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The expression of eukaryotic genes can be regulated at several stages, including the translation of mRNA. It is known that the structure of mRNA can affect both the efficiency of interaction with the translation apparatus in general and the choice of translation initiation sites. To study the translated fraction of the transcriptome, experimental methods of analysis were developed, the most informative of which is ribosomal profiling (RP, Ribo-seq). Originally developed for use in yeast systems, this method has been adapted for research in translation mechanisms in many plant species. This technology includes the isolation of the polysomal fraction and high-performance sequencing of a pool of mRNA fragments associated with ribosomes. Comparing the results of transcript coverage with reads obtained using the ribosome profiling with the transcriptional efficiency of genes allows the translation efficiency to be evaluated for each transcript. The exact positions of ribosomes determined on mRNA sequences allow determining the translation of open reading frames and switching between the translation of several reading frames – a phenomenon in which two or more overlapping frames are read from one mRNA and different proteins are synthesized. The advantage of this method is that it provides quantitative estimates of ribosome coverage of mRNA and can detect relatively rare translation events. Using this technology, it was possible to identify and classify plant genes by the type of regulation of their expression at the transcription, translation, or both levels. Features of the mRNA structure that affect translation levels have been revealed: the formation of G2 quadruplexes and the presence of specific motifs in the 5’-UTR region, GC content, the presence of alternative translation starts, and the influence of uORFs on the translation of downstream mORFs. In this review, we briefly reviewed the RP methodology and the prospects for its application to study the structural and functional organization and regulation of plant gene expression.

Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium-Arthrospira platensis Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown.IMPORTANCE While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis, a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic.

In this paper, a methodology for experimental investigation of chemical and thermal structure of weakly stretched counterflow flames under terrestrial conditions is proposed. The non-premixed counterflow flames are stabilized in a narrow channel between quartz plates, and the flame gases are sampled by a microprobe inserted via a thin slit in one of the quartz plates. The gas samples are then analyzed by mass spectrometry. The results of the measurements of mole fraction profiles of the main components of methane-air non-premixed flames, namely, CH4, O2, H2O, CO2, and CO, are presented. The temperature profiles are also reconstructed using the measurement data for the gas composition. The experimental profiles are compared to the results of the 3D numerical simulations undertaken within the global reaction mechanisms (one- and four-step) and a detailed reaction mechanism (San-Diego). The results of this work clearly show that the thermal and chemical structures of the counterflow flame in the planar channel are essentially non-one-dimensional, and 3D-calculations are necessary to correctly predict the flame behavior in this configuration. The methodology demonstrated in the current work can be successfully employed for the investigation of the low stretched counterflow flames of various hydrocarbon fuels and fuel blends. This will allow verifying and developing the reaction kinetic models capable of quantitative prediction of weakly stretched flame behavior in confined conditions. [ABSTRACT FROM AUTHOR]

Barley (Hordeum vulgare L.) grain pigmentation is caused by two types of phenolic compounds: anthocyanins (which are flavonoids) give a blue or purple color, and melanins (which are products of enzymatic oxidation and polymerization of phenolic compounds) give a black or brown color. Genes Ant1 and Ant2 determine the synthesis of purple anthocyanins in the grain pericarp, whereas melanins are formed under the control of the Blp1 gene in hulls and pericarp tissues. Unlike anthocyanin synthesis, melanin synthesis is poorly understood. The objective of the current work was to reveal features of the phenylpropanoid biosynthesis pathway functioning in melanin-accumulating barley grains. For this purpose, comparative transcriptomic and metabolomic analyses of three barley near-isogenic lines accumulating anthocyanins, melanins, or both in the grain, were performed. A comparative analysis of mRNA libraries constructed for three stages of spike development (booting, late milk, and early dough) showed transcriptional activation of genes encoding enzymes of the general phenylpropanoid pathway in all the lines regardless of pigmentation; however, as the spike matured, unique transcriptomic patterns associated with melanin and anthocyanin synthesis stood out. Secondary activation of transcription of the genes encoding enzymes of the general phenylpropanoid pathway together with genes of monolignol synthesis was revealed in the line accumulating only melanin. This pattern differs from the one observed in the anthocyanin-accumulating lines, where — together with the genes of general phenylpropanoid and monolignol synthesis pathways — flavonoid biosynthesis genes were found to be upregulated, with earlier activation of these genes in the line accumulating both types of pigments. These transcriptomic shifts may underlie the observed differences in concentrations of phenylpropanoid metabolites analyzed in the grain at a late developmental stage by high-performance liquid chromatography. Both melanin-accumulating lines showed an increased total level of benzoic acids. By contrast, anthocyanin-accumulating lines showed higher concentrations of flavonoids and p-coumaric and ferulic acids. A possible negative effect of melanogenesis on the total flavonoid content and a positive influence on the anthocyanin content were noted in the line accumulating both types of pigments. As a conclusion, redirection of metabolic fluxes in the phenylpropanoid biosynthesis pathway occurs when melanin is synthesized.

Abstract Background Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut virome is far from being fully characterized, and additional groups of phages, including highly abundant ones, continue to be discovered by metagenome mining. A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. Together with advanced approaches for sequence assembly and powerful methods of sequence analysis, this revised framework offers the opportunity to discover and classify unknown phage taxa in the human gut. Results A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3738 apparently complete phage genomes that represent 451 putative genera. Several of these phage genera are only distantly related to previously identified phages and are likely to found new families. Two of the candidate families, “Flandersviridae” and “Quimbyviridae”, include some of the most common and abundant members of the human gut virome that infect Bacteroides, Parabacteroides, and Prevotella. The third proposed family, “Gratiaviridae,” consists of less abundant phages that are distantly related to the families Autographiviridae, Drexlerviridae, and Chaseviridae. Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. Comparative genomic analysis of the three candidate phage families revealed features without precedent in phage genomes. Some “Quimbyviridae” phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. Several “Flandersviridae” phages encode enzymes of the isoprenoid pathway, a lipid biosynthesis pathway that so far has not been known to be manipulated by phages. The “Gratiaviridae” phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species. Conclusions Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. Addition of these phylogenetically classified, diverse, and distinct phages to public databases will facilitate taxonomic decomposition and functional characterization of human gut viromes. Video abstract

Abstract Constituting one of Earth’s major biomes, steppes are characterised by naturally treeless extra-tropical vegetation. The formation of the Eurasian steppe belt, the largest steppe region in the world, began in Central Asia during the Neogene. In the glacial stages of the Pleistocene, steppe displaced forest vegetation, which in turn recolonised the area during the warmer interglacial periods, thus affecting the distribution of plants adapted to these habitats. Krascheninnikovia ceratoides (Chenopodiaceae) is a plant characteristic of dry steppe and semi-desert formations. Earlier studies showed that the ancestor of this autochthonous steppe element originated in Central Asia during the Miocene/Pliocene, i.e., in the same region and at the same time as the first appearance of steppe vegetation. However, as the extant lineages of Krascheninnikovia ceratoides diversified only 2.2 ± 0.9 Mya, it may represent a modern element of current dry steppe and semi-desert formations, rather than a component of the first steppe precursors of the Miocene. As such, it may have capitalised on the climatic conditions of the cold stages of the Quaternary to expand its range and colonise suitable habitats outside of its area of origin. To test this hypothesis, phylogeographic methods were applied to high-resolution genotyping-by-sequencing data. Our results indicate that Krascheninnikovia originated in western Central Asia and the Russian Altai, then spread to Europe in the West, and reached North America in the East. The populations of eastern Central Asia and North America belong to the same clade and are genetically clearly distinct from the Euro-Siberian populations. Among the populations west of the Altai Mountains, the European populations are genetically distinct from all others, which could be the result of the separation of populations east and west of the Urals caused by the Pleistocene transgressions of the Caspian Sea.

De novo transcriptome assembly is an important stage of RNA-seq data computational analysis. It allows the researchers to obtain the sequences of transcripts presented in the biological sample of interest. The availability of accurate and complete transcriptome sequence of the organism of interest is, in turn, an indispensable condition for further analysis of RNA-seq data. Through years of transcriptomic research, the bioinformatics community has developed a number of assembler programs for transcriptome reconstruction from short reads of RNA-seq libraries. Different assemblers makes it possible to conduct a de novo transcriptome reconstruction and a genome-guided reconstruction. The majority of the assemblers working with RNA-seq data are based on the De Bruijn graph method of sequence reconstruction. However, specif ics of their procedures can vary drastically, as do their results. A number of authors recommend a hybrid approach to transcriptome reconstruction based on combining the results of several assemblers in order to achieve a better transcriptome assembly. The advantage of this approach has been demonstrated in a number of studies, with RNA-seq experiments conducted on the Illumina platform. In this paper, we propose a hybrid approach for creating a transcriptome assembly of the barley Hordeum vulgare isogenic line Bowman and two nearly isogenic lines contrasting in spike pigmentation, based on the results of sequencing on the IonTorrent platform. This approach implements several de novo assemblers: Trinity, Trans-ABySS and rnaSPAdes. Several assembly metrics were examined: the percentage of reference transcripts observed in the assemblies, the percentage of RNA-seq reads involved, and BUSCO scores. It was shown that, based on the summation of these metrics, transcriptome meta-assembly surpasses individual transcriptome assemblies it consists of.

Plant surface properties are crucial determinants of resilience to abiotic and biotic stresses. The outer layer of the plant cuticle consists of chemically diverse epicuticular waxes. The WAX INDUCER1/SHINE subfamily of APETALA2/ETHYLENE RESPONSIVE FACTORS regulates cuticle properties in plants. In this study, four barley genes homologous to the Arabidopsis thaliana AtWIN1 gene were mutated using RNA-guided Cas9 endonuclease. Mutations in one of them, the HvWIN1 gene, caused a recessive glossy sheath phenotype associated with β-diketone deficiency. A complementation test for win1 knockout (KO) and cer-x mutants showed that Cer-X and WIN1 are allelic variants of the same genomic locus. A comparison of the transcriptome from leaf sheaths of win1 KO and wild-type plants revealed a specific and strong downregulation of a large gene cluster residing at the previously known Cer-cqu locus. Our findings allowed us to postulate that the WIN1 transcription factor in barley is a master mediator of the β-diketone biosynthesis pathway acting through developmental stage- and organ-specific transactivation of the Cer-cqu gene cluster.

CO2 methanation was studied in the presence of nickel catalysts obtained by the solid-state combustion method. Complexes with a varying number of ethylenediamine molecules in the coordination sphere of nickel were chosen as the precursors of the active component of the catalysts. Their synthesis was carried out without the use of solvents, which made it possible to avoid the stages of their separation from the solution and the utilization of waste liquids. The composition and structure of the synthesized complexes were confirmed by elemental analysis, IR spectroscopy, powder XRD and XPS methods. It was determined that their thermal decomposition in the combustion wave proceeds in multiple stages with the formation of NiO and Ni(OH)2, which are reduced to Ni0. Higher ethylenediamine content in the complex leads to a higher content of metal in the solid products of combustion. However, different ratios of oxidized and reduced forms of nickel do not affect the initial activation temperature of nickel catalysts in the presence of CO2. It was noted that, after activation, the sample obtained from [Ni(C2H8N2)2](NO3)2 exhibited the highest activity in CO2 methanation. Thus, this complex is a promising precursor for CO2 methanation catalysts, and its synthesis requires only a small amount of ethylenediamine.

Solanum tuberosum L. (common potato) is one of the most important crops produced almost all over the world. Genomic sequences of potato opens the way for studying the molecular variations related to diversification. We performed a reconstruction of genomic sequences for 15 tetraploid potato cultivars grown in Russia using short reads. Protein-coding genes were identified; conserved and variable parts of pan-genome and the repertoire of the NBS-LRR genes were characterized. For comparison, we used additional genomic sequences for twelve South American potato accessions, performed analysis of genetic diversity, and identified the copy number variations (CNVs) in two these groups of potato. Genomes of Russian potato cultivars were more homogeneous by CNV characteristics and have smaller maximum deletion size in comparison with South American ones. Genes with different CNV occurrences in two these groups of potato accessions were identified. We revealed genes of immune/abiotic stress response, transport and five genes related to tuberization and photoperiod control among them. Four genes related to tuberization and photoperiod were investigated in potatoes previously (phytochrome A among them). A novel gene, homologous to the poly(ADP-ribose) glycohydrolase (PARG) of Arabidopsis, was identified that may be involved in circadian rhythm control and contribute to the acclimatization processes of Russian potato cultivars.

This paper presents a study of the flammability and thermal decomposition products of glass fiber-reinforced epoxy resin (GFRER) with the addition of cardanol-based phosphorus-containing benzoxazine monomer (CBz) and graphene and their combinations in different proportions (up to 20 wt.%). The addition of CBz alone or in combination with graphene resulted in an increase in the limiting oxygen index (LOI) and self-extinguishing in the UL-94 HB test. The flame-retardant samples had better tensile mechanical properties than the sample without additives. The differential mass-spectrometric thermal analysis (DMSTA) of the thermal decomposition products of GFRER without additives and with the addition of CBz and graphene was carried out. CBz addition promoted the thermal decomposition of high-molecular-weight products of epoxy resin decomposition in the condensed phase and at the same time decreased the time of release of low-molecular-weight thermal decomposition products into the gas phase. Graphene addition resulted in an increase in the relative intensities of high-molecular-mass peaks compared to GFRER without additives. [ABSTRACT FROM AUTHOR]

The Acorus calamus group, or sweet flag, includes important medicinal plants and is classified into three species: A. americanus (diploid), A. verus (tetraploid), and A. calamus (sterile triploid of hybrid origin). Members of the group are famous as components of traditional Indian medicine, and early researchers suggested the origin of the sweet flag in tropical Asia. Subsequent research led to an idea of the origin of the triploid A. calamus in the Amur River basin in temperate Asia, because this was the only region where both diploids and tetraploids were known to co-occur and be capable of sexual reproduction. Contrary to this hypothesis, triploids are currently very rare in the Amur basin. Here, we provide the first evidence that all three species occur in Kazakhstan. The new records extend earlier data on the range of A. verus for c. 1800 km. Along the valley of the Irtysh River in Kazakhstan and the adjacent Omsk Oblast of Russia, A. verus is recorded in the south, A. americanus in the north, and A. calamus is common in between. We propose the Irtysh River valley as another candidate for a cradle of the triploid species A. calamus. It is possible that the range of at least one parent species (A. americanus) has contracted through competition with its triploid derivative species, for which the Irtysh River floods provide a tool for downstream range expansion. We refine our earlier data and show that the two parent species have non-overlapping ranges of variation in a quantitative metric of leaf aerenchyma structure. [ABSTRACT FROM AUTHOR]

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The paper presents the results of research into the influence of the titanium foil thickness on the impact response of metal-ceramic ZrO2/Ti/ZrO2/Ti composites consisting of nonrigidly joined plane-parallel layers. The difference is shown between the deformation behavior of the metal foils in composites with foil thicknesses of 100, 200, and 500 μm. It is found that an increase in the thickness of reinforcing metal layers leads to a higher structure dispersion in the deformation localization zone. The deformation and fracture features of each layer of the composites are studied in detail. A comparative analysis is made of the structural characteristics of materials before and after impact loading. [ABSTRACT FROM AUTHOR]

A comprehensive study was performed on the supramolecular ordering and optical properties of thin nanostructured glycerohydrogel sol-gel plates based on chitosan L- and D-aspartate and their individual components in the X-ray, UV, visible, and IR ranges. Our comparative analysis of chiroptical characteristics, optical collimated transmittance, the average cosine of the scattering angle, microrelief and surface asymmetry, and the level of structuring shows a significant influence of the wavelength range of electromagnetic radiation and the enantiomeric form of aspartic acid on the functional characteristics of the sol-gel materials. At the macrolevel of the supramolecular organization, a complex topography of the surface layer and a dense amorphous–crystalline ordering of polymeric substances were revealed, while at the nanolevel, there were two forms of voluminous scattering domains: nanospheres with diameters of 60–120 nm (L-) and 45–55 nm (D-), anisometric particles of lengths within ~100–160 (L-) and ~85–125 nm (D-), and widths within ~10–20 (L-) and ~20–30 nm (D-). The effect of optical clearing on glass coated with a thin layer of chitosan L-(D-)aspartate in the near-UV region was discovered (observed for the first time for chitosan-based materials). The resulting nanocomposite shape-stable glycerohydrogels seem promising for sensorics and photonics. [ABSTRACT FROM AUTHOR]

A solvent-free method was proposed for the synthesis of hexaimidazolecobalt(II) nitrate and perchlorate complexes—[Co(C3H4N2)6](NO3)2 and [Co(C3H4N2)6](ClO4)2—by adding cobalt salts to melted imidazole. The composition, charge state of the metal, and the structure of the resulting complexes were confirmed by elemental analysis, XPS, IR spectroscopy, and XRD. The study of the thermochemical properties of the synthesized complexes showed that [Co(C3H4N2)6](NO3)2 and [Co(C3H4N2)6](ClO4)2 are thermally stable up to 150 and 170 °C, respectively. When the critical temperature of thermal decomposition is reached, oxidative two-stage gasification is observed. In this case, the organic component of the [Co(C3H4N2)6](NO3)2 complex undergoes almost complete gasification to form Co3O4 with a slight admixture of CoO, which makes it attractive as a component of gas-generation compositions, like airbags. [ABSTRACT FROM AUTHOR]

Commonly considered bispecific, Acorus is one of the most phylogenetically isolated angiosperm genera that forms the order Acorales sister to the rest of the monocots. The Acorus calamus group is widely distributed in the Holarctic regions of Eurasia and America and has strong medicinal and other practical uses since prehistoric times. Earlier studies interpreted native diploids and invasive triploids occurring in North America as two species that differed in morphology and distribution ranges. In contrast, diploids, triploids, and tetraploids occurring in Eurasia are commonly interpreted as one species because they reportedly cannot be distinguished in collections. We resolve the controversy over taxonomic concepts between Eurasia and America and provide the first detailed multidisciplinary account of Acorus in temperate Asia. We used plastid and nuclear markers, leaf anatomy, seed micromorphology, pollen stainability, flow cytometry, and direct chromosome counts. Diploids and tetraploids show stable molecular and micromorphological differences. Triploids are their sterile hybrids, with the plastid genome inherited from the diploid parent. Diploids of America and Asia tend to differ in leaf characters. Coadaptative coexistence with pollinating beetles Platamartus jakowlewi and Sibirhelus corpulentus (Kateretidae) is conserved between diploids and tetraploids and over a distance of 4700 km between Japan and Western Siberia. Diploids are self‐compatible and can set seeds in the absence of kateretid beetles. Tetraploids are self‐incompatible and/or cannot set seeds in the absence of Platamartus and Sibirhelus. Diploids (A. americanus) and tetraploids (A. verus) are two biological species; the former has two subspecies. Acorus calamus should be restricted to triploids; it apparently first evolved in temperate Asia. Diploids mostly occur in much cooler climates than triploids and tetraploids. Accessions of A. verus and A. calamus from tropical Asia are apparently derived from ancient introductions. Our data provide a new framework for the pharmacological use of Acorus. [ABSTRACT FROM AUTHOR]

In this work, NiO and NiO–SiO2 are studied using X-ray diffraction and the method of atomic-pair radial distribution. Using X-ray phase analysis, it is determined that the sizes of NiO particles have a coherent-scattering region of more than 100 nm, while the NiO–SiO2 sample has particle sizes of about 2–3 nm. However, full-profile simulation using the Rietveld method does not allow one to describe the effects observed during diffraction: asymmetry of the peaks, the appearance of an additional shoulder of peak 111 in the region of small angles; therefore, the method of atomic-pair radial distribution is used to analyze the structure. When simulating the experimental curve of the atomic-pair radial distribution, 3 different models are used: pure NiO, a mixture of NiO and Ni2SiO4, as well as a modified NiO model with Si embedded into the crystal lattice. The latter model is created based on the assumption of the incorporation of silicon into the NiO structure, as can be evidenced by the X-ray diffraction data. According to the results of simulation of the curve of the atomic-pair radial distribution, it is the latter model that provides the best description of the observed effects: a significantly increased unit-cell parameter in comparison with the sample without the addition of SiO2, as well as decreased cation–oxygen distances in the structure while the distances between cations are increased. [ABSTRACT FROM AUTHOR]

Here, the authors analyze 4907 Circular Metagenome Assembled Genomes from human microbiomes and identify and characterize nearly 600 diverse genomes of crAss-like phages, finding two putative families with unusual genomic features, including high density of self-splicing introns and inteins.

Abstract Following the game‐changing high‐pressure CO (HiPco) process that established the first facile route toward large‐scale production of single‐walled carbon nanotubes, CO synthesis of cm‐sized graphene crystals of ultra‐high purity grown during tens of minutes is proposed. The Boudouard reaction serves for the first time to produce individual monolayer structures on the surface of a metal catalyst, thereby providing a chemical vapor deposition technique free from molecular and atomic hydrogen as well as vacuum conditions. This approach facilitates inhibition of the graphene nucleation from the CO/CO2 mixture and maintains a high growth rate of graphene seeds reaching large‐scale monocrystals. Unique features of the Boudouard reaction coupled with CO‐driven catalyst engineering ensure not only suppression of the second layer growth but also provide a simple and reliable technique for surface cleaning. Aside from being a novel carbon source, carbon monoxide ensures peculiar modification of catalyst and in general opens avenues for breakthrough graphene‐catalyst composite production.