Analysis of Codon Usage Patterns of Six Sequenced Brachypodium distachyon Lines Reveals a Declining CG Skew of the CDSs from the 5′-ends to the 3′-ends

Brachypodium distachyon, a new monocotyledonous model plant, has received wide attention in biological research due to its small genome and numerous genetic resources. Codon usage bias is an important feature of genes and genomes, and it can be used in transgenic and evolutionary studies. In this study, the nucleotide compositions and patterns of codon usage bias were calculated using Codon W. Additionally, an ENC plot, Parity rule 2 and correspondence analyses were used to explore the major factors influencing codon usage bias patterns. The numbers of hydrogen bonds and skews were used to analyze the GC trend in the 5′-ends of the coding sequences. The results showed that minor differences in the codon usage bias patterns were revealed by the ENC plot, Parity rule 2 and correspondence analyses. The analyses of the CG-skew and the number of hydrogen bonds showed a declining trend in the number of cytosines at the 5′-ends of the CDSs (from the 5′-ends to the 3′-ends), indicating that GC may play a major role in codon usage bias. In addition, our results laid a foundation for the study of codon usage bias patterns in Brachypodium genus and suggested that the GC plays a major role in determining these patterns.

SkewDB: A comprehensive database of GC and a 10 other skews for over 28,000 chromosomes and plasmids

ABSTRACTGC skew denotes the relative excess of G nucleotides over C nucleotides on the leading versus the lagging replication strand of eubacteria. While the effect is small, typically around 2.5%, it is robust and pervasive. GC skew and the analogous TA skew are a localized deviation from Chargaff’s second parity rule, which states that G and C, and T and A occur with (mostly) equal frequency even within a strand.Most bacteria also show the analogous TA skew. Different phyla show different kinds of skew and differing relations between TA and GC skew.This article introduces an open access database (https://skewdb.org) of GC and 10 other skews for over 28,000 chromosomes and plasmids. Further details like codon bias, strand bias, strand lengths and taxonomic data are also included. The SkewDB database can be used to generate or verify hypotheses. Since the origins of both the second parity rule, as well as GC skew itself, are not yet satisfactorily explained, such a database may enhance our understanding of microbial DNA.

Oblik punomoći za sklapanje ugovora o prijenosu poslovnog udjela u svjetlu odluke Visokog trgovačkog suda od 11. prosinca 2019.

The High Commercial Court held that the power of attorney to enter into a share transfer agreement must be executed in the form required for the share transfer agreement itself – that of a notarial act or a private document certified by a public notary. In the absence of such form, the share transfer agreement is invalid. This paper examines whether this conclusion is justified. Although the High Commercial Court correctly applied the requirement of “parity” between the form of an agreement and the power of attorney for its conclusion, this rule should be restricted whenever the form’s primary purpose is not the protection of the parties. Furthermore, other statutes suggest that the share transfer agreement can be entered into on the basis of a written power of attorney with the signature authenticated by a public notary. Finally, even if the “parity” rule is literally applied, the absence of parity does not cause the invalidity of the share transfer agreement, but only its temporary ineffectiveness, which can be cured by the principal’s approval.

Tetranucleotide Profile of Herpesvirus DNA

Introduction. Herpesvirus DNAs (about 90% of the total genomic sequences of the Herpesvirales family presented in GenBank) contain at a minimum concentration one of the two tetranucleotides, CTAG or TCGA. The “underrepresentation” of CTAG was previously observed only in the DNA of some bacteria and phages. The aim of the study was the further analysis of the formal characteristics of herpesvirus DNA, as well as their comparison with the density of the virus/host DNA microhomology and with the genomic macrostructure of herpes viruses.Materials and methods. Twenty strains and isolates of each of the five types of human herpes viruses (HHV1, HHV2, HHV3, HHV4, HHV5), 10 strains of HHV8, 5 strains of HHV6A, 4 strains of HHV6B and 3 strains of HHV7 were analyzed. GenBank tools were used to determine the frequency of tetranucleotides, and human DNA fragments with size matched herpesvirus DNA were used for comparison.Results. Minimum CTAG concentration in DNA of herpes viruses is mainly characteristic of two- and singlesegment genomes with direct or inverted terminal repeats (classes A,D,E), while the minimum TCGA density is characteristic mainly for DNA that is significantly less structured (classes B,C,F). By increasing CTAG density, human herpes viruses form a sequence close to the sequence of increasing the homology density of 20 nt with human DNA, which also correlates with the macrostructure of DNA. A parallel of this minimization with the DNA structure of herpes viruses or with their belonging to one or another subfamily — as well as the context of the “minimal” CpG (that is, TCGA) — is not noted in the literature. Although herpesvirus DNA is quite large (125– 295 Kb), some of them (for example, HHV4, HHV5 and HHV7 DNA) show noticeable deviations from the second DNA parity rule, and can thus serve as a component of the molecular signature.The Discussion suggests possible hypotheses for the origin of some of the observed phenomena.

Aus für Thüringer Paritätsgesetz. Zum Urteil des Verfassungsgerichtshofs Thüringen vom 15 . Juli 2020 – VerfGH 2/20

Thuringia’s electoral law stipulates a parity rule for its next state parliament election . Each political party’s electoral list should alternately be filled by female and male candidates . The Constitutional Court of Thuringia revoked the law . The Court ruled that the parity regulation compromised voters’ and candidates’ constitutional right to freedom and equality of choice as well as political parties’ right to freedom of action and equal opportunities . The ruling is commented approvingly in the result .

The importance of Chargaff’s second parity rule for genomic signatures in metagenomics

An important problem in metagenomic data analysis is to identify the source organism, or at least taxon, of each sequence. Most methods tackle this problem in two steps by using an alignment-free approach: first the DNA sequences are represented as points of a real n-dimensional space via a mapping function then either clustering or classification algorithms are applied. Those mapping functions require to be genomic signatures: the dissimilarity between the mapped points must reflect the degree of phylogenetic similarity of the source species. Designing good signatures for metagenomics can be challenging due to the special characteristics of metagenomic sequences; most of the existing signatures were not designed accordingly and they were tested only on error-free sequences sampled from a few dozens of species.In this work we analyze comparatively the goodness of existing and novel signatures based on tetranu-cleotide frequencies via statistical models and computational experiments; we also study how they are affected by the generalized Chargaff’s second parity rule (GCSPR), which states that in a given sequence longer than 50kbp, inverse oligonucleotides are approximately equally frequent. We analyze 38 million sequences of 150 bp-1,000 bp with 1% base-calling error, sampled from 1,284 microbes. Our models indicate that GCSPR reduces strand-dependence of signatures, that is, their values are less affected by the source strand; GCSPR is further exploited by some signatures to reduce the intra-species dispersion. Two novel signatures stand out both in the models and in the experiments: the combination signature and the operation signature. The former achieves strand-independence without grouping oligonucleotides; this could be valuable for alignment-free sequence comparison methods when distinguishing inverse oligonucleotides matters. Operation signature sums the frequencies of reverse, complement, and inverse tetranucleotides; having 72 features it reduces the computational intensity of the analysis.