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Small study finds acute exercise is associated with epigenetic alteration of muscle through methylation.  This study found a hypomethylation of the genes PGC-1alpha, PDK4, and PPAR-delta with a respondent increase in expression.  The methylation activity was in the promoter region of these genes.

TNF-alpha associated with muscle loss and weakness.  TNF-alpha may also decrease testosterone production/secretion resulting in muscle loss.  

Testosterone given to elderly men with low "serum" testosterone shown to increase IGF-1 and increased muscle growth and strength.  So, this study shows that testosterone in men, seems to increase HGH production and thus increase IGF-1 production.  This may be the mechanism by which testosterone promotes muscle growth and increase in strength in men.

Great review of the Hypogonadal-obesity-adipocytokine hypothesis.

T3 induces beneficial oxidative changes in muscles through its interaction with mitochondrial receptors.  PGC-1alpha and PPAR-gamma were involved in this process.  The important point here is that T3 is increasing oxidative function of muscle through interaction with mitochondria.

Study looked at muscle loss in older men and found that low activity, type II diabetes, low Total Testosterone and low free Testosterone, and increased PTH are associated with an increased muscle loss 

Skeletal muscles are much more than just about contraction.  There produce inflammatory cytokines and other signals that have endocrine-like effects.  This article calls them myokines.  A decrease in physical activity would leave an altered myokine response effecting the liver, adipose tissue, immune system and pancreatic function.

Testosterone therapy in men with low T is associated with an increase in protein synthesis and thus an increase in muscle mass.

Testosterone promotes muscle mass increase through increased protein synthesis.

Testosterone increases muscle satellite cells in men.

gut microflora and its impact on muscle loss/muscle growth.  Not just for lean versus fat evaluation.

Online article reviewing the physiologic adaptation of muscle to resistance training.  The author used the evidence here to point to the most productive resistance training protocol--the RE effort.  The RE effort is the high repetition, lower weight regimen.  However, the RE to failure is critical to the success of RE.

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This study proposes that immediate post-resistance training protein helps to stimulate muscle growth. Recovery from training is just as important as the training itself.

Creatine supplementation shown to improve muscle recovery in injury.  The dosing included the standard loading dose at 0.3 g/kg of body weight divided in multiple doses.  Maintenance was at 0.1 g/kg of body weight.

Only abstract available here, but muscle loss associated with low Testosterone in men with AWS.

Only abstract available here--high Estradiol:Testosterone, thus high aromatase activity, increased abdominal fat and reduced lean muscle mass.  The authors also reported an higher bone mineral density, but that pales in the comparison of the metabolic dysfunction of high fat and low muscle mass causes.

great review of cirrhosis and BCCA supplementation.