Polyacetylene Derivatives from the Polypore Fungus (Fistulina hepatica, Agaricomycetes) and Their Antimicrobial Activity.

Chemical investigation of the polypore fungus Fistulina hepatica resulted in the isolation of five compounds, including four new polyacetylenic fatty acid derivatives - isocinnatriacetin B (1), isocinnatriacetin A (2), cinna-triacetin C (3) and ethylcinnatriacetin A (4) together with one known polyacetylene fatty acid derivative - cinnatriacetin A (5). The structures were elucidated using spectroscopic methods (UV, NMR, HR-ESIMS) along with comparison to literature data. Antibacterial activity screening of compounds 1-5 against ESKAPE bacterial strains in vitro with zones of inhibition (ZOI) was performed and MIC values were established for the most active compounds (3 and 4). Together with that morphological and growth parameters under solid-phase cultivation were also researched.

New benzoquinone pigments from the hydnoid fungus Sarcodontia setosa and their biosynthetic relationship.

Chemical investigation of the hydnoid fungus Sarcodontia setosa resulted in the isolation of five compounds, including two new sarcodontic acid derivatives - setosic acid (1) and 7,8-dehydrohomosarcodontic acid (2) along with three known benzoquinone pigments - sarcodontic acid (3), 4,5-dehydrosarcodontic acid (4) and dihydrosarcodontic acid (5). The structures were elucidated using spectroscopic methods (UV, NMR and HR-ESIMS). The biosynthetic relationship of the isolated compounds is proposed and discussed. Antibacterial activity screening of compounds 1-5 against ESKAPE bacterial strains in vitro with zones of inhibition was performed and MIC values were established for the most active compounds (3 and 5).

Organic matter composition and greenhouse gas production of thawing subsea permafrost in the Laptev Sea.

Subsea permafrost represents a large carbon pool that might be or become a significant greenhouse gas source. Scarcity of observational data causes large uncertainties. We here use five 21-56 m long subsea permafrost cores from the Laptev Sea to constrain organic carbon (OC) storage and sources, degradation state and potential greenhouse gas production upon thaw. Grain sizes, optically-stimulated luminescence and biomarkers suggest deposition of aeolian silt and fluvial sand over 160 000 years, with dominant fluvial/alluvial deposition of forest- and tundra-derived organic matter. We estimate an annual thaw rate of 1.3 ± 0.6 kg OC m-2 in subsea permafrost in the area, nine-fold exceeding organic carbon thaw rates for terrestrial permafrost. During 20-month incubations, CH4 and CO2 production averaged 1.7 nmol and 2.4 µmol g-1 OC d-1, providing a baseline to assess the contribution of subsea permafrost to the high CH4 fluxes and strong ocean acidification observed in the region.

Diversity of ESI-MS Based Phosphatidylcholine Profiles in Basidiomycetes.

Phosphatidylcholines (PC) are the main membrane lipid constituents comprising more than 50% of total glycerophospholipids. They coordinate a number of cell functions, particularly cell growth, homeostasis, secretion, recognition and communication. In basidial fungi PC are synthesized via the Kennedy pathway as well as through methylation of phosphatidylethanolamines (PE) and then undergo remodeling in Lands cycle that replaces fatty acids in PC molecules. The molecular profile of PC is determined by the genetic features that are characteristic for every species and depend on the environment. Here we present the results of ESI-MS based analyses of PC profiles of 38 species of basidiomycetes belonging to Agaricales (12), Polyporales (17), Russulales (5), Gleophyllales (2), Cantharellales (1), Auriculariales (1), Phallales (1). Although the variety of PC molecular species of basidiomycetes is rather diverse (20-38 molecular species in every profile), only 1-3 main molecular species represent 70-90% of total PC content. The most abundant of them are C36:4 and C36:3, followed by C34:1, C34:2, C36:5, C36:2. In the majority of basidiomycetes, C36:4 reaches up to 50-70% of total PC molecular species. Based on the results of hierarchical cluster analysis four main types of PC profiles which characterized the studied fungi independently from their taxonomic position, ecology, trophic status, and hyphal differentiation have been revealed. Comparative analyses of studied fungi using PCA method have shown that species of Polyporales differ from those of Agaricales by higher variability of PC profiles.

Source apportionment of methane escaping the subsea permafrost system in the outer Eurasian Arctic Shelf.

The East Siberian Arctic Shelf holds large amounts of inundated carbon and methane (CH4). Holocene warming by overlying seawater, recently fortified by anthropogenic warming, has caused thawing of the underlying subsea permafrost. Despite extensive observations of elevated seawater CH4 in the past decades, relative contributions from different subsea compartments such as early diagenesis, subsea permafrost, methane hydrates, and underlying thermogenic/ free gas to these methane releases remain elusive. Dissolved methane concentrations observed in the Laptev Sea ranged from 3 to 1,500 nM (median 151 nM; oversaturation by ∼3,800%). Methane stable isotopic composition showed strong vertical and horizontal gradients with source signatures for two seepage areas of δ13C-CH4 = (-42.6 ± 0.5)/(-55.0 ± 0.5) ‰ and δD-CH4 = (-136.8 ± 8.0)/(-158.1 ± 5.5) ‰, suggesting a thermogenic/natural gas source. Increasingly enriched δ13C-CH4 and δD-CH4 at distance from the seeps indicated methane oxidation. The Δ14C-CH4 signal was strongly depleted (i.e., old) near the seeps (-993 ± 19/-1050 ± 89‰). Hence, all three isotope systems are consistent with methane release from an old, deep, and likely thermogenic pool to the outer Laptev Sea. This knowledge of what subsea sources are contributing to the observed methane release is a prerequisite to predictions on how these emissions will increase over coming decades and centuries.

Data on the genome analysis of the wood-rotting fungus Steccherinum ochraceum LE-BIN 3174.

In the present article, we report data on the whole-genome sequencing of wood-rotting (white-rot) fungus Steccherinum ochraceum LE-BIN 3174. The S. ochraceum LE-BIN 3174 genome consists of 770 scaffolds (N50 = 62,812 bp) with the total length of assembly ∼35 Mb. The structural annotation of the genome resulted in the prediction of 12,441 gene models, among which 181 were models of tRNA-coding genes, and 12,260 - protein-coding genes. The protein-coding genes were annotated with different databases (Pfam, InterPro, eggNOG, dbCAN, and MEROPS). The whole genome sequence and functional annotation provide an important information for the deep investigation of biochemical processes that take place during the late stages of wood decomposition by Basidiomycetes. The Whole Genome project of S. ochraceum LE-BIN 3174 had been deposited at DDBJ/ENA/GenBank under the accession RWJN00000000. The version described in this work is version RWJN00000000.1. For further interpretation of the data provided in this article, please refer to the research article "Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum" [1].

Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum.

Steccherinum ochraceum is a white rot basidiomycete with wide ecological amplitude. It occurs in different regions of Russia and throughout the world, occupying different climatic zones. S. ochraceum colonizes stumps, trunks, and branches of various deciduous (seldom coniferous) trees. As a secondary colonizing fungus, S. ochraceum is mainly observed at the late decay stages. Here, we present the de novo assembly and annotation of the genome of S. ochraceum, LE-BIN 3174. This is the 8th published genome of fungus from the residual polyporoid clade and the first from the Steccherinaceae family. The obtained genome provides a first glimpse into the genetic and enzymatic mechanisms governing adaptation of S. ochraceum to an ecological niche of pre-degraded wood. It is proposed that increased number of carbohydrate-active enzymes (CAZymes) belonging to the AA superfamily and decreased number of CAZymes belonging to the GH superfamily reflects substrate preferences of S. ochraceum. This proposition is further substantiated by the results of the biochemical plate tests and exoproteomic study, which demonstrates that S. ochraceum assumes the intermediate position between typical primary colonizing fungi and litter decomposers or humus saprotrophs. Phylogenetic analysis of S. ochraceum laccase and class II peroxidase genes revealed the distinct evolutional origin of these genes in the Steccherinaceae family.

Photobiological properties of phthalocyanine photosensitizers Photosens, Holosens and Phthalosens: A comparative in vitro analysis.

Photobiological properties of phthalocyanine photosensitizers, namely, clinically approved Photosens and new compounds Holosens and Phthalosens were analyzed on transitional cell carcinoma of the urinary bladder (T24) and human hepatic adenocarcinoma (SK-HEP-1). Photosens is a sulfated aluminum phthalocyanine with the number of sulfo groups 3.4, which is characterized by a high degree of hydrophilicity, slow cellular uptake, localization in lysosomes and the lowest photodynamic activity. Holosens is an octacholine zinc phthalocyanine, a cationic compound with significant charge. Holosens more efficiently enters the cells; it is localized in Golgi apparatus in addition to lysosomes and exhibits a significant inhibitory effect on cell viability upon irradiation. The highest photodynamic activity was demostrated by Phthalosens. Phthalosens is a metal-free analog of Photosens with a number of sulfo groups 2.5, which determines its amphiphilicity. Phthalosens is characterized by the highest rate of cellular uptake through the outer cell membrane, localization in cell membrane as well as in lysosomes and Golgi apparatus, and the highest activity upon irradiation among the photosensitizers studied. In general, changes in the physicochemical properties of Holosens and Phthalosens ensured an increase in their efficiency in vitro compared to Photosens. The features of accumulation, intracellular distribution and their interrelation with photodynamic activity, revealed in this work, indicate the prospects of Phthalosens and Holosens for clinical practice.

White-rot basidiomycetes Junghuhnia nitida and Steccherinum bourdotii: Oxidative potential and laccase properties in comparison with Trametes hirsuta and Coriolopsis caperata.

White-rot basidiomycetes from the poorly studied residual polyporoid clade of Polyporales order Junghuhnia nitida (Pers.) Ryvarden and Steccherinum bourdotii Saliba & A. David grow as secondary xylotrohps on well decomposed woody materials. The main objective of the current study was to compare oxidative potential, growth, production of oxidative enzymes and laccase properties of J. nitida and S. bourdotii with that of typical primary xylotrohps Trametes hirsuta (Wulfen) Lloyd and Coriolopsis caperata (Berk.) Murrill, belonging to the core polyporoid clade. For the first time we report species J. nitida and S. bourdotii as active laccase producers. New laccases from J. nitida and S. bourdotii were purified and characterized. They had an identical molecular weight of 63 kDa and isoelectric points of 3.4 and 3.1, respectively. However, the redox potential of the T1 copper site for both J. nitida (610 mV) and S. bourdotii (640 mV) laccases was lower than those for T. hirsuta and C. caperata laccases. The new laccases showed higher temperature optima and better thermal stability than T. hirsuta and C. caperata laccases. Their half-lives were more than 40 min at 70 °C. The laccases from J. nitida and S. bourdotii showed higher affinity to syringyl-type phenolic compounds than T. hirsuta and C. caperata laccases. The oxidative potential of studied fungi as well as the properties of their laccases are discussed in terms of the fungal life-style.

Multimodal approach in assessment of the response of breast cancer to neoadjuvant chemotherapy.

The ability for noninvasive visualization of functional changes of a tumor's oxygenation and circulatory system offers new advantages for prognosis and monitoring of the treatment efficacy. The results of breast cancer oxygen state study under chemotherapy action obtained by diffuse optical spectroscopy (DOS) in combination with Doppler ultrasonic imaging are presented. Complex use of optical and ultrasound methods gives complementary information about the size of the tumor node, peculiarities of its vascular bed, rate of its blood flow as well as oxygenation, and provide a picture of the tumor response to treatment. Comparison with tumor pathologic response allowed to identify differences in the changes of these parameters depending on the degree of pathological tumor response to chemotherapy. It was demonstrated that fourth and fifth degrees of therapeutic pathomorphism may be predicted by the increase of oxygen saturation level after the first cycle of chemotherapy. If the reduction or absence of the oxygen saturation dynamics is observed, first or second degree of pathological tumor response can be expected. Additional ultrasound investigation of the tumors may be useful for observation of the dynamics of tumor blood flow thereby for understanding the reasons of induced chemotherapy oxygenation changes. The proposed approach based on DOS and ultrasonography may be applied for monitoring of breast tumors under therapy and prediction of their sensitivity.

Optical coherence tomography-based angiography device with real-time angiography B-scans visualization and hand-held probe for everyday clinical use.

This work is dedicated to the development of the OCT system with angiography for everyday clinical use. Two major problems were solved during the development: compensation of specific natural tissue displacements, induced by contact scanning mode and physiological motion of patients (eg, respiratory and cardiac motions) and online visualization of vessel cross-sections to provide feedback for the system operator.

Optical coherence tomography in gynecology: a narrative review.

Modern gynecologic practice requires noninvasive diagnostics techniques capable of detecting morphological and functional alterations in tissues of female reproductive organs. Optical coherence tomography (OCT) is a promising tool for providing imaging of biotissues with high resolution at depths up to 2 mm. Design of the customized probes provides wide opportunities for OCT use in gynecology. This paper contains a retrospective insight into the history of OCT employment in gynecology, an overview of the existing gynecologic OCT probes, including those for combination with other diagnostic modalities, and state-of-the-art application of OCT for diagnostics of tumor and nontumor pathologies of female genitalia. Perspectives of OCT both in diagnostics and treatment planning and monitoring in gynecology are overviewed.

Current rates and mechanisms of subsea permafrost degradation in the East Siberian Arctic Shelf.

The rates of subsea permafrost degradation and occurrence of gas-migration pathways are key factors controlling the East Siberian Arctic Shelf (ESAS) methane (CH4) 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 CH4 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 CH4 release in the Arctic.

Siberian Arctic black carbon sources constrained by model and observation.

Black carbon (BC) in haze and deposited on snow and ice can have strong effects on the radiative balance of the Arctic. There is a geographic bias in Arctic BC studies toward the Atlantic sector, with lack of observational constraints for the extensive Russian Siberian Arctic, spanning nearly half of the circum-Arctic. Here, 2 y of observations at Tiksi (East Siberian Arctic) establish a strong seasonality in both BC concentrations (8 ng⋅m-3 to 302 ng⋅m-3) and dual-isotope-constrained sources (19 to 73% contribution from biomass burning). Comparisons between observations and a dispersion model, coupled to an anthropogenic emissions inventory and a fire emissions inventory, give mixed results. In the European Arctic, this model has proven to simulate BC concentrations and source contributions well. However, the model is less successful in reproducing BC concentrations and sources for the Russian Arctic. Using a Bayesian approach, we show that, in contrast to earlier studies, contributions from gas flaring (6%), power plants (9%), and open fires (12%) are relatively small, with the major sources instead being domestic (35%) and transport (38%). The observation-based evaluation of reported emissions identifies errors in spatial allocation of BC sources in the inventory and highlights the importance of improving emission distribution and source attribution, to develop reliable mitigation strategies for efficient reduction of BC impact on the Russian Arctic, one of the fastest-warming regions on Earth.

The East Siberian Arctic Shelf: towards further assessment of permafrost-related methane fluxes and role of sea ice.

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.

Criteria for pathology recognition in optical coherence tomography of fallopian tubes.

An increase of infertility and chronic pelvic pains syndrome, a growing level of latent diseases of this group, as well as a stably high percentage (up to 25% for infertility and up to 60% for the chronic pelvic pains syndrome) of undetermined origin raises the requirement for novel introscopic diagnostic techniques. We demonstrate abilities of optical coherence tomography (OCT) as a complementary technique to laparoscopy in diagnostics of fallopian tubes pathologies. We have acquired OCT images of different parts of fallopian tubes in norm and with morphologically proven pathology. Based on comparative analysis of the OCT data and the results of histological studies, we have worked out the subjective OCT criteria for distinguishing between unaltered and pathologic tissues. The developed criteria are verified in blind recognition tests. Diagnostic efficacy of OCT diagnostics in the case ofpelvic inflammatory diseases has been statistically evaluated, and high diagnostic accuracy (88%) is shown. Basing of the subjective criteria, an attempt to develop independent criteria aimed for automated recognition of pathological states in fallopian tubes is undertaken. Enhanced diagnostic accuracy (96%) of the developed independent criteria is demonstrated.

Comparative study of tumor hypoxia by diffuse optical spectroscopy and immunohistochemistry in two tumor models.

The capabilities of diffuse optical spectroscopy for noninvasive assessing of oxygen status in experimental tumors have been demonstrated. Specific features of the distribution of total hemoglobin, oxygenated hemoglobin, deoxygenated hemoglobin, and blood-oxygen saturation were shown on two tumor models having different histological structure and functional characteristics. The results obtained by the optical technique were verified by immunohistochemical study of tissue samples marked with exogenous marker of hypoxia--pimonidazole.

Extensive methane venting to the atmosphere from sediments of the East Siberian Arctic Shelf.

Remobilization to the atmosphere of only a small fraction of the methane held in East Siberian Arctic Shelf (ESAS) sediments could trigger abrupt climate warming, yet it is believed that sub-sea permafrost acts as a lid to keep this shallow methane reservoir in place. Here, we show that more than 5000 at-sea observations of dissolved methane demonstrates that greater than 80% of ESAS bottom waters and greater than 50% of surface waters are supersaturated with methane regarding to the atmosphere. The current atmospheric venting flux, which is composed of a diffusive component and a gradual ebullition component, is on par with previous estimates of methane venting from the entire World Ocean. Leakage of methane through shallow ESAS waters needs to be considered in interactions between the biogeosphere and a warming Arctic climate.