Yu Ermeng

Cloning, mRNA expression and bioinformatic analysis of full length type collagen alpha 1 I cDNA from grass carp (Ctenopharyngodon idellus)

TypeⅠcollagen, as a number of collagen family, is the most abundant collagen and major components of the extracellular matrices of all metazoan life, and plays crucial roles in differentiation, formation of collagen fibers and tissue remodeling after injury, etc. Type Ⅰ collagen alpha 1(COL1A1) cDNA of grass carp (Ctenopharyngodon idella) was isolated through the RT-PCR and RACE approaches. The cDNA was 5 772-bp in length, including a 4 347-bp CDS (coding sequence) and encoded a polypeptide of 1 449 aa. The homology of COL1A1 amino acid with relative species (zebrafish, goldfish, etc.) was as high as 93% with zebra fish and goldfish. The protein peptide molecular weight was 137.2 ku and theoretical pI was 5.44 using ProtParam software on line. The protein peptides of COL1A1 possessed 6 α-helixes, 12 β-sheets, others of ruleless coil regions, and 18 regions of triple helical repeats, 22 low complexity regions, 17 function domains. There were two calcium-binding sites and one zinc-binding site in the COL1A1 protein peptide. COL1A1 mRNA was determined in all the tested 8 tissues (muscle, intestine, hepatopancreas, gill, skin, fin, kidney and spleen) of grass carp by semi- quantitative RT-PCR, and the mRNAs expression in gill, kidney, skin and fin significantly higher than other tissues (P0.05). The structure and bioinformatics characteristics of the COL1A1 from grass carp may help to further understand the function of COL1A1 gene in the repair process of damaged tissue in the grass carp.

Effect of C/N ratio on bioflocs formation and water quality in zero-water exchange grass crap tanks

Biofloc technology(BFT)was recently proposed as a new approach towards more sustainable practices that lower environmental impacts and prevent diseases incidence.In order to explore required adaptive C/N of bioflocs formation,the effects of C/N on bioflocs formation,water quality and growth performance of grass carp in zero-water exchange tanks were investigated.A locally formulated and prepared feed containing 30% crude protein with C/N ratio 10.8 was applied to all ponds.In order to raise the C/N ratio of the feed input to 15,20 and 25,glucose was applied separately as a source of carbohydrate in addition to artificial feed.The results showed that when the C/N was over 15,the bioflocs could effectively regulate water quality,reduce ammonia and nitrite concentration;the bioflocs volume index(FVI)was increasing with gradual increase in breeding time and stabilized on 14 d in each group;With the C/N increased,the crude protein content of bioflocs groups was significantly higher(P0.05)than that of control groups,but there was a decreasing trend in the growth of grass carp.Overall,when C/N was 15 in the biofloc technology used in the breeding of grass carp,this ratio could effectively promote the bioflocs formation and reduce ammonia nitrogen and nitrite nitrogen levels.

Analysis of bacterial community structure of Bio-Floc by PCR-DGGE

Bio-Floc consists of phytoplankton,bacteria,aggregates of living and dead particulate organic matter,and grazers of the bacteria.It not only can regulate water quality,but also can supply the food protein for breeding animals.For the study of bacterial community structure of Bio-Floc in freshwater culture systems,the key technologies of Israeli Avnimelech team about Bio-Floc in the field of aquaculture were used in this paper.Glucose was added as the carbon source which makes a C∶ N ratio of 20∶ 1 be maintained during the experiment.The bacterial communities of Bio-Floc were analyzed by using the PCR-DGGE(PCR-denaturing gradient gel electrophoresis)on the 5th,10th,and 15th day,respectively.The results indicated that the similarity of bacterial communities was highest on the 5th day and 10th day which was 67.4%,and was lowest on the 5th day and 15th day which was 40.5%.Diversity of bacterial species in the Bio-Floc was maximal on the 10th day and minimal on the 15 day.The acquired sequences of 24 bands in DGGE gel were performed by BLAST searches against NCBI database,and the sequences including the closely related sequences were aligned with Clustal W program in BioEdit software for phylogenetic analysis.The main microbes represented by 24 main bands in DGGE gel were Alphaproteobacteria,Gammaproteobacteria,Betaproteobacteria,Actinobacteria,Bacilli and Bacteroidetes.Among these bacteria,the α-,β-,and γ-proteobacteria are the major bacterial groups,but Actinobacteria bacteria exist on the 10th day and the 15th day.α-proteobacteria was the dominant bacteria during the entire process.The specific bacteria at different stages were usually the flocculant-producing bacteria:Acidovorax,Aeromonas,Agrobacterium only for 5th day;Bacillus,Rhodococcus for 10th day and 15th day,respectively.This study first found that the composition and diversity of bacteria of the Bio-Floc used in freshwater aquaculture systems are extremely rich.The study of functional microbial composition of the Bio-Floc may help to lay the foundation for the further application of the bio-floc technology in actual aquaculture production.

Identification and expression analysis of miRNA in hybrid snakehead by deep sequencing approach and their targets prediction

MicroRNAs (miRNAs) play important regulatory roles in numerous biological processes, but there is no report on miRNAs of hybrid snakehead. In this study, four independent small RNA libraries were constructed from the spleen, liver kidney and muscle of hybrid snakehead. These libraries were sequenced using deep sequencing technology, as result, a total of 1,067,172, 1,152,002, 1,653,941 and 970,866 clean reads from these four libraries were obtained. 252 known miRNAs and 63 putative novel miRNAs in these small RNA dataset were identified. The stem-loop RT-qPCR analysis indicated that eight known miRNAs and two novel miRNAs show different expression in eight different kinds of tissues. For better understanding the functions of miRNAs, 95,947 predicated target genes were analyzed by GO and their pathways, the results indicated that these targets of the identified miRNAs are involved in a broad range of physiological functions.

Community characteristics of the macrozoobenthos and bioassessment of water quality in aquaculture ponds of the Pearl River Delta

Pearl River Delta is one of the main aquaculture areas in China. In order to understand the community structures of mac⁃ rozoobenthos and further assess the water quality in aquaculture ponds, a field investigation of macrozoobenthos and environmental parameters was conducted in 30 ponds with six aquaculture models during July to August 2016. The results showed that a total of 18 species belonging to 14 genera and 3 phyla were identified, and the species number of oligochaeta, aquatic insect, and mollusca was 7, 7, and 4, respectively. The dominant taxa of macrozoobenthos were the Limnodrilus claparedeianus, Limnodrilus sp., and Chironomus sp., which have strong tolerances to pollution. The average species number among the six model ponds had no signifi⁃ cant differences. However, the density and biomass were significantly different, and which were significant higher in two models ( juvenile and adult fish, respectively) of hybrid snakehead (Channa maculate♀×Channa arguss♂) than the other four model ponds. Pearson correlation analyses showed that the TN and TP were the main factors influencing the density and biomass of macro⁃ zoobenthos in aquaculture ponds of Pearl River Delta. The density and biomass of oligochaeta were only positively correlated with TN, while which of chironomids were significantly affected by TN and TP. The water quality of 30 aquaculture ponds were assessed using Shannon⁃Wiener index, Margalef index, and Biotic index. It suggested that the Shannon⁃Wiener index was not appropriate for