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Background Utilization of quantitative proteomics data on the network level is still a challenge in proteomics data analysis. Currently existing models use sophisticated, sometimes hard to implement analysis techniques. Our aim was to generate a relatively simple strategy for quantitative proteomics data analysis in order to utilize as much of the data generated in a proteomics experiment as possible. Results In this study, we applied label-free proteomics, and generated a network model utilizing both qualitative, and quantitative data, in order to examine the early host response to Human Immunodeficiency Virus type 1 (HIV-1). A weighted network model was generated based on the amount of proteins measured by mass spectrometry, and analysis of weighted networks and functional sub-networks revealed upregulation of proteins involved in translation, transcription, and DNA condensation in the early phase of the viral life-cycle. Conclusion A relatively simple strategy for network analysis was created and applied to examine the effect of HIV-1 on host cellular proteome. We believe that our model may prove beneficial in creating algorithms, allowing for both quantitative and qualitative studies of proteome change in various biological and pathological processes by quantitative mass spectrometry. Electronic supplementary material The online version of this article (10.1186/s12859-019-2990-3) contains supplementary material, which is available to authorized users.

Floodplains are valuable scenes of water management and nature conservation. A better understanding of their geomorphological characteristic helps to understand the main processes involved. We performed a classification of floodplain forms in a naturally developed area in Hungary using a Digital Terrain Model (DTM) of aerial laser scanning. We derived 60 geomorphometric variables from the DTM and prepared a geomorphological map of 265 forms (crevasse channels, point bars, swales, levees). Random Forest classification was conducted with Recursive Feature Elimination (RFE) on the objects (mean pixel values by forms) and on the pixels of the variables. We also evaluated the classification probabilities (CP), the spatial uncertainties (SU), and the overfitting in the function of the number of the variables. We found that the object-based method had a better performance (95%) than the pixel-based method (78%). RFE helped to identify the most important 13–20 variables, maintaining the high model performance and reducing the overfitting. However, CP and SU were not efficient measures of classification accuracy as they were not in accordance with the class level accuracy metric. Our results help to understand classification results and the specific limits of laser scanned DTMs. This methodology can be useful in geomorphologic mapping.

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The sorption of phosphate on soils is studied by radioisotopic tracer method. Two consecutive processes with rather different rates were differentiated: namely the heterogeneous isotope exchange between the phosphate in the soil solution and the weakly sorbed phosphate (fast reaction), and the transformation of weakly sorbed phosphate to tightly sorbed phosphate (slow reaction). In this paper, it is shown how the rate constants of these two processes can be determined by a radiotracer with a relatively short half-life.

Background The health of plants is heavily influenced by the intensively researched plant microbiome. The microbiome has to cope with the plant’s defensive secondary metabolites to survive and develop, but studies that describe this interaction are rare. In the current study, we describe interactions of endophytic fungi with a widely researched chemical defense system, the glucosinolate - myrosinase - isothiocyanate system. The antifungal isothiocyanates are also of special interest because of their beneficial effects on human consumers. Results Seven endophytic fungi were isolated from horseradish roots (Armoracia rusticana), from the genera Fusarium, Macrophomina, Setophoma, Paraphoma and Oidiodendron. LC-ESI-MS analysis of the horseradish extract incubated with these fungi showed that six of seven strains could decompose different classes of glucosinolates. Aliphatic, aromatic, thiomethylalkyl and indolic glucosinolates were decomposed by different strains at different rates. SPME-GC-MS measurements showed that two strains released significant amounts of allyl isothiocyanate into the surrounding air, but allyl nitrile was not detected. The LC-ESI-MS analysis of many strains’ media showed the presence of allyl isothiocyanate - glutathione conjugate during the decomposition of sinigrin. Four endophytic strains also accepted sinigrin as the sole carbon source. Isothiocyanates inhibited the growth of fungi at various concentrations, phenylethyl isothiocyanate was more potent than allyl isothiocyanate (mean IC50 was 2.30-fold lower). As a control group, ten soil fungi from the same soil were used. They decomposed glucosinolates with lower overall efficiency: six of ten strains had insignificant or weak activities and only three could use sinigrin as a carbon source. The soil fungi also showed lower AITC tolerance in the growth inhibition assay: the median IC50 values were 0.1925 mM for endophytes and 0.0899 mM for soil fungi. Conclusions The host’s glucosinolates can be used by the tested endophytic fungi as nutrients or to gain competitive advantage over less tolerant species. These activities were much less apparent among the soil fungi. This suggests that the endophytes show adaptation to the host plant’s secondary metabolites and that host metabolite specific activities are enriched in the root microbiome. The results present background mechanisms enabling an understanding of how plants shape their microbiome. Electronic supplementary material The online version of this article (10.1186/s12870-018-1295-4) contains supplementary material, which is available to authorized users.

Linking the conservation of cultural heritage and natural values provides a unique opportunity for preserving traditional landscapes and receives an increased awareness from stakeholders and society. Ancient burial mounds are proper objects of such projects as they are iconic landscape elements of the Eurasian steppes and often act as refugia for grassland specialist species. The aim of this project was to reintroduce grassland plant species to burial mounds for representing them as cultural monuments with the associated biodiversity for the public. The effectiveness of seed sowing, transplanting greenhouse-grown plants and individuals from threatened populations on burial mounds in Hortobágy National Park, Hungary was tested. The following questions were answered: (1) which method is the most effective for species introduction? (2) which species can establish most successfully? (3) how does management affect the species establishment rates? It was found advisable to use a combination of seed sowing and transplanting greenhouse-grown plants. Sowing was found as a cost-effective method for introducing large-seeded species, whilst introduction of greenhouse-grown transplants warranted higher establishment rates for a larger set of species. Transplanting adult individuals was more reliable regardless of management regimes, however this method is labour-intensive and expensive. Intensive management, like mowing with heavy machinery and intensive grazing, should be avoided in the first few years after introduction. The authors highlighted the fact that introducing characteristic grassland species on cultural monuments offers a great opportunity to link issues of landscape and biodiversity conservation. This project demonstrated that, by the revitalisation of cultural monuments, cultural ecosystem services can also be restored.

In our study, by investigating reambulated soil profiles from the Nagy-Sárrét region in Hungary, we attempt to determine the extent of changes which have occurred due to effects which impacted the landscape in terms of the soil chemistry properties of soil profiles exposed during the Kreybig soil survey more than 70 years ago. Based on the results, in the areas used as grassland, we observed a decrease in pH and an increase in the humus content of the topsoil. The increased CaCO3 following the chemical improvement of the soil which was used as cropland is still characteristic of the area. During the past decades, the investigated soils have been affected by significant changes with regard to water management, which have also modified the investigated parameters. We have classified the reambulated soil profiles among the Solonetz, Vertisol, and Gleysol reference groups based on the World Reference Base of Soil Resources (WRB) diagnostic system.

In 2017 the European Goldfinch (Carduelis carduelis) was voted to be the “bird of the year” in Hungary. This is a partially migrant species; most of the European populations are resident, however, its breeding range extends to East from the Sweden-Poland-Moldova axis towards the Yenisei with some of the populations wintering in Kazakhstan and South of Turkey. The European Goldfinch is classified within the Carduelinae subfamily including approximately a hundred species. Several taxonomic changes were introduced in this group during the last fifteen years, however, we still do not understand much of their origin and evolutionary history. My aim in this paper is to collect existing knowledge on the phylogeny and evolution of the Carduelinae finches and their allies, with a particular focus on the European Goldfinch and its closest relatives. Furthermore, here I point out uncertainties in different phylogenetic sources of finches, which careful consideration can be useful in similar evolutionary studies. Finally, I summarise some vision for future research.

We aimed to introduce and test the “seed mass–distribution range trade‐off” hypothesis, that is, that range size is negatively related to seed mass due to the generally better dispersal ability of smaller seeds. Studying the effects of environmental factors on the seed mass and range size of species, we also aimed to identify habitats where species may be at risk and need extra conservation effort to avoid local extinctions. We collected data for seed mass, global range size, and indicators for environmental factors of the habitat for 1,600 species of the Pannonian Ecoregion (Central Europe) from the literature. We tested the relationship between species’ seed mass, range size, and indicator values for soil moisture, light intensity, and nutrient supply. We found that seed mass is negatively correlated with range size; thus, a seed mass–distribution range trade‐off was validated based on the studied large species pool. We found increasing seed mass with decreasing light intensity and increasing nutrient availability, but decreasing seed mass with increasing soil moisture. Range size increased with increasing soil moisture and nutrient supply, but decreased with increasing light intensity. Our results supported the hypothesis that there is a trade‐off between seed mass and distribution range. We found that species of habitats characterized by low soil moisture and nutrient values but high light intensity values have small range size. This emphasizes that species of dry, infertile habitats, such as dry grasslands, could be more vulnerable to habitat fragmentation or degradation than species of wet and fertile habitats. The remarkably high number of species and the use of global distribution range in our study support our understanding of global biogeographic processes and patterns that are essential in defining conservation priorities.

Among the segments of economic development and shifts in the Miskolc agglomeration the present study introduces some characteristics of the functional, sectoral and regional differentiation of economic transformation. The functional, sectoral and geographical distribution of business corporations in the 35 settlements of the Miskolc agglomeration in 2016 may help to interpret and assess economic processes adapted to local characteristics in the past quarter-century. During the research, only those operating businesses were considered that had net sales of 20 million HUF or more in 2015. An empirical study of 640 active businesses in 35 settlements reveals the regional inequalities and sectoral concentration of the economy. The intensity of the spatial structure of the economy is uneven within the Miskolc agglomeration and spatial specialization can also be observed in the economic hinterland of Miskolc. The economic development induced significant changes in the spatial structure of three towns (Felsőzsolca, Nyékládháza, and Alsózsolca). Services (e.g. personal, distributive, and services for other businesses) as well as commerce, logistics and leisure functions concentrated in these towns strengthened their positions in the spatial structure. In addition, the technological and industrial parks of these towns are playing an increasing role. However, the towns of the agglomeration cannot or can hardly be regarded as economic competitors of Miskolc, i.e. the urban region has not become polycentric, and the inhabitants of these towns are not totally independent of Miskolc. In the case of Sajóbábony (due to its special situation) and Szikszó (despite its economic recovery) the functional, sectoral and regional transformation is not clear yet. Of the villages, only four (Kistokaj, Mályi, Szirmabesenyő, Hernádnémeti) could significantly improve their economic positions, and were able to rival the dynamically transforming three towns of the agglomeration. On the outer edge of the agglomeration the dynamism and the impact of businesses on the formation of the structure of the economic space is less and less detectable. Here, settlement differentiation is also influenced by transport accessibility, the innovation capabilities of local communities and other geographical factors.

Itaconic acid is used as a bio-based, renewable building block in the polymer industry. It is produced by submerged fermentations of the filamentous fungus Aspergillus terreus from molasses or starch, but research over the efficient utilization of non-food, lignocellulosic plant biomass is soaring. The objective of this study was to test whether the application of two key cultivation parameters for obtaining itaconic acid from D-glucose in high yields – Mn2+ ion deficiency and high concentration of the carbon source – would also occur on D-xylose, the principal monomer of lignocellulose. To this end, a carbon and energy balance for itaconic acid formation was established, which is 0.83 moles/mole D-xylose. The effect of Mn2+ ions on itaconic acid formation was indeed similar to that on D-glucose and maximal yields were obtained below 3 μg L–1 Mn2+ ions, which were, however, only 0.63 moles of itaconic acid per mole D-xylose. In contrast to the case on D-glucose, increasing D-xylose concentration over 50 g L–1 did not change the above yield. By-products such as xylitol and α-ketoglutarate were found, but in total they remained below 2% of the concentration of D-xylose. Mass balance of the fermentation with 110 g L–1D-xylose revealed that >95% of the carbon from D-xylose was accounted as biomass, itaconic acid, and the carbon dioxide released in the last step of itaconic acid biosynthesis. Our data show that the efficiency of biomass formation is the critical parameter for itaconic acid yield from D-xylose under otherwise optimal conditions.

l-Arabinose and d-galactose are the principal constituents of l-arabinogalactan, and also co-occur in other hemicelluloses and pectins. In this work we hypothesized that similar to the induction of relevant glycoside hydrolases by monomers liberated from these plant heteropolymers, their respective catabolisms in saprophytic and phytopathogenic fungi may respond to the presence of the other sugar to promote synergistic use of the complex growth substrate. We showed that these two sugars are indeed consumed simultaneously by Aspergillus nidulans, while l-arabinose is utilised faster in the presence than in the absence of d-galactose. Furthermore, the first two genes of the Leloir pathway for d-galactose catabolism - encoding d-galactose 1-epimerase and galactokinase - are induced more rapidly by l-arabinose than by d-galactose eventhough deletion mutants thereof grow as well as a wild type strain on the pentose. d-Galactose 1-epimerase is hyperinduced by l-arabinose, d-xylose and l-arabitol but not by xylitol. The results suggest that in A. nidulans, l-arabinose and d-xylose - both requiring NADPH for their catabolisation - actively promote the enzyme infrastructure necessary to convert β-d-galactopyranose via the Leloir pathway with its α-anomer specific enzymes, into β-d-glucose-6-phosphate (the starting substrate of the oxidative part of the pentose phosphate pathway) even in the absence of d-galactose.

Our aim in this article is to establish weighted Hardy-type inequalities in a broad family of means. In other words, for a fixed vector of weights $(\lambda_{n})_{n=1}^{\infty}$ and a weighted mean $\mathscr{M}$ , we search for the smallest extended real number $C$ such that ¶ \[\sum_{n=1}^{\infty}\lambda_{n}\mathscr{M}((x_{1},\ldots ,x_{n}),(\lambda_{1},\ldots,\lambda_{n}))\le C\sum_{n=1}^{\infty}\lambda_{n}x_{n}\quad \text{for all }x\in \ell_{1}(\lambda).\] The main results provide a complete answer in the case when $\mathscr{M}$ is monotone and satisfies the weighted counterpart of the Kedlaya inequality. In particular, this is the case if $\mathscr{M}$ is symmetric, concave, and the sequence $(\frac{\lambda_{n}}{\lambda_{1}+\cdots+\lambda_{n}})_{n=1}^{\infty}$ is nonincreasing. In addition, we prove that if $\mathscr{M}$ is a symmetric and monotone mean, then the biggest possible weighted Hardy constant is achieved if $\lambda$ is the constant vector.

Co-cultivation of the endophytic fungus Fusarium tricinctum with Streptomyces lividans on solid rice medium led to the production of four new naphthoquinone dimers, fusatricinones A–D (1–4), and a new lateropyrone derivative, dihydrolateropyrone (5), that were not detected in axenic fungal controls. In addition, four known cryptic compounds, zearalenone (7), (−)-citreoisocoumarin (8), macrocarpon C (9) and 7-hydroxy-2-(2-hydroxypropyl)-5-methylchromone (10), that were likewise undetectable in extracts from fungal controls, were obtained from the co-culture extracts. The known antibiotically active compound lateropyrone (6), the depsipeptides enniatins B (11), B1 (12) and A1 (13), and the lipopeptide fusaristatin A (14), that were present in axenic fungal controls and in co-culture extracts, were upregulated in the latter. The structures of the new compounds were elucidated by 1D and 2D NMR spectra as well as by HRESIMS data. The relative and absolute configuration of dihydrolateropyrone (5) was elucidated by TDDFT-ECD calculations.

Covering: 2012 to 2018 The principles and applicability of optical rotation, and electronic and vibrational circular dichroism aided by quantum chemical calculations are presented to determine absolute configuration and conformation through examples of stereochemical analysis of natural products with emphasis on the possibility of combined analysis and pitfalls for natural product chemists.

Five new biscembranoids, bistrochelides A–E (3–7), were isolated together with glaucumolides A (1) and B (2) from the soft coral Sarcophyton trocheliophorum. Their structures and absolute configurations were determined by spectroscopic methods, X-ray crystal diffraction, and DFT/NMR (density functional theory/nuclear magnetic resonance) and TDDFT/ECD (time-dependent density functional theory/electronic circular dichroism) calculations. A new approach is introduced to determine the relative configuration of a stereocenter through the dynamic evaluation of the mean absolute errors (MAEs) between the investigated diastereoisomers, moving from an “extended” to a more diagnostic “restricted” set of atoms. This research leads to the structure revision of glaucumolides A and B. In in vitro immunomodulatory screening, compounds 1 and 4 significantly induced the proliferation of CD3+ T cells, while compounds 1 and 5 significantly increased the CD4+/CD8+ ratio at 3 μM.

Chub (Squalius cephalus L. 1758) specimens of three age groups with different types of diet were collected in November 2013 in the River Szamos/Somes, Hungary. The Ca, K, Mg, Na, Cd, Cr, Cu, Fe, Mn, Pb, Sr and Zn concentrations were analyzed in the muscle, gills and liver samples of chub by microwave assisted plasma-atomic emission spectrometry (MP-AES). The Kruskal–Wallis test revealed significant differences among different age groups based on the trace element concentrations in the liver, muscle and gills. The trace element concentration pattern in muscle and liver of different age groups differed, may be according to the different diet types of the groups. Meanwhile no differentiation among the age groups based on the trace element concentration in the gills was observed, probably because the pattern of trace elements in the gills is related to the habitat preference, which does not differ during the life-span of chub. In contrast to expectations, trace element concentrations in juveniles were the highest in most cases, certainly because of their specific diet, relatively fast metabolic rate and inadequately developed detoxification system. Only the copper concentrations in liver increased with fish age. Considerable concentrations of trace elements in the tissues of juveniles were observed in the case of elements whose concentrations in the River Szamos were higher in 2013 than in previous years. According to this phenomenon, trace element patterns in the tissues of juveniles may be good indicators of recent pollution of watercourses.

In the face of worldwide habitat loss, the role of human-shaped habitats in conserving biodiversity is becoming increasingly important. Due to their special cultural role, cemeteries can preserve parts of the native vegetation when the surrounding landscape becomes degraded. However, these special refuges are threatened by human encroachment and changing management practices. The aim of this study was to understand how urbanization affects the conservation value of cemeteries, indicated by orchids as flagship species for biodiversity conservation. We analyzed species richness, abundance and the presence of threatened orchid taxa in cemeteries from 631 differently sized Turkish settlements along an urban-rural gradient. To understand driving patterns determining the conservation value, we performed detailed characterization of 288 cemeteries in terms of woody vegetation (tree cover and proportion of native trees) and overall structure (age, density and type of graves). Conservation value was highest in rural cemeteries. Rural cemeteries were smaller, contained more traditional and less densely situated graves, but their woody vegetation was similar to urban cemeteries. The proportion of native trees was positively related to species richness, abundance and presence of threatened orchid taxa, after taking into account area, altitude and geographical location of cemeteries. In addition, cemetery structure (age and density of graves) predicted species richness. Our results indicate that urbanization and modern changes in human activity have a strong impact on the conservation value of Turkish cemeteries. Practices maintaining traditional burial habits and environment-friendly management of cemeteries deserve more moral and financial support.

Amorphisation effect on the surface of SnTe and GeTe samples under low Ar+ ion energy sputtering (160 eV) has been firstly observed. Scanning electron microscopy and Raman spectroscopy methods were used for the investigation. Microscope images show that ion bombardment changes significantly the morphology of SnTe and GeTe sample surfaces. Comparative Raman spectroscopy studies of the as-prepared and sputtered surfaces revealed that sputtering changes not only the surface morphology, but also the crystal structure of samples. Due to sputtering, the initial crystalline GeTe sample surface completely changed to amorphous, while the SnTe sample surface changed to a mixed amorphous-crystalline structure. This means that on the surface of IVB group binary tellurides an amorphisation can be evoked by low energy Ar+ ion bombardment, up to a few hundred electron volts energy.

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Plant thin cell layers (TCLs), which consist of a few layers of cells, are typically 0.5–1 mm thick. After the first application of TCLs to tobacco in 1943, and after 45 years of their practical application to plant tissue culture, TCLs have proven to be an effective tool for the in vitro culture of dozens of plant species. Their higher productivity compared to conventional explants has made TCLs continually relevant and useful in plant research and applied plant biotechnology. On the 45th anniversary of TCLs, this mini-review highlights the emergence of about a dozen new studies published in the past three years (2016–2018) that employed TCLs in either basic tissue culture or applied in vitro biotechnology. These new results emerged for medicinal plants (Bacopa monnieri, Scutellaria ocmulgee, Urginea altissima, Withania coagulans ), fruit trees (Rubus spp.), vegetables (Allium ascalonicum, Allium schoenoprasum), a conifer (Pinus patula ), ornamental plants including Lilium and three orchids (Dendrobium aqueum, Dendrobium aphyllum, Malaxis wallichii ), and a model plant (Arabidopsis thaliana ). In plant biotechnology, TCLs have a rich history and their continued use and future application to plant tissue culture or genetic transformation is promising.

SUMMARYWe have studied how individual decisions about timing of breeding and nest location affected the reproductive success of rooks by tracing the formation of a rook breeding colony in Hortobágy NP (Hungary), during the breeding season in 1999.We have found that birds who built nests earlier also laid eggs earlier and had larger clutch size but had no had more offspring than late nesters. Distance of the nest from the centre or edge of the colony did not affect the reproductive success though rooks generally settled closer to the centre and further from the edge than it can be expected by assuming random distribution. The colony showed high breeding synchrony since date of egg laying varied less than date of nesting but synchrony did not influence the breeding success. Hatchling’s survival rate and number of offspring increased with local nest density and rooks clustered their nests more than it can be expected by random settlement. Nest sites of early and late nesters did not differ regarding the distance from the centre or the edge of the colony but late nesters chose nest sites in more densely populated regions.The results indicate that individuals may follow different strategies to increase their reproductive success. It is prospectively advantageous to build the nest and lay eggs earlier, in turn, it’s worth nesting in already more densely nested areas for late beginners. We suggest that a game theoretical approach may be useful if we try to understand the adaptive significance of colonial breeding.

We report the synthesis of some novel β-lactam hybrids of 2-mercaptobenzothiazole and benzoquinoline. These compounds were synthesized by a [2 + 2]-cycloaddition reaction of imines 8a-d and ketenes derived from substituted acetic acids. The reaction was totally diastereoselective leading exclusively to the formation of cis-β-lactams 10a-m. All products were obtained in good to excellent yields and their structures were established based on IR, 1H NMR, 13C NMR spectral data and elemental analysis. Schiff bases 8a-d and β-lactam hybrids 10a-m were evaluated for antimicrobial activities against six bacterial species. The minimum inhibitory concentration (MIC) values indicate that two of the β-lactams, 10k and 10m, have good activities against the two Gram-negative bacteria, E. coli and P. aeruginosa, while three of the Schiff bases, 8a-c, are active against P. aeruginosa and the Gram-positive pathogen S. aureus. The molecular and cellular basis for these observed antibacterial properties are not determined. Moreover, the five most active compounds showed acceptably low cytotoxicity (less than 25% cell growth inhibition after 72 h of incubation) against the MCF-7 cell line, and below 10% in vitro hemolytic activity at 50 and 200 µM concentrations. These results suggest a need for further inquiry into the reason for why these compounds are bioactive, and as to what their full biological activities and antibiotic potential may be. The cis stereochemistry of β-lactam 10a was confirmed by X-ray crystallographic studies.

Small, cysteine-rich and cationic antifungal proteins from natural sources are promising candidates for the development of novel treatment strategies to prevent and combat infections caused by drug-resistant fungi. However, limited information about their structure and antifungal mechanism hampers their future applications. In the present study, we determined the solution structure, dynamics and associated solvent areas of the Neosartorya (Aspergillus) fischeri antifungal protein NFAP. Genome mining within the genus revealed the presence of orthologous genes in N. fischeri and Neosartorya spathulata, and genes encoding closely related proteins can be found in Penicillium brasiliensis and Penicillium oxalicum. We show that the tertiary structure of these putative proteins can be resolved using the structure of NFAP as reliable template for in silico prediction. Localization studies with fluorescence-labelled protein pointed at an energy-dependent uptake mechanism of NFAP in the sensitive model fungus Neurospora crassa and subsequent cytoplasmic localization coincided with cell-death induction. The presented results contribute to a better understanding of the structure/function relationship of NFAP and related proteins and pave the way towards future antifungal drug development.

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D-ribose and D-arabinose differ only by the steric orientation of their C2-OH groups. The initial reactions and emergence of RNA depended on the position, reactivity, and flexibility of the C2-OH moiety in the ribose molecule. The steric relationship of the C2- and C3-OH groups favored the selection of ribose, ribonucleotide, and RNA synthesis and excluded the possibility of xenonucleic acid-based life on Earth. This brief review provides a hypothesis based on the absence of nucleotides and enzymes under prebiotic conditions and on the polymerization of ribose 5-phosphate units leading to the polarized formation of the ribose-phosphate backbone. The strong covalent bond formation in the sugar-phosphate backbone was followed by the somewhat less reactive interaction between ribose and nucleobase and supplemented by even weaker hydrogen-bonded and stacking interactions. This hypothesis proposes a scheme how prebiotic random-sequence RNA was formed under abiotic conditions and hydrolyzed to oligomers and nucleotides. The term random-sequence prebiotic RNA refers to nucleobases attached randomly to the ribose-phosphate backbone and not to cellular RNA sequences as proteins and cells did not probably exist at the time of abiotic RNA formation. It is hypothesized that RNA generated under abiotic conditions containing random nucleobases was hydrolyzed to nucleotides that served as a pool for the selected synthesis of genetic RNA.

An increasing number of infections originating from probiotic use are reported worldwide, with the majority of such cases caused by the yeast Saccharomyces 'boulardii', a subtype of S. cerevisiae. Reliably linking infectious cases to probiotic products requires unequivocal genotyping data, however, these techniques are often time-consuming and difficult to implement in routine diagnostics. This leads to a widespread lack of genetic data regarding the origin of Saccharomyces infections. We propose a quick and reliable PCR-based protocol for the identification of S. 'boulardii' based on a combined analysis of interdelta fingerprinting and microsatellite typing. By applying various typing methods and our proposed method to the clinical yeast collection of a Hungarian hospital we show that probiotic origin is common among clinical Saccharomyces, and that the new multiplex method enables rapid and unequivocal identification of probiotic yeast infections. This method can be applied for the identification of yeast infection sources, helping decisions on probiotic use.

The effect of long-term laboratory maintenance on the biological diversity and certain oenolological properties of wine yeasts was investigated by the analysis of 17 strains isolated from Tokaj (Hungary) wines more than a century ago and maintained since then in culture collections. The analysis of the D1/D2 domains of the large subunit ribosomal RNA genes and the ITS sequences assigned them all to S. cerevisiae but divided them into two groups. One group showed sequence identity with wine strains occurring mainly in countries of the region. The combined results of the interdelta, RAPD, microsatellite-primed PCR (MSP), mtDNA and karyotype analyses found both groups diverse and defined each strain as unique, demonstrating that the long period of maintenance under identical conditions has not resulted in convergent evolution in their genomes. High diversity was detected also in certain phenotypic traits of oenological relevance (osmotolerance, killer phenotype, production of glycerol, ethanol, H2S and volatile acids). In the microvinification experiments all strains performed better than the laboratory strain S288c and were comparable to the industrial strain used as a control or even surpassed it in certain parameters. Thus, the oenological abilities of wine yeasts can be preserved over long periods of maintenance under laboratory conditions.

Three new compounds (9-11) were isolated together with eight known analogues from the fungus Pseudallescheria boydii associated with the South China Sea soft coral Sinularia sandensis. The structures of the new compounds were elucidated on the basis of the spectroscopic analysis, and the absolute configurations including the sulfur stereogenic center of a sulfoxide moiety were determined by comparison of experimental ECD spectra to TDDFT/ECD calculations. Epimeric chiral sulfoxides differing in the absolute configuration of the sulfur chirality center could be efficiently distinguished and assigned by comparing the experimental ECD to those of calculations for the sulfur epimers. In the in vitro biotests for osteoclastogenesis effects, compounds 1, 5, 7, and 10 exhibited a stimulatory activity, while compound 3 displayed an inhibitory activity.

Ethyl-3-formyl-6-methoxy-(2H)-chromene-2-carboxylate was transformed to N-substituted 1,2-dihydrochromeno[2,3-c]pyrrol-3-ones in a domino reductive amination–lactamization reaction. Isomerization of the double bond and the inherently labile stereogenic center was studied, and HPLC-ECD analysis of a chiral 1,2-dihydrochromeno[2,3-c]pyrrol-3(3aH)-one derivative aided by TDDFT-ECD calculation allowed configurational assignment of the separated enantiomers. Antiproliferative activity of the products was demonstrated on the CaCo-2 human epithelial colorectal adenocarcinoma cell line.

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The class Laboulbeniomycetes comprises biotrophic parasites associated with arthropods and fungi. Two orders are currently recognized, Pyxidiophorales and Laboulbeniales. Herpomyces is an isolated genus of Laboulbeniales, with species that exclusively parasitize cockroaches (Blattodea). Here, we evaluate 39 taxa of Laboulbeniomycetes with a three-locus phylogeny (nrSSU, ITS, nrLSU) and propose a new order in this class. Herpomycetales accommodates a single genus, Herpomyces, with currently 26 species, one of which is described here based on morphological and molecular data. Herpomyces shelfordellae is found on Shelfordella lateralis cockroaches from Hungary, Poland, and the USA. We also build on the six-locus dataset from the Ascomycota Tree of Life paper (Schoch and colleagues, 2009) to confirm that Laboulbeniomycetes and Sordariomycetes are sister classes, and we apply laboulbeniomyceta as a rankless taxon for the now well-resolved node that describes the most recent common ancestor of both classes.

DNA methylation is a process of epigenetic modification that can alter the functionality of a genome. Using whole-genome bisulfite sequencing, this study quantify the level of DNA methylation in the epigenomes of two diploid apple (Malus x domestica) scion cultivars ('McIntosh' and 'Húsvéti rozmaring') derived from three environmental conditions: in vivo mother plants in an orchard, in vitro culture, and acclimatized in vitro plants. The global DNA methylation levels were not dependent on the source of plant material, and the average level of DNA methylation was 49.77%, 34.65% and 8.77% in CpG, CHG and CHH contexts, respectively. Significant differences in DNA methylation were identified in 586 (specifically 334, 201 and 131 in CpG, CHG and CHH contexts, respectively) out of 45,116 genes, including promoter and coding sequences. These were classified as differentially methylated genes (DMGs). This is a 1.3% difference in the level of DNA methylation of genes in response to a change in the environment. Differential methylation was visualised by MA plots and functional genomic maps were established for biological processes, molecular functions and cellular components. When the DMGs were considered, in vitro tissue culture resulted in the highest level of methylation, but it was lower in acclimatized in vitro plants which was similar to that in the mother tree. Methylation patterns of the two scions differed, indicating cultivar-specific epigenetic regulation of gene expression during adaptation to various environments. After selecting genes that displayed differences larger than ±10% in CpG and CHG contexts, or larger than ±1.35% in the CHH context from among the DMGs, they were annotated in Blast2 GO v5.1.12 for Gene Ontology. DMGs identified as MD07G1113000 (protein transport), MD08G1041600 (extracellular space), MD09G1054800 (phosphatidic acid binding), and MD10G1265800 (not annotated) were methylated in all three contexts in in vitro shoots. These DNA methylation results suggest that epigenetic changes may contribute to the adaptation of apple to environmental changes by modifying the epigenome and thereby gene expression.

Cholesterol, an essential lipid component of cellular plasma membranes, regulates fluidity, mechanical integrity, raft structure and may specifically interact with membrane proteins. Numerous effects on ion channels by cholesterol, including changes in current amplitude, voltage dependence and gating kinetics, have been reported. We have previously described such changes in the voltage-gated potassium channel Kv1.3 of lymphocytes by cholesterol and its analog 7-dehydrocholesterol (7DHC). In voltage-gated channels membrane depolarization induces movement of the voltage sensor domains (VSD), which is transmitted by a coupling mechanism to the pore domain (PD) to open the channel. Here, we investigated whether cholesterol effects were mediated by the VSD to the pore or the PD was the direct target. Specificity was tested by comparing Kv1.3 and Kv10.1 channels having different VSD-PD coupling mechanisms. Current recordings were performed with two-electrode voltage-clamp fluorometry, where movement of the VSDs was monitored by attaching fluorophores to external cysteine residues introduced in the channel sequence. Loading the membrane with cholesterol or 7DHC using methyl-β-cyclodextrin induced changes in the steady-state and kinetic parameters of the ionic currents while leaving fluorescence parameters mostly unaffected in both channels. Non-stationary noise analysis revealed that reduction of single channel conductance rather than that of open probability caused the observed current decrease. Furthermore, confocal laser scanning and stimulated emission depletion microscopy demonstrated significant changes in the distribution of these ion channels in response to sterol loading. Our results indicate that sterol-induced effects on ion channel gating directly target the pore and do not act via the VSD.

The changes of the surface morphology of poly(tetrafluoroethylene) due to proton irradiation was investigated. 1 MeV proton beam was used for the irradiations with relatively low current densities, in the range of 10–100,000 pA/mm2. The applied ion fluences ranged from 0.1 to 2500 nC/mm2 (6.24 * 1010–1.56 * 1015 ion/cm2). The surface was characterized by interference contrast microscopy, surface profilometry and scanning electron microscopy. The results show that at each current density the surface can be machined, and the etching depth is increasing with increasing ion fluence, up to a certain point. However, in each case there is a threshold value, between 50 and 100 nC/mm2, where the process turns back. First, the etching depth starts to decrease. Later, by further increasing the delivered ion fluence, an opposite process begins and the surface becomes protruding.

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International audience; Spliceosomal twin introns (stwintrons) are introns where any of the three consensus sequences involved in splicing is interrupted by another intron (internal intron). In Aspergillus nidulans, a donor-disrupted stwintron (intron-1) is extant in the transcript encoding a reticulon-like protein. The orthologous transcript of Aspergillus niger can be alternatively spliced; the exon downstream the stwintron could be skipped by excising a sequence that comprises this stwintron, the neighbouring intron-2, and the exon bounded by these. This process involves the use of alternative 3' splice sites for the internal intron, the resulting alternative intervening sequence being a longer 3'-extended stwintron. In 29 species of Onygenales, a multi-step splicing process occurs in the orthologous transcript, in which a complex intervening sequence including the stwintron and neigbouring intron-2, generates by three splicing reactions a "second order intron" which must then be excised with a fourth splicing event. The gene model in two species can be envisaged as one canonical intron (intron-1) evolved from this complex intervening sequence of nested canonical introns found elsewhere in Onygenales. Postulated splicing intermediates were experimentally verified in one or more species. This work illustrates a role of stwintrons in both alternative splicing and the evolution of intron structure.

One of the promising directions of the combined approach is the design of dual-acting antibiotics - heterodimeric structures on the basis of antimicrobial agents of different classes. In this study a novel series of azithromycin-glycopeptide conjugates were designed and synthesized. The structures of the obtained compounds were confirmed using NMR spectroscopy and mass spectrometry data including MS/MS analysis. All novel hybrid antibiotics were found to be either as active as azithromycin and vancomycin against Gram-positive bacterial strains or have superior activity in comparison with their parent antibiotics. One compound, eremomycin-azithromycin conjugate 16, demonstrated moderate activity against Enterococcus faecium and Enterococcus faecalis strains resistant to vancomycin, and equal to vancomycin's activity for the treatment of mice with Staphylococcus aureus sepsis.

Glucopyranosylidene-spiro-benzo[ b][1,4]oxazinones were obtained via the corresponding 2-nitrophenyl glycosides obtained by two methods: (a) AgOTf-promoted glycosylation of 2-nitrophenol derivatives by O-perbenzoylated methyl (α-d-gluculopyranosyl bromide)heptonate or (b) Mitsunobu-type reactions of O-perbenzoylated methyl (α-d-gluculopyranose)heptonate with bulky 2-nitrophenols in the presence of diethyl azodicarboxylate (DEAD) and PPh3. Catalytic hydrogenation (H2-Pd/C) or partial reduction (e.g., H2-Pd/C, pyridine) of the 2-nitro groups led to spiro-benzo[ b][1,4]oxazinones and spiro-benzo[ b][1,4]-4-hydroxyoxazinones by spontaneous ring closure of the intermediate 2-aminophenyl or 2-hydroxylamino glycosides, respectively. The analogous 2-aminophenyl thioglycosides, prepared by reactions of O-perbenzoylated methyl (α-d-gluculopyranosyl bromide)heptonate with 2-aminothiophenols, were cyclized in m-xylene at reflux temperature to the corresponding spiro-benzo[ b][1,4]thiazinones. O-Debenzoylation was effected by Zemplen transesterification in both series. Spiro-configurations were determined by NMR and electronic circular dichroism time-dependent density functional theory (ECD-TDDFT) methods. Inhibition assays with rabbit muscle glycogen phosphorylase b showed (1' R)-spiro{1',5'-anhydro-d-glucitol-1',2-benzo[ b][1,4]oxazin-3(4 H)-one} and (1' R)-spiro{1',5'-anhydro-d-glucitol-1',2-benzo[ b][1,4]thiazin-3(4 H)-one} to be the most efficient inhibitors (27 and 28% inhibition at 625 μM, respectively). Plant growth tests with white mustard and garden cress indicated no effect except for (1' R)-4-hydroxyspiro{1',5'-anhydro-d-glucitol-1',2-benzo[ b][1,4]oxazin-3(4 H)-one} with the latter plant to show modest inhibition of germination (95% relative to control).

Matrix-assisted laser desorption ionization and electrospray ionization mass spectrometry (MALDI-MS and ESI-MS) were used for the characterization of epoxidized soybean and linseed oils, which are important raw materials in the biopolymer production. The recently invented data mining approach, mass-remainder analysis (MARA), was implemented for the analysis of these types of complex natural systems. Different epoxidized triglyceride mass spectral peak series were identified, and the number of carbon atoms and epoxide groups was determined. The fragmentation mechanisms of the epoxidized triglyceride (ETG) adducts formed with different cations (such as H+, Na+, Li+, and NH4+) were explored. As a novel approach, the evaluation of the clear fragmentation pathways of the sodiated ETG adducts enabled the estimation of the epoxidized fatty acid compositions of these types of oils by MS/MS.

Structural changes (martensitic transformation, rearrangements of martensitic variants) in shape memory alloys have an intermittent character that is accompanied by the emission of different (thermal, acoustic, and magnetic) noises, which are fingerprints of the driven criticality, resulting in a damped power-law behaviour. We will illustrate what kinds of important information can be obtained on the structural changes in shape memory alloys. It was established that the power exponents of distributions of acoustic emission (AE) parameters (energy, amplitude, etc.), belonging to martensitic transformations, show quite a universal character and depend only on the symmetry of the martensite. However, we have shown that the asymmetry of the transformation (the exponents are different for the forward and reverse transformations) results in as large differences as those due to the martensite symmetry. We will also demonstrate how the recently introduced AE clustering method can help to identify the different contributions responsible for the asymmetry. The usefulness of the investigations of time correlations between the subsequent events and correlations between acoustic and magnetic noise events in ferromagnetic shape memory alloys will be demonstrated too. Finally, examples of acoustic and magnetic emissions during variant rearrangements (superplastic or superelastic behaviour) in the martensitic state will be described.

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Maintenance of the endothelial cell (EC) barrier is critical to vascular homeostasis and a loss of barrier integrity results in increased vascular permeability. While the mechanisms that govern increased EC permeability have been under intense investigation over the past several decades, the processes regulating the preservation/restoration of the EC barrier remain poorly understood. Herein we show that the extracellular purines, adenosine (Ado) and adenosine 5'-[γ-thio]-triphosphate (ATPγS) can strengthen the barrier function of human lung microvascular EC (HLMVEC). This ability involves protein kinase A (PKA) activation and decreases in myosin light chain 20 (MLC20) phosphorylation secondary to the involvement of MLC phosphatase (MLCP). In contrast to Ado, ATPγS-induced PKA activation is accompanied by a modest, but significant decrease in cyclic adenosine monophosphate (cAMP) levels supporting the existence of an unconventional cAMP-independent pathway of PKA activation. Furthermore, ATPγS-induced EC barrier strengthening does not involve the Rap guanine nucleotide exchange factor 3 (EPAC1) which is directly activated by cAMP but is instead dependent upon PKA-anchor protein 2 (AKAP2) expression. We also found that AKAP2 can directly interact with the myosin phosphatase-targeting protein MYPT1 and that depletion of AKAP2 abolished ATPγS-induced increases in transendothelial electrical resistance. Ado-induced strengthening of the HLMVEC barrier required the coordinated activation of PKA and EPAC1 in a cAMP-dependent manner. In summary, ATPγS-induced enhancement of the EC barrier is EPAC1-independent and is instead mediated by activation of PKA which is then guided by AKAP2, in a cAMP-independent mechanism, to activate MLCP which dephosphorylates MLC20 resulting in reduced EC contraction and preservation.

Accurate and reliable probabilistic forecasts of hydrological quantities like runoff or water level are beneficial to various areas of society. Probabilistic state-of-the-art hydrological ensemble prediction models are usually driven with meteorological ensemble forecasts. Hence, biases and dispersion errors of the meteorological forecasts cascade down to the hydrological predictions and add to the errors of the hydrological models. The systematic parts of these errors can be reduced by applying statistical post-processing. For a sound estimation of predictive uncertainty and an optimal correction of systematic errors, statistical post-processing methods should be tailored to the particular forecast variable at hand. Former studies have shown that it can make sense to treat hydrological quantities as bounded variables. In this paper, a doubly truncated Bayesian model averaging (BMA) method, which allows for flexible post-processing of (multi-model) ensemble forecasts of water level, is introduced. A case study based on water level for a gauge of river Rhine, reveals a good predictive skill of doubly truncated BMA compared both to the raw ensemble and the reference ensemble model output statistics approach.