The influence of forest habitat type on infections with spp. in south-western Poland.

This study investigates the prevalence of spp. in tick populations in different forest habitat types (broadleaf forest, mixed broadleaf and coniferous forest, and coniferous forest) in south-western Poland. During the survey periods from April to June 2018 and 2019 a total of 494 ticks, including 374 nymphs, 60 females and 60 males, were tested for infections by nested PCR targeting the A gene.

The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes.

Synonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding.

New insights into the criteria of functional heterozygosity of the Apis mellifera complementary sex determining gene-Discovery of a functional allele pair differing by a single amino acid.

The complementary sex determiner (csd) gene is responsible for controlling the sex-determination molecular switch in western honey bees (Apis mellifera): bees that are heterozygous for csd develop into females, whereas bees that are hemizygous or homozygous develop into males. The homozygous diploid males are destroyed at an early stage of their development. It has been proposed that the minimal number of amino acid differences between two csd alleles needed to fully determine femaleness is five and it has also been shown that smaller differences may result in forming an evolutionary intermediate that is not fully capable of female determination, but has increased fitness compared to the homozygous genotype.

The structure of the genetic code as an optimal graph clustering problem.

The standard genetic code (SGC) is the set of rules by which genetic information is translated into proteins, from codons, i.e. triplets of nucleotides, to amino acids.

The influence of local environmental factors in southwestern Poland on the abundance of Ixodes ricinus and prevalence of infection with Borrelia burgdorferi s.l. and B. miyamotoi.

Ticks are important ectoparasites and vectors of pathogens that cause disease in humans and animals. The natural habitat of Ixodes ricinus ticks is forests, which are convenient habitats to search for hosts, including reservoir hosts, and therefore can be an important habitat source of tick-borne pathogens. The aim of the study was to assess the usefulness of detailed forest habitat-type maps to estimate the tick-borne risk at a local scale (Lower Silesia, SW Poland).

Model of Genetic Code Structure Evolution under Various Types of Codon Reading.

The standard genetic code (SGC) is a set of rules according to which 64 codons are assigned to 20 canonical amino acids and stop coding signal. As a consequence, the SGC is redundant because there is a greater number of codons than the number of encoded labels. This redundancy implies the existence of codons that encode the same genetic information.

Models of genetic code structure evolution with variable number of coded labels.

It is assumed that at the early stage of cell evolution its translation machinery was characterized by high noise, i.e. ambiguous assignment of codons to amino acids in the genetic code, which initially encoded only few amino acids.

Some theoretical aspects of reprogramming the standard genetic code.

Reprogramming of the standard genetic code to include non-canonical amino acids (ncAAs) opens new prospects for medicine, industry, and biotechnology. There are several methods of code engineering, which allow us for storing new genetic information in DNA sequences and producing proteins with new properties. Here, we provided a theoretical background for the optimal genetic code expansion, which may find application in the experimental design of the genetic code.

Basic principles of the genetic code extension.

Compounds including non-canonical amino acids (ncAAs) or other artificially designed molecules can find a lot of applications in medicine, industry and biotechnology. They can be produced thanks to the modification or extension of the standard genetic code (SGC). Such peptides or proteins including the ncAAs can be constantly delivered in a stable way by organisms with the customized genetic code.

Optimization of the standard genetic code in terms of two mutation types: Point mutations and frameshifts.

The distinct structure and universality of the standard genetic code (SGC) have fascinated the scientists ever since the first amino acid assignments were discovered. There are several hypotheses trying to explain the origin and evolution of this code. One of them postulates that the SGC evolved to minimize harmful effects of amino acid replacements in proteins, caused by mutations and translational errors.

The influence of different types of translational inaccuracies on the genetic code structure.

Background: The standard genetic code is a recipe for assigning unambiguously 21 labels, i.e. amino acids and stop translation signal, to 64 codons.

Many alternative and theoretical genetic codes are more robust to amino acid replacements than the standard genetic code.

We evaluated the differences between the standard genetic code (SGC) and its known alternative variants in terms of the consequences of amino acids replacements. Furthermore, the properties of all the possible theoretical genetic codes, which differ from the SGC by one, two or three changes in codon assignments were also tested. Although the SGC is closer to the best theoretical codes than to the worst ones due to the minimization of amino acid replacements, from 10% to 27% of the all possible theoretical codes minimize the effect of these replacements better than the SGC.

The optimality of the standard genetic code assessed by an eight-objective evolutionary algorithm.

Background: The standard genetic code (SGC) is a unique set of rules which assign amino acids to codons. Similar amino acids tend to have similar codons indicating that the code evolved to minimize the costs of amino acid replacements in proteins, caused by mutations or translational errors. However, if such optimization in fact occurred, many different properties of amino acids must have been taken into account during the code evolution.

Correction: Optimization of the standard genetic code according to three codon positions using an evolutionary algorithm.

[This corrects the article DOI: 10.1371/journal.pone.

Optimization of the standard genetic code according to three codon positions using an evolutionary algorithm.

Many biological systems are typically examined from the point of view of adaptation to certain conditions or requirements. One such system is the standard genetic code (SGC), which generally minimizes the cost of amino acid replacements resulting from mutations or mistranslations. However, no full consensus has been reached on the factors that caused the evolution of this feature.

Role of recombination and faithfulness to partner in sex chromosome degeneration.

Sex determination in mammals is strongly linked to sex chromosomes. In most cases, females possess two copies of X chromosome while males have one X and one Y chromosome. It is assumed that these chromosomes originated from a pair of homologous autosomes, which diverged when recombination between them was suppressed.

The influence of habitat preferences on shell morphology in ecophenotypes of Trochulus hispidus complex.

Trochulus hispidus and T. sericeus are hairy snails widely distributed in Europe. They differ in shell morphology and are usually found in various land habitats.

Uneven distribution of complementary sex determiner (csd) alleles in Apis mellifera population.

The complementary sex determiner (csd) gene determines the sex of the western honey bee (Apis mellifera L.). Bees that are heterozygous at the csd locus develop into females; whereas hemizygous bees develop into males.

Optimization of amino acid replacement costs by mutational pressure in bacterial genomes.

Mutations are considered a spontaneous and random process, which is important component of evolution because it generates genetic variation. On the other hand, mutations are deleterious leading to non-functional genes and energetically costly repairs. Therefore, one can expect that the mutational pressure is optimized to simultaneously generate genetic diversity and preserve genetic information.

Representations of Search Spaces in the Problem of Mutational Pressure Optimization According to Protein-Coding Sequences.

The proper representation of the search space is the fundamental step in every optimization task, because it has a decisive impact on the quality of potential solutions. In particular, this problem appears when the search spaces are nonstandard and complex, with the large number of candidate solutions that differ from classical forms usually investigated. One of such spaces is the set of continuous-time, homogenous, and stationary Markov processes.

The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons.

There are two main forces that affect usage of synonymous codons: directional mutational pressure and selection. The effectiveness of protein translation is usually considered as the main selectional factor. However, biased codon usage can also be a byproduct of a general selection at the amino acid level interacting with nucleotide replacements.

The role of crossover operator in evolutionary-based approach to the problem of genetic code optimization.

One of theories explaining the present structure of canonical genetic code assumes that it was optimized to minimize harmful effects of amino acid replacements resulting from nucleotide substitutions and translational errors. A way to testify this concept is to find the optimal code under given criteria and compare it with the canonical genetic code. Unfortunately, the huge number of possible alternatives makes it impossible to find the optimal code using exhaustive methods in sensible time.

Optimization of Mutation Pressure in Relation to Properties of Protein-Coding Sequences in Bacterial Genomes.

Most mutations are deleterious and require energetically costly repairs. Therefore, it seems that any minimization of mutation rate is beneficial. On the other hand, mutations generate genetic diversity indispensable for evolution and adaptation of organisms to changing environmental conditions.