Комбинаторные свойства сайтов рестрикции

Restriction sites are the strings in DNA recognised by their specific enzymes. Recognition of the sites is provided by their combinatoric pattern. This study presents some results obtained from 6-nucleotide long restriction sites analysis using duplet strength and editing distance methodsРассмотрены комбинаторные свойства сайтов рестрикции, обеспечивающие механизм узнавания этих сайтов специальными ферментам

Комбинаторные свойства сайтов рестрикции

Restriction sites are the strings in DNA recognised by their specific enzymes. Recognition of the sites is provided by their combinatoric pattern. This study presents some results obtained from 6-nucleotide long restriction sites analysis using duplet strength and editing distance methodsРассмотрены комбинаторные свойства сайтов рестрикции, обеспечивающие механизм узнавания этих сайтов специальными ферментам

DNA methylation changes in clonally propagated oil palm

One of the main challenges faced by the oil palm industry is fruit abnormalities, such as the “mantled” phenotype that can lead to reduced yields. This clonal abnormality is an epigenetic phenomenon and has been linked to the hypomethylation of a transposable element within the EgDEF1 gene. To understand the epigenome changes in clones, methylomes of clonal oil palms were compared to methylomes of seedling-derived oil palms. Whole-genome bisulfite sequencing data from seedlings, normal, and mantled clones were analyzed to determine and compare the context-specific DNA methylomes. In seedlings, coding and regulatory regions are generally hypomethylated while introns and repeats are extensively methylated. Genes with a low number of guanines and cytosines in the third position of codons (GC3-poor genes) were increasingly methylated towards their 3′ region, while GC3-rich genes remain demethylated, similar to patterns in other eukaryotic species. Predicted promoter regions were generally hypomethylated in seedlings. In clones, CG, CHG, and CHH methylation levels generally decreased in functionally important regions, such as promoters, 5′ UTRs, and coding regions. Although random regions were found to be hypomethylated in clonal genomes, hypomethylation of certain hotspot regions may be associated with the clonal mantling phenotype. Our findings, therefore, suggest other hypomethylated CHG sites within the Karma of EgDEF1 and hypomethylated hotspot regions in chromosomes 1, 2, 3 and 5, are associated with mantling

Triple nuclear collisions - a new method to explore the matter properties under new extreme conditions

We suggest to explore an entirely new method to experimentally and theoretically study the phase diagram of strongly interacting matter based on the triple nuclear collisions (TNC).We simulated the TNC using the UrQMD 3.4 model at the beam center of- mass collision energies √SNN = 200 GeV and √SNN = 2.76 TeV. It is found that in the most central and simultaneous TNC the initial baryonic charge density is about 3 times higher than the one achieved in the usual binary nuclear collisions at the same energies. As a consequence, the production of protons and Λ-hyperons is increased by a factor of 2 and 1.5, respectively. Using the MIT Bag model equation we study the evolution of the central cell in TNC and demonstrate that for the top RHIC energy of collision the baryonic chemical potential is 2-2.5 times larger than the one achieved in the binary nuclear collision at the same time of reaction. Based on these estimates, we show that TNC offers an entirely new possibility to study the QCD phase diagram at very high baryonic charge densities