Institute of Chemistry, Far Eastern Branch of the Russian Academy of Sciences

Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10-15 years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis, Collophora (as Collophorina), Cryomyces, Dematiopleospora, Heterospora (as Heterosporicola), Lithophila, Palmomyces (as Palmaria) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae. Four species of Lalaria, which were invalidly published are transferred to Taphrina and validated as new combinations. Catenomycopsis Tibell & Constant. is reduced under Chaenothecopsis Vain., while Dichomera Cooke is reduced under Botryosphaeria Ces. & De Not. (Art. 59).

Today East Asia harbors many "relict" plant species whose ranges were much larger during the Paleogene-Neogene and earlier. The ecological and climatic conditions suitable for these relict species have not been identified. Here, we map the abundance and distribution patterns of relict species, showing high abundance in the humid subtropical/warm-temperate forest regions. We further use Ecological Niche Modeling to show that these patterns align with maps of climate refugia, and we predict species' chances of persistence given the future climatic changes expected for East Asia. By 2070, potentially suitable areas with high richness of relict species will decrease, although the areas as a whole will probably expand. We identify areas in southwestern China and northern Vietnam as long-term climatically stable refugia likely to preserve ancient lineages, highlighting areas that could be prioritized for conservation of such species.

The plasma electrolytic oxidation is an innovative method for the surface treatment of titanium and its alloys. This review provides an overview of the historical development of the process and summarizes the current state of the art. The chemical as well as the electro- and plasma-chemical basics of the layer forming mechanisms, which comprises the substrate/electrolyte interface before discharge initiation and the different types and stages of plasma electrolytic discharge phenomena are explained within the context of titanium-based materials. How these phenomena can be influenced by the use of suitable electrolytes and controlled by the electrical regime is described. Subsequently, the microstructures and composition of the layers are described in detail, and the properties for specific applications are then discussed. The resistance of a PEO coating to corrosive environments, tribological factors, and alternating mechanical stress is viewed critically, and the extensive functional properties such as physiological compatibility, photocatalytic activity, and decorative properties are revealed. Finally, examples of various practical applications in the medical engineering, aviation, automotive, and environmental technology fields, as well as other branches of industry, are presented.

Heat stress (HS) is expected to be of increasing worldwide concern in the near future, especially with regard to crop yield and quality as a consequence of rising or varying temperatures as a result of global climate change. HS response (HSR) is a highly conserved mechanism among different organisms but shows remarkable complexity and unique features in plants. The transcriptional regulation of HSR is controlled by HS transcription factors (HSFs) which allow the activation of HS-responsive genes, among which HS proteins (HSPs) are best characterized. Cell wall remodeling constitutes an important component of plant responses to HS to maintain overall function and growth; however, little is known about the connection between cell wall remodeling and HSR. Pectin controls cell wall porosity and has been shown to exhibit structural variation during plant growth and in response to HS. Pectin methylesterases (PMEs) are present in multigene families and encode isoforms with different action patterns by removal of methyl esters to influencing the properties of cell wall. We aimed to elucidate how plant cell walls respond to certain environmental cues through cell wall-modifying proteins in connection with modifications in cell wall machinery. An overview of recent findings shed light on PMEs contribute to a change in cell-wall composition/structure. The fine-scale modulation of apoplastic calcium ions (Ca2+) content could be mediated by PMEs in response to abiotic stress for both the assembly and disassembly of the pectic network. In particular, this modulation is prevalent in guard cell walls for regulating cell wall plasticity as well as stromal aperture size, which comprise critical determinants of plant adaptation to HS. These insights provide a foundation for further research to reveal details of the cell wall machinery and stress-responsive factors to provide targets and strategies to facilitate plant adaptation.

An updated classification of the order Hymenoptera is provided with the current numbers of genera and species described so far specified. The order is composed of 2 suborders, 27 superfamilies, 132 families, 8423 extant genera with an additional 685 extinct genera. Considered one of the most species-rich insects orders a total of 153088 extant species have been described, in addition to 2429 extinct species.

Sustained release of methane (CH(4)) to the atmosphere from thawing Arctic permafrost may be a positive and significant feedback to climate warming. Atmospheric venting of CH(4) from the East Siberian Arctic Shelf (ESAS) was recently reported to be on par with flux from the Arctic tundra; however, the future scale of these releases remains unclear. Here, based on results of our latest observations, we show that CH(4) emissions from this shelf are likely to be determined by the state of subsea permafrost degradation. We observed CH(4) emissions from two previously understudied areas of the ESAS: the outer shelf, where subsea permafrost is predicted to be discontinuous or mostly degraded due to long submergence by seawater, and the near shore area, where deep/open taliks presumably form due to combined heating effects of seawater, river run-off, geothermal flux and pre-existing thermokarst. CH(4) emissions from these areas emerge from largely thawed sediments via strong flare-like ebullition, producing fluxes that are orders of magnitude greater than fluxes observed in background areas underlain by largely frozen sediments. We suggest that progression of subsea permafrost thawing and decrease in ice extent could result in a significant increase in CH(4) emissions from the ESAS.

Abstract The rates of subsea permafrost degradation and occurrence of gas-migration pathways are key factors controlling the East Siberian Arctic Shelf (ESAS) methane (CH 4 ) emissions, yet these factors still require assessment. It is thought that after inundation, permafrost-degradation rates would decrease over time and submerged thaw-lake taliks would freeze; therefore, no CH 4 release would occur for millennia. Here we present results of the first comprehensive scientific re-drilling to show that subsea permafrost in the near-shore zone of the ESAS has a downward movement of the ice-bonded permafrost table of ∼14 cm year −1 over the past 31–32 years. Our data reveal polygonal thermokarst patterns on the seafloor and gas-migration associated with submerged taliks, ice scouring and pockmarks. Knowing the rate and mechanisms of subsea permafrost degradation is a prerequisite to meaningful predictions of near-future CH 4 release in the Arctic.

Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.

The ascomycete order Diaporthales includes a number of plant pathogenic fungi such as Cryphonectria parasitica, the chestnut blight fungus, as well as many asexually reproducing fungi without known sexual states. Relationships among genera in the Diaporthales were evaluated as a basis for the recognition of families and to provide a taxonomic framework for the asexually reproducing diaporthalean fungi. Phylogenetic relationships were determined based on analyses of large subunit (LSU) nuclear ribosomal DNA (nrDNA) sequences. Within the Diaporthales 82 sequences representing 69 taxa were analyzed. Results suggest the presence of at least six major lineages within the Diaporthales recognized as the Gnomoniaceae sensu stricto, Melanconidaceae sensu stricto, Schizoparme complex including the anamorph genera Coniella and Pilidiella, Cryphonectria-Endothia complex, Valsaceae sensu stricto, and Diaporthaceae sensu stricto. In addition, six teleomorphic and anamorphic taxa fell within the Diaporthales but were not allied with any of the six lineages.

New monolithic nanocomposite silica biomaterials were synthesized on the basis of various natural polysaccharides and recently introduced completely water-soluble precursor tetrakis(2-hydroxyethyl) orthosilicate. The sol-gel processes were performed in aqueous solutions without the addition of organic solvents and catalysts. The silica polymerization was promoted by the polysaccharides through acceleration and catalytic effect on the processes. By introducing poly(vinyl alcohol) or poly(ethylene oxide) in the precursor solution, it was shown that the jellification took place in the case of the hydroxyl-containing polymer. Therefore, it was suggested that the catalysis was caused by a formation of hydrogen bonds between hydroxyl groups in macromolecules and products of precursor hydrolysis (silanols). It was also demonstrated that the polysaccharides radically changed the structure of biomaterials. In place of the cross-linked nanoparticles, there was a three-dimensional network from crossed or branched fibers and uncrossed spherical particles that filled the mesh space. The density of network, thickness of fibers, and properties of synthesized biomaterials depended on the polysaccharide type, charged degree of their macromolecule, and concentration. By varying these parameters, it was possible to manipulate the structural organization of hybrid polysaccharide-silica nanocomposites.

Abstract Aims Classification of vegetation is an essential tool to describe, understand, predict and manage biodiversity. Given the multiplicity of approaches to classify vegetation, it is important to develop international consensus around a set of general guidelines and purpose‐specific standard protocols. Before these goals can be achieved, however, it is necessary to identify and understand the different choices that are made during the process of classifying vegetation. This paper presents a framework to facilitate comparisons between broad‐scale plot‐based classification approaches. Results Our framework is based on the distinction of four structural elements (plot record, vegetation type, consistent classification section and classification system) and two procedural elements (classification protocol and classification approach). For each element we describe essential properties that can be used for comparisons. We also review alternative choices regarding critical decisions of classification approaches; with a special focus on the procedures used to define vegetation types from plot records. We illustrate our comparative framework by applying it to different broad‐scale classification approaches. Conclusions Our framework will be useful for understanding and comparing plot‐based vegetation classification approaches, as well as for integrating classification systems and their sections.

It is known that the rolA, rolB, and rolC genes of Agrobacterium rhizogenes T-DNA affect processes of plant development and activate the synthesis of secondary metabolites in transformed plant cells. Although a synergistic activity of the rol genes on root formation is well-documented, little is known about their individual and combined action on secondary metabolism. In the present investigation, we provide evidence indicating that individual rolA, rolB, and rolC genes are capable of increasing biosynthesis of anthraquinones (AQs) in transformed calli of Rubia cordifolia. The stimulatory effect was due to the increased transcription of a key gene of AQ biosynthesis, the isochorismate synthase (ICS) gene. The strongest AQ-stimulating activity was shown for an R. cordifolia culture expressing rolB at high levels, where rolB ensured a 15-fold increase of AQ accumulation compared with the control, non-transformed calli. A tyrosine phosphatase inhibitor abolished the rolB-induced increase of AQ production, thus indicating the involvement of tyrosine (de)phosphorylation in the rolB-mediated AQ stimulation. The rolA- and rolC-expressing cultures produced 2.8- and 4.3-fold higher levels of AQs, respectively, when compared with the control calli. However, the effect of rolA, rolB, and rolC on AQ biosynthesis was not synergistic because rolA and rolC apparently attenuated the stimulatory effect of rolB on AQ biosynthesis. Therefore, the rol-gene-mediated signals that promote root formation and those which activate biosynthesis of secondary metabolites seem to have a point of divergence.

Rosmarinic acid (RA) is one of the first secondary metabolites produced in plant cell cultures in extremely high yields, up to 19% of the cell dry weight. More complex derivatives of RA, such as rabdosiin and lithospermic acid B, later were also obtained in cell cultures at high yields. RA and its derivatives possess promising biological activities, such as improvement of cognitive performance, prevention of the development of Alzheimer's disease, cardioprotective effects, reduction of the severity of kidney diseases and cancer chemoprevention. The TNF-α-induced NF-κB signaling pathway has emerged as a central target for RA. Despite these impressive activities and high yields, the biotechnological production of these metabolites on an industrial scale has not progressed. We summarized data suggesting that external stimuli, the Ca(2+)-dependent NADPH oxidase pathway and processes of protein phosphorylation/dephosphorylation are involved in the regulation of biosynthesis of these substances in cultured plant cells. In spite of growing information about pathways regulating biosynthesis of RA and its derivatives in cultured plant cells, the exact mechanism of regulation remains unknown. We suggest that further progress in the biotechnology of RA and its derivatives can be achieved by using new high-throughput techniques.

BACKGROUND: There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. RESULTS: We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. CONCLUSIONS: Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.

Many species have mitochondrial DNA lineages that are phylogenetically intermixed with other species, but studies have rarely tested the cause of such paraphyly. In this study, we tested two hypotheses that could explain mitochondrial paraphyly of Holarctic gadwalls (Anas strepera) with respect to Asian falcated ducks (A. falcata). First, hybridization could have resulted in falcated duck mitochondrial DNA (mtDNA) introgressing into the gadwall gene pool. Second, gadwalls and falcated ducks could have diverged so recently that mtDNA lineages have not sorted to reciprocal monophyly. We used coalescent analyses of three independent loci to distinguish between these two hypotheses. Two lines of evidence support introgression. First, analyses of the three loci combined show that some introgression is necessary to explain current genetic diversity in gadwalls. Second, we generated alternative predictions regarding time since divergence estimated from mtDNA: falcated ducks and gadwalls would have diverged between 65,000 and 700,000 years before present (ybp) under the introgression hypothesis and between 11,000 and 76,000 ybp under the incomplete lineage sorting hypothesis. The two independent nuclear introns indicated that these species diverged between 210,000 and 5,200,000 ybp, which did not overlap the predicted time for incomplete lineage sorting. These analyses also suggested that ancient introgression ( approximately 14,000 ybp) has resulted in the widespread distribution and high frequency of falcated-like mtDNA (5.5% of haplotypes) in North America. This is the first study to use a rigorous quantitative framework to reject incomplete lineage sorting as the cause of mitochondrial paraphyly.

Bionanocomposites are a novel class of nanosized materials. They contain the constituent of biological origin and particles with at least one dimension in the range of 1–100 nm. There are similarities with nanocomposites but also fundamental differences in the methods of preparation, properties, functionalities, biodegradability, biocompatibility, and applications. The article includes two parts. Bionanocomposite definition and classification along with nanoparticles, biomaterials, and methods of their preparation are initially reviewed. Then, novel approaches developed by our team are presented. The first approach concerns the preparation of bionanocomposites from chitosan and nanoparticles. It is based on the regulated charging of polysaccharide by the gradual shift of solution pH. When charges appear, the biomacromolecules come into the electrostatic interactions with negatively charged nanoparticles that cause the jellification of solutions. It is also applied to form films. They have a nacre-like structure from stacked planar nanoparticles separated by aligned biomacromolecules. The second approach deals with the biomimicking mineralization of biopolymers by using a novel silica precursor. Its advantage over the current sol-gel processing is in the compatibility and regulation of processes and structure of generated silica. Another example of the mineralization is presented by titania. Syntheses are performed in anhydrous ethylene glycol. Processes and structure of bionanocomposites are regulated by water that is added in an amount to only hydrate functional groups in the carbohydrate macromolecule.

The polyfunctional nature of chitosan enables its application as a polymer ligand not only for the recovery, separation, and concentration of metal ions, but for the fabrication of a wide spectrum of functional materials. Although unmodified chitosan itself is the unique cationic polysaccharide with very good complexing properties toward numerous metal ions, its sorption capacity and selectivity can be sufficiently increased and turned via chemical modification to meet requirements of the specific applications. In this review, which covers results of the last decade, we demonstrate how different strategies of chitosan chemical modification effect metal ions binding by O-, N-, S-, and P-containing chitosan derivatives, and which mechanisms are involved in binding of metal cation and anions by chitosan derivatives.

Abstract Aim Zoogeographic patterns in the Himalayas and their neighbouring Southeast Asian mountain ranges include elevational parapatry and ecological segregation, particularly among passerine bird species. We estimate timings of lineage splits among close relatives from the north Palaearctic, the Sino‐Himalayan mountain forests and from adjacent Southeast Asia. We also compare phylogeographic affinities and timing of radiation among members of avian communities from different elevational belts. Location East Asia. Methods We reconstructed molecular phylogenies based on a mitochondrial marker (cytochrome b ) and multilocus data sets for seven passerine groups: Aegithalidae, Certhiidae ( Certhia ), Fringillidae ( Pyrrhula ), Paridae ( Periparus ), Phylloscopidae, Regulidae and Timaliidae ( Garrulax sensu lato ). Molecular dating was carried out using a Bayesian approach applying a relaxed clock in beast . Time estimates were inferred from three independent calibrations based on either a fixed mean substitution rate or fixed node ages. The biogeographic history of each group was reconstructed using a parsimony‐based approach. Results Passerine radiation in Southeast Asia can be divided into roughly three major phases of separation events. We infer that an initial Miocene radiation within the Southeast Asian region included invasions of (sub)tropical faunal elements from the Indo‐Burmese region to the Himalayan foothills and further successive invasions to Central Asia and Taiwan towards the early Pliocene. During two further Pliocene/Pleistocene phases, the subalpine mountain belt of the Sino‐Himalayas was initially invaded by boreal species with clear phylogenetic affinities to the north Palaearctic taiga belt. Most terminal splits between boreal Himalayan/Chinese sister taxa were dated to the Pleistocene. Main conclusions Extant patterns of elevational parapatry and faunal transition in the Sino‐Himalayas originated from successive invasions from different climatic regions. The initiation of Southeast Asian passerine diversification and colonization of the Himalayan foothills in the mid‐Miocene coincides with the postulated onset of Asian monsoon climate and the resulting floral and faunal turnovers. Patterns of elevational parapatry were established by southward invasions of boreal avifaunal elements to the subalpine Sino‐Himalayan forest belt that were strongly connected to climate cooling towards the end of the Pliocene. Current patterns of allopatry and parapatry in boreal species (groups) were shaped through Pleistocene forest fragmentation in East Asia.

The results of the Internet discussion on the classification of urban soils aimed at evaluating their possible inclusion into the modern Russian soil classification system adopted by a wide range of specialists are presented. The first step was to address the urban diagnostic horizons as the basis for identifying soil types according to the rules of the Russian soil classification. New diagnostic horizons were proposed for urban soils: urbic (UR), filled compost-mineral (RAT), and filled peat (RT). The combination of these horizons with other diagnostic horizons and layers of technogenic materials correspond to different soil types. At the subtype level, the diagnostic properties (qualifiers) that may reflect both natural phenomena (gley, alkalinity) and technogenic impacts on the soils (urbistratified; phosphatic; or poorly expressed urban—ur, rat, rt) are used. Some corrections were proposed for the system of parent materials in urban environments. Urban soils formerly described in another nomenclature—urbanozems, urbiquasizems, and culturozems—are correlated with the taxa in all the trunks of the system. The proposals accepted can be used for the next updated version of the new Russian soil classification system.

Asian-origin avian influenza (AI) viruses are spread in part by migratory birds. In Alaska, diverse avian hosts from Asia and the Americas overlap in a region of intercontinental avifaunal mixing. This region is hypothesized to be a zone of Asia-to-America virus transfer because birds there can mingle in waters contaminated by wild-bird-origin AI viruses. Our 7 years of AI virus surveillance among waterfowl and shorebirds in this region (1998-2004; 8,254 samples) showed remarkably low infection rates (0.06%). Our findings suggest an Arctic effect on viral ecology, caused perhaps by low ecosystem productivity and low host densities relative to available water. Combined with a synthesis of avian diversity and abundance, intercontinental host movements, and genetic analyses, our results suggest that the risk and probably the frequency of intercontinental virus transfer in this region are relatively low.