Institute of Hydrobiology, Chinese Academy Of Sciences
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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
Transcriptional and subcellular characterization of interferon induced protein-35 (IFP35) in mandarin fish, Siniperca chuatsi
No full textInterferon (IFN)-stimulated genes (ISGs) exert multiple functions in immune system, and IFN-induced protein 35 (IFP35), which is a member of ISG, has been suggested to be involved in numerous cellular activities including the regulation of antiviral immunity in mammals. However, the role of IFP35 in fish innate immunity remains largely unknown. In the present study, we characterized the IFP35 gene in mandarin fish Siniperca chuatsi, which contains two conserved Nmi/IFP35 homology domains (NIDs) at C-terminus, but no leucine zipper motif, with its genomic DNA sequence consisting of eight exons and seven introns. High and constitutive mRNA level of IFP35 was observed in all examined tissues, with the highest level being observed in gills. Moreover, the IFP35 gene was significantly induced in vivo for 120 h following the infection of infectious spleen and kidney necrosis virus (ISKNV), and its mRNA and protein level was also significantly induced in vitro following the treatment of poly I: C, IFNh, IFNc, as well as IFN-gamma. The subcellular localization results indicated that exogenous IFP35 protein was mainly located in cytoplasm, while endogenous IFP35 protein was transferred into, or aggregated around, the nucleus with the induction of poly I:C or IFNs. The dual luciferase activity analysis indicated that the IFP35 promoter was activated by type I and type II IFNs through ISRE site. It is considered that IFP35 in fish is involved in antiviral, as well as in IFN-induced innate immunity
Life history flexibility of Drunella submontana Brodsky, 1930 (Ephemeroptera: Ephemerellidae) along altitude gradients in Shennongjia National Park, China
No full textWe investigated the life history of Drunella submontana Brodsky, 1930 using the size-frequency method at four sites at different altitudes (from 590 m to 2180 m) in Shennongjia National Park, Central China. Monthly samples of larvae were taken over a two-year period (May 2015-April 2017). Drunella submontana was considered exhibit three overlapping life cycle types: univoltinism with a short egg stage, univoltinism with a long egg stage and semivoltinism. Under diverse climatic habitats in the river ecosystem in Shennongjia National Park, some physicochemical parameters (such as temperature, conductivity, salinity, total dissolved solids and pH) of water showed significantly differences, and the developmental time of D. submontana prolongated from low to high altitudes. High larva density and the short egg stage appeared in middle altitude
Nitrate removal from low carbon-to-nitrogen ratio wastewater by combining iron-based chemical reduction and autotrophic denitrification
No full textNitrate removal from low carbon-to-nitrogen ratio (C/N) wastewater has always been a knotty problem due to the deficiency of organics. Here, a novel iron-based chemical reduction and autotrophic denitrification (ICAD) system was developed. ICAD system could maintain average nitrate removal efficiency of 97.2% for 131 days with feeding 20.3 mg NO3--N/L at hydraulic retention time (HRT) of 24 h. The optimal operational conditions was further explored, and results demonstrated that average nitrate removal efficiency of 85.5% and 98.4% could be achieved at HRT of 12 h and 24 h (influent 20.3 mg NO3--N/L), while average nitrate removal efficiency could reach 96.3% at optimal HRT of 12 h (influent 10.3 mg NO3--N/L). Hydrogenophaga, which can carry out hydrogenotrophic denitrification, showed a positive correlation with nitrate removal efficiency of the ICAD system. Low cost and simple operation make the ICAD system suitable for large-scale application.</p
Dynamic nano-Ag colloids cytotoxicity to and accumulation by Escherichia coli: Effects of Fe3+, ionic strength and humic acid
No full textReleased Ag ions or/and Ag particles are believed to contribute to the cytotoxicity of Ag nanomaterials, and thus, the cytotoxicity and mechanism of Ag nanomaterials should be dynamic in water due to unfixed Ag particle:Agthorn ratios. Our recent research found that the cytotoxicity of PVP-Ag nanoparticles is attributable to Ag particles alone in 3 hr bioassays, and shifts to both Ag particles and released Ag+ in 48 hr bioassays. Herein, as a continued study, the cytotoxicity and accumulation of 50 and 100 nm Ag colloids in Escherichia coli were determined dynamically. The cytotoxicity and mechanisms of nanoAg colloids are dynamic throughout exposure and are derived from both Ag ions and particles. Ag accumulation by E. coli is derived mainly from extracellular Ag particles during the initial 12 hr of exposure, and thereafter mainly from intracellular Ag ions. Fe3thorn accelerates the oxidative dissolution of nano-Ag colloids, which results in decreasing amounts of Ag particles and particle-related toxicity. Nathorn stabilizes nano- Ag colloids, thereby decreasing the bioavailability of Ag particles and particle-related toxicity. Humic acid (HA) binds Agthorn to form Agthorn -HA, decreasing ion-related toxicity and binding to the E. coli surface, decreasing particle-related toxicity. HA in complex conditions showed a stronger relative contribution to toxicity and accumulation than Nathorn or Fe3thorn. The results highlighted the cytotoxicity and mechanism of nano- Ag colloids are dynamic and affected by environmental factors, and therefore exposure duration and water chemistry should be seriously considered in environmental and health risk assessments. (c) 2019 The Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V.</p
Effects of sediment oxidation on phosphorus transformation in three large shallow eutrophic lakes in China
No full textOxidation of surface sediments is an important means for altering phosphorus (P) exchanges across sediment-water interface (SWI) in shallow lakes. In this study, the potential and composition of regenerated oxidation capacity (OC) of surface sediments were evaluated in three large shallow lakes (Tai Lake, Chao Lake, and Dianchi Lake) in China; the transformation of sedimentary P was quantified through P fractionation scheme. The composition of the regenerated OC differed among these three lakes, with Fe(III) and SO42- dominant in Dianchi Lake, Mn(IV) and Fe(III) in Chao Lake and Tai Lake. Oxidation of sediments enhanced the transformation of sedimentary P and altered P exchanges across the SWI. In Chao Lake, the HCl-P was transformed to BD-P; in Tai Lake, the NaOH-P was involved too, and transformed to BD-P; whereas in Dianchi Lake, an increase in NH4Cl-P was also observed except for the transformation from HCl-P to BD-P. The sediment-to-water flux of P was enhanced with 0.17 mg/g DW in Dianchi Lake and 0.08 mg/g DW in Chao Lake, while a contrary water-to-sediment flux of P was observed in Tai Lake, reaching 0.01 mg/g DW. This study advances our knowledge on the impacts of sediment oxidation on P cycles in lakes, which will be beneficial to eutrophication control.</p
The physiological response of Arundo donax and characteristics of anodic bacterial community in BE-CW systems: Effects of the applied voltage
No full textThe performance of bioelectrochemically assisted constructed wetland systems planted with Arundo donax were evaluated at applied voltages of 1, 2, 3 and 5 V. The RGR and Proline (Pro) results implied a positive response at the proper applied voltage. In the 3-V group, the RGR sharply climbed to a maximum over two stages, and the Pro reached a higher level of 256.25 mu g/g at the end of the first stage without an additional organic carbon source. This result indicated that A. donax was attempting to adapt the 3-V stress via physiological self-regulation and the growth was nearly unaffected. However, in the 5-V group, the great increase in Pro and withering of the aboveground A. donax showed that the voltage stress had become lethal and the plant was not able to endure it through physiological regulation. In addition, Anodic microbial community compositions accumulating on graphite felts were analyzed via high-throughput sequencing. Results showed that there were two clear clusters at different applied voltages. One cluster was assembled from the anodic region of the 0-V and 1-V groups, and the other was collected from the 2-V and 3-V samples. At the phylum level, Proteobacteria, Firmicutes and Bacteroidetes were the most common phyla among the samples. However, at the genus level, the dominant genera varied with the applied voltage. The relative abundance of Desulfovibrio increased with increased applied voltage. The highest total nitrogen removal rate in the 2-V group was closely related to the high abundance of the Acinetobacter genus. Moreover, Exiguobacterium became dominant only in the 5-V sample, suggesting that this genus strongly depended on the interactive environment of exudes from A. donax and applied voltage.</p
Environmental influence on the euglenoid species diversity and their abundance in Museum Lake, Thiruvananthapuram, India
No full textTwenty-three species belonging to the class Euglenophyceae were recorded from the Museum Lake, Thiruvananthapuram, India. A canonical correspondence analysis (CCA) between environmental variables and the dominant euglenophytes indicated interaction with certain physical and chemical parameters, in particular rainfall, electrical conductivity and phosphate versus their distribution in the Museum Lake. The dominant species were Euglena deses, Trachelomonas hispida and Trachelomonas volvocina. The CCA results indicate interaction between a variety of environmental parameters and species abundance. A closer examination suggests some external factor (e.g. evaporation) affecting water quality rather than the environment changing the algal biomass. With low rainfall the phosphate concentration increased from 1.5 to 6.9 mg P/l (likely as a result of anoxic conditions in the muddy bottom) and simultaneously nitrate was (partly) taken up by these dominant algae, as a result of which N : P ratios decreased from 4.5 to 0.7. The present study shows that the dominant euglenoid species co-occur in relatively hard water with high phosphorus concentration, and can be considered as useful bio-indicators in assessing the health and extent of deterioration of a lake ecosystem
Dynamic Phosphoproteome Profiling of Zebrafish Embryonic Fibroblasts during Cold Acclimation
No full textTemperature affects almost all aspects of the fish life. To cope with low temperature, fish have evolved the ability of cold acclimation for survival. However, intracellular signaling events underlying cold acclimation in fish remain largely unknown. Here, the formation of cold acclimation in zebrafish embryonic fibroblasts (ZF4) is monitored and the phosphorylation events during the process are investigated through a large-scale quantitative phosphoproteomic approach. In total, 11 474 phosphorylation sites are identified on 4066 proteins and quantified 5772 phosphosites on 2519 proteins. Serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation accounted for 85.5%, 13.3%, and 1.2% of total phosphosites, respectively. Among all phosphosites, 702 phosphosites on 510 proteins show differential regulation during cold acclimation of ZF4 cells. These phosphosites are divided into six clusters according to their dynamic changes during cold exposure. Kinase-substrate prediction reveals that mitogen-activated protein kinase (MAPK) among the kinase groups is predominantly responsible for phosphorylation of these phosphosites. The differentially regulated phosphoproteins are functionally associated with various cellular processes such as regulation of actin cytoskeleton and MAPK signaling pathway. These data enrich the database of protein phosphorylation sites in zebrafish and provide key clues for the elucidation of intracellular signaling networks during cold acclimation of fish
Disodium 2-oxoglutarate promotes carbon flux into astaxanthin and fatty acid biosynthesis pathways in Haematococcus
No full textImproving carbon availability in astaxanthin production is pivotal in Haematococcus industry. In this study, disodium 2-oxoglutarate (2-OG-2Na) was observed to be a potential carbon regulator to increase the astaxanthin content. To illustrate its efficacy in astaxanthin production, key genes and enzyme were analyzed. Upon 2-OG-2Na treatment, genes ipi, bkt and crtR-b were up regulated, concomitantly, carotenoids and astaxanthin content increased by 15.4% and 14.0% at 120 h, respectively; additionally, Acetyl-CoA carboxylase was activated, consistent with 1.27-fold increase in fatty acids content. PUFAs increased earlier as fatty acids assembly gene fad was up-regulated to 20.56. It was also found that cell division was not compromised. Altogether, it was suggested that increased carbon skeletons were re-directed into the astaxanthin and fatty acids biosynthesis pathway. Furthermore, 2-OG-2Na was applied in ten Haematococcus strains. Of these strains, astaxanthin contents were accelerated with average net increase of 10.48%, exhibiting a scalable paradigm for commercial production.</p