Use of comparative transcriptome analysis to identify candidate genes related to albinism in channel catfish (Ictalurus punctatus)

Zhang, Shiyong; Li, Xiang; Pan, Jianlin; Wang, Minghua; Zhong, Liqiang; Wang, Jiang; Qin, Qin; Liu, Hongyan; Shao, Junjie; Chen, Xiaohui; Bian, Wenji

doi:10.1016/j.aquaculture.2018.09.055

Cited by 13 publications

(3 citation statements)

References 62 publications

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“…The protein/energy ratio can affect the growth performance, feed efficiency, and body composition of fish. Fish body composition could be affected by protein synthesis, protein deposition rate, and protein related transcriptome changes [73,74,75]. In the present study, the moisture content in the whole body, muscle, and liver were negatively related to dietary P/E ratios.…”

Section: Discussionmentioning

confidence: 53%

Growth and Metabolic Response of Chinese Perch to Different Dietary Protein-to-Energy Ratios in Artificial Diets

Alam

Liang

Liu

et al. 2019

IJMS

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The effect of dietary nutrients on novel farm species has always garnered wide research and economic interest. Chinese perch, an economically important carnivorous fish, accepts an artificial diet after taming, so it is essential to evaluate and optimize the nutritional and metabolic demands of this species. However, little is known about the effect of an artificial diet on the growth and metabolism of Chinese perch. Therefore, the present study evaluated the growth and metabolic responses of Chinese perch to experimental diets with different dietary protein/energy (P/E) ratios. Five isoenergetic diets (18 kJ/g) with graded levels of P/E ratios of 30.58, 33.22, 35.90, 38.6, and 41.35 mg/kJ (named A, B, C, D, and E) were formulated. A total of 225 Chinese perch (64.89 ± 0.28 g) were divided into five groups (triplicate tanks for each group), distributed into 15 (350 L) fiberglass tanks, and fed twice a day at 4% of fish wet body weight with the respective P/E ratio diets for 10 weeks. Compared with the other groups, Chinese perch in Group C showed significantly improved growth performance, weight gain (WG), specific growth rate (SGR), viscerosomatic index (VSI), hepatosomatic index (HSI), intraperitoneal fat (IPF), feed utilization, feed intake (FI), feed conversion ratio (FCR), protein efficiency ratio (PER), protein retention efficiency (PRE), energy retention efficiency (ERE), and feed efficiency (FE) as well as whole-body, muscle, and liver composition. Chinese perch in Group A, on the other hand, had the lowest growth performance, feed utilization, and body composition compared with the other groups. The activities of nitrogen metabolism-related enzymes (alanine aminotransferase (ALT), aspartate aminotransferase (AST) glutamate dehydrogenase (GDH), and adenosine 5′-monophosphate deaminase (AMPD)) as well as the mRNA expression of the GDH and AMPD genes were significantly lower than those in the other groups. Similarly, the expression of NPY and AgRp were significantly higher in Group C compared with the other groups. However, the gene expression of CART and POMC was not affected by the dietary P/E ratios. In Group A, the expression of mTOR, S6K, and 4EBP1 was significantly lower and that of AMPK, LKB1, and eEF2 was significantly higher when compared with the other groups. Biochemical analysis of blood showed that ALT, AST, total protein (TP), alkaline phosphatase (ALP), glucose (GLU), blood urea nitrogen (BUN), and triglyceride (TG) levels were also affected by the dietary P/E ratio. From our results, we concluded that Chinese perch growth performance and nutrient metabolism were significantly affected by the P/E ratio of the artificial diet. Second-order polynomial regression analysis revealed that Chinese perch growth performance was optimal at a P/E ratio of 37.98 in the artificial diet.

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Section: Discussionmentioning

confidence: 53%

Growth and Metabolic Response of Chinese Perch to Different Dietary Protein-to-Energy Ratios in Artificial Diets

Alam

Liang

Liu

et al. 2019

IJMS

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“…The dietary requirement of protein and dietary energy is closely related to one another. The inclusion of suitable non‐protein energy sources (carbohydrates and lipids) can spare protein for growth and lower the feed cost (Ali, Al‐Ogaily, Al‐Asgah, Goddard, & Ahmed, 2008; Zhang et al., 2019). In the present study, WG, SGR and PER were increased with increasing dietary P/E ratios from 17.84 to 22.19 mg/kJ, after that it decreased with further increase in dietary P/E ratio (from 24.46 to 26.50 mg/kJ), which showed a plateaued at 22.19 mg/kJ (P/E).…”

Section: Discussionmentioning

confidence: 99%

Effect of dietary protein‐to‐energy ratios on growth performance, body composition, feed utilization and nitrogen metabolism enzyme of Cirrhinus mrigala

et al. 2020

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The present study was conducted to encompass the effect of dietary protein‐to‐energy ratios on growth performance, feed utilization, body composition and nitrogen metabolism enzymes of Cirrhinus mrigala. Five Iso‐energetic diets (16 kJ/g) with graded levels of P/E ratios (17.84, 19.79, 22.19, 24.46 and 26.50 mg/kJ) named as A, B, C, D and E were formulated. A total of 300 C. mrigala fingerlings (initial body weight 17.8 ± 0.12 g) were equally distributed into five groups (in triplicate). Each group was fed twice a day at 4% wet body weight with respective P/E ratio diets for 8 weeks. Highest weight gain, specific growth rate, protein efficiency ratio and protein retention efficiency were observed in group C with the lowest, feed conversion ratio, Hepatosomatic index and Viscerosomatic index as compared to other groups. Furthermore, the whole‐body and muscle tissue composition were also significantly (p < .05) influenced by the P/E ratios in diets. Among all groups, group C was significantly higher in crude protein and ash contents, with comparatively low lipids level and moisture contents compared to other groups. Additionally, the activities of nitrogen metabolism enzymes, Aspartate amino transferase, Alkaline amino transaminase, Glutamate dehydrogenase and Adenosine 5′‐monophosphate deaminase (AST, ALT, GDH and AMPD) were significantly (p < .05) increased with the increasing of P/E ratios in diets. Our results showed that on the basis of second‐order polynomial regression analysis of feed conversion ratio, the optimal dietary P/E ratio of C. mrigala (fingerlings) was 22.61 mg/kJ.

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“…Such as WWW, Internet, citation networks among scientific journals or authors, social systems and biological systems. Among which, biological systems are typical complex systems [1,[7][8][9][10][11][12][13][14][15][16] .…”

Section: Introductionmentioning

confidence: 99%

Statistical Identification of Important Nodes in Biological Systems

Wang

2021

J Syst Sci Complex

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Biological systems can be modeled and described by biological networks. Biological networks are typical complex networks with widely real-world applications. Many problems arising in biological systems can be boiled down to the identification of important nodes. For example, biomedical researchers frequently need to identify important genes that potentially leaded to disease phenotypes in animal and explore crucial genes that were responsible for stress responsiveness in plants. To facilitate the identification of important nodes in biological systems, one needs to know network structures or behavioral data of nodes (such as gene expression data). If network topology was known, various centrality measures can be developed to solve the problem; while if only behavioral data of nodes were given, some sophisticated statistical methods can be employed. This paper reviewed some of the recent works on statistical identification of important nodes in biological systems from three aspects, that is, 1) in general complex networks based on complex networks theory and epidemic dynamic models; 2) in biological networks based on network motifs; and 3) in plants based on RNA-seq data. The identification of important nodes in a complex system can be seen as a mapping from the system to the ranking score vector of nodes, such mapping is not necessarily with explicit form. The three aspects reflected three typical approaches on ranking nodes in biological systems and can be integrated into one general framework. This paper also proposed some challenges and future works on the related topics. The associated investigations have potential real-world applications in the control of biological systems, network medicine and new variety cultivation of crops.

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Use of comparative transcriptome analysis to identify candidate genes related to albinism in channel catfish (Ictalurus punctatus)

Cited by 13 publications

References 62 publications

Growth and Metabolic Response of Chinese Perch to Different Dietary Protein-to-Energy Ratios in Artificial Diets

Growth and Metabolic Response of Chinese Perch to Different Dietary Protein-to-Energy Ratios in Artificial Diets

Effect of dietary protein‐to‐energy ratios on growth performance, body composition, feed utilization and nitrogen metabolism enzyme of Cirrhinus mrigala

Statistical Identification of Important Nodes in Biological Systems

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