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The study investigates the representation of the vaccine against COVID-19 in “editorial”, “opinion” and “analysis” articles. The study draws on the appraisal model as a linguistic tool to analyze the attitudinal language of the articles, the differences in which have the potential to be the ground for differentiating “opinion”, “editorial”, and “analysis” texts. The selected 30 articles belong to the period from March 2020 to January 2021, when the importance of the vaccine was unprecedented and all political and economic factors moved to the background. The findings indicate no significant differences in the types of evaluations used, though demonstrate some tendencies that constitute grounds for further research in the field: 1) “analysis” texts draw on less evaluative elements than “editorial” and “opinion”; 2) “opinion” texts demonstrate a balance of appreciation and judgment; 3) there is a dominance of judgment in “editorial” texts. The paper demonstrates that all texts judge the vaccines as effective tools and avoid emotional or negative evaluations.

The ways of explication of evidentiality in analytical articles of the English-language press are investigated. 30 articles of newspapers “The Washington Post”, “The Guardian”, “The Independent” for 2021 are analyzed. The classification of evidential values is presented on the basis of two indicators: the source of information and its degree of reliability. Three types of evidentiality have been identified: direct evidentiality (there is a clear indication of the source of information); impersonal evidentiality (lack of an identified source of information); author’s evidentiality (based on the author’s conclusions). The results of the study showed a significant superiority of direct evidentiality (74 %), realized through the precise indication of the source of information and the use of the author’s “we”. It was revealed that impersonal evidentiality is not typical for an analytical article (6 %). This is due to its specific characteristics: the desire for objectivity and transparency of the data provided. It is noted that this type of evidentiality is realized through adverbs, indicating an anonymous source and using collective nouns. It is shown that the author’s evidentiality is found in 20 % of cases and is realized through filler words, main sentences like that means, adverbs, impersonal sentences using verbs of perception, constructions “to be + adjective with a probability value”, modal verbs.

The article dwells on the two main types of the analytical articles - argumentative and reasoning - which are the results of the variations in the analytical block of the genre composition. It is demonstrated that the argumentative analytical article has a fixed structure which unwinds horizontally or vertically and consists of arguments which support and counter the thesis. It is shown that the reasoning analytical article is aimed at answering an open question, which means that there can’t be a stated structure of the analytical block. The typical elements of this type are description of the main aspects of the situation, coverage of the main views on the issue, explanation of the events and their interconnection, consideration of the possible reactions and consequences.

Humans are well-versed in reasoning about the behaviors of physical objects and choosing actions accordingly to accomplish tasks, while it remains a major challenge for AI. To facilitate research addressing this problem, we propose a new testbed that requires an agent to reason about physical scenarios and take an action appropriately. Inspired by the physical knowledge acquired in infancy and the capabilities required for robots to operate in real-world environments, we identify 15 essential physical scenarios. For each scenario, we create a wide variety of distinct task templates, and we ensure all the task templates within the same scenario can be solved by using one specific strategic physical rule. By having such a design, we evaluate two distinct levels of generalization, namely the local generalization and the broad generalization. We conduct an extensive evaluation with human players, learning agents with varying input types and architectures, and heuristic agents with different strategies. Inspired by how human IQ is calculated, we define the physical reasoning quotient (Phy-Q score) that reflects the physical reasoning intelligence of an agent. Our evaluation shows that 1) all agents are far below human performance, and 2) learning agents, even with good local generalization ability, struggle to learn the underlying physical reasoning rules and fail to generalize broadly. We encourage the development of intelligent agents that can reach the human level Phy-Q score. Website: https://github.com/phy-q/benchmark

The article deals with the analysis of the balance of opinion in the newspaper, which is originally realized through editorial and op-ed genres. We analyzed 20 articles from “The Wall Street Journal” and “The New York Times” in the genres of editorial and op-ed about events in Afghanistan in August 2021, which were interpreted differently in mass media due to the role of the White House. The findings prove that in the context of new digital reality the op-ed has lost its original function of conveying alternative positions to the ones stated in the editorial; at the same time newspapers tend to advocate the positions shared by the political parties they have historically developed close relations with: “The Wall Street Journal” - with the Republican Party, “The New York Times” - the Democratic Party.

Protein synthesis on ribosomes is considered the main process in cell life. Regulation of ribosomal protein gene expression plays an important role in the balanced synthesis of proteins and RNA in ribosomal biogenesis. This review is focused on some features of autoregulation of ribosomal protein synthesis in prokaryotes. Inhibition of the synthesis of ribosomal proteins encoded by 12 operons by mechanisms of competition , "entrapment", and retroregulation are discussed. Examples of regulation of protein synthesis by individual ribosomal proteins and their complexes are presented.

Potato virus Y (PVY) is one of the most common and harmful plant viruses. Translation of viral RNA starts with the interaction between the plant cap-binding translation initiation factors eIF4E and viral genome-linked protein (VPg) covalently attached to the viral RNA. Disruption of this interaction is one of the natural mechanisms of plant resistance to PVY. The multigene eIF4E family in the potato (Solanum tuberosum L.) genome contains genes for the translation initiation factors eIF4E1, eIF4E2, and eIF(iso)4E. However, which of these factors can be recruited by the PVY, as well as the mechanism of this interaction, remain obscure. Here, we showed that the most common VPg variant from the PVY strain NTN interacts with eIF4E1 and eIF4E2, but not with eIF(iso)4E. Based on the VPg, eIF4E1, and eIF4E2 models and data on the natural polymorphism of VPg amino acid sequence, we suggested that the key role in the recognition of potato cap-binding factors belongs to the R104 residue of VPg. To verify this hypothesis, we created VPg mutants with substitutions at position 104 and examined their ability to interact with potato eIF4E factors. The obtained data were used to build the theoretical model of the VPg-eIF4E2 complex that differs significantly from the earlier models of VPg complexes with eIF4E proteins, but is in a good agreement with the current biochemical data.

Humans are well-versed in reasoning about the behaviors of physical objects and choosing actions accordingly to accomplish tasks, while it remains a major challenge for AI. To facilitate research addressing this problem, we propose a new testbed that requires an agent to reason about physical scenarios and take an action appropriately. Inspired by the physical knowledge acquired in infancy and the capabilities required for robots to operate in real-world environments, we identify 15 essential physical scenarios. We create a wide variety of distinct task templates, and we ensure all the task templates within the same scenario can be solved by using one specific strategic physical rule. By having such a design, we evaluate two distinct levels of generalization, namely the local generalization and the broad generalization. We conduct an extensive evaluation with human players, learning agents with varying input types and architectures, and heuristic agents with different strategies. Inspired by how human IQ is calculated, we define the physical reasoning quotient (Phy-Q score) that reflects the physical reasoning intelligence of an agent using the physical scenarios we considered. Our evaluation shows that 1) all agents are far below human performance, and 2) learning agents, even with good local generalization ability, struggle to learn the underlying physical reasoning rules and fail to generalize broadly. We encourage the development of intelligent agents that can reach the human level Phy-Q score. Website: https://github.com/phy-q/benchmark, For the associated website, see https://github.com/phy-q/benchmark

Ribosomal protein L1 is a conserved two-domain protein that is involved in formation of the L1 stalk of the large ribosomal subunit. When there are no free binding sites available on the ribosomal 23S RNA, the protein binds to the specific site on the mRNA of its own operon (L11 operon in bacteria and L1 operon in archaea) preventing translation. Here we show that the regulatory properties of the r-protein L1 and its domain I are conserved in the thermophilic bacteria Thermus and Thermotoga and in the halophilic archaeon Haloarcula marismortui. At the same time the revealed features of the operon regulation in thermophilic bacteria suggest presence of two regulatory regions.

Aminoacyl-RNA synthetases (aaRSs) are among the key enzymes of protein biosynthesis. They are responsible for conducting the first step in the protein biosynthesis, namely attaching amino acids to the corresponding tRNA molecules both in cytoplasm and mitochondria. More and more research demonstrates that mutations in the genes encoding aaRSs lead to the development of various neurodegenerative diseases, such as incurable Charcot–Marie–Tooth disease (CMT) and distal spinal muscular atrophy. Some mutations result in the loss of tRNA aminoacylation activity, while other mutants retain their classical enzyme activity. In the latter case, disease manifestations are associated with additional neuron-specific functions of aaRSs. At present, seven aaRSs (GlyRS, TyrRS, AlaRS, HisRS, TrpRS, MetRS, and LysRS) are known to be involved in the CMT etiology with glycyl-tRNA synthetase (GlyRS) being the most studied of them.

The conserved two-domain ribosomal protein (r-protein) L1 is a structural part of the L1 stalk of the large ribosomal subunit and regulates the translation of the operon that comprises its own gene. The regulatory properties of the bacterial r-protein L1 have only been studied in detail for Escherichia coli; however, there were no such studies for other bacteria, in particular, Thermus thermophilus and Thermotoga maritima, which are more evolutionarily ancient. It is known that domain I of the r-protein L1 might have regulatory properties of the whole protein. The aim of this study was to identify regulatory sites on the mRNA of T. thermophilus and T. maritima that interact with r-proteins L1, as well as with their domains I from the same organisms. An analysis of the mRNA of the L11 operon T. thermophilus showed the presence of one potential binding site of the L1 r-protein, two such regions were found also in the mRNA sequence of the L11 operon of T. maritima. The dissociation constants for the L1 proteins from T. thermophilus and T. maritima and their domains I with mRNA fragments from the same organisms that contain the supposed L1-binding sites were determined by surface plasmon resonance. It has been shown that the ribosomal proteins L1 as their domains I bind specific fragments of mRNA from the same organisms that may suggest regulatory activity of the L1 protein in the T. thermophilus and T. maritima and conservatism of the principles of L1-RNA interactions.

State governments and universities’ officials now realize that modern elite universities represent the source of national and cultural pride, the stock of human capital that ensures prosperity of any country. Elitism and prestige of a university are determined by the position it occupies in different ratings. This position depends heavily on science citation indexes for published academic papers. However most high quality, peer-reviewed scientific journals accept articles in English and require standard scientific communication language. The article advances the general principle of the English-language academic writing, analyses existing recommendations and reveals difficulties regarding the problem. The authors develop some techniques for training in academic writing which they introduce in Peter the Great St. Petersburg Polytechnic University. To estimate proposed techniques, academic writing skills of participants were measured before and after the training. The significant improvement was identified. So the proposed techniques can be applied to broaden professional and academic competences of the students. That will increase the number of publications in high quality scientific journals, provide more opportunities for students to participate in international conferences and seminars, and serve the aim of improving University image.

The use of rendering in learning foreign languages is a widespread method in the foreign language learning process. We determine rendering as a process of reading, analyzing a text and summing up its main ideas. The use of rendering is aimed at comprehending, remembering and producing a foreign language as well as emulating the specific of different text genres. The present study explores specific features of an analytical article that must be taken into consideration in learning rendering. By analytical article we mean an objective text, aimed at analyzing/clarifying a situation. However, it sees an increase of subjectivity, which leads to growth of language means’ use, among which contrast plays a considerable role. Contrast as the phenomenon of mutual opposition of text units is considered as one of the semantic and stylistic types of the text organization used in order to put forward the important information introduced by the author. Contrast in an analytical article could be expressed in two forms: 1) explicit form of contrast based on systemic opposition of lexical units in the text (we can use antonyms as well as some stylistic devices which express opposition like oxymoron, antheses, paradox), and 2) implicit form where text units could be considered as contrasting only in the context of the whole text. Analyzing the articles most students ignore the phenomenon of contrast and therefore misrepresent the main gist of the text. This study is intended to illustrate the difficulties in rendering of an analytical article and to help students interpret the text correctly.

The Sm and Sm-like proteins are widely distributed among bacteria, archaea and eukarya. They participate in many processes related to RNA-processing and regulation of gene expression. While the function of the bacterial Lsm protein Hfq and eukaryotic Sm/Lsm proteins is rather well studied, the role of Lsm proteins in Archaea is investigated poorly. In this work, the RNA-binding ability of an archaeal Hfq-like protein from Methanococcus jannaschii has been studied by X-ray crystallography, anisotropy fluorescence and surface plasmon resonance. It has been found that MjaHfq preserves the proximal RNA-binding site that usually recognizes uridine-rich sequences. Distal adenine-binding and lateral RNA-binding sites show considerable structural changes as compared to bacterial Hfq. MjaHfq did not bind mononucleotides at these sites and would not recognize single-stranded RNA as its bacterial homologues. Nevertheless, MjaHfq possesses affinity to poly(A) RNA that seems to bind at the unstructured positive-charged N-terminal tail of the protein.

A correlation between the ligand–protein affinity and the identification of the ligand in the experimental electron density maps obtained by X-ray crystallography has been tested for a number of RNA-binding proteins. Bacterial translation regulators ProQ, TRAP, Rop, and Hfq together with their archaeal homologues SmAP have been used. The equilibrium dissociation constants for the N-methyl-anthraniloyl-labelled adenosine and guanosine monophosphates titrated by the proteins have been determined by the fluorescent anisotropy measurements. The estimated stability of the nucleotide–protein complexes has been matched with a presence of the nucleotides in the structures of the proposed nucleotide–protein complexes. It has been shown that the ribonucleotides can be definitely identified in the experimental electron density maps at equilibrium dissociation constant

Ribosomal protein L1 consists of two domains connected by two oppositely directed fragments of the polypeptide chain in a hinge-resembling fashion. The domain arrangement determines the overall shape of the protein, corresponding to an open or a closed conformation. Ribosomal L1 proteins from archaea demonstrate the open conformation in both isolated and RNA-bound forms. RNA-free ribosomal L1 proteins from bacteria display the closed conformation, whereas in complex with RNA these proteins exist in an open conformation similar to their archaeal counterparts. Analysis of all available L1 amino-acid sequences shows that in comparison to the archaeal proteins, the bacterial proteins possess an extra residue in one of the two interdomain fragments which could be responsible for their closed conformation. To verify this suggestion, a Thermus thermophilus L1 mutant lacking one residue in the fragment corresponding to the hinge was obtained and its crystal structure was solved. It was found that this mutation transformed the closed conformation of the bacterial L1 protein into an open conformation similar to that of the archaeal L1 proteins.

Ribosomal protein L1 has a dual function as a ribosomal protein binding 23S rRNA and as a translational repressor binding its mRNA. L1 is a two-domain protein with N- and C-termini located in domain I. Earlier it was shown that L1 interacts with the same targets on both rRNA and mRNA mainly through domain I. We have suggested that domain I is necessary and sufficient for specific RNA-binding by L1. To test this hypothesis, a truncation mutant of L1 from Thermus thermophilus, representing domain I, was constructed by deletion of the central part of the L1 sequence, which corresponds to domain II. It was shown that the isolated domain I forms stable complexes with specific fragments of both rRNA and mRNA. The crystal structure of the isolated domain I was determined and compared with the structure of this domain within the intact protein L1. This comparison revealed a close similarity of both structures. Our results confirm our suggestion that in protein L1 its domain I alone is sufficient for specific RNA binding, whereas domain II stabilizes the L1-rRNA complex.

The RNA-binding ability of ribosomal protein L1 is of profound interest, since L1 has a dual function as a ribosomal structural protein that binds rRNA and as a translational repressor that binds its own mRNA. Here, we report the crystal structure at 2.6 A resolution of ribosomal protein L1 from the bacterium Thermus thermophilus in complex with a 38 nt fragment of L1 mRNA from Methanoccocus vannielii. The conformation of RNA-bound T.thermophilus L1 differs dramatically from that of the isolated protein. Analysis of four copies of the L1-mRNA complex in the crystal has shown that domain II of the protein does not contribute to mRNA-specific binding. A detailed comparison of the protein-RNA interactions in the L1-mRNA and L1-rRNA complexes identified amino acid residues of L1 crucial for recognition of its specific targets on the both RNAs. Incorporation of the structure of bacterial L1 into a model of the Escherichia coli ribosome revealed two additional contact regions for L1 on the 23S rRNA that were not identified in previous ribosome models.

The RNA-binding ability of ribosomal protein L1 is of profound interest since the protein has a dual function as a ribosomal protein binding rRNA and as a translational repressor binding its mRNA. Here, we report the crystal structure of ribosomal protein L1 in complex with a specific fragment of its mRNA and compare it with the structure of L1 in complex with a specific fragment of 23S rRNA determined earlier. In both complexes, a strongly conserved RNA structural motif is involved in L1 binding through a conserved network of RNA-protein H-bonds inaccessible to the solvent. These interactions should be responsible for specific recognition between the protein and RNA. A large number of additional non-conserved RNA-protein H-bonds stabilizes both complexes. The added contribution of these non-conserved H-bonds makes the ribosomal complex much more stable than the regulatory one.

Ribosomal protein L1, as part of the L1 stalk of the 50S ribosomal subunit, is implicated in directing tRNA movement through the ribosome during translocation. High-resolution crystal structures of four mutants (T217V, T217A, M218L and G219V) of the ribosomal protein L1 fromThermus thermophilus(TthL1) in complex with a specific 80 nt fragment of 23S rRNA and the structures of two of these mutants (T217V and G219V) in the RNA-unbound form are reported in this work. All mutations are located in the highly conserved triad Thr-Met-Gly, which is responsible for about 17% of all protein–RNA hydrogen bonds and 50% of solvent-inaccessible intermolecular hydrogen bonds. In the mutated proteins without bound RNA the RNA-binding regions show substantial conformational changes. On the other hand, in the complexes with RNA the structures of the RNA-binding surfaces in all studied mutants are very similar to the structure of the wild-type protein in complex with RNA. This shows that formation of the RNA complexes restores the distorted surfaces of the mutant proteins to a conformation characteristic of the wild-type protein complex. Domain I of the mutated TthL1 and helix 77 of 23S rRNA form a rigid body identical to that found in the complex of wild-type TthL1 with RNA, suggesting that the observed relative orientation is conserved and is probably important for ribosome function. Analysis of the complex structures and the kinetic data show that the number of intermolecular contacts and hydrogen bonds in the RNA–protein contact area does not correlate with the affinity of the protein for RNA and cannot be used as a measure of affinity.

The crystal structure of the isolated full-length ribosomal L1 stalk, consisting of Thermus thermophilus ribosomal protein L1 in complex with a specific 80-nucleotide fragment of 23S rRNA, has been solved for the first time at high resolution. The structure revealed details of protein-RNA interactions in the L1 stalk. Analysis of the crystal packing enabled the identification of sticky sites on the protein and the 23S rRNA which may be important for ribosome assembly and function. The structure was used to model different conformational states of the ribosome. This approach provides an insight into the roles of domain II of L1 and helix 78 of rRNA in ribosome function.

The formation of a specific and stable complex between two (macro)molecules implies complementary contact surface regions. We used ribosomal protein L1, which specifically binds a target site on 23S rRNA, to study the influence of surface modifications on the protein−RNA affinity. The threonine residue in the universally conserved triad Thr−Met−Gly significant for RNA recognition and binding was substituted by phenylalanine, valine and alanine, respectively. The crystal structure of the mutant Thr217Val of the isolated domain I of L1 from Thermus thermophilus (TthL1) was determined. This structure and that of two other mutants, which had been determined earlier, were analysed and compared with the structure of the wild type L1 proteins. The influence of structural changes in the mutant L1 proteins on their affinity for the specific 23S rRNA fragment was tested by kinetic experiments using surface plasmon resonance (SPR) biosensor analysis. Association rate constants undergo minor changes, whereas dissociation rate constants displayed significantly higher values in comparison with that for the wild type protein. The analysed L1 mutants recognize the specific RNA target site, but the mutant L1−23S rRNA complexes are less stable compared to the wild type complexes. Copyright © 2010 John Wiley & Sons, Ltd.

The crystal structure of a hybrid complex between the bacterial ribosomal protein L1 from Thermus thermophilus and a Methanococcus vannielii mRNA fragment containing an L1-binding site was determined at 2.1 A resolution. It was found that all polar atoms involved in conserved protein-RNA hydrogen bonds have high values of density in the electron-density map and that their hydrogen-bonding capacity is fully realised through interactions with protein atoms, water molecules and K(+) ions. Intermolecular contacts were thoroughly analyzed in the present crystals and in crystals of previously determined L1-RNA complexes. It was shown that extension of the RNA helices providing canonical helix stacking between open-open or open-closed ends of RNA fragments is a common feature of these and all known crystals of complexes between ribosomal proteins and RNAs. In addition, the overwhelming majority of complexes between ribosomal proteins and RNA molecules display crystal contacts formed by the central parts of the RNA fragments. These contacts are often very extensive and strong and it is proposed that they are formed in the saturated solution prior to crystal formation.

RNA chaperone activity is defined as the ability of proteins to either prevent RNA from misfolding or to open up misfolded RNA conformations. One-third of all large ribosomal subunit proteins from E. coli display this activity, with L1 exhibiting one of the highest activities. Here, we demonstrate via the use of in vitro trans- and cis-splicing assays that the RNA chaperone activity of L1 is conserved in all three domains of life. However, thermophilic archaeal L1 proteins do not display RNA chaperone activity under the experimental conditions tested here. Furthermore, L1 does not exhibit RNA chaperone activity when in complexes with its cognate rRNA or mRNA substrates. The evolutionary conservation of the RNA chaperone activity among L1 proteins suggests a functional requirement during ribosome assembly, at least in bacteria, mesophilic archaea and eukarya. Surprisingly, rather than facilitating catalysis, the thermophilic archaeal L1 protein from Methanococcus jannaschii (MjaL1) completely inhibits splicing of the group I thymidylate synthase intron from phage T4. Mutational analysis of MjaL1 excludes the possibility that the inhibitory effect is due to stronger RNA binding. To our knowledge, MjaL1 is the first example of a protein that inhibits group I intron splicing.