Identification of DNA Methylation Changes in European Beech Seeds during Desiccation and Storage.

Ageing and deterioration of seeds is a major problem for the maintenance of seed quality and viability during long-term storage. Prediction of early stages of seed deterioration in order to point out the plantlets' regeneration time is a major challenge of successful storage. In preserved seeds, damages accumulate within cells at the rate mainly related to their moisture content and temperature of storage. Current research reveals global alterations in DNA methylation in lipid-rich intermediate seeds during desiccation and storage at various regimes covering nonoptimal and optimal conditions. We show for the first time that monitoring of 5-methylcytosine (m5C) level in seeds can be used as a truly universal viability marker regardless of postharvest category of seeds and their composition. For seeds stored up to three years, in varied conditions, moisture content, temperature, and time of storage had significant influence on seedling emergence and DNA methylation (p < 0.05). Similarities among lipid-rich intermediate and orthodox seeds regarding different reactions of embryonic axes and cotyledons to desiccation are newly revealed. Along with previous studies on seeds dramatically different in desiccation tolerance (recalcitrant vs. orthodox), results regarding lipid-rich seeds positioned in-between (intermediate) prove that maintaining global DNA methylation status is crucial for maintaining seed viability.

Lycopene ­ the impact of supplementation on the skin aging process / Likopen ­ wplyw suplementacji na proces starzenia sie skóry.

The skin aging process is affected by multiple different factors (including sun exposure, smoking, poor diet) and reactive oxygen species (ROS). Under their influence, the skin becomes weaker, mainly elastin and collagen fibers are damaged. The amount of lipids is also reduced, leading to the death of the skin cells. The presence of free radicals also blocks the natural ability of the epidermis to regenerate. Each of these factors determines the acceleration of the signs of aging. To some extent, our body is able to deal with the free radicals by producing antioxidants. Regular supplementation is also a beneficial solution. Lycopene is a red pigment naturally found in tomatoes and is a known antioxidant. Among the carotenoids, it is the strongest singlet oxygen quencher and scavenger of peroxygen radicals, making it an important defense mechanism in the human body. The aim of this paper is to present the biological properties of lycopene in relation to its beneficial effect on the aging process of the skin.

T-psi-C: user friendly database of tRNA sequences and structures.

tRNAs have been widely studied for their role as genetic code decoders in the ribosome during translation, but have recently received new attention due to the discovery of novel roles beyond decoding, often in connection with human diseases. Yet, existing tRNA databases have not been updated for more than a decade, so they do not contain this new functional information and have not kept pace with the rate of discovery in this field. Therefore, a regularly updated database that contains information about newly discovered characteristics of tRNA molecules and can be regularly updated is strongly needed. Here, we report the creation of the T-psi-C database (http://tpsic.igcz.poznan.pl), an up-to-date collection of tRNA sequences that contains data obtained from high-throughput tRNA sequencing, e.g. all isoacceptors and isodecoders for human HEK293 cells. This database also contains 3D tRNA structures obtained from Protein Data Bank and generated using homology modeling. The T-psi-C database can be continuously updated by any member of the scientific community, and contains its own application programming interface (API), which allows users to retrieve or upload data in JSON format. Altogether, T-psi-C is user-friendly, easy to develop and an up-to-date source of knowledge about tRNAs.

Epigenetic on Earth and in Space / Epigenetyka na Ziemi i w kosmosie.

The year 1961 went down in history with exceptional scientific achievements. On May 13, the journal Nature published two articles on the first isolation of messenger ribonucleic acid (mRNA), which is an intermediate product between a gene and a protein. Just two weeks later, on May 27, the first letter of the genetic code, phenylalanine, was discovered. These discoveries made it possible to understand how genetic information is encoded and processed, thus causing the dynamic development of molecular biology. The breakthroughs of 1961 concerned not only nucleic acids. On April 12, the first human, Yuri Gagarin, entered space. Eight years later, in 1969, Neil Armstrong made his first walk on the moon, uttering the famous phrase: It is a small step for man, but a great leap for humanity. The era of conquering and learning about the cosmos has begun, mainly motivated by the natural curiosity of man and the desire to learn about the surrounding reality. The environmental factors in space are very different from terrestrial conditions, which raises questions about their effects on living organisms. In search of answers, a variety of scientific research has been carried out at the International Space Station (ISS) for over twenty years. As space travel is set to become more common in the near future, detailed studies of the effects of long-term space missions on the human body are required. These studies are currently carried out, among others using molecular biology techniques that enable detailed analysis of nucleic acids and proteins, but not only. The breakthrough achievements of 1961 initiated the development both in the field of molecular biology and the science of space, thanks to which today, 60 years after those events, we can combine knowledge and technological achievements from both fields to analyze and understand changes at the molecular level that occur as a result of being in organisms in outer space.

100 years of RNA. The Diamond Jubilee of Information RNA / 100 lat RNA. Diamentowy jubileusz informacyjnego RNA.

The year 2021 marks not only 60 years since the discovery of messenger RNA and the genetic code. Already 100 yaers passed since RNA was discovered. On the occasion of this special anniversary, we would like to recall the most important events in the history of nucleic acids that led to the above discoveries. We remind the beginning of a new era in science caused by the isolation of nuclein and then nucleic acid, whose components and properties were gradually learned, often by little-known researchers. The distinction of RNA and DNA and the analysis of their occurrence in cells made it possible to formulate the first conclusions about the functions of these compounds. Conclusions on the ratio of nitrogenous bases in DNA led to the knowledge of the structure of the double helix, triggering an avalanche of questions about the essence of transmission of genetic information. Answers began to emerge with the discovery of mRNA, and knowledge of the first three nucleotides encoding an amino acid caused a race to decipher the genetic code. The above discoveries are the foundation of molecular biology. The diamond jubilee coincided with the development of an mRNA-based vaccine against the SARS-CoV-2.

The Reverse Transcriptase/RNA Maturase Protein MatR Is Required for the Splicing of Various Group II Introns in Brassicaceae Mitochondria.

Group II introns are large catalytic RNAs that are ancestrally related to nuclear spliceosomal introns. Sequences corresponding to group II RNAs are found in many prokaryotes and are particularly prevalent within plants organellar genomes. Proteins encoded within the introns themselves (maturases) facilitate the splicing of their own host pre-RNAs. Mitochondrial introns in plants have diverged considerably in sequence and have lost their maturases. In angiosperms, only a single maturase has been retained in the mitochondrial DNA: the matR gene found within NADH dehydrogenase 1 (nad1) intron 4. Its conservation across land plants and RNA editing events, which restore conserved amino acids, indicates that matR encodes a functional protein. However, the biological role of MatR remains unclear. Here, we performed an in vivo investigation of the roles of MatR in Brassicaceae. Directed knockdown of matR expression via synthetically designed ribozymes altered the processing of various introns, including nad1 i4. Pull-down experiments further indicated that MatR is associated with nad1 i4 and several other intron-containing pre-mRNAs. MatR may thus represent an intermediate link in the gradual evolutionary transition from the intron-specific maturases in bacteria into their versatile spliceosomal descendants in the nucleus. The similarity between maturases and the core spliceosomal Prp8 protein further supports this intriguing theory.

Prediction of secondary and tertiary structures of human BC200 RNA (BCYRN1) based on experimental and bioinformatic cross-validation.

Based on experimental and bioinformatic approaches, we present the first empirically established complete secondary structure of human BC200 RNA. BC200 RNA is a brain-specific non-messenger RNA with a confirmed regulatory role in dendritic translation in neurons. Although the involvement of human BC200 RNA in various types of tumour and Alzheimer's disease has been repeatedly confirmed, the exact secondary structure remains not fully elucidated. To determine the secondary structure of BC200 RNA in vitro, we performed partial hydrolysis with sequence-specific nucleases and lead-induced cleavage. We also examined the availabilities of putative single-stranded regions and base-pairing interactions via specific DNAzymes and RNase H assay. To determine the complete spatial folding of BC200 RNA, we used experimental data as constraints in structure prediction programs and performed a comparison of results obtained by several algorithms using different criteria. Based on the experimental-derived secondary structure of BC200 RNA, we also predicted the tertiary structure of BC200 RNA. The presented combination of experimental and bioinformatic approaches not only enabled the determination of the most reliable secondary and tertiary structures of human BC200 RNA (largely in agreement with the previous phylogenetic model), but also verified the compatibility and potential disadvantages of utilizing in silico structure prediction programs.

Interaction of small molecules with polynucleotide repeats and frameshift site RNA.

This mini-review describes the interaction between small molecules and RNA, in addition to its application either in treating RNA-associated diseases or detecting target molecules. In the case of RNA-associated disease treatment, the designed small molecules interact with RNA sites, forming adducts and providing successful therapeutic strategies over oligonucleotides. On the other hand, synthetically designed RNA moieties (aptamers) interact with target molecules like toxins, drugs, hormones; these interactions are useful in the detection, quantification or separation of these target moieties.

Biological activity of N6-furfuryladenosine / Aktywnosc biologiczna N6-furfuryloadenozyny.

Cytokinins are a group of plant hormones which play an important role in plant growth and development. They produce various effects when applied to intact plants. They particularly stimulate protein synthesis and participate in cell cycle control. First discovered cytokinin was N6-furfuryladenine (kinetin). It is a strong inhibitor of proteins and nucleic acids oxidation in vitro and in vivo. Both kinetin and its ribosides (N6-furfuryladenosine, kinetin riboside) as natural compounds occur in the milk of coconuts on the nanomole level. Kinetin riboside selectively inhibits the proliferation of cancer cells and induce their apoptosis. This review focuses on the kinetin riboside occurrence, and primarily on its metabolism, and biological activity.

[Life as a way of the functioning of matter - Theory of organic being of Jedrzej Sniadecki]. / Zycie jako sposób istnienia materii ­ Teoria jestestw organicznych Jedrzeja Sniadeckiego.

In 2018 we celebrate the 250th anniversary of the Jedrzej Sniadecki's birth. This work aims to show the importance of his thoughts for the development of natural sciences. He studied at some of the largest universities in Europe, where he met great scientists of the enlightenment. The effects can be seen in his works. He was remembered as a founder of Polish biochemistry, anthropology and pathology, also as the author of chemical terminology and language. The essence of his thoughts is "Theory of Organic being", which is an attempt to answer the question: "what is life?". Jedrzej Sniadecki introduced a new definition of life based on the term "organic power". This work shows how import are the thoughts of Jedrzej Sniadecki in the context of the times in which he lived, as well as the following development of natural sciences, what makes him and his theories worth memory.

Impact of PKCε downregulation on autophagy in glioblastoma cells.

BACKGROUND: Several efforts have been focused on identification of pathways involved in malignancy, progression, and response to treatment in Glioblastoma (GB). Overexpression of PKCε was detected in histological samples from GB, anaplastic astrocytoma, and gliosarcoma and is considered an important marker of negative disease outcome. In multiple studies on GB, autophagy has been shown as a survival mechanism during cellular stress, contributing to resistance against anti-cancer agents. The main object of this research was to determine the influence of PKCε downregulation on the expression of genes involved in autophagy pathways in glioblastoma cell lines U-138 MG and U-118 MG with high PKCε level. METHODS: We conducted siRNA-mediated knockdown of PKCε in glioblastoma cell lines and studied the effects of autophagy pathway. The expression of autophagy-related genes was analyzed using qPCR and Western blot analysis was carried out to assess protein levels. Immunostaining was used to detect functional autophagic maturation process. RESULTS: We found that these cell lines exhibited a high basal expression of autophagy-related genes. Our results suggest that the loss of PKCε contributes to the downregulation of genes involved in autophagy pathways. Moreover, most of the changes we observed in Western blot analysis and endogenous immunofluorescence experiments confirmed dysfunction of autophagy programs. We found that knockdown of PKCε induced a decrease in the expression of Beclin1, Atg5, PI3K, whereas the expression of other autophagy-related proteins mTOR and Bcl2 was increased. Treatment of control siRNA glioma cells with rapamycin-induced autophagosome formation and increase in LC3-II level and caused a decrease in the expression of p62. Additionally, PKCε siRNA caused a diminution in the Akt phosphorylation at Ser473 and in the protein level in both cell lines. Moreover, we observed reduction in the adhesion of glioblastoma cells, accompanied by the decrease in total FAK protein level and phosphorylation. CONCLUSIONS: Effects of down-regulation of PKCε in glioma cells raised the possibility that the expression of PKCε is essential for the autophagic signal transduction pathways in these cells. Thus, our results identify an important role of PKCε in autophagy and may, more importantly, identifyit as a novel therapeutic target.

5SRNAdb: an information resource for 5S ribosomal RNAs.

Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA-protein interactions and molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across three domains of life. Here, we give an overview of new developments in the database and associated web tools since 2002, including updates to database content, curation processes and user web interfaces.

[Origins of molecular life sciences. Polish context]. / Poczatki molekularnych nauk o zyciu - Kontekst Polski

Different scientific disciplines such as physics, genetics or biochemistry crossed over into molecular biology in the last century. The Polish state didn't existed at the beginning of XX century, but the territory for a large number of scientists was not a limitation in delineating new routes, making fundamental discoveries or training the new generation of distinguished people of sciences. We want to tell the story of roots of molecular biology from the Polish perspective and outline its importance, by bringing closer the most essential discoveries of elite scientists in different fields of life science, associated with Poland and its territory.

Histone demethylase JMJD3 at the intersection of cellular senescence and cancer.

Cellular senescence is defined by an irreversible growth arrest and is an important biological mechanism for suppression of tumor formation. Although deletion/mutation to DNA sequences is one mechanism by which cancer cells can escape senescence, little is known about the epigenetic factors contributing to this process. Histone modifications and chromatin remodeling related to the function of a histone demethylase, jumonji domain-containing protein 3 (JMJD3; also known as KDM6B), play an important role in development, tissue regeneration, stem cells, inflammation, and cellular senescence and aging. The role of JMJD3 in cancer is poorly understood and its function may be at the intersection of many pathways promoted in a dysfunctional manner such as activation of the senescence-associated secretory phenotype (SASP) observed in aging.

The path to the genetic code.

In December of 1966 the last nucleotide triplet in the genetic code has been assigned (Brenner et al., 1967 [1]) thus completing years of studies aimed at deciphering the nature of the relationship between the sequences of genes and proteins. The end product, the table of the genetic code, was a crowning achievement of the quest to unravel the basic mechanisms underlying functioning of all living organisms on the molecular level.

Inhibition of HIV-1 gp41 expression with hammerhead ribozymes.

Despite great progress in the treatment of AIDS, HIV-1 remains one of the major concerns as a human pathogen. One of the therapeutic strategies against viral infections is the application of catalytic ribonucleic acids (ribozymes) that can significantly reduce expression of a target gene by site-specific hydrolysis of its mRNA. In the present paper, we report a study on the activity of several variants of hammerhead ribozymes targeting a conserved region within mRNA encoding HIV-1 envelope glycoprotein gp41. On the basis of the data from in vitro assays and gene silencing in the cultured cells, we propose a new hammerhead ribozyme targeting the gp41-encoding sequence that can be potentially used as a therapeutic agent in AIDS treatment. Moreover, we demonstrate that the hydrolytic activity of the ribozyme in the intracellular environment cannot be inferred solely from the results of in vitro experiments.

Global 5-methylcytosine alterations in DNA during ageing of Quercus robur seeds.

BACKGROUND AND AIMS: Epigenetic regulation plays an important role in the management of plant growth, development and response to stress factors, and several reports have indicated that DNA methylation plays a critical role in seed development and viability. This study examines changes in 5-methylcytosine (m(5)C) levels in the DNA of seeds during ageing, a process that has important implications for plant conservation and agriculture. METHODS: Changes in the global level of m(5)C were measured in mature seeds of oak, Quercus robur. The extent of DNA methylation was measured using a protocol based on two-dimensional thin-layer chromatography. Viability of seeds was determined by germination and seedling emergence tests. KEY RESULTS: An ageing-related decrease in total m(5)C during storage of recalcitrant seeds was highly and significantly correlated with a decrease in seed viability, as reflected by a reduction in germination (r = 0·8880) and seedling emergence (r = 0·8269). CONCLUSIONS: The decrease in viability during ageing of Q. robur seeds is highly correlated with a global decline in the amount of m(5)C in genomic DNA, and it is possible that this may represent a typical response to ageing and senescence in recalcitrant seeds. Potential mechanisms that drive changes in genomic DNA methylation during ageing are discussed, together with their implications for seed viability.

'Click' chemistry synthesis and capillary electrophoresis study of 1,4-linked 1,2,3-triazole AZT-systemin conjugate.

The Cu(I) catalyzed Huisgen 1,3-dipolar azide-alkyne cycloaddition (CuAAC) was applied for a nucleoside-peptide bioconjugation. Systemin (Sys), an 18-aa plant signaling peptide naturally produced in response to wounding or pathogen attack, was chemically synthesized as its N-propynoic acid functionalized analog (Prp-Sys) using the SPPS. Next, CuAAC was applied to conjugate Prp-Sys with 3'-azido-2',3'-dideoxythymidine (AZT), a model cargo molecule. 1,4-Linked 1,2,3-triazole AZT-Sys conjugate was designed to characterize the spreading properties and ability to translocate of cargo molecules of systemin. CuAAC allowed the synthesis of the conjugate in a chemoselective and regioselective manner, with high purity and yield. The presence of Cu(I) ions generated in situ drove the CuAAC reaction to completion within a few minutes without any by-products. Under typical separation conditions of phosphate 'buffer' at low pH and uncoated fused bare-silica capillary, an increasing peak intensity assigned to triazole-linked AZT-Sys conjugate was observed using capillary electrophoresis (CE) during CuAAC. CE analysis showed that systemin peptides are stable in tomato leaf extract for up to a few hours. CE-ESI-MS revealed that the native Sys and its conjugate with AZT are translocated through the tomato stem and can be directly detected in stem exudates. The results show potential application of systemin as a transporter of low molecular weight cargo molecules in tomato plant and of CE method to characterize a behavior of plant peptides and its analogs.

Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint.

Hammerhead ribozyme is a versatile tool for down-regulation of gene expression in vivo. Owing to its small size and high activity, it is used as a model for RNA structure-function relationship studies. In the present paper we describe a new extended hammerhead ribozyme HH-2 with a tertiary stabilizing motif constructed on the basis of the tetraloop receptor sequence. This ribozyme is very active in living cells, but shows low activity in vitro. To understand it, we analysed tertiary structure models of substrate-ribozyme complexes. We calculated six unique catalytic core geometry parameters as distances and angles between particular atoms that we call the ribozyme fingerprint. A flanking sequence and tertiary motif change the geometry of the general base, general acid, nucleophile and leaving group. We found almost complete correlation between these parameters and the decrease of target gene expression in the cells. The tertiary structure model calculations allow us to predict ribozyme intracellular activity. Our approach could be widely adapted to characterize catalytic properties of other RNAs.