchii, an Antarctic fish species with notoriously challenging tissue for nuclear extraction. We describe steps for pulverizing frozen heart tissue, library construction, and sequencing. This protocol can provide a valuable reference for isolating nuclei from other cryopreserved marine fish tissues.
- Toll-like receptor evolution: does temperature matter?Publication . Sousa, Carmen; Fernandes, Stefan A.; Cardoso, João; Wang, Ying; Zhai, Wanying; Guerreiro, Pedro; Chen, Liangbiao; Canario, A.V.M.; Power, DeborahToll-like receptors (TLRs) recognize conserved pathogen-associated molecular patterns (PAMPs) and are an ancient and well-conserved group of pattern recognition receptors (PRRs). The isolation of the Antarctic continent and its unique teleost fish and microbiota prompted the present investigation into Tlr evolution. Gene homologues of tlr members in teleosts from temperate regions were present in the genome of Antarctic Nototheniidae and the non-Antarctic sister lineage Bovichtidae. Overall, in Nototheniidae apart from D. mawsoni, no major tlr gene family expansion or contraction occurred. Instead, lineage and species-specific changes in the ectodomain and LRR of Tlrs occurred, particularly in the Tlr11 superfamily that is well represented in fish. Positive selective pressure and associated sequence modifications in the TLR ectodomain and within the leucine-rich repeats (LRR), important for pathogen recognition, occurred in Tlr5, Tlr8, Tlr13, Tlr21, Tlr22, and Tlr23 presumably associated with the unique Antarctic microbiota. Exposure to lipopolysaccharide (Escherichia coli O111:B4) Gram negative bacteria did not modify tlr gene expression in N. rossii head-kidney or anterior intestine, although increased water temperature (+4 degrees C) had a significant effect.
- Transcriptome analysis of Immune Response against Streptococcus agalactiae infection in the Nile Tilapia GIFT StrainPublication . Zhou, Tao; Fang, Zhihua; Duarte, Daniel F. C.; Fernandes, Stefan A.; Lu, Ying; Guo, Jing; Gui, Lang; Chen, LiangbiaoStreptococcus agalactiae (group B streptococcus, GBS), a broad-spectrum pathogen, causes great economic losses in fish aquaculture, especially the industry of tilapia. Until now, the knowledge of the immune response mechanism against S. agalactiae infection in tilapia has been limited. In the present study, the gill transcriptome of the tilapia from the GBS and the phosphate buffered saline (PBS) groups were sequenced. The transcriptomic analysis results presented the differentially expressed genes (DEGs) at different time points (DEGs number, 6 h: 2122, 9 h: 1851, 15 h: 1791, and 18 h: 2395) after GBS injection, and significantly enriched immune-related gene ontology (GO) terms such as the innate immune response. The significantly enriched immune pathways included the Toll-like receptor signaling pathway, the nucleotide oligomerization domain (NOD)-like receptor signaling pathway, the cytosolic-DNA sensing pathway, and the intestinal immune network for Immunoglobulin A (IgA) production. Most of the DEGs in Toll-like receptor signaling, NOD-like receptor signaling, and cytosolic-DNA sensing pathways presented upregulations at 18 h, which indicated that the innate immune pathways were activated. Two immune-related pathways (phagosome and cell adhesion molecules) were significantly enriched at all time points, suggesting that these two pathways might also play important roles in the immune response against the GBS infection. The results of HE staining showed that the gills of tilapia were damaged seriously at 9 h post-infection, which might be due to the possibility of pyroptosis resulting from the changes of DEGs in the NODlike receptor signaling pathway. This study provided new insight into the mechanisms of gill damage in fish infected with S. agalactiae.
- Transcriptomic down-regulation of immune system components in barrier and hematopoietic tissues after lipopolysaccharide injection in antarctic notothenia coriicepsPublication . Sousa, Carmen; Power, Deborah; Guerreiro, Pedro M; Louro, Bruno; Chen, Liangbiao; Canario, AdelinoThe environmental conditions and isolation in the Antarctic have driven the evolution of a unique biodiversity at a macro to microorganism scale. Here, we investigated the possible adaptation of the teleost Notothenia coriiceps immune system to the cold environment and unique microbial community of the Southern Ocean. The fish immune system was stimulated through an intraperitoneal injection of lipopolysaccharide (LPS 0111:B4 from E. coli) and the tissue transcriptomic response and plasma biochemistry were analyzed 7 days later and compared to a sham injected control. Gene transcription in the head-kidney, intestine and skin was significantly modified by LPS, although tissues showed different responsiveness, with the duodenum most modified and the skin the least modified. The most modified processes in head-kidney, duodenum and skin were related to cell metabolism (up-regulated) and the immune system (comprising 30% of differentially expressed genes). The immune processes identified were mostly down-regulated, particularly interleukins and pattern recognition receptors (PRRs), nucleotide-binding oligomerization domain-like receptors and mannose receptors, unlike the toll-like receptors response commonly described in other teleost fish. The modified transcriptional response was not mirrored by a modified systemic response, as the circulating levels of enzymes of innate immunity, lysozyme and antiproteases, were not significantly different from the untreated and sham control fish. In conclusion, while the N. coriiceps immune system shares many features with other teleosts there are also some specificities. Further studies should better characterize the PRRs and their role in Antarctic teleosts, as well as the importance of the LPS source and its consequences for immune activation in teleosts.
- Transcriptomic responses to low temperature stress in the Nile tilapia, Oreochromis niloticusPublication . Zhou, Tao; Gui, Lang; Liu, Mingli; Li, Wenhao; Hu, Peng; Duarte, Daniel F. C.; Niu, Hongbo; Chen, LiangbiaoThe Nile tilapia, Oreochrornis niloticus, is a species of high economic value and extensively cultured. The limited stress tolerance of this species to a low temperature usually leads to mass mortality and great loss. Nevertheless, there is limited information on the molecular mechanisms underlying the susceptibility to low temperature in the tilapia. In this study, tilapia was treated at 28 degrees C to a lethal temperature of 8 degrees C by a gradual decrement. Transcriptomic response of the immune organ, kidney, in tilapia was characterized using RNA-seq. In total, 2191 genes were annotated for significant expression, which were mainly associated with metabolism and immunity. Pathway analysis showed that immune-related pathways of phagosome and cell adhesion molecules (CAMs) pathway were significantly down-regulated under low temperature. Moreover, ferroptosis, a significantly changed pathway involved in tissue damage and acute renal failure, is reported here for the first time. The levels of serum parameters associated with kidney damage such as urea and uric acid (UA) increased significantly under low temperature. The immunofluorescence staining of the kidney showed that cell apoptosis occurred at low temperature. The results of the present study indicate that exposure to low temperature can cause kidney disfunction and down-regulate the immune-related pathway in the kidney of tilapia. This study provides new insight into the mechanism of kidney damage in fish under low temperature.