This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.
2 CB Cowey (1995) Protein and amino acid requirements: a critique of methods. J Appl Ichthyol 11, 199–204.
3 RL Naylor , RW Hardy , DP Bureau , et al. (2009) Feeding aquaculture in an era of finite resources. Proc Natl Acad Sci U S A 106, 15103–15110.
CG Carter & RC Hauler (2000) Fish meal replacement by plant meals in extruded feeds for Atlantic salmon, Salmo salar L. Aquaculture
5 SJ Kaushik , JP Cravedi , JP Lalles , et al. (1995) Partial or total replacement of fish meal by soybean protein on growth, protein utilization, potential estrogenic or antigenic effects, cholesterolemia and flesh quality in rainbow trout, Oncorhynchus mykiss. Aquaculture 133, 257–274.
DM Gatlin , FT Barrows , P Brown , et al. (2007) Expanding the utilization of sustainable plant products in aquafeeds: a review. Aquac Res
M Pack , M Rodehutscord , S Jacobs , et al. (1995) Amino acid requirements of rainbow trout (Oncorhynchus mykiss) II. Protein deposition as function of dietary methionine, threonine and arginine. J Appl Ichthyol
10 GL Rumsey , JW Page & ML Scott (1983) Methionine and cystine requirements of rainbow trout. Prog Fish Cult 45, 139–143.
H Sveier , H Nordås , GE Berge , et al. (2001) Dietary inclusion of crystalline d- and l-methionine: effects on growth, feed and protein utilization, and digestibility in small and large Atlantic salmon (Salmo salar L.). Aquac Nutr
12 K Kino & J Okumura (1986) Improvement of body weight and nitrogen balance of chicks fed histidine-free or lysine-free diets with supplementation of graded levels of sulfur-containing amino acids. Poult Sci 65, 1736–1740.
RA Bradshaw , WW Brickey & KW Walker (1998) N-Terminal processing: the methionine aminopeptidase and Nα-acetyl transferase families. Trends Biochem Sci
14 S Métayer-Coustard , H Mameri , I Seiliez , et al. (2010) Methionine deprivation regulates the S6K1 pathway and protein synthesis in avian QM7 myoblasts without activating the GCN2/eIF2 alpha cascade. J Nutr 140, 1539–1545.
S Tesseraud , S Métayer-Coustard , S Boussaid , et al. (2007) Insulin and amino acid availability regulate atrogin-1 in avian QT6 cells. Biochem Biophys Res Commun
16 W B'chir , A-C Maurin , V Carraro , et al. (2013) The eIF2α/ATF4 pathway is essential for stress-induced autophagy gene expression. Nucleic Acids Res 41, 7683–7699.
18 D Dardevet , I Rieu , P Fafournoux , et al. (2003) Leucine: a key amino acid in ageing-associated sarcopenia? Nutr Res Rev 16, 61–70.
19 SR Kimball & LS Jefferson (2004) Regulation of global and specific mRNA translation by oral administration of branched-chain amino acids. Biochem Biophys Res Commun 313, 423–427.
F Yoshizawa (2004) Regulation of protein synthesis by branched-chain amino acids in vivo
. Biochem Biophys Res Commun
S Takagi , S Shimeno , H Hosokawa , et al. (2001) Effect of lysine and methionine supplementation to a soy protein concentrate diet for red sea bream Pagrus major
. Fisheries Sci
TG Gaylord & FT Barrows (2009) Multiple amino acid supplementations to reduce dietary protein in plant-based rainbow trout, Oncorhynchus mykiss, feeds. Aquaculture
26 M Espe , EM Hevrøy , B Liaset , et al. (2008) Methionine intake affect hepatic sulphur metabolism in Atlantic salmon, Salmo salar. Aquaculture 274, 132–141.
M Lansard , S Panserat , E Plagnes-Juan , et al. (2011)
l-Leucine, l-methionine, and l-lysine are involved in the regulation of intermediary metabolism-related gene expression in rainbow trout hepatocytes. J Nutr
PM Craig , A Massarsky & TW Moon (2013) Understanding glucose uptake during methionine deprivation in incubated rainbow trout (Oncorhynchus mykiss) hepatocytes using a non-radioactive method. Comp Biochem Physiol B Biochem Mol Biol
SJ Kaushik & I Seiliez (2010) Protein and amino acid nutrition and metabolism in fish: current knowledge and future needs. Aquac Res
32 MM Bradford (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein–dye binding. Anal Biochem 72, 248–254.
I Belghit , S Panserat , B Sadoul , et al. (2013) Macronutrient composition of the diet affects the feeding-mediated down regulation of autophagy in muscle of rainbow trout (O. mykiss). PLOS ONE
34 W Dai , S Panserat , JA Mennigen , et al. (2013) Post-prandial regulation of hepatic glucokinase and lipogenesis requires the activation of TORC1 signalling in rainbow trout (Oncorhynchus mykiss). J Exp Biol 216, 4483–4492.
I Seiliez , S Panserat , M Lansard , et al. (2011) Dietary carbohydrate-to-protein ratio affects TOR signaling and metabolism-related gene expression in the liver and muscle of rainbow trout after a single meal. Am J Physiol Regul Integr Comp Physiol
36 I Seiliez , J-C Gabillard , M Riflade , et al. (2012) Amino acids downregulate the expression of several autophagy-related genes in rainbow trout myoblasts. Autophagy 8, 364–375.
37 I Seiliez , GC Taty Taty , J Bugeon , et al. (2013) Myostatin induces atrophy of trout myotubes through inhibiting the TORC1 signaling and promoting ubiquitin–proteasome and autophagy–lysosome degradative pathways. Gen Comp Endocrinol 186, 9–15.
38 I Seiliez , J Gutierrez , C Salmerón , et al. (2010) An in vivo and in vitro assessment of autophagy-related gene expression in muscle of rainbow trout (Oncorhynchus mykiss). Comp Biochem Physiol B Biochem Mol Biol 157, 258–266.
39 MW Pfaffl , GW Horgan & L Dempfle (2002) Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30, e36.
41 M Mambrini , AJ Roem , JP Carvèdi , et al. (1999) Effects of replacing fish meal with soy protein concentrate and of dl-methionine supplementation in high-energy, extruded diets on the growth and nutrient utilization of rainbow trout, Oncorhynchus mykiss. J Anim Sci 77, 2990–2999.
42 AJ Jackson & BS Capper (1982) Investigations into the requirements of the tilapia Sarotherodon mossambicus for dietary methionine, lysine and arginine in semi-synthetic diets. Aquaculture 29, 289–297.
43 K-I Kim , TB Kayes & CH Amundson (1992) Requirements for sulfur amino acids and utilization of d-methionine by rainbow trout (Oncorhynchus mykiss). Aquaculture 101, 95–103.
SR Kimball , LM Shantz , RL Horetsky , et al. (1999) Leucine regulates translation of specific mRNAs in L6 myoblasts through mTOR-mediated changes in availability of eIF4E and phosphorylation of ribosomal protein S6. J Biol Chem
45 SR Kimball & LS Jefferson (2002) Control of protein synthesis by amino acid availability. Curr Opin Clin Nutr 5, 63–67.
AK Sikalidis , KM Mazor , M Kang , et al. (2013) Total 4EBP1 is elevated in liver of rats in response to low sulfur amino acid intake. J Amino Acids
47 AK Sikalidis & MH Stipanuk (2010) Growing rats respond to a sulfur amino acid-deficient diet by phosphorylation of the α subunit of eukaryotic initiation factor 2 heterotrimeric complex and induction of adaptive components of the integrated stress response. J Nutr 140, 1080–1085.
TG Anthony , BJ McDaniel , RL Byerley , et al. (2004) Preservation of liver protein synthesis during dietary leucine deprivation occurs at the expense of skeletal muscle mass in mice deleted for eIF2 kinase GCN2. J Biol Chem
M Sandri (2010) Autophagy in skeletal muscle. FEBS Lett
Y Chen & DJ Klionsky (2011) The regulation of autophagy – unanswered questions. J Cell Sci
51 A Cuervo (2004) Autophagy: many paths to the same end. Mol Cell Biochem 263, 55–72.
J Kim , M Kundu , B Viollet , et al. (2011) AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1. Nat Cell Biol
N Mizushima & T Yoshimori (2007) How to interpret LC3 immunoblotting. Autophagy
54 DJ Klionsky , F Abdalla , H Abeliovich , et al. (2012) Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 8, 445–554.
55 S Mordier , C Deval , D Béchet , et al. (2000) Leucine limitation induces autophagy and activation of lysosome-dependent proteolysis in C2C12 myotubes through a mammalian target of rapamycin-independent signaling pathway. J Biol Chem 275, 29900–29906.
S Lorin , MJ Tol , C Bauvy , et al. (2013) Glutamate dehydrogenase contributes to leucine sensing in the regulation of autophagy. Autophagy
57 C Mammucari , G Milan , V Romanello , et al. (2007) FoxO3 controls autophagy in skeletal muscle in vivo. Cell Metab 6, 458–471.
J Füllgrabe , DJ Klionsky & B Joseph (2013) Histone post-translational modifications regulate autophagy flux and outcome. Autophagy
D Attaix & D Taillandier (1998) The critical role of the ubiquitin–proteasome pathway in muscle wasting in comparison to lysosomal and Ca2+-dependent systems. In Advances in Molecular and Cell Biology, pp. 235–266 [ EE Bittar and AJ Rivett , editors]. Stamford, CT: JAI Press.
SH Lecker , RT Jagoe , A Gilbert , et al. (2004) Multiple types of skeletal muscle atrophy involve a common program of changes in gene expression. FASEB J
T Kumamoto , S Fujimoto , T Ito , et al. (2000) Proteasome expression in the skeletal muscles of patients with muscular dystrophy. Acta Neuropathol (Berl)
63 DJ Glass (2010) Signaling pathways perturbing muscle mass. Curr Opin Clin Nutr 13, 225–229.
P Bonaldo & M Sandri (2013) Cellular and molecular mechanisms of muscle atrophy. Dis Model Mech
S Schiaffino , KA Dyar , S Ciciliot , et al. (2013) Mechanisms regulating skeletal muscle growth and atrophy. FEBS J
S Tesseraud , I Bouvarel , A Collin , et al. (2009) Daily variations in dietary lysine content alter the expression of genes related to proteolysis in chicken pectoralis major muscle. J Nutr
67 RA Frost , GJ Nystrom , LS Jefferson , et al. (2007) Hormone, cytokine, and nutritional regulation of sepsis-induced increases in atrogin-1 and MuRF1 in skeletal muscle. Am J Physiol Endocrinol Metab 292, E501–E512.
M Sandri (2013) Protein breakdown in muscle wasting: role of autophagy–lysosome and ubiquitin–proteasome. Int J Biochem Cell Biol
69 S Cohen , B Zhai , SP Gygi , et al. (2012) Ubiquitylation by Trim32 causes coupled loss of desmin, Z-bands, and thin filaments in muscle atrophy. J Cell Biol 198, 575–589.
A Hishiya , S Iemura , T Natsume , et al. (2006) A novel ubiquitin-binding protein ZNF216 functioning in muscle atrophy. EMBO J