PRIME EDITING - a new method of editing genes / PRIME EDITING - nowa metoda edycji genów.

The Prime Editing method introduces the expected manipulations within a given genome with a Cas9-nicase and pegRNA structure and a reverse transcriptase, which is responsible for the synthesis of the segment, which is then incorporated into the edited strand. This technique is based on the previously discovered CRISPR/Cas9 method. It differs from CRISPR/Cas9 in the absence of double cracks within the DNA helix, which is due to its complex structure, including the presence of additional elements, i. e. the reverse transcriptase and the matrix within the pegRNA. PE is used to modify the DNA double helix. The work deals mainly with the creation and improvement as well as testing of the modern Prime Editing method. Information on the structure and functioning of the system is provided, as well as the research carried out so far with the use of PE, carried out within the genomes of cells derived from plant, animal, and human organisms, is described. The paper also contains information on the potential benefits and hopes related to the use of this innovative method.

Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach.

The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminating Cervidae species, with BLOG and WEKAs SMO classifier performing the best.

An Overview of Factors Affecting the Functional Quality of Common Wheat (Triticum aestivum L.).

Wheat (Triticum aestivum L.) is one of the most important crops worldwide, and, as a resilient cereal, it grows in various climatic zones. Due to changing climatic conditions and naturally occurring environmental fluctuations, the priority problem in the cultivation of wheat is to improve the quality of the crop. Biotic and abiotic stressors are known factors leading to the deterioration of wheat grain quality and to crop yield reduction. The current state of knowledge on wheat genetics shows significant progress in the analysis of gluten, starch, and lipid genes responsible for the synthesis of the main nutrients in the endosperm of common wheat grain. By identifying these genes through transcriptomics, proteomics, and metabolomics studies, we influence the creation of high-quality wheat. In this review, previous works were assessed to investigate the significance of genes, puroindolines, starches, lipids, and the impact of environmental factors, as well as their effects on the wheat grain quality.

CRISPR/Cas as the intelligent immune system of bacteria and archea / CRISPR/Cas jako inteligentny system immunologiczny bakterii i archea.

The invention of CRISPR is considered to be one of the most breakthrough discoveries in recent years in the history of biology, biotechnology, medicine, as well as the pharmaceutical and agricultural industries. The methods developed using CRISPR create new, previously unattainable possibilities that can significantly improve the quality of life. From the invention of this intelligent immune system to the present day, much research has been done using the CRISPR/Cas systems. The result of these studies was the development of a modern tool for genetic manipulation, which allows for the introduction of many modifications within the DNA, which may contribute to the silencing of the expression of given genes or their overexpression through e.g. mutations or deletions. The paper describes the application of the method for genetic manipulation with the use of the second class system ­ CRISPR/Cas9 and the advantages of this method and its advantage over the previously used genetic engineering tools, as well as its limitations and disadvantages, which significantly limit the possibility of its application. The potential use of the method was also presented as well as the research carried out with the use of CRSPR/Cas9.

Natural Molecular Mechanisms of Plant Hyperaccumulation and Hypertolerance towards Heavy Metals.

The main mechanism of plant tolerance is the avoidance of metal uptake, whereas the main mechanism of hyperaccumulation is the uptake and neutralization of metals through specific plant processes. These include the formation of symbioses with rhizosphere microorganisms, the secretion of substances into the soil and metal immobilization, cell wall modification, changes in the expression of genes encoding heavy metal transporters, heavy metal ion chelation, and sequestration, and regenerative heat-shock protein production. The aim of this work was to review the natural plant mechanisms that contribute towards increased heavy metal accumulation and tolerance, as well as a review of the hyperaccumulator phytoremediation capacity. Phytoremediation is a strategy for purifying heavy-metal-contaminated soils using higher plants species as hyperaccumulators.

Sequentiality of beetle communities in the longitudinal gradient of a lowland river in the context of the river continuum concept.

The main goal of the study was to recognize the mechanisms underlying assemblage structuring of aquatic beetle fauna inhabiting a medium-sized, lowland river exposed to anthropogenic pressures. An attempt was made to identify the impact of numerous abiotic factors on how beetle communities are formed, with particular emphasis on geomorphological and landscape-related factors, which tend to be omitted from many studies of aquatic organisms. Our intention was to refer the results of our study to the general assumptions of the River Continuum Concept. Field studies were conducted in 2010, at 13 sites located along the Krapiel River (north-western Poland). In total, 3,269 beetles were captured, representing 120 species and five ecological groups: crenophiles, rheophiles, rheobionts, stagnobionts a and stagnobionts b, which differ in environmental preferences. The core of the identified fauna was composed of stagnobionts, while rheophiles and rheobionts accounted for only 20% of the entire collected material. The formation of beetle assemblages was affected both by local factors, with an impact on aquatic environments, and by geomorphological factors, influencing a larger catchment. This was reflected in the high degree of conformity between dendrograms presenting similarities in the fauna at the studied sites, including the clustering of sites based on the abiotic factors that differentiated these sites. The presence of buffer zones, surfaces of patches denoted as "marshes" (marshland surface), "shrubs" (shrub surface), and "forests" (forest surface), and the distance to those patches seem to be the most important landscape factors affecting beetle communities. Of the factors influencing the aquatic environment, the following exerted the strongest effect: insolation, vegetation cover, presence of organic matter and BOD5, and anthropogenic pressure. The changes in assemblages of beetles determined in our study in the particular sections of the river course were a consequence of the effects of both internal factors and external ones, originating from the entire river's catchment, which is in accord with the basic assumptions of the RCC.

Horizontal Gene Transfer Involving Chloroplasts.

Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.

SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species.

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3-8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.

New record of a parasitising species of Hydrachna (Acari, Hydrachnidia) on water beetles Eretesgriseus (Fabricius, 1781) (Coleoptera, Dytiscidae, Dytiscinae, Eretini).

The larvae of water mites of the genus Hydrachna parasitise water bugs and water beetles. Larvae of the genus Hydrachna attach to the thorax and abdomen sternites and tergites under the elytra. Up to now six species of Hydrachna were recorded from Iran, but there are no records on larvae parasitising on water beetles. There is some information about parasitising of Hydrachna on water beetles from the genus Eretes, which is very well adapted to dry climate. The aim of this paper is to describe the morphology of an unknown larva of the genus Hydrachna, found on Eretesgriseus.

Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis.

The genus Secale is small but very diverse. Despite the high economic importance, phylogenetic relationships of rye species have not been fully determined, and they are extremely important for the process of breeding of new cultivars that can be enriched with functional traits derived from wild rye species. The study analyzed the degree of relationship of 35 accessions of the genus Secale, representing 13 most often distinguished species and subspecies, originating from various seed collections in the world, based on the analysis of non-coding regions of the chloroplast (cpDNA) and mitochondrial genome (mtDNA), widely used in phylogenetic and population plant studies, because of a higher rate of evolution than the coding regions. There was no clear genetic structure between different species and subspecies, which may indicated the introgression between these taxa. The obtained data confirmed that S. vavilovii was very similar to S. cereale, which confirmed the assumption that they might share a common ancestor. The results also confirmed the divergence of S. sylvestre from other species and subspecies of rye. Areas that may be useful molecular markers in studies on closely related species of the genus Secale were also indicated.

"Expression of genes encoding protein disulfide isomerase (PDI) in cultivars and lines of common wheat with different baking quality of flour".

BACKGROUND: The subject of this research was to investigate the level of expression of genes encoding protein disulfide isomerase (PDI) in cultivars and lines of wheat with different baking value of flour. PDI plays a key role in the formation of disulfide bonds in newly formed proteins. Each of cultivars and lines had a specific set of high molecular weight glutenin subunits (HMW-GS). Based on the presence of individual subunits, the potential baking value is predicted. Sometimes this value is not confirmed during technological analysis. Since there are cases where flour has a better or worse value than expected on the basis of the genotype, the expression of PDI genes was considered as a potential cause for discrepancies mentioned. RESULTS: Analysis focused on three stages of grain development. The expression level of PDI genes was compared between wheat cultivars and lines with different genotype-phenotype combinations, which means diversified sets of HMW-GS combined with diversified qualitative classification. The highest expression level of PDI was noticed at early stage of grain development, which is consistent with the function of PDI. The expression level was evaluated by the real-time PCR technique. CONCLUSION: Results obtained in this work did not allow for a clear statement of decisive significance of PDI in the context of shaping the final baking value. The results of this work contribute to an ever more in-depth understanding of the mechanisms governing baking value, and thus to the progress of the selection of new varieties with more beneficial properties.

Characterization of Genes Encoding Protein Disulfide Isomerase in Wheat Including the Specific Role of PDI in the Formation of Gluten.

The results of phylogenetic analyses revealed that the family of plant PDI may comprise of at least eight different subfamilies with varying numbers and positions of active centers while retention signals in the endoplasmic reticulum may be present or absent. At least one gene has been cloned for each phylogenetic group. Other phylogenetic analyses have indicated that the family of PDIlike proteins consists of ten classes, the first five of which include proteins equipped with two thioredoxin domains. These results indicate complexity and diversity of the family of protein disulfide isomerase in plants. The study of molecular characteristics of PDI in some cereal species have shown that this enzyme participates in the maturation of secretory proteins and also in the formation of albuminous substances in endosperm, in the mechanism of formation of disulfide bonds and polymerization of gluten polypeptides in wheat. The mechanism of formation of disulfide linkage was tested through in vitro experiments. However, it is not entirely certain whether it reflects their formation in vivo. The results of researches suggest that protein folding and disulfide bond formation occurs in the endoplasmic reticulum. PDI plays a prominent role among enzymes involved in posttranslational modification of proteins. The main goal of this work is to present research data on protein disulfide isomerase, which may be a leading research objective in the area of wheat gluten and the impact of PDI on the baking quality of wheat flour.