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.
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.
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.
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.
A filamentous benthic cyanobacteria, strain USMAC16, was isolated from the High Arctic Svalbard archipelago, Norway, and a combination of morphological, ultrastructural and molecular characterisation (16S rRNA gene sequence) used to identify to species level. Cell dimensions, thylakoid arrangement and apical cell shape are consistent with the Pseudanabaena genus description. The molecular characterisation of P. catenata gave 100% similarity with Pseudanabaena catenata SAG 1464-1, originally reported from Germany. Strain USMAC16 was cultured under a range of temperature and photoperiod conditions, in solid and liquid media, and harvested at exponential phase to examine its phenotypic plasticity. Under different culture conditions, we observed considerable variations in cell dimensions. The longest cell (5.91±0.13 μm) was observed at 15°C under 12:12 light:dark, and the widest cell (3.24±0.06 μm) at 4°C under 12:12 light: dark in liquid media. The study provides baseline data documenting the morphological variation of P. catenata in response to changing temperature regimes.
Nitritation, the first stage of ammonia removal process is known to be limiting for total process performance. Ammonia oxidizing bacteria (AOB) which perform this process are obligatory activated sludge habitants, a mixture consisting of Bacteria, Protozoa and Metazoa used for biological wastewater treatment. Due to this fact they are an interesting bacterial group, from both the technological and ecological point of view. AOB changeability and biodiversity analyses both in wastewater treatment plants and lab-scale reactors are performed on the basis of 16S rRNA gene sequences using PCR-DGGE (Polymerase Chain Reaction – Denaturing Gradient Gel Electrophoresis) as a molecular biology tool. AOB researches are usually led with nested PCR. Because the application of nested PCR is laborious and time consuming, we have attempted to check the possibility of using only first PCR round to obtain DGGE fingerprinting of microbial communities. In this work we are comparing the nested and non-nested PCR-DGGE monitoring of an AOB community and presenting advantages and disadvantages of both methods used. The experiment revealed that PCR technique is a very sensitive tool for the amplification of even a minute amount of DNA sample. But in the case of nested-PCR, the sensitivity is higher and the template amount could be even smaller. The nested PCR-DGGE seems to be a better tool for AOB community monitoring and complexity research in activated sludge, despite shorter fragments of DNA amplification which seems to be a disadvantage in the case of bacteria identification. It is recommended that the sort of analysis approach should be chosen according to the aim of the study: nested-PCR-DGGE for community complexity analysis, while PCR-DGGE for identification of the dominant bacteria.
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.
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.
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.
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.