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3

Codon usage optimization is still pretty much heurestic. The most common factor we think are important in E. Coli are: optimization to highly expressed genes, i.e. maximization of codon adaptation index [http://www.ncbi.nlm.nih.gov/pubmed/19359587/] keeping the optimal GC content [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0107319] ...


10

You can validate the interactions by knockding down (KD) or overexpressing (OE) a gene and checking the change in expression levels of the downstream nodes. You can do this in a high throughput fashion using microarray or RNAseq. For protein you can do an LC-MS. However this method cannot help you in: Differentiating direct vs indirect interactions Finding ...


0

Yes, that mixture of shapes can happen. Differences in the nucleotide base sequences between the two alleles of a gene can lead to differences in amino acid sequence, which in some cases large differences in protein shape. One example would be if one allele changed a cystine codon to any other codon, leading to loss of a disulfide bond needed to stabilize ...



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