Chinese Academy of Fishery Sciences

About: Chinese Academy of Fishery Sciences is a nonprofit organization based out in Beijing, China. It is known for research contribution in the topics: Population & Gene. The organization has 8107 authors who have published 7929 publications receiving 92095 citations. The organization is also known as: Zhōngguó shuǐchǎn Kēxuéyánjiūyuàn & Chinese Academy of Fishery Sciences.

RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data

Abstract: RNA-Seq has become one of the most widely used applications based on next-generation sequencing technology. However, raw RNA-Seq data may have quality issues, which can significantly distort analytical results and lead to erroneous conclusions. Therefore, the raw data must be subjected to vigorous quality control (QC) procedures before downstream analysis. Currently, an accurate and complete QC of RNA-Seq data requires of a suite of different QC tools used consecutively, which is inefficient in terms of usability, running time, file usage, and interpretability of the results. We developed a comprehensive, fast and easy-to-use QC pipeline for RNA-Seq data, RNA-QC-Chain, which involves three steps: (1) sequencing-quality assessment and trimming; (2) internal (ribosomal RNAs) and external (reads from foreign species) contamination filtering; (3) alignment statistics reporting (such as read number, alignment coverage, sequencing depth and pair-end read mapping information). This package was developed based on our previously reported tool for general QC of next-generation sequencing (NGS) data called QC-Chain, with extensions specifically designed for RNA-Seq data. It has several features that are not available yet in other QC tools for RNA-Seq data, such as RNA sequence trimming, automatic rRNA detection and automatic contaminating species identification. The three QC steps can run either sequentially or independently, enabling RNA-QC-Chain as a comprehensive package with high flexibility and usability. Moreover, parallel computing and optimizations are embedded in most of the QC procedures, providing a superior efficiency. The performance of RNA-QC-Chain has been evaluated with different types of datasets, including an in-house sequencing data, a semi-simulated data, and two real datasets downloaded from public database. Comparisons of RNA-QC-Chain with other QC tools have manifested its superiorities in both function versatility and processing speed. We present here a tool, RNA-QC-Chain, which can be used to comprehensively resolve the quality control processes of RNA-Seq data effectively and efficiently.

Compensatory growth in juvenile Chinese sturgeon (Acipenser sinensis): effects of starvation and subsequent feeding on growth and body composition

Abstract: Summary Compensatory growth (CG) of juvenile Acipenser sinensis was investigated over a test period of 70 days. 120 fish (mean ± SD, 75.24 ± 3.56 g) were divided into five feeding groups including one control group receiving continuous feeding (S0) and four experimental groups with food deprivation for 3 days (S3), 7 days (S7), 14 days (S14) and 28 days (S28), respectively. All starved fish resumed feeding comparable to S0. Fish in S3 and S7 reached in the end essentially the same weights as the control fish, indicating that complete compensatory growth occurred. Although the specific growth rates in S14 or S28 were greater than in the S0 after re-feeding, neither S14 nor S28 fish reached the same body weight of S0 fish at the end of the re-feeding period, but showed partial compensation only. With progressing starvation, muscle moisture and ash content increased significantly, lipid increased obviously in the first 7 days and thereafter decreased remarkable, protein content changed indistinctively during the first 7 days and thereafter decreased significantly, while muscle glycogen content declined obviously in the first 14 days but had a clear rise after 28 days. In the liver, moisture and protein contents raised significantly, while crude fat decreased remarkably; liver glycogen showed the same performance profile as did muscle glycogen. These results indicated that lipid and glycogen was the better nutrient during starvation than to mobilize protein in the A. sinensis juveniles.

The effect of ultrafiltered fish protein hydrolysate level on growth performance, protein digestibility and mRNA expression of PepT1 in juvenile turbot (Scophthalmus maximus L.)

Abstract: The intention of the study was to investigate the effect of ultrafiltered fish protein hydrolysate (UF) level on growth, feed utilization, apparent digestibility coefficients and proximal intestine peptide transporter 1 (PepT1) mRNA level for juvenile turbot (Scophthalmus maximus L.). Experimental diets (UF-0, UF-5, UF-10, UF-15 and UF-20) were prepared containing about 68% plant protein, and fish meal protein was, respectively, replaced by 0%, 5%, 10%, 15% and 20% UF of dietary protein. Diet PP contained about 78% plant protein, and diet CAA contained about 10% crystalline amino acid mixture. All diets were fed to seven triplicate groups of turbot (initial weight 16.05 ± 0.03 g) for 68 days. Fish fed diet UF-10 had an increasing tendency in growth compared with diets contained UF, while dietary UF level was not significantly correlated with specific growth rate and feed intake. Feed efficiency, protein efficiency ratio and protein productive value significantly correlated with dietary UF level, and fish fed diets contained low-level UF had higher digestibility than that diets UF-0, PP and CAA. There was a decreasing tendency in PepT1 expression level with dietary UF level. The results indicated that low-level UF showed a positive effect on growth and feed utilization in juvenile turbot.