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Amino acid residue doublet propensity in the protein–RNA interface and its application to RNA interface prediction
TLDR
A new residue-based propensity is introduced, which gives a measure of residue pairing preferences in the RNA interface of a protein (residue doublet interface propensity), which contains much more information than the sum of two singlet propensities alone. Expand
Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions.
TLDR
Phylogenetic analysis of eRF1s supports the hypothesis that the genetic code in ciliates has deviated independently several times from the universal genetic code, and that different ciliate e RF1s may have undergone different processes to change the codon specificity. Expand
Highly Divergent Actins from Karyorelictean, Heterotrich, and Litostome Ciliates1
TLDR
The putative amino acid sequences of the newly determined actin genes were found to be highly divergent as expected from previous findings of other ciliate actins, indicating that act in genes are highly diverse even within the phylum Ciliophora. Expand
A single amino acid substitution alters omnipotent eRF1 of Dileptus to euplotes-type dualpotent eRF1: standard codon usage may be advantageous in raptorial ciliates.
TLDR
The results indicate that R128 is one of the key residues preserving the ability to recognize all three stop codons, especially UGA, in Dileptus, and a possible advantage that ciliates from the Litostomatea class may gain from using the standard genetic code. Expand
A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement
TLDR
The hypothetical chromosomes by comparison with the channel catfish demonstrated the usefulness of the striped catfish genome as a marker resource and developed genomic resources for the stripedCatfish. Expand
In silico studies for the interaction of tumor necrosis factor-alpha (TNF-α) with different saponins from Vietnamese ginseng (Panax vietnamesis)
TLDR
Tumor necrosis factor-alpha (TNF-α) is a cytokine that plays an important role in inflammatory process and tumor development and triterpene saponins have a good binding affinity with protein TNF- α. Expand
The relation between the stop codon reassignment and the specificity of eukaryotic release factor 1 (eRF1) in Blepharisma (第40回日本原生動物学会大会講演要旨)
In Blepharisma, the universal stop codon UGA has been known to reassign to sense codon (Trp). The reassignment of the codon UGA implies that eRF1 (the stop codon-recognizing protein) may loses itsExpand
Ciliates use both variant and universal genetic codes: evidence of omnipotent eRF1s in the class Litostomatea.
TLDR
Examination of the capacity of the translation termination factor eRF1 for recognizing stop codons in litostome ciliates showed that Didinium and Dileptus e RF1s efficiently recognize all three stopcodons, the first experimental evidence that strongly supports the hypothesis that litostomes use universal genetic code. Expand
Metagenome Sequences from the Environment of Diseased Otter Clams, Lutraria rhynchaena, from a Farm in Vietnam
Otter clam farming in Vietnam has recently encountered difficulties due to swollen-siphon disease. Here, we report the metagenome sequences of microorganisms extracted from the siphon tissue ofExpand
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