The disruption of circadian rhythmicity of gene expression in the hippocampus and associated structures in Gria2R/R mice; a comparison with C57BL/6J and Adar2-/- mice strains.

Adar2-/- mice are a widely used model for studying the physiological consequences of reduced RNA editing. These mice are viable only when the Q/R editing site of the Gria2 subunit of the AMPA receptor is constitutively mutated to the codon for arginine, and Gria2R/R mice often serve as the sole control for Adar2-/- mice. Our study aimed to investigate whether ADAR2 inactivity and the Gria2R/R phenotype affect the rhythmicity of the circadian clock gene pattern and the expression of Gria1 and Gria2 subunits in the suprachiasmatic nucleus (SCN), hippocampus, parietal cortex and liver. Our data show that Gria2R/R mice completely lost circadian rhythmicity in the hippocampus compared to Adar2-/- mice. Compared to C57BL/6J mice, the expression profiles in the hippocampus and parietal cortex of Gria2R/R mice differ to the same extent as in Adar2-/-. No alterations were detected in the circadian profiles in the livers. These data suggest that the natural gradual postnatal increase in the editing of the Q/R site of the Gria2 subunit may be important for the development of circadian clockwork in some brain structures, and the use of Gria2R/R mice as the only control to Adar2-/- mice in the experiments dependent on the hippocampus and parietal cortex should therefore be considered.

CRISPR/Cas9-Mediated Knock-Out of the MtCLE35 Gene Highlights Its Key Role in the Control of Symbiotic Nodule Numbers under High-Nitrate Conditions.

Legume plants have the ability to establish a symbiotic relationship with soil bacteria known as rhizobia. The legume-rhizobium symbiosis results in the formation of symbiotic root nodules, where rhizobia fix atmospheric nitrogen. A host plant controls the number of symbiotic nodules to meet its nitrogen demands. CLE (CLAVATA3/EMBRYO SURROUNDING REGION) peptides produced in the root in response to rhizobial inoculation and/or nitrate have been shown to control the number of symbiotic nodules. Previously, the MtCLE35 gene was found to be upregulated by rhizobia and nitrate treatment in Medicago truncatula, which systemically inhibited nodulation when overexpressed. In this study, we obtained several knock-out lines in which the MtCLE35 gene was mutated using the CRISPR/Cas9-mediated system. M. truncatula lines with the MtCLE35 gene knocked out produced increased numbers of nodules in the presence of nitrate in comparison to wild-type plants. Moreover, in the presence of nitrate, the expression levels of two other nodulation-related MtCLE genes, MtCLE12 and MtCLE13, were reduced in rhizobia-inoculated roots, whereas no significant difference in MtCLE35 gene expression was observed between nitrate-treated and rhizobia-inoculated control roots. Together, these findings suggest the key role of MtCLE35 in the number of nodule numbers under high-nitrate conditions, under which the expression levels of other nodulation-related MtCLE genes are reduced.

Functional Modules in the Meristems: "Tinkering" in Action.

BACKGROUND: A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem). CONCLUSIONS: The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.

Identification and Expression Analysis of the C-TERMINALLY ENCODED PEPTIDE Family in Pisum sativum L.

The C-TERMINALLY ENCODED PEPTIDE(CEP) peptides play crucial roles in plant growth and response to environmental factors. These peptides were characterized as positive regulators of symbiotic nodule development in legume plants. However, little is known about the CEP peptide family in pea. Here, we discovered in pea genome 21 CEP genes (PsCEPs), among which three genes contained additional conserved motifs corresponding to the PIP (PAMP-induced secreted peptides) consensus sequences. We characterized the expression patterns of pea PsCEP genes based on transcriptomic data, and for six PsCEP genes with high expression levels in the root and symbiotic nodules the detailed expression analysis at different stages of symbiosis and in response to nitrate treatment was performed. We suggest that at least three PsCEP genes, PsCEP1, PsCEP7 and PsCEP2, could play a role in symbiotic nodule development, whereas the PsCEP1 and PsCEP13 genes, downregulated by nitrate addition, could be involved in regulation of nitrate-dependent processes in pea. Further functional studies are required to elucidate the functions of these PsCEP genes.

Ordering motivation and Likert scale ratings: When a numeric scale is not necessarily better.

Measuring psychological attributes, such as motivation, typically involves rating scales, assuming that an attribute can be ordered, and that ratings represent this order. Previously, only the first assumption had been tested, albeit limited. First, we checked the ordinal structure of motivation, looking at whether people can establish transitive relations between motivation levels in pairwise comparisons; and we found different ordering patterns: strict transitive, weak transitive, changing order, and intransitivity. The rate of intransitivity was similar to that found previously and was somewhat higher than we obtained when we asked participants to compare definitely quantitative attributes (such as weight). Second, we checked if specific ordering patterns were related to individual interpretations of the statements that deviated from expected motivation types. Indeed, about a third of participants miscategorized statements, and these deviant interpretations were related to intransitivity as well as weak transitivity. Third, we checked whether Likert ratings represent the order of motives obtained from pairwise comparisons. We found rather homomorphic representation: ratings correlated with the order, but they did not differentiate between different ordering patterns and hierarchies of motives. We conclude that the Likert rating scale provides less information about respondents than pairwise ordering. The findings question the mainstream practice of using rating scales without testing underlying assumptions.

Creating a list of word alignments from parallel Russian simplification data.

This work describes the development of a list of monolingual word alignments taken from parallel Russian simplification data. This word lists can be used in such lexical simplification tasks as rule-based simplification applications and lexically constrained decoding for neural machine translation models. Moreover, they constitute a valuable source of information for developing educational materials for teaching Russian as a second/foreign language. In this work, a word list was compiled automatically and post-edited by human experts. The resulting list contains 1409 word pairs in which each "complex" word has an equivalent "simpler" (shorter, more frequent, modern, international) synonym. We studied the contents of the word list by comparing the frequencies of the words in the pairs and their levels in the special CEFR-graded vocabulary lists for learners of Russian as a foreign language. The evaluation demonstrated that lexical simplification by means of single-word synonym replacement does not occur often in the adapted texts. The resulting list also illustrates the peculiarities of the lexical simplification task for L2 learners, such as the choice of a less frequent but international word.

Vascular plants occurrences in the Southern Urals industrial towns (Sterlitamak and Salavat).

Background: The paper presents datasets of plant species of two industrial cities Sterlitamak and Salavat (Republic of Bashkortostan) is presented. These cities are part of the Southern Bashkortostan urban agglomeration and are amongst the three largest in the Republic. The population of Sterlitamak is about 276,000. There are large oil refineries and other large industrial transport infrastructure facilities. Datasets are prepared on the basis of long-time field research by Ya. Golovanov (2008 - 2016). Technical preparation of the datasets was carried out by M. Lebedeva and M. Drap. The herbarium samples are stored in the herbarium collections of the South Ural Botanical Garden Institute and the Ufa Institute of Biology (UFA). The data paper describes three datasets on species occurrences. It presents occurrences of species in different types of habitats (anthropogenically transformed and semi-natural). The datasets consists of 5,462 occurrence records totally. Most of the records (5,359) are georeferenced. New information: The total number of records in three datasets is 5,462. They contain of vascular plant species occurrences in the two industrial cities of the Southern Urals (Sterlitamak and Salavat). There are both alien and natural species occurrences in different types of habitats (antropogenically transformed and semi-natural).

A Fullerene-Platinum Complex for Direct Functional Patterning of Single Metal Atom-Embedded Carbon Nanostructures.

The development of patterning materials ("resists") at the nanoscale involves two distinct trends: one is toward high sensitivity and resolution for miniaturization, the other aims at functionalization of the resists to realize bottom-up construction of distinct nanoarchitectures. Patterning of carbon nanostructures, a seemingly ideal application for organic functional resists, has been highly reliant on complicated pattern transfer processes because of a lack of patternable precursors. Herein, we present a fullerene-metal coordination complex as a fabrication material for direct functional patterning of sub-10 nm metal-containing carbon structures. The attachment of one platinum atom per fullerene molecule not only leads to significant improvement of sensitivity and resolution but also enables stable atomic dispersion of the platinum ions within the carbon matrix, which may gain fundamentally new interest in functional patterning of hierarchical carbon nanostructures.

At the Root of Nodule Organogenesis: Conserved Regulatory Pathways Recruited by Rhizobia.

The interaction between legume plants and soil bacteria rhizobia results in the formation of new organs on the plant roots, symbiotic nodules, where rhizobia fix atmospheric nitrogen. Symbiotic nodules represent a perfect model to trace how the pre-existing regulatory pathways have been recruited and modified to control the development of evolutionary "new" organs. In particular, genes involved in the early stages of lateral root development have been co-opted to regulate nodule development. Other regulatory pathways, including the players of the KNOX-cytokinin module, the homologues of the miR172-AP2 module, and the players of the systemic response to nutrient availability, have also been recruited to a unique regulatory program effectively governing symbiotic nodule development. The role of the NIN transcription factor in the recruitment of such regulatory modules to nodulation is discussed in more details.

A Comparative Study of Educational Texts for Native, Foreign, and Bilingual Young Speakers of Russian: Are Simplified Texts Equally Simple?

Studies on simple language and simplification are often based on datasets of texts, either for children or learners of a second language. In both cases, these texts represent an example of simple language, but simplification likely involves different strategies. As such, this data may not be entirely homogeneous in terms of text simplicity. This study investigates linguistic properties and specific simplification strategies used in Russian texts for primary school children with different language backgrounds and levels of language proficiency. To explore the structure and variability of simple texts for young readers of different age groups, we have trained models for multiclass and binary classification. The models were based on quantitative features of texts. Subsequently, we evaluated the simplification strategies applied to readers of the same age with different linguistic backgrounds. This study is particularly relevant for the Russian language material, where the concept of easy and plain language has not been sufficiently investigated. The study revealed that the three types of texts cannot easily be distinguished from each other by judging the performance of multiclass models based on various quantitative features. Therefore, it can be said that texts of all types exhibit a similar level of accessibility to young readers. In contrast, binary classification tasks demonstrated better results, especially in the R-native vs. non R-native track (with 0.78 F1-score), these results may indicate that the strategies used for adapting or creating texts for each type of audience are different.

Dialog between Kingdoms: Enemies, Allies and Peptide Phytohormones.

Various plant hormones can integrate developmental and environmental responses, acting in a complex network, which allows plants to adjust their developmental processes to changing environments. In particular, plant peptide hormones regulate various aspects of plant growth and development as well as the response to environmental stress and the interaction of plants with their pathogens and symbionts. Various plant-interacting organisms, e.g., bacterial and fungal pathogens, plant-parasitic nematodes, as well as symbiotic and plant-beneficial bacteria and fungi, are able to manipulate phytohormonal level and/or signaling in the host plant in order to overcome plant immunity and to create the habitat and food source inside the plant body. The most striking example of such phytohormonal mimicry is the ability of certain plant pathogens and symbionts to produce peptide phytohormones of different classes. To date, in the genomes of plant-interacting bacteria, fungi, and nematodes, the genes encoding effectors which mimic seven classes of peptide phytohormones have been found. For some of these effectors, the interaction with plant receptors for peptide hormones and the effect on plant development and defense have been demonstrated. In this review, we focus on the currently described classes of peptide phytohormones found among the representatives of other kingdoms, as well as mechanisms of their action and possible evolutional origin.

A database of weed plants in the European part of Russia.

BACKGROUND: Weeds are plants that, although not specially cultivated, grow and often adapt to growing in arable lands. They form an ecological variant of flora, as a historically-formed set of species growing on cultivated soils. For the rational use of the chemical and biological crop protection products and to produce safe and high-quality food, up-to-date data on the floristic diversity of weeds and the patterns of its geographical change are required. The need for a weeds' database arises that allows many specialists to work together independently. However, the great value of any database lies not in its existence, but in the accumulation of data that can be used to analyse the factors affecting the species diversity of weeds. NEW INFORMATION: A dataset of weed species diversity and their distribution in the European part of Russia, based on the results of the authors' own research from 1999 to 2019, has been created.The dataset includes 24,284 observations of occurrences of weed plants, which were obtained on the basis of 2,049 relevés of segetal plant communities in seven regions of the European part of Russia. In total, the dataset includes information about 329 species of vascular plants growing in 65 farmlands: cereals, spring and winter crops, industrial crops, row crops and perennial grasses (Tretyakova et al. 2020).

Nitrate-Induced CLE Peptide Systemically Inhibits Nodulation in Medicago truncatula.

Legume plants form nitrogen-fixing nodules in symbiosis with soil bacteria rhizobia. The number of symbiotic nodules is controlled at the whole-plant level with autoregulation of nodulation (AON), which includes a shoot-acting CLV1-like receptor kinase and mobile CLE (CLAVATA3/ENDOSPERM SURROUNDING REGION-related) peptides that are produced in the root in response to rhizobia inoculation. In addition to rhizobia-induced CLE peptides, nitrate-induced CLE genes have been identified in Lotus japonicus and Glycine max, which inhibited nodulation when overexpressed. However, nitrate-induced CLE genes that systemically suppress nodulation in AON-dependent manner have not been identified in Medicago truncatula. Here, we found that MtCLE35 expression is activated by both rhizobia inoculation and nitrate treatment in M. truncatula, similarly to L. japonicus CLE genes. Moreover, we found that MtCLE35 systemically suppresses nodulation in AON-dependent manner, suggesting that MtCLE35 may mediate nitrate-induced inhibition of nodulation in M. truncatula.

The emergence of hypervirulent blaNDM-1-positive Klebsiella pneumoniae sequence type 395 in an oncology hospital.

Fifteen hypermucoviscous isolates (13 blaNDM-1-positive) obtained from 11 oncology patients were analyzed by whole genome sequencing, and selected isolates were assessed in a murine model of sepsis. ST395/K2 isolates harboring rmpA, rmpA2, peg-344, aerobactin, enterobactin, yersiniabactin, type I fimbriae, etc. displayed maximal virulence in the mouse lethality assay (LD50 = 102 CFU). ST147/K20 isolates lacking yersiniabactins were relatively less virulent (LD50 = 104 CFU), ST395/K2 isolates lacking rmpA, rmpA2, peg-344, and aerobactin, but harboring yersiniabactin demonstrated minimal virulence (LD50 = 105 CFU). Isolates represent various paths and stages of evolution directed towards convergence of multidrugresistant classical Klebsiella pneumoniae and hypervirulent K. pneumoniae.

Emergence and Rearrangement of Dynamic Supramolecular Aggregates Visualized by Interferometric Scattering Microscopy.

Studying dynamic self-assembling systems in their native environment is essential for understanding the mechanisms of self-assembly and thereby exerting full control over these processes. Traditional ensemble-based analysis methods often struggle to reveal critical features of the self-assembly that occur at the single particle level. Here, we describe a label-free single-particle assay to visualize real-time self-assembly in aqueous solutions by interferometric scattering microscopy. We demonstrate how the assay can be applied to biphasic reactions yielding micellar or vesicular aggregates, detecting the onset of aggregate formation, quantifying the kinetics at the single particle level, and distinguishing sigmoidal and exponential growth of aggregate populations. Furthermore, we can follow the evolution in aggregate size in real time, visualizing the nucleation stages of the self-assembly processes and record phenomena such as incorporation of oily components into the micelle or vesicle lumen.

Coupled Metabolic Cycles Allow Out-of-Equilibrium Autopoietic Vesicle Replication.

We report chemically fuelled out-of-equilibrium self-replicating vesicles based on surfactant formation. We studied the vesicles' autocatalytic formation using UPLC to determine monomer concentration and interferometric scattering microscopy at the nanoparticle level. Unlike related reports of chemically fuelled self-replicating micelles, our vesicular system was too stable to surfactant degradation to be maintained out of equilibrium. The introduction of a catalyst, which introduces a second catalytic cycle into the metabolic network, was used to close the first cycle. This shows how coupled catalytic cycles can create a metabolic network that allows the creation and perseverance of fuel-driven, out-of-equilibrium self-replicating vesicles.

Cytokinin biosynthesis genes expressed during nodule organogenesis are directly regulated by the KNOX3 protein in Medicago truncatula.

Cytokinin is an important regulator of symbiotic nodule development. Recently, KNOTTED1-LIKE HOMEOBOX 3 transcription factor (TF) was shown to regulate symbiotic nodule development possibly via the activation of cytokinin biosynthesis genes. However, the direct interaction between the KNOX3 TF and its target genes has not been investigated up to date. Here, using EMSA analysis and SPR-based assay, we found that MtKNOX3 homeodomain directly binds to the regulatory sequences of the MtLOG1, MtLOG2, and MtIPT3 genes involved in nodulation in Medicago truncatula. Moreover, we showed that MtLOG2 and MtIPT3 expression patterns partially overlap with MtKNOX3 expression in developing nodules as it was shown by promoter:GUS analysis. Our data suggest that MtKNOX3 TF may directly activate the MtLOG1, MtLOG2, and MtIPT3 genes during nodulation thereby increasing cytokinin biosynthesis in developing nodules.

Plant tumors: a hundred years of study.

MAIN CONCLUSION: The review provides information on the mechanisms underlying the development of spontaneous and pathogen-induced tumors in higher plants. The activation of meristem-specific regulators in plant tumors of various origins suggests the meristem-like nature of abnormal plant hyperplasia. Plant tumor formation has more than a century of research history. The study of this phenomenon has led to a number of important discoveries, including the development of the Agrobacterium-mediated transformation technique and the discovery of horizontal gene transfer from bacteria to plants. There are two main groups of plant tumors: pathogen-induced tumors (e.g., tumors induced by bacteria, viruses, fungi, insects, etc.), and spontaneous ones, which are formed in the absence of any pathogen in plants with certain genotypes (e.g., interspecific hybrids, inbred lines, and mutants). The causes of the transition of plant cells to tumor growth are different from those in animals, and they include the disturbance of phytohormonal balance and the acquisition of meristematic characteristics by differentiated cells. The aim of this review is to discuss the mechanisms underlying the development of most known examples of plant tumors.

The Green Box: An Electronically Versatile Perylene Diimide Macrocyclic Host for Fullerenes.

The powerful electron accepting ability of fullerenes makes them ubiquitous components in biomimetic donor-acceptor systems that model the intermolecular electron transfer processes of Nature's photosynthetic center. Exploiting perylene diimides (PDIs) as components in cyclic host systems for the noncovalent recognition of fullerenes is unprecedented, in part because archetypal PDIs are also electron deficient, making dyad assembly formation electronically unfavorable. To address this, we report the strategic design and synthesis of a novel large, macrocyclic receptor composed of two covalently strapped electron-rich bis-pyrrolidine PDI panels, nicknamed the "Green Box" due to its color. Through the principle of electronic complementarity, the Green Box exhibits strong recognition of pristine fullerenes (C60/70), with the noncovalent ground and excited state interactions that occur upon fullerene guest encapsulation characterized by a range of techniques including electronic absorption, fluorescence emission, NMR and time-resolved EPR spectroscopies, cyclic voltammetry, mass spectrometry, and DFT calculations. While relatively low polarity solvents result in partial charge transfer in the host donor-guest acceptor complex, increasing the polarity of the solvent medium facilitates rare, thermally allowed full electron transfer from the Green Box to fullerene in the ground state. The ensuing charge separated radical ion paired complex is spectroscopically characterized, with thermodynamic reversibility and kinetic stability also demonstrated. Importantly, the Green Box represents a seminal type of C60/70 host where electron-rich PDI motifs are utilized as recognition motifs for fullerenes, facilitating novel intermolecular, solvent tunable ground state electronic communication with these guests. The ability to switch between extremes of the charge transfer energy continuum is without precedent in synthetic fullerene-based dyads.

Identification and Expression Analysis of Medicago truncatula Isopentenyl Transferase Genes (IPTs) Involved in Local and Systemic Control of Nodulation.

Cytokinins are essential for legume plants to establish a nitrogen-fixing symbiosis with rhizobia. Recently, the expression level of cytokinin biosynthesis IPTs (ISOPENTENYLTRANSFERASES) genes was shown to be increased in response to rhizobial inoculation in Lotus japonicus, Medicago truncatula and Pisum sativum. In addition to its well-established positive role in nodule primordium initiation in root cortex, cytokinin negatively regulates infection processes in the epidermis. Moreover, it was reported that shoot-derived cytokinin inhibits the subsequent nodule formation through AON (autoregulation of nodulation) pathway. In L. japonicus, LjIPT3 gene was shown to be activated in the shoot phloem via the components of AON system, negatively affecting nodulation. However, in M. truncatula, the detailed analysis of MtIPTs expression, both in roots and shoots, in response to nodulation has not been performed yet, and the link between IPTs and AON has not been studied so far. In this study, we performed an extensive analysis of MtIPTs expression levels in different organs, focusing on the possible role of MtIPTs in nodule development. MtIPTs expression dynamics in inoculated roots suggest that besides its early established role in the nodule primordia development, cytokinin may be also important for later stages of nodulation. According to expression analysis, MtIPT3, MtIPT4, and MtIPT5 are activated in the shoots in response to inoculation. Among these genes, MtIPT3 is the only one the induction of which was not observed in leaves of the sunn-3 mutant defective in CLV1-like kinase, the key component of AON, suggesting that MtIPT3 is activated in the shoots in an AON-dependent manner. Taken together, our findings suggest that MtIPTs are involved in the nodule development at different stages, both locally in inoculated roots and systemically in shoots, where their expression can be activated in an AON-dependent manner.