Institute of Hydrobiology, Chinese Academy Of Sciences
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The involvement of TNF-alpha and TNF-beta as proinflammatory cytokines in lymphocyte-mediated adaptive immunity of Nile tilapia by initiating apoptosis
No full textTumor necrosis factors (TNFs) are pleiotropic cytokines with important functions in homeostasis and disease pathogenesis. Recent advances have shown that TNFs are also involved in the regulation of adaptive immune responses. However, the knowledge about how TNF participates in and regulates adaptive immune response in early vertebrates is still limited. In present study, we identified two isoforms of TNF, TNF-alpha and TNF-beta, from Nile tilapia Oreochromis niloticus (On-TNF-alpha and beta). After analyzing the sequence characteristics, we investigated their regulatory roles in adaptive immune response of this fish species. On-TNF-alpha and beta are evolutionarily conserved compare with their homologs from other vertebrates. Both TNFs were distributed in a wide range of tissues in O. niloticus, and with relative higher expression level in gill. After the animals were infected by Streptococcus agalactiae, mRNA levels of On-TNF-alpha and TNF-beta in spleen lymphocytes were significantly upregulated during the primary response stage of adaptive immunity. Meanwhile, both TNF proteins in spleen lymphocytes were also dramatically elevated during the adaptive immune stage after bacterial infection. These results indicate the potential participation of On-TNF-alpha and TNF-beta in adaptive immune response of Nile tilapia. Furthermore, OnTNF-alpha and beta transcripts were obviously augmented, once spleen lymphocytes were activated by T cell-specific mitogen PHA. More importantly, both recombinant On-TNF-alpha and beta could induce the apoptosis of head kidney leukocytes of Nile tilapia. And On-TNF-beta but not On-TNF-alpha promoted the apoptosis by activating caspase-8 in the target cells. Altogether, our study revealed that TNF-alpha and TNF-beta participated in the lymphocyte mediated adaptive immune response of Nile tilapia by initiating the apoptosis, and thus shed novel perspective for the regulatory mechanism of adaptive immunity in teleost
An identified PfHMGB1 promotes microcystin-LR-induced liver injury of yellow catfish (Pelteobagrus fulvidraco)
No full textMicrocystin-LR (MC-LR) is a potent hepatotoxin that can cause liver inflammation and injury. However, the mode of action of related inflammatory factors is not fully understood. PfHMGB1 is an inflammatory factor induced at the mRNA level in the liver of juvenile yellow catfish (Pelteobagrus fulvidraco) that were intraperi-toneally injected with 50 mu g/kg MC-LR. The PfHMGB1 mRNA level was highest in the liver and muscle among 11 tissues examined. The full-length cDNA sequence of PfHMGB1 was cloned and overexpressed in E. coli, and the purified protein rPfHMGB1 demonstrated DNA binding affinity. Endotoxin-free rPfHMGB1 (6-150 mu g/mL) also showed dose-dependent hepatotoxicity and induced inflammatory gene expression of primary hepatocytes. PfHMGB1 antibody (anti-PfHMGB1) in vitro reduced MC-LR (30 and 50 mu mol/L)-induced hepatotoxicity, suggesting PfHMGB1 is important in the toxic effects of MC-LR. In vivo study showed that MC-LR upregulated PfHMGB1 protein in the liver. The anti-PfHMGB1 blocked its counterpart and reduced ALT/AST activities after MC-LR exposure. Anti-PfHMGB1 partly neutralized MC-LR-induced hepatocyte disorganization, nucleus shrinkage, mitochondria, and rough endoplasmic reticula destruction. These findings suggest that PfHMGB1 promotes MC-LR-induced liver damage in the yellow catfish. HMGB1 may help protect catfish against widespread microcystin pollution
Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae
No full textAbstractBackgroundLoaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated.ResultsIn this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3?bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11?Ma), furthermore, mtDNA introgression might occur (14.40?Ma) between ancestral species of Cobitis and ancestral species of Misgurnus.ConclusionsThe current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family
A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs
No full textHigh-throughput RNA sequencing unveiled the complexity of transcriptome and significantly increased the records of long noncoding RNAs (lncRNAs), which were reported to participate in a variety of biological processes. Identification of lncRNAs is a key step in lncRNA analysis, and a bunch of bioinformatics tools have been developed for this purpose in recent years. While these tools allow us to identify lncRNA more efficiently and accurately, they may produce inconsistent results, making selection a confusing issue. We compared the performance of 41 analysis models based on 14 software packages and different data sets, including high-quality data and low-quality data from 33 species. In addition, computational efficiency, robustness, and joint prediction of the models were explored. As a practical guidance, key points for lncRNA identification under different situations were summarized. In this investigation, no one of these models could be superior to others under all test conditions. The performance of a model relied to a great extent on the source of transcripts and the quality of assemblies. As general references, FEELnc_all_cl, CPC, and CPAT_mouse work well in most species while COME, CNCl, and IncScore are good choices for model organisms. Since these tools are sensitive to different factors such as the species involved and the quality of assembly, researchers must carefully select the appropriate tool based on the actual data. Alternatively, our test suggests that joint prediction could behave better than any single model if proper models were chosen. All scripts/data used in this research can be accessed at http://bioinfo.ihb.ac.cn/elit
Grass carp cGASL negatively regulates interferon activation through autophagic degradation of MAVS
No full textIn mammals, cyclic GMP-AMP synthase (cGAS) is a crucial cytosolic DNA sensor responsible for activating the interferon (IFN) response. A cGAS-like (cGASL) gene was previously identified from grass carp Ctenopharyngodon idellus, which is evolutionarily closest to cGAS but not a true ortholog of cGAS. Here, we found that grass carp cGASL targets mitochondrial antiviral signaling protein (MAVS) for autophagic degradation to negatively regulate fish IFN response. Firstly, the transcriptional level of cellular cgasl was upregulated by poly I:C stimulation, and overexpression of cGASL significantly decreased poly I:C- and MAVS-induced promoter activities and transcriptional levels of IFN and IFN-stimulated genes (ISGs). In addition, cGASL associated with MAVS and prompted autophagic degradation of MAVS in a dose-dependent manner. Finally, overexpression of cGASL attenuated MAVS-mediated cellular antiviral response. These results collectively indicate that cGASL negatively regulates fish IFN response by triggering autophagic degradation of MAVS
Stock enhancement of Culter mongolicus : Assessment of growth, recapture and release size in the Yangtze lakes
No full textThe release of piscivorous fishes is considered crucial to alleviate eutrophication and fish miniaturization, as well as to develop sustainable fisheries management strategy for Yangtze lakes. In order to promote the stock enhancement programme of a new released piscivorous fish species Culter mongolicus, growth, recapture rates, reproduction and impact of size-at-release for hatchery-reared juveniles were evaluated in three Yangtze shallow lakes during a five-year period. C. mongolicus displayed important growth capability with a body weight reaching commercial size (> 500 g) during the second released year and about 1500 g in the third year. However, a sharp decline of growth appeared quickly after several years of releasing, indicating possible issue of density-dependent growth caused by over-stocking. The recapture rates for one-month-old juveniles were less than 5%, but increased to more than 20 % when one-year-old fingerlings were selected as release size. Gonad examination and catch analysis showed that released juveniles could not succeed in building the recruitment stock due to over fishing. Thus hatchery-reared juveniles should be released annually. Management actions that prioritize the release of fewer but larger fingerlings will improve the recapture rate and subsequent economic benefit. A new stock enhancement strategy that changes the present release-catch cycle from two years to one was proposed accordingly
Microplastics in freshwater sediment: A review on methods, occurrence, and sources
No full textThere is a rising concern regarding the accumulation of microplastics in the aquatic ecosystems. However, compared to the marine environment, the occurrence, transport, and diffusion of microplastics in freshwater sediment are still open questions. This paper summarizes and compares the methods used in previous studies and provides suggestions for sampling and analysis of microplastics in freshwater sediment. This paper also reviews the findings on microplastics in freshwater sediment, including abundance, morphological characteristics, polymer types, sources, and factors affecting the abundance of microplastics in freshwater sediment. The results show that microplastics are ubiquitous in the investigated sediment of rivers, lakes, and reservoirs, with an abundance of 2-5 orders of magnitude across different regions. Low microplastics concentration was observed in the Ciwalengke River with an average abundance of 30.3 +/- 15.9 items/kg. In particular, an extremely high abundance of microplastics was recorded in the urban recipient in Norway reaching 12,000-200,000 items/kg. Fibers with particle size less than 1 mm are the dominant shape for microplastics in freshwater sediment. In addition, the most frequently recorded colors and types are white/transparent, and PE/PS, respectively. Finally, we conclude that the consistency of morphological characteristics and components of microplastics between the beach or marine sediments and freshwater sediments may be an indicator of these interlinkages and source-pathways. Microplastics in freshwater sediment need further research and exploration to identify its spatial and temporal variations and driving force through further field sampling and implementation of standard and uniform analytical methodologies. (C) 2020 Elsevier B.V. All rights reserved
Geographical Variability of Mineral Elements and Stability of Restrictive Mineral Elements in Terrestrial Cyanobacteria Across Gradients of Climate, Soil, and Atmospheric Wet Deposition Mineral Concentration
No full textTerrestrial cyanobacteria Nostoc commune is an ideal species to study the geographical variation of mineral elements of soil cyanobacteria at the species level. Here, we first address the following questions: (1) from where are these mineral elements, (2) are there geographical variations for these mineral elements, and if so, (3) which environmental factors drive the geographical variation of these mineral elements? Second, we tested whether the soil cyanobacterial mineral elements followed the "restrictive element stability hypothesis" of higher plants. Finally, we explored the effect of mineral geographic variation on ecological adaptation of soil cyanobacteria. We collected N. commune samples across gradients of climate, soil, and atmospheric wet deposition mineral concentration in mainland China. We measured fifteen minerals, including five macroelements (N, Ca, K, Fe, P), five microelements (Mn, Zn, Cu, Co, Se), and five heavy metals (Pb, Cr, As, Cd, Hg). We found that five elements (P, Cu, Zn, Co, Pb) had significant geographical variation. They increased as the distance from the equator increased and decreased as the distance from the prime meridian increased. Mean annual precipitation and mean annual temperature explained most of the variation. We did not find any significant correlations between the mineral element contents in N. commune and the minerals in soil and rainfall, except for P. There was no significant correlation between the variation coefficients of different elements and their actual detected contents and their potential physiological required contents. The statistical results of our experiment did not support the "restrictive element stability hypothesis." We speculated that net accumulation of mineral elements in cyanobacterial cells and extracellular polysaccharides (EPS) might play an important role for terrestrial cyanobacteria in the adaptation to dry and cold conditions
Ecological effects of wastewater treatment modifications on infauna communities off the coast of Orange County, California
No full textThe Orange County Sanitation District (OCSD) is a public agency that provides treatment of wastewater for residents in Orange County, California. The final effluent characteristics at OCSD have been altered in the last 18 years due to the similar to 20-fold increase of sodium hypochlorite usage for disinfecting waste streams from 2002 to 2010, implementation of the Ground Water Replenishment System (GWRS) in 2008, and conversion to full secondary treatment, together with a major reduction of sodium hypochlorite usage in 2011. This study analyzed infauna data gathered from 1994 to 2016 at the zone of initial dilution (ZID) and reference stations located on the San Pedro Shelf to assess the effects of these treatment process changes on biota in the receiving water. Impacts to the infauna community within the ZID were observed during the period of high chlorine usage, including the increased proportion of the pollution tolerant polychaete Capitella capitata complex from 6.2% in 2003 to nearly 60% in 2010, the lowest Infaunal Trophic Index score in 2009, and the highest Benthic Response Index score in 2006. The degradation of the infauna community in the ZID was correlated with chlorination and was coincidental with the initiation of the GWRS. The infauna community at the ZID recovered rapidly after the implementation of full secondary treatment as indicated by the significant reduction of the relative abundance of C. capitata complex from 59.8% in 2010 to less than 0.1% after 2012, and by the markedly improved community health index scores. This study demonstrated the composition and biointegrity of the infauna community at the ZID varied in response to changes in the wastewater treatment process. Caution should be exercised at wastewater treatment plants when relatively higher dosages of sodium hypochlorite are used over a multi-year period, as this may negatively impact aquatic biota in the receiving water. (C) 2020 Elsevier B.V. All rights reserved
IRF11 regulates positively type I IFN transcription and antiviral response in mandarin fish, Siniperca chuatsi
No full textIn vertebrates, a total of eleven interferon (IFN) regulatory factors (IRFs), IRF1 to IRF11 are reported, with the conserved presence of IRF1 to IRF9 in all classes of vertebrates. However, IRF10 has been reported only in fish and birds, and IRF11 seems to be a fish specific IRF member. In this study, IRF11 in mandarin fish Siniperca chuatsi was found upregulated following virus infection, and IRF11 was localized constitutively in nucleus as revealed through immunofluorescence test. The overexpression and/or luciferase reporter assays showed that IRF11 can induce transcriptionally the ISRE activity, and the expression of type I IFNs, IFNc and IFNh, as well as the IFN-stimulated gene, Mx, thus inhibiting the Siniperca chuatsi rhabdovirus (SCRV) replication as indicated in the reduced expression of virus protein genes. It is thus suggested that IRF11 in mandarin fish and probably in other teleost fish can exert its antiviral effect through the upregulation of type I IFNs and ISGs