BACKGROUND While idiopathic pulmonary fibrosis (IPF) is one of the most common forms of interstitial lung disease, the aetiology of IPF is poorly understood. Familial cases of pulmonary fibrosis suggest a genetic basis for some forms of the disease. Recent reports have linked genetic mutations in surfactant protein C (SFTPC) with familial forms of pulmonary fibrosis, including one large family ...

An experiment was conducted to study the effects of substitution soybean meal (SBM) with canola meal (CM) and formulated diets based on total and digestible amino acid on performance, egg quality, organs weight and blood parameters of laying hens from 73 to 83 weeks of age. A total of 128 laying hens were distributed by completely randomized design in a 2×2 factorial arrangement with 2 protein ...

Evolutionary models measure the probability of amino acid substitutions occurring over different evolutionary distances. We examine various evolutionary models based on empirically derived amino acid substitution matrices. The models are constructed using the PAM and BLOSUM amino acid substitution matrices. We rescale these matrices by raising them to powers to model substitution patterns that ...

Background: CDKN2A, encoding two important tumor suppressor proteins p16 and p14, is a tumor suppressor gene. Mutations in this gene and subsequently the defect in p16 and p14 proteins lead to the downregulation of RB1/p53 and cancer malignancy. To identify the structural and functional effects of mutations, various powerful bioinformatics tools are available. The aim of this study is the ident...

Natural selection operating on amino acid substitution at single amino acid sites can be detected by comparing the rates of synonymous (r(S)) and nonsynonymous (r(N)) nucleotide substitution at single codon sites. Amino acid substitutions can be classified as conservative or radical according to whether they retain the properties of the substituted amino acid. Here methods for comparing the rat...

The mineralocorticoid hormone, aldosterone, is known to play a role in sodium homeostasis. We serendipitously found, however, highly significant association between single-nucleotide polymorphisms in the aldosterone synthase gene and plasma glucose levels in a large population of Chinese and Japanese origin. Two polymorphisms--one in the putative promoter (T-344C) and another resulting in a lys...

BACKGROUND AND AIM The present study was designed to consider whether amino acid substitution polymorphisms in O6-methylguanine-DNA methyltransferase (MGMT) and DNA methyl transferase 1 (DNMT1) genes may be associated with the genetic susceptibility to sporadic colorectal cancer. PATIENTS AND METHODS We assessed eight non-synonymous polymorphisms of these two genes by PCR/pyrosequencing. Our ...

Previous studies on human mitochondrial genomes showed that the ratio of intra-specific diversities at nonsynonymous-to-synonymous positions was two to ten times higher than the ratio of interspecific divergences at these positions, suggesting an excess of slightly deleterious nonsynonymous polymorphisms. However, such an overabundance of nonsynonymous single nucleotide polymorphisms (SNPs) was...

Stearoyl-CoA desaturase (SCD) is a rate-limiting enzyme in the biosynthesis of monounsaturated fatty acids (MUFA). A number of studies support the hypothesis that SCD gene regulation and polymorphism may affect fatty acid composition and fat quality in meat and milk. Single nucleotide polymorphisms in the coding region of the bovine stearoyl-CoA desaturase gene have been predicted to result in ...

This paper introduces a method for identifying empirically conserved amino acid substitution groups. In contrast with existing approaches that view amino acid substitution as a pairwise phenomenon, the method presented here identifies conserved groups of amino acids using a data structure called a conditional distribution matrix. The conditional distribution matrix extends the concept of a pair...