The Bulletin of the Polish Academy of Sciences: Technical Sciences (Bull.Pol. Ac.: Tech.) is published bimonthly by the Division IV Engineering Sciences of the Polish Academy of Sciences, since the beginning of the existence of the PAS in 1952. The journal is peer‐reviewed and is published both in printed and electronic form. It is established for the publication of original high quality papers from multidisciplinary Engineering sciences with the following topics preferred: Artificial and Computational Intelligence, Biomedical Engineering and Biotechnology, Civil Engineering, Control, Informatics and Robotics, Electronics, Telecommunication and Optoelectronics, Mechanical and Aeronautical Engineering, Thermodynamics, Material Science and Nanotechnology, Power Systems and Power Electronics.

Journal Metrics: JCR Impact Factor 2018: 1.361, 5 Year Impact Factor: 1.323, SCImago Journal Rank (SJR) 2017: 0.319, Source Normalized Impact per Paper (SNIP) 2017: 1.005, CiteScore 2017: 1.27, The Polish Ministry of Science and Higher Education 2017: 25 points.

Abbreviations/Acronym: Journal citation: Bull. Pol. Ac.: Tech., ISO: Bull. Pol. Acad. Sci.-Tech. Sci., JCR Abbrev: B POL ACAD SCI-TECH Acronym in the Editorial System: BPASTS.

Prof. Andrzej Dziembowski of the PAS Institute of Biochemistry and Biophysics, laureate of this year’s Prize of the Foundation for Polish Science (FNP), talks about RNA-degrading enzymes, the role of yeast in studies that help humans, and two different types of scientists.

In this study the quality of total RNA, isolated from fresh spermatozoa, was compared between boars with good and poor semen freezability (GSF and PSF, respectively). Semen from 3 boars with GSF exhibited significantly higher total motility, mitochondrial function, plasma membrane integrity and reduced lipid peroxidation compared with 3 boars with PSF after cryo- preservation. There were variations in the quality of RNA isolated from spermatozoa of boars with GSF and PSF. Boars with GSF exhibited mainly full-length, intact RNA, whereas substantial amounts of degraded RNA were detected in spermatozoa from boars with PSF. Further under- standing of the biological relevance of RNAs in sperm function is critical to improve the freezabil- ity of boar semen.

RNA extraction involves several main stages, regardless of the method of extraction: homogenization, effective denaturation of proteins from RNA, inactivation of ribonuclease and removal of any DNA, protein, and some residual contamination. Isolation of undamaged intact RNA is challenging when the related tissue contains high levels of polysaccharides and phenols. Several efforts have been made towards the comparison and optimization of extraction and purification methods for RNA from plant tissues. This is dictated by the necessity of obtaining RNA of a good quality and in a sufficient quantity for further molecular analyzes. Plant storage organs (such as bulbs or seeds) rich in polysaccharide and polyphenolic compounds present distinct challenges for total RNA isolation. Such components, considered in this case as contamination, may bind and co-precipitate with nucleic acids and negatively affect later assays. Since standard routine protocols yield unacceptable results in bulbs, we have designed a new method for RNA extraction. We used two modified procedures (based on CTAB and sarkosyl reagents) of RNA extraction from so called “difficult plant material” and compared them to a popular RNA isolation base on the column isolation kit and TriPure reagent. Our modified protocols dealt with problems of both RNA degradation and low yield caused by co-purification with polysaccharides present in plant bulbs. In this study we have shown that improvement of the CTAB and sarkosyl method with a lyophilization step of plant tissues leads to isolation of high quality RNA from difficult material like storage organs of bulbous plants. The main changes in the procedure compared to the previously described methods concerned the different order of lithium chloride and sodium acetate addition, lithium chloride concentration increase and modification of centrifugation conditions. Gel electrophoresis and spectrophotometer analysis confirmed the high quality and integrity of the obtained RNA. The modified procedures allowed for obtaining a satisfying amount of RNA concentration in the range from 280 to 950 ng/μl depending on the plant species. Thus, the demonstrated RNA isolation methods are efficient and can be used for plant material rich in polysaccharides, such as bulbs.

This study characterizes mycorrhiza helper bacteria (MHB) from selected unpolluted locations as well as subjected to industrial emissions. To determine the species of bacteria isolated from the roots of ectomycorrhizal pine and birch, a method based on the sequence analysis of a 16S rRNA gene was used. The isolated bacteria were initially characterized by available biochemical methods and phenotypic observation. On the selected bacteria representatives isolation of DNA was performed, on which the PCR reaction was carried out. In this way amplified samples were automatically sequenced and the obtained results were compared to public databases. Among the isolated bacteria Pseudomonas fluorescens SBW25 and Burkholderia xenovorans LB400 species were dominant.

The current study is the first phylogenetic and secondary RNA structure analysis of Dactylogyrus species parasitising gill filaments of Iraqi cyprinid fishes. Most previous phylogenetic studies have targeted on primary DNA sequence data. Nevertheless, RNA secondary configuration is principally helpful in systematics since they comprise features that do not appear in the primary sequence and provide morphological information. The primary objective was molecular-based identification of Dactylogyrids species using evolutionary tree and secondary RNA structure prediction. A total of 681 fish were collected from the Lesser Zab River in the northeast of Iraq in the sub-district of Altun-Kopru from August 2016 to September 2017 and brought to the Zoology Research Laboratory, Salahaddin University-Erbil, Iraq. All fish were classified as 18 cyprinid species. The species of Dactylogyrus were identified by the 28S rDNA subunit using PCR and sequencing methods, and the obtained nucleotide sequences were then compared with the available GenBank sequences. Phylogenetic relationships were concluded using Neighbour-Joining (NJ), Maximum Likelihood (ML), and Minimum Evolution (ME) methods. The results justify the validation of 11 Dactylogyrus species (three of them were newly recorded in Iraq). Additionally, out of nine infected fish species, seven of them were regarded as a new host for Dactylogyrus species. Secondary RNA configuration prediction using minimum free energy was considered as a hopeful tool for species identification. This was considered the first comprehensive phylogenetic study in the area. It was concluded that PCR sequencing, phylogenetic and secondary RNA analysis were proper molecular methods for identifying Dactylogyrids species on the gills of fishes.

An outstanding Polish biochemist, laureate of the Foundation for Polish Science Prize in 2007, member of the Polish Academy of Sciences, a head of the Department of Molecular Biomedicine at the Institute of Bioorganic Chemistry, PAS in Poznan

Professor Wlodzimierz Krzyzosiak’s research path led from the structural chemistry of nucleic acids, through molecular genetics and cancer genetics to molecular medicine. In the last years, Professor's scientific activity focused on understanding the role of RNA in the pathogenesis of human neurological diseases caused by the expansion of repetitive sequences. He also developed new methods of experimental therapy for this group of disorders using antisense oligonucleotides and RNA interference technology. He analyzed the factors influencing the microRNA biogenesis and used this knowledge to improve RNA interference technology tools in therapeutic approaches. Overall, Professor Krzyżosiak coauthored more than 130 publications, which have been cited more than 3500 times so far.

Cells of a multicellular organism are genetically identical but differ in structure and function. This heterogeneity is created by several epigenetic mechanisms during the development of the organism. The epigenetic changes- including DNA methylation, histone post-translational modifications, chromatin remodeling and RNA interference have all been shown to control chromatin structure and regulate a plethora of cellular and organismal processes. There is a strong evidence that epigenetics play a crucial role in the development of diseases such as cancer, schizophrenia or metabolic disorders. The epigenetic regulation underlie memory formation or adaptation to external stimuli. The extent to which environmental effects can provoke epigenetic responses represents an exciting area of future research. Here we review the current knowledge about the epigenetic mechanisms and their relation to the human health and disease.

Resonance assignment remains one of the hardest stages in RNA tertiary structure determination with the use of Nuclear Magnetic Resonance spectroscopy. We propose an evolutionary algorithm being a tool for an automatization of the procedure. NOE pathway, which determines the assignments, is constructed during an analysis of possible connections between resonances within aromatic and anomeric region of 2D-NOESY spectra resulting from appropriate NMR experiments. Computational tests demonstrate the performance of the evolutionary algorithm as compared with the exact branch-and-cut procedure applied for the experimental and simulated spectral data for RNA molecules.

Ammonia-oxidizing bacteria communities were evaluated in a completely mixed, laboratory scale membrane reactor (MBR) working under anoxic conditions for 5 months. The microorganisms in activated sludge were fed a synthetic medium containing 66-150 mg NH4 +-N/l. The age of the activated sludge in MBR was 50 days and the hydraulic retention time (HRT) was 3.3 days. The estimation of the diversity and complexity of the AOB community together with the identification of the dominant bacteria in the activated sludge under anoxic conditions were performed using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing. Molecular analysis of the microbial community carried out with two microbial molecular markers, 16S rRNA gene and amoA gene, suggested that nitrification was led by a Nitrosomonas-like species. In the biocenosis of the investigated bioreactor, oxygen was the crucial selective parameter. The results obtained in this work showed that amoA gene research is more suitable to study the stability and effectiveness of ammonia oxidation. This information emphasizes the necessity of the usage of molecular markers based on functional genes instead of ribosomal ones in order to present the actual state of the process performed in bioreactors. It was also stated that Nitrosomonas -like bacteria are able to perform nitritation even in anoxic environment, that is probably the reason why these bacteria are the most common AOB in different bioreactors.

Despite the considerable progress that has recently been made in medicine, the treatment of viral infections is still a problem remaining to be solved. This especially concerns infections caused by newly emerging patogenes such as: human immunodeficiency virus, hepatitis C virus or SARS-coronavirus. There are several lines of evidence that the unusual genetic polymorphism of these viruses is responsible for the observed therapeutic difficulties. In order to determine whether some parameters describing a very complex and variable viral population can be used as prognostic factors during antiviral treatment computational methods were applied. To this end, the structure of the viral population and virus evolution in the organisms of two patients suffering from chronic hepatitis C were analyzed. Here we demonstrated that phylogenetic trees and Hamming distances best reflect the differences between virus populations present in the organisms of patients who responded positively and negatively to the applied therapy. Interestingly, the obtained results suggest that based on the elaborated method of virus population analysis one can predict the final outcome of the treatment even before it has started.

In this short communication describing experiments carried out on the larvae of two insects, Unaspis euonymi Comstock (feeding on Euonymus japonicus Thunb.) and Dynaspidiotus britannicus Newstead (feeding on Laurus nobilis L.), we evaluate for the first time the efficiency of using DNA insecticides in the control of sap-sucking insects, including armored scale insects. Over a period of 10 days, high insect mortality was detected in both U. euonymi and D. britannicus, accompanied by a significant decrease in the concentration of target RNAs. At the same time, no visible changes were observed when the leaves of the host plants were subjected to treatment with DNA insecticides for one month. The results show the high efficiency of DNA insecticides used against hemipteran insect pests. It is noteworthy that the high efficiency of DNA insecticides and their low cost in comparison with RNA preparations provides a safe and extremely promising potential vehicle for the control of sap-sucking insects.

5.8S ribosomal RNA plays an important role in protein synthesis and eukaryotic ribosome translocation. Contact DNA insecticides based on antisense fragments of 5.8S ribosomal RNA gene of gypsy moth Lymantria dispar L. showed prospective insecticidal activity on its larvae. The most pronounced insecticidal effect was found for antisense fragments 10 and 11 nucleotides long (oligoRIBO-10 and oligoRIBO-11), whereas 12 nucleotides long fragment (oligoRIBO-12) caused the lowest level of insect mortality. This data corresponds to results obtained earlier using rabbit reticulocyte and wheat germ extracts, where maximum inhibition of protein synthesis was observed when a relevant oligomer 10-11 nucleotides long was used, whilst longer chain lengths resulted in reduced inhibition. Using oligoRIBO-11 fragment we have shown penetration of antisense oligonucleotides to insect cells through insects’ exoskeletons. MALDI technique registered the penetration of the oligoRIBO-11 fragment into insect cells after 30 min and a significant response of insect cells to the applied oligonucleotide after 60 min, which indicates not only that the oligonucleotide enters the insect cells, but also the synthesis of new substances in response to the applied DNA fragment. Contact DNA insecticides developed from the L. dispar 5.8S ribosomal RNA gene provide a novel biotechnology for plant protection using unmodified antisense oligonucleotides.

Obviously, the moment has come in agriculture and forestry when we must decide to gradually abandon (where possible) non-selectively acting chemical insecticides, taking into consideration the overall decrease in the total biomass of insects, especially pollinators, and the increased number of diseases and human deaths directly or indirectly associated with chemical insecticides. Yet with the world facing the rapid growth of human populations, the annual reduction of cultivated areas, and substantial losses from insect pests, most experts believe that no serious alternative to chemical insecticides exists. However, there is definitely room to create more well-tailored chemical insecticides. And there is hope, in the form of effective DNA insecticides able to provide an adequate level of safety for non-target organisms. In this short communication describing experiments carried out on the larvae of Ceroplastes japonicus Green (feeding on Ilex aquifolium Linnaeus), we show for the first time the enormous potential for the use of DNA insecticides in the control of soft scale insects and how they could replace non-selective organophosphate insecticides.

Here we investigate the microbiomes of the soil samples from the Yamal Peninsula (the surroundings of Salekhard city, Russian Federation) using a high-throughput sequencing approach. The main goal was to investigate the impact of mining on soils within the following regeneration, both during the reclamation practice and natural self-growth. Several quarries were studied, engaged in sand, clay and chromatic ores mining. The taxonomic analysis of the soil microbiomes revealed 50 bacterial and archaeal phyla; among the dominant phyla were: Proteobacteria, Actinobacteria, Acidobacteria, Chroloflexi, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, Bacteroidetes, AD3, and Nitrospirae. Compared to the typical tundra soil, which was chosen as a control, the disturbed soils had increased biodiversity and total counts for soil bacteria, archaea, and fungi, especially in the cryosolic horizon. The different mining strategies caused significantly different transformations of soil microbiomes, which was less pronounced for self-growth compared to reclaimed quarries. This isolation of the reclaimed quarry was mainly associated with the increase of the amount of acidobacteria (fam. Koribacteraceae and Acidobacteriaceae and order Ellin6513), some proteobacterial taxa (fam. Syntrophobacteraceae), and Chloroflexi (fam. Thermogemmatisporaceae). The study also revealed bacteria, which tend to be specific for marine tundra environments: gemmatimonadetes from the order N1423WL and Chloroflexi bacteria from the order Gitt-GS-136.