Three-dimensional algebraic models, also called Genetic Hotels, are developed to represent the Standard Genetic Code, the Standard tRNA Code (S-tRNA-C), and the Human tRNA code (H-tRNA-C). New algebraic concepts are introduced to be able to describe these models, to wit, the generalization of the 2n-Klein Group and the concept of a subgroup coset with a tail. We found that the H-tRNA-C displayed broken symmetries in regard to the S-tRNA-C, which is highly symmetric. We also show that there are only 12 ways to represent each of the corresponding phenotypic graphs of amino acids. The averages of statistical centrality measures of the 12 graphs for each of the three codes are carried out and they are statistically compared. The phenotypic graphs of the S-tRNA-C display a common triangular prism of amino acids in 10 out of the 12 graphs, whilst the corresponding graphs for the H-tRNA-C display only two triangular prisms. The graphs exhibit disjoint clusters of amino acids when their polar requirement values are used. We contend that the S-tRNA-C is in a frozen-like state, whereas the H-tRNA-C may be in an evolving state.

Seven‐membered ring lactones fused to coumarin scaffolds were obtained via a palladium‐catalyzed regioselective intramolecular alkoxycarbonylation under a CO atmosphere. Cyclocarbonylation of 3‐allyl‐4‐hydroxycoumarin derivatives was accessed in the absence of hydrogen gas, acidic conditions, or any other additives. The results of the control experiments revealed the importance of pKa of the substrate for initiating the reaction.

We examined statistical correlations between the frequencies of seven proposed nucleosome positioning motifs and the densities of repetitive sequences in the human genome. For both parametric and non-parametric measures of statistical correlations there is a tendency for repetitive sequence density to be negatively correlated with the density of R/Y-based nucleosome positioning motifs, while being positively correlated with that of W/S-based motifs. These results largely hold even when motifs are examined only within repeat-filtered sequences. The RRRRRYYYYY motif and its 5-base shift YYYYYRRRRR, in particular, is over-represented in the human genome; and its negative correlation is consistently present at different regions and at different length scales. For some other nucleosome positioning motifs, the relationship with repeats can be regional or length scale dependent. Considering the importance of nucleosome formation in epigenetic regulations, these results may provide new insight to the evolution of repetitive sequences.

No abstract

Recently, Trifonov's group proposed a 10-mer DNA motif YYYYYRRRRR as a solution of the long-standing problem of sequence-based nucleosome positioning. To test whether this generic decamer represents a biological meaningful signal, we compare the distribution of this motif in primates and Archaea, which are known to contain nucleosomes, and in Eubacteria, which do not possess nucleosomes. The distribution of the motif is analyzed by the mutual information function (MIF) with a shifted version of itself (MIF profile). We found common features in the patterns of this generic decamer on MIF profiles among primate species, and interestingly we found conspicuous but dissimilar MIF profiles for each Archaea tested. The overall MIF profiles for each chromosome in each primate species also follow a similar pattern. Trifonov's generic decamer may be a highly conserved motif for the nucleosome positioning, but we argue that this is not the only motif. The distribution of this generic decamer exhibits previously unidentified periodicities, which are associated to highly repetitive sequences in the genome. Alu repetitive elements contribute to the most fundamental structure of nucleosome positioning in higher Eukaryotes. In some regions of primate chromosomes, the distribution of the decamer shows symmetrical patterns including inverted repeats.