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To investigate the dematiaceous fungal profile of patients with ocular mycoses attending a tertiary eye care hospital in Coimbatore, India METHODS: The identification of dematiaceous fungus based on their morphology, their genotypes, and the measurement of the minimum inhibitory concentrations (MICs) using microdilution method of routinely used antifungal drugs were all compared.A total of 148 dematiaceous fungi were isolated during a study period of 27 months. Isolates were confirmed as Curvularia spp. (n = 98), Exserohilum spp. (n = 32), Alternaria spp. (n = 14), Exophiala spp. (n = 2), Cladosporium sp. (n = 1) and Aureobasidium sp. (n = 1). Out of 50 well grown isolates characterized genotypically based on the amplification and sequencing of the ITS region of the ribosomal RNA gene cluster and subsequent BLAST analysis, Curvularia lunata (n = 24), C. aeria (n = 1), C. spicifera (n = 8), C. hawaiiensis (n = 1), C. maydis (n = 2), C. papendorfii (n = 2), C. geniculata (n = 3), C. tetramera (n = 2) and Exs. rostratum (n = 7) were identified. In vitro antifungal susceptibilities of the most tested dematiaceous isolates showed that voriconazole had a MICVoriconazole proved to be the most effective drug against the pigmented filamentous fungi, followed by amphotericin B, itraconazole and econazole.

Cryptococcosis, a life-threatening fungal infection, frequently occurs in patients suffering from AIDS. The treatment of the disease is hampered by the limited number of the effective drugs and the increasing resistance; therefore, to find new active substances is needed. As meningitis is the most serious infection affecting the AIDS patients, effective drugs have to be capable of entering to the central nervous system. Ecdysteroids are natural bioactive molecules with considerable anabolic activity and without toxic side effects on humans. The aim of this work was to study the anti-cryptococcal activity of a natural ecdysteroid, 20E, and its three semi-synthetic derivatives obtained by structural modification of the original molecule. We established the minimum inhibitory concentration of the compounds with microdilution method and demonstrated their fungicidal activity by flow cytometry and cultivation of the drug-treated cells. The interaction of the compounds with each other and efflux transporter inhibitors was assessed by checkerboard titration method. Two derivatives, 20E-EOx and 20E-ZOx, inhibited the growth of Cryptococcus neoformans with minimum inhibitory concentration 2 mg/mL and 1 mg/mL, respectively; both compounds possess fungicidal effect. A combination of the ecdysteroids with each other and verapamil resulted in additive interaction. This study confirmed that structural modification of an originally non-antimicrobial molecule can enhance its effectiveness.

Abstract Monotopic membrane-bound flavoproteins, sulfide:quinone oxidoreductases (SQRs), have a variety of physiological functions, including sulfide detoxification. SQR enzymes are classified into six groups. SQRs use the flavin adenine dinucleotide (FAD) cofactor to transfer electrons from sulfide to quinone. A type VI SQR of the photosynthetic purple sulfur bacterium, Thiocapsa roseopersicina (TrSqrF), has been previously characterized, and the mechanism of sulfide oxidation has been proposed. This paper reports the characterization of quinone binding site (QBS) of TrSqrF composed of conserved aromatic and apolar amino acids. Val331, Ile333, and Phe366 were identified near the benzoquinone ring of enzyme-bound decylubiquinone (dUQ) using the TrSqrF homology model. In silico analysis revealed that Val331 and Ile333 alternately connected with the quinone head group via hydrogen bonds, and Phe366 and Trp369 bound the quinones via hydrophobic interactions. TrSqrF variants containing alanine (V331A, I333A, F366A) and aromatic amino acid (V331F, I333F, F366Y), as well as a C-terminal α-helix deletion (CTD) mutant were generated. These amino acids are critical for quinone binding and, thus, catalysis. Spectroscopic analyses proved that all mutants contained FAD. I333F replacement resulted in the lack of the charge transfer complex. In summary, the interactions described above maintain the quinone molecule’s head in an optimal position for direct electron transfer from FAD. Surprisingly, the CTD mutant retained a relatively high level of specific activity while remaining membrane-anchored. This is a unique study because it focuses on the QBS and the oxidative stage of a type VI sulfide-dependent quinone reduction. Key points • V331, I333, F366, and W369 were shown to interact with decylubiquinone in T. roseopersicina SqrF • These amino acids are involved in proper positioning of quinones next to FAD • I333 is essential in formation of a charge transfer complex from FAD to quinone Graphical abstract

IntroductionLand use changes have seriously fragmented grasslands leading to extensive biodiversity loss worldwide. Habitat fragmentation affects grasslands at both local and landscape scales, adversely affecting the probability of species colonisation and extinction. In our study, we addressed the effects of fragment size and landscape-scale habitat connectivity on the vegetation composition in two grassland types, i.e., loess steppe fragments (situated on kurgans) and sand steppe fragments of the Pannonian forest steppe region.MethodsWe collected frequency data on vascular plant species in 12 1 m × 1 m quadrats in altogether 60 fragments along a connectivity gradient in sand steppes and loess steppe fragments. We analysed whether habitat specialists, generalists and exotic species were affected by the level of fragmentation based on species richness and traits related to local persistence (life span, clonality and soil seed bank type) and dispersal (dispersal strategy and seed mass) in the two grassland types using linear mixed-effects models.ResultsBased on our results, both fragment size and landscape-scale connectivity were important in shaping the trait composition of the vegetation. We observed more fragmentation effects in generalist than in specialist species. We found that isolation resulted in fewer specialist species with autochorous dispersal strategy in loess steppe fragments, but, at the same time, also fewer exotics. Isolated loess steppe fragments harboured fewer generalist species with persistent seed bank. Large loess steppe fragments supported more wind-dispersed species than smaller ones. In isolated sand steppe fragments, generalists were more frequent with endozoochorous dispersal strategy and without clonal propagation. Life span, clonal propagation and seed mass did not depend on the level of fragmentation in the two grassland types.DiscussionOur results imply that both sand and loess steppe fragments can rely to some extent on the persistence of clonal perennial specialist and generalist species in small and isolated patches to mitigate fragmentation effects. In conclusion, these processes should be supported by the preservation of large fragments, increase of habitat connectivity combined with targeted management of exotic species.

Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhibit coordinated and highly cell-type-specific inclusion. We found two distinct combination patterns: those distinguishing neural cell types, enriched in TSS-exon, exon-polyadenylation-site and non-adjacent exon pairs, and those with multiple configurations within one cell type, enriched in adjacent exon pairs. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons, implying that coordination can be rapidly established during evolution. SnISOr-Seq enables cell-type-specific long-read isoform analysis in human brain and in any frozen or hard-to-dissociate sample.

The rotifer-specific exogenic biopolymer, named Rotimer and its related molecular processes are affected by physical and chemical factors (e.g., temperature, pH or metal ions); however, the study of biological influences (e.g., the presence protozoa) concerning the particle-dependent reproduction (egg laying) and 'biopolymer producing capacity' (BPC) of rotifers is the objective of the present work. Non-planktonic rotifer species (Philodina acuticornis, Adineta vaga, Euchlanis dilatata, and Lecane bulla) were studied in paired micrometazoa-protozoa co-cultures involving Paramecium, Diplonema, and Amoeba. These protozoa can be beneficial food sources, enhancing reproduction, or even toxic factors for the above-mentioned animals, but can also function as particle-like mechanical stimulators. Furthermore, current studies reveal that bdelloids, similarly to monogonants, produce filamentous exudate; moreover, the body of bdelloids is covered by their exudate, unlike that of monogonants, especially in the case of A. vaga. A mathematical formula was developed as an improved version of a previously published viability marker to characterize the BPC and the relative amount of produced exudate in different conditions. Rotifer species secreting biopolymers appear to be a general trait indicating a common evolutionary background (e.g., calcium- and particle dependency) of such molecules; therefore, the BPC becomes an experiential sublethal influencing marker to these micrometazoans.

Fusarium graminearum and F. culmorum cause the most widespread wheat disease Fusarium head blight (FHB). The present study describes that the Fusarium inoculation of the wheat spikes caused systemic changes in the key elements of the antioxidant/detoxification defence system in the flag leaf during the grain filling period in wheat lines differing in biotic stress susceptibility to explore changes in some components of the response. According to our data, the inoculation with both F. graminearum and F. culmorum at the anthesis changed significantly the activities of superoxide dismutase (SOD) and guaiacol peroxidase (POD) enzymes, as well as the glutathione transferase (GST) activity in the flag leaves of the selected wheat lines approx. two weeks later after the infection. In silico approach supported the expressional up-regulation of various GST genes upon Fusarium infection. Based on our results, GST sequences TaGSTF26 and TaGSTU120 were among the series of important stress response genes, which were transcriptionally up-regulated, thus possibly playing a role in the systemic response to Fusarium infection, where TaGSTF26 might have an important role in the successful defence. These GSTs can serve as effective markers of the detoxification process for breeders and plant protection in the future.

Fumonisin B1 (FB1) is a harmful mycotoxin produced by Fusarium species, which results in oxidative stress leading to cell death in plants. FB1 perturbs the metabolism of sphingolipids and causes growth and yield reduction. This study was conducted to assess the role of ethylene in the production and metabolism of reactive oxygen species in the leaves of wild type (WT) and ethylene receptor mutant Never ripe (Nr) tomato and to elucidate the FB1-induced phytotoxic effects on the photosynthetic activity and antioxidant mechanisms triggered by FB1 stress. FB1 exposure resulted in significant ethylene emission in a concentration-dependent manner in both genotypes. Moreover, FB1 significantly affected the photosynthetic parameters of PSII and PSI and activated photoprotective mechanisms, such as non-photochemical quenching in both genotypes, especially under 10 µM FB1 concentration. Further, the net photosynthetic rate and stomatal conductance were significantly reduced in both genotypes in a FB1 dose-dependent manner. Interestingly, lipid peroxidation and loss of cell viability were also more pronounced in WT as compared to Nr leaves indicating the role of ethylene in cell death induction in the leaves. Thus, FB1-induced oxidative stress affected the working efficiency of PSI and PSII in both tomato genotypes. However, ethylene-dependent antioxidant enzymatic defense mechanisms were activated by FB1 and showed significantly elevated levels of superoxide dismutase (18.6%), ascorbate peroxidase (129.1%), and glutathione S-transferase activities (66.62%) in Nr mutants as compared to WT tomato plants confirming the role of ethylene in the regulation of cell death and defense mechanisms under the mycotoxin exposure.

We introduce a novel population genetic approach suitable to model the origin and relationships of populations, using new computation methods analyzing Hg frequency distributions. Hgs were selected into groups which show correlated frequencies in subsets of populations, based on the assumption that correlations were established in ancient separation, migration and admixture processes. Populations are defined with this universal Hg database, then using unsupervised artificial intelligence, central vectors (CVs) are determined from local condensations of the Hg-distribution vectors in the multidimensional point system. Populations are clustered according to their proximity to CVs. We show that CVs can be regarded as approximations of ancient populations and real populations can be modeled as weighted linear combinations of the CVs using a new linear combination algorithm based on a gradient search for the weights. The efficacy of the method is demonstrated by comparing Copper Age populations of the Carpathian Basin to Middle Age ones and modern Hungarians. Our analysis reveals significant population continuity since the Middle Ages, and the presence of a substrate component since the Copper Age.

The fungal membrane contains ergosterol instead of cholesterol, which offers a specific point of attack for the defense against pathogenic fungi. Indeed, most antifungal agents target ergosterol or its biosynthesis.

The cultivation and consumption of sweet potato (Ipomoea batatas) are increasing globally. As the usage of chemical fertilizers and pest control agents during its cultivation may lead to soil, water and air pollution, there is an emerging need for environment-friendly, biological solutions enabling increased amounts of healthy crop and efficient disease management. Microbiological agents for agricultural purposes gained increasing importance in the past few decades. Our goal was to develop an agricultural soil inoculant from multiple microorganisms and test its application potential in sweet potato cultivation. Two Trichoderma strains were selected: Trichoderma ghanense strain SZMC 25217 based on its extracellular enzyme activities for the biodegradation of plant residues, and Trichoderma afroharzianum strain SZMC 25231 for biocontrol purposes against fungal plant pathogens. The Bacillus velezensis strain SZMC 24986 proved to be the best growth inhibitor of most of the nine tested strains of fungal species known as plant pathogens, therefore it was also selected for biocontrol purposes against fungal plant pathogens. Arthrobacter globiformis strain SZMC 25081, showing the fastest growth on nitrogen-free medium, was selected as a component with possible nitrogen-fixing potential. A Pseudomonas resinovorans strain, SZMC 25872, was selected for its ability to produce indole-3-acetic acid, which is among the important traits of potential plant growth-promoting rhizobacteria (PGPR). A series of experiments were performed to test the selected strains for their tolerance to abiotic stress factors such as pH, temperature, water activity and fungicides, influencing the survivability in agricultural environments. The selected strains were used to treat sweet potato in two separate field experiments. Yield increase was observed for the plants treated with the selected microbial consortium (synthetic community) in comparison with the control group in both cases. Our results suggest that the developed microbial inoculant has the potential to be used in sweet potato plantations. To the best of our knowledge, this is the first report about the successful application of a fungal-bacterial consortium in sweet potato cultivation.

Mucormycosis is an invasive fungal infection caused by certain members of the fungal order of Mucorales. The species most frequently identified as the etiological agents of mucormycosis belong to the genera Rhizopus, Lichtheimia, and Mucor. The frequency of systemic mucormycosis has been increasing, mainly because of increasing numbers of susceptible patients. Furthermore, Mucorales display intrinsic resistance to the majority of routinely used antifungal agents (e.g., echinocandins and short-tailed azoles), which limits the number of possible therapeutic options. All the above-mentioned issues urge the improvement of molecular identification methods and the discovery of new antifungal targets and strategies. Spore coat proteins (CotH) constitute a kinase family present in many pathogenic bacteria and fungi and participate in the spore formation in these organisms. Moreover, some of them can act as virulence factors being receptors of the human GRP78 protein during Rhizopus delemar-induced mucormycosis. We identified 17 cotH-like genes in the Mucor lusitanicus genome database. Successful disruption of five cotH genes in Mucor was performed using the CRISPR-Cas9 system. The CotH3 and CotH4 proteins play a role in adaptation to different temperatures as well as in developing the cell wall structure. We also show CotH4 protein is involved in spore wall formation by affecting the total chitin content and, thus, the composition of the spore wall. The role of CotH3 and CotH4 proteins in virulence was confirmed in two invertebrate models and a diabetic ketoacidosis (DKA) mouse model. IMPORTANCE Current treatment options for mucormycosis are inadequate, resulting in high mortality rates, especially among immunosuppressed patients. The development of novel therapies for mucormycosis has been hampered by lack of understanding of the pathogenetic mechanisms. The importance of the cell surface CotH proteins in the pathogenesis of Rhizopus-mediated mucormycosis has been recently described. However, the contribution of this family of proteins to the virulence of other mucoralean fungi and their functionality in vital processes remain undefined. Through the use of the CRISPR-Case9 gene disruption system, we demonstrate the importance of several of the CotH proteins to the virulence of Mucor lusitanicus by using three infection models. We also report on the importance of one of these proteins, CotH4, to spore wall formation by affecting chitin content. Therefore, our studies extend the importance of CotH proteins to Mucor and identify the mechanism by which one of the CotH proteins contributes to the development of a normal fungal cell wall, thereby indicating that this family of proteins can be targeted for future development of novel therapeutic strategies of mucormycosis.

Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×–11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data.

Invasive tree species are a significant threat to native flora. They modify the environment with their allelopathic substances and inhibit the growth of native species by shading, thus reducing diversity. The most effective way to control invasive plants is to prevent their spread which requires identifying the environmental parameters promoting it. Since there are several types of invasive plant databases available, determining which database type is the most relevant for investigating the occurrence of alien plants is of great importance. In this study, we compared the efficiency and reliability of point-based (EUROSTAT Land Use and Coverage Area Frame Survey (LUCAS)) and polygon-based (National Forestry Database (NFD)) databases using geostatistical methods in ArcGIS software. We also investigated the occurrence of three invasive tree species (Ailanthus altissima, Elaeagnus angustifolia, and Robinia pseudoacacia) and their relationships with soil, hydrological, and climatic parameters such as soil organic matter content, pH, calcium carbonate content, rooting depth, water-holding capacity, distance from the nearest surface water, groundwater depth, mean annual temperature, and mean annual precipitation with generalized linear models in R-studio software. Our results show that the invasion levels of the tree species under study are generally over-represented in the LUCAS point-based vegetation maps, and the point-based database requires a dataset with a larger number of samples to be reliable. Regarding the polygon-based database, we found that the occurrence of the invasive species is generally related to the investigated soil and hydrological and climatic factors.

In this study, two long-read sequencing (LRS) techniques, MinION from Oxford Nanopore Technologies and Sequel from the Pacific Biosciences, were used for the transcriptional characterization of a prototype baculovirus, Autographa californica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, and thereby distinguish between transcript isoforms, mono- and polycistronic RNAs, and overlapping transcripts. Altogether, we detected 875 transcript species, of which 759 were novel and 116 were annotated previously. These RNA molecules include 41 novel putative protein coding transcripts [each containing 5′-truncated in-frame open reading frames (ORFs), 14 monocistronic transcripts, 99 polygenic RNAs, 101 non-coding RNAs, and 504 untranslated region isoforms. This work also identified novel replication origin-associated transcripts, upstream ORFs, cis-regulatory sequences and poly(A) sites. We also detected RNA methylation in 99 viral genes and RNA hyper-editing in the longer 5′-UTR transcript isoform of the canonical ORF 19 transcript.

Cancer chemotherapeutics usually have serious side effects. Targeting the special properties of cancer and activation of the anticancer drug in the tumor microenvironment in situ may decrease the intensity of the side effects and improve the efficacy of therapy. In this study, half-sandwich Rh complexes are introduced, which may be activated at the acidic, extracellular pH of the tumor tissue. The synthesis and aqueous stability of mixed-ligand complexes with a general formula of [Rh(η5-Cp*)(N,N/O)(N)]2+/+ are reported, where (N,N/O) indicates bidentate 8-quinolate, ethylenediamine and 1,10-phenanthroline and (N) represents the releasable monodentate ligand with a nitrogen donor atom. UV-visible spectrophotometry, 1H NMR, and pH-potentiometry were used to determine the protonation constants of the monodentate ligands, the proton dissociation constants of the coordinated water molecules in the aqua complexes, and the formation constants of the mixed-ligand complexes. The obtained data were compared to those of the analogous Ru(η6-p-cymene) complexes. The developed mixed-ligand complexes were tested in drug-sensitive and resistant colon cancer cell lines (Colo205 and Colo320, respectively) and in four bacterial strains (Gram-positive and Gram-negative, drug-sensitive, and resistant) at different pH values (5–8). The mixed-ligand complexes with 1-methylimidazole displayed sufficient stability at pH 7.4, and their activation was found in cancer cells with decreasing pH; moreover, the mixed-ligand complexes demonstrated antimicrobial activity in Gram-positive and Gram-negative bacteria, including the resistant MRSA strain. This study proved the viability of incorporating releasable monodentate ligands into mixed-ligand half-sandwich complexes, which is supported by the biological assays.

Natural compounds are a suitable alternative to synthetic food preservatives due to their natural origin and health-promoting properties. In the current study, phenolic–phenolic and phenolic–synthetic combinations were tested for their antibiofilm formation, anti-planktonic growth, and anti-adhesion properties against Debaryomyces hansenii, Wickerhamomyces anomalus (formerly Pichia anomala), Schizosaccharomycespombe, and Saccharomyces cerevisiae. The phenolics were vanillin and cinnamic acid, while the synthetic preservatives were sodium benzoate, potassium sorbate, and sodium diacetate. The vanillin–cinnamic acid combination had synergistic effect in all the tested yeasts for the biofilm inhibition with a fractional inhibitory concentration index (FICI) of ≤0.19 for W. anomalus, 0.25 for S. pombe, 0.31 for S. cerevisiae, and 0.5 for D. hansenii. Most of the phenolic–synthetic combinations had indifferent interaction regarding biofilm formation. The vanillin–cinnamic acid combination also had higher activity against spoilage yeasts adhesion on the abiotic surface and planktonic growth compared to the phenolic–synthetic combinations. For the phenolic–synthetic anti-planktonic activity, synergistic interaction was present in all the vanillin–synthetic combinations in S. pombe, vanillin–sodium benzoate and vanillin–potassium sorbate in S. cerevisiae, vanillin–sodium benzoate in W. anomalus, and cinnamic acid–sodium diacetate in S. pombe. These results suggest a novel antimicrobial strategy that may broaden the antimicrobial spectrum and reduce compound toxicity against food spoilage yeasts.

Accumulating evidence indicates that there are substantial species differences in the properties of mammalian neurons, yet theories on circuit activity and information processing in the human brain are based heavily on results obtained from rodents and other experimental animals. This knowledge gap may be particularly important for understanding the neocortex, the brain area responsible for the most complex neuronal operations and showing the greatest evolutionary divergence. Here, we examined differences in the electrophysiological properties of human and mouse fast-spiking GABAergic basket cells, among the most abundant inhibitory interneurons in cortex. Analyses of membrane potential responses to current input, pharmacologically isolated somatic leak currents, isolated soma outside-out patch recordings, and immunohistochemical staining revealed that human neocortical basket cells abundantly express hyperpolarization-activated cyclic nucleotide-gated cation (HCN) channel isoforms HCN1 and HCN2 at the cell soma membrane, whereas these channels are sparse at the rodent basket cell soma membrane. Antagonist experiments showed that HCN channels in human neurons contribute to the resting membrane potential and cell excitability at the cell soma, accelerate somatic membrane potential kinetics, and shorten the lag between excitatory postsynaptic potentials and action potential generation. These effects are important because the soma of human fast-spiking neurons without HCN channels exhibit low persistent ion leak and slow membrane potential kinetics, compared with mouse fast-spiking neurons. HCN channels speed up human cell membrane potential kinetics and help attain an input–output rate close to that of rodent cells. Computational modeling demonstrated that HCN channel activity at the human fast-spiking cell soma membrane is sufficient to accelerate the input–output function as observed in cell recordings. Thus, human and mouse fast-spiking neurons exhibit functionally significant differences in ion channel composition at the cell soma membrane to set the speed and fidelity of their input–output function. These HCN channels ensure fast electrical reactivity of fast-spiking cells in human neocortex.

Recently, selenium containing derivatives have attracted more attention in medicinal chemistry. In the present work, the anticancer activity of symmetrical selenoesters was investigated by studying the reversal of efflux pump-related and apoptosis resistance in sensitive and resistant human colon adenocarcinoma cells expressing the ABCB1 protein. The combined effect of the compounds with doxorubicin was demonstrated with a checkerboard assay. The ABCB1 inhibitory and the apoptosis-inducing effects of the derivatives were measured with flow cytometry. Whole transcriptome sequencing was carried out on Illumina platform upon the treatment of resistant cells with the most potent derivatives. One ketone and three methyl ester selenoesters showed synergistic or weak synergistic interaction with doxorubicin, respectively. Ketone selenoesters were the most potent ABCB1 inhibitors and apoptosis inducers. Nitrile selenoesters could induce moderate early and late apoptotic processes that could be explained by their ABCB1 modulating properties. The transcriptome analysis revealed that symmetrical selenoesters may influence the redox state of the cells and interfere with metastasis formation. It can be assumed that these symmetrical selenocompounds possess toxic, DNA-damaging effects due to the presence of two selenium atoms in the molecule, which may be augmented by the presence of symmetrical groups., This research was funded by the projects SZTE ÁOK-KKA 2018/270-62-2 of the University of Szeged, Faculty of Medicine and GINOP-2.3.2-15-2016-00038 (Hungary). The study was supported by the Szeged Foundation for Cancer Research (Szegedi Rákkutatásért Alapítvány). G.S. was supported by the János Bolyai Research Scholarship (BO/00158/22/5) of the Hungarian Academy of Sciences.

The most widespread nature-based solution for mitigating climate change is tree planting. When realized as forest restoration in historically forested biomes, it can efficiently contribute to the sequestration of atmospheric carbon and can also entail significant biodiversity and ecosystem service benefits. Conversely, tree planting in naturally open biomes can have adverse effects, of which water shortage due to increased evapotranspiration is among the most alarming ones. Here we assessed how soil texture affects the strength of the trade-off between tree cover and water balance in the forest-steppe biome, where the global pressure for afforestation is threatening with increasing tree cover above historical levels. Here we monitored vertical soil moisture dynamics in four stands in each of the most common forest types of lowland Hungary on well-drained, sandy (natural poplar groves, and Robinia and pine plantations) and on poorly drained, silty-clayey soils (natural oak stands and Robinia plantations), and neighboring grasslands. We found that forests on sand retain moisture in the topsoil (approx. 20 cm) throughout the year, but a thick dry layer develops below that during the vegetation period, significantly impeding groundwater recharge. Neighboring sandy grasslands showed an opposite pattern, with often dry topsoil but intact moisture reserves below, allowing deep percolation. In contrast, forests on silty-clayey soils did not desiccate lower soil layers compared neighboring grasslands, which in turn showed moisture patterns similar to sandy grasslands. We conclude that, in water-limited temperate biomes where landscape-wide water regime depends on deep percolation, soil texture should drive the spatial allocation of tree-based climate mitigation efforts. On sand, the establishment of new forests should be kept to a minimum and grassland restoration should be preferred. The trade-off between water and carbon is less pronounced on silty-clayey soils, making forest patches and wooded rangelands viable targets for both climate mitigation and ecosystem restoration.

Several reports have suggested a role for Corynebacterium striatum as an opportunistic pathogen. The authors have conducted a retrospective study at the Clinical Center of the University of Szeged, Hungary, between 2012 and 2021 that revealed significantly increased rifampicin resistance in this species. This work aimed to investigate the reasons behind this phenomenon. The data were collected corresponding to the period between 1 January 2012 and 31 December 2021 at the Department of Medical Microbiology, University of Szeged. To characterize the resistance trends, the antibiotic resistance index was calculated for each antibiotic in use. Fourteen strains with different resistance patterns were further analyzed with Fourier-transform infrared spectroscopy using the IR Biotyper®. The decline in C. striatum sensitivity to rifampicin seen during the COVID-19 pandemic may have been attributable to the use of Rifadin® to treat concomitant Staphylococcus aureus infections. The fact that the IR Biotyper® typing method revealed that the rifampicin-resistant C. striatum strains were closely related supports this hypothesis. The IR Biotyper® infrared spectroscopy proved to be a modern and fast method to support effective antimicrobial stewardship programs.

The detection and analysis of protein complexes is essential for understanding the functional mechanism and cellular integrity. Recently, several techniques for detecting and analysing protein complexes from Protein–Protein Interaction (PPI) dataset have been developed. Most of those techniques are inefficient in terms of detecting, overlapping complexes, exclusion of attachment protein in complex core, inability to detect inherent structures of underlying complexes, have high false-positive rates and an enrichment analysis. To address these limitations, we introduce a special structural-based weighted network approach for the analysis of protein complexes based on a Weighted Edge, Core-Attachment and Local Modularity structures (WECALM). Experimental results indicate that WECALM performs relatively better than existing algorithms in terms of accuracy, computational time, and p-value. A functional enrichment analysis also shows that WECALM is able to identify a large number of biologically significant protein complexes. Overall, WECALM outperforms other approaches by striking a better balance of accuracy and efficiency in the detection of protein complexes.

A series of four indolo[2,3-e]benzazocines HL1–HL4 and two indolo[2,3-f]benzazonines HL5–and HL6, as well as their respective copper(II) complexes 1–6 were synthesized and characterized by 1H and 13C NMR spectroscopy, ESI...

Assemblysomes are EDTA- and RNase-resistant ribonucleoprotein (RNP) complexes of paused ribosomes with protruding nascent polypeptide chains. They have been described in yeast and human cells for the proteasome subunit Rpt1, and the disordered N-terminal part of the nascent chain was found to be indispensable for the accumulation of the Rpt1-RNP into assemblysomes. Motivated by this, to find other assemblysome-associated RNPs we used bioinformatics to rank subunits of Saccharomyces cerevisiae protein complexes according to their N-terminal disorder propensity. The results revealed that gene products involved in DNA repair are enriched among the top candidates. The Sgs1 DNA helicase was chosen for experimental validation. We found that indeed nascent chains of Sgs1 form EDTA-resistant RNP condensates, assemblysomes by definition. Moreover, upon exposure to UV, SGS1 mRNA shifted from assemblysomes to polysomes, suggesting that external stimuli are regulators of assemblysome dynamics. We extended our studies to human cell lines. The BLM helicase, ortholog of yeast Sgs1, was identified upon sequencing assemblysome-associated RNAs from the MCF7 human breast cancer cell line, and mRNAs encoding DNA repair proteins were overall enriched. Using the radiation-resistant A549 cell line, we observed by transmission electron microscopy that 1,6-hexanediol, an agent known to disrupt phase-separated condensates, depletes ring ribosome structures compatible with assemblysomes from the cytoplasm of cells and makes the cells more sensitive to X-ray treatment. Taken together these findings suggest that assemblysomes may be a component of the DNA damage response from yeast to human.

Background The growth and productivity of plants are largely dependent on the availability of various mineral nutrients, of which some are required at relatively higher concentrations and are termed as macronutrients, while others are required in low amounts and are termed as micronutrients. Both macro- and micro-nutrients are considered as essential elements as their deficiency can result in severe growth defects in plants. Moreover, some of the recent studies have highlighted the role of even non-essential elements in plants. Iodine is one such non-essential element that, at low concentrations, exhibits positive effects on plant growth. Scope In this review, we discuss the effects of iodine on plants including its uptake and transportation, and the current understanding of the pathways responsible for its functioning as a biostimulant. Moreover, we provide evidence that supports the role of iodine as a biostimulant of growth and stress responses in plants. Conclusion Iodine, in the range of 0.20 to 10 mu M, has been documented to regulate the (1) expression of various genes, and (2) activity and structure of various proteins by protein iodination to improve biomass production and defense responses in plants. Further, a growing body of evidence also suggests a role of iodine in the maintenance of ROS homeostasis in plants under normal as well as challenging environmental conditions.

The increased rate of twinning has pointed out newer challenges in clinical practices related to gestational complications, intrauterine growth restriction, perinatal mortality, and comorbidities. As a twin pregnancy progresses, the increased demand for oxygen supply can easily disrupt the redox homeostasis balance and further impose a greater challenge for the developing fetuses. A substantial birth-weight difference acts as an indicator of a deficit in oxygenation or blood flow to one of the fetuses, which might be related to a low bioavailable nitric oxide level. Therefore, in this study, we focused on networks involved in the adjustment of oxygen supply, like the activation of inducible and endothelial nitric oxide synthase (NOS3) along with free radical and lipid peroxide formation in mature twin pairs with high birth-weight differences. The selected parameters were followed by immunofluorescence staining, fluorescence-activated cell sorting analysis, and biochemical measurements in the umbilical cord vessels and fetal red blood cells. Based on our data set, it is clear that the lower-weight siblings are markedly exposed to persistent intrauterine hypoxic conditions, which are connected to a decreased level in NOS3 activation. Furthermore, the increased level of peroxynitrite aggravates lipid peroxidation and induces morphological and functional damage and loss in redox homeostasis.

We report the synthesis and characterization of a group of benzoylhydrazones (Ln) derived from 2-carbaldehyde-8-hydroxyquinoline and benzylhydrazides containing distinct para substituents (R = H, Cl, F, CH3, OCH3, OH and NH2, for L1-7, respectively; in L8 isonicotinohydrazide was used instead of benzylhydrazide). Cu(II) complexes were prepared by reaction of each benzoylhydrazone with Cu(II) acetate. All compounds were characterized by elemental analysis and mass spectrometry as well as by FTIR, UV-visible absorption, NMR or electron paramagnetic resonance spectroscopies. Complexes isolated in the solid state (1–8) are either formulated as [Cu(HL)acetate] (with L1 and L4) or as [Cu(Ln)]3 (n = 2, 3, 5, 6, 7 and 8). Single crystal X-ray diffraction studies were done for L5 and [Cu(L5)]3, confirming the trinuclear formulation of several complexes. Proton dissociation constants, lipophilicity and solubility were determined for all free ligands by UV-Vis spectrophotometry in 30% (v/v) DMSO/H2O. Formation constants were determined for [Cu(LH)], [Cu(L)] and [Cu(LH−1)] for L = L1, L5 and L6, and also [Cu(LH−2)] for L = L6, and binding modes are proposed, [Cu(L)] predominating at physiological pH. The redox properties of complexes formed with L1, L5 and L6 are investigated by cyclic voltammetry; the formal redox potentials fall in the range of +377 to +395 mV vs. NHE. The binding of the Cu(II)-complexes to bovine serum albumin was evaluated by fluorescence spectroscopy, showing moderate-to-strong interaction and suggesting formation of a ground state complex. The interaction of L1, L3, L5 and L7, and of the corresponding complexes with calf thymus DNA was evaluated by thermal denaturation. The antiproliferative activity of all compounds was evaluated in malignant melanoma (A-375) and lung (A-549) cancer cells. The complexes show higher activity than the corresponding free ligand, and most complexes are more active than cisplatin. Compounds 1, 3, 5, and 8 were selected for additional studies: while these complexes induce reactive oxygen species and double-strand breaks in both cancer cells, their ability to induce cell-death by apoptosis varies. Within the set of compounds tested, 8 emerges as the most promising one, presenting low IC50 values, and high induction of oxidative stress and DNA damage, which eventually lead to high rates of apoptosis.

Key message Dolines may provide important safe havens for many plant species and play a key role in maintaining biodiversity. The combined effects of forest age and topographic position influence the biodiversity patterns of these unique habitats. Forest managers, conservationists, and researchers need to work together in order to maintain the species richness and composition of these habitats under environmental changes. Context Dolines are the most prominent geomorphological features in many karst landscapes that may provide important microhabitats for many species. Aims We aim to contribute to a better understanding of how forest age and topographic position influence the plant species richness and composition of vascular plants within doline habitats. Methods We studied the effects of forest age (four age classes: from 5- to 10-year-old stands to more than 90-year-old stands), topographic position (south-facing slope, bottom, and north-facing slope), and their interaction on the distribution of vascular plants and mean Ellenberg indicator values in dolines using detrended correspondence analysis and mixed-effects models. Diagnostic species for the forest age classes and topographic positions were also determined. Results Different groups of vascular plant species usually showed significant preferences for certain topographic positions and/or forest age classes in dolines. In general, the number of species in all studied groups of plants increased after a few years of canopy removal. The number of plant species in almost all groups was lowest in dolines covered with 40–45-year-old forests. The moist and nutrient-rich doline bottoms covered with 90–120-year-old forests harboured many climate change vulnerable plant species. Conclusions Forest age and topographic position considerably influence the species richness and composition of vascular plants in dolines; therefore, forest managers and conservationists need to consider their potential impacts when evaluating the effects of climate warming on karst landscapes.

Pomegranate peel powder (PPP) is increasingly used as a bioadsorbent to decontaminate wastewaters due to its adsorptive characteristics. The application of nutrient-fortified bioadsorbents as alternatives to chemical fertilizers can provide an innovative and eco-friendly approach for sustainable waste management. Nevertheless, there is extremely limited information regarding their effects on the growth of agricultural crops. We investigated the effects of raw and nutrient-fortified PPPs on oilseed rape (Brassica napus). Our results showed that the concentration-dependent in vitro phytotoxicity of high PPP doses (germination indices were 109.6%, 63.9%, and 8.9% at the applied concentrations of 0.05%, 0.5%, and 5%) was diminished by the application of nutrient-fortified PPPs (germination indices were 66.0–83.4% even at the highest doses). In pot experiments, most PPP treatments (especially Raw-PPP and the mixture of N- and P-fortified PPPs) promoted the development of aboveground plant parts. Reorganization of the pattern of protein tyrosine nitration in the root tissues indicated that the plants were acclimated to the presence of PPPs, and thus, PPP treatment induced no or low-level stress. Our findings confirmed that several doses of PPP supplementation were beneficial for the model crop plant when applied in soil. We anticipate that our study will be a foundation for future investigations involving more plant species and soil types, which can contribute to the introduction of nutrient-fortified PPPs as sustainable biofertilizers.

The emergence, survival, growth and maintenance of autoreactive (AR) B-cell clones, the hallmark of humoral autoimmunity, leave their footprints in B-cell receptor repertoires. Collecting IgH sequences related to polyreactive (PR) ones from adaptive immune receptor repertoire (AIRR) datasets make the reconstruction and analysis of PR/AR B-cell lineages possible. We developed a computational approach, named ImmChainTracer, to extract members and to visualize clonal relationships of such B-cell lineages. Our approach was successfully applied on the IgH repertoires of patients suffering from monogenic hypomorphic RAG1 and 2 deficiency (pRD) or polygenic systemic lupus erythematosus (SLE) autoimmune diseases to identify relatives of AR IgH sequences and to track their fate in AIRRs. Signs of clonal expansion, affinity maturation and class-switching events in PR/AR and non-PR/AR B-cell lineages were revealed. An extension of our method towards B-cell expansion caused by any trigger (e.g., infection, vaccination or antibody development) may provide deeper insight into antigen specific B-lymphogenesis.

Ageing is driven by the progressive, lifelong accumulation of cellular damage. Autophagy (cellular self-eating) functions as a major cell clearance mechanism to degrade such damages, and its capacity declines with age. Despite its physiological and medical significance, it remains largely unknown why autophagy becomes incapable of effectively eliminating harmful cellular materials in many cells at advanced ages. Here we show that age-associated defects in autophagic degradation occur at both the early and late stages of the process. Furthermore, in the fruit fly Drosophila melanogaster, the myotubularin-related (MTMR) lipid phosphatase egg-derived tyrosine phosphatase (EDTP) known as an autophagy repressor gradually accumulates in brain neurons during the adult lifespan. The age-related increase in EDTP activity is associated with a growing DNA N6-adenine methylation at EDTP locus. MTMR14, the human counterpart of EDTP, also tends to accumulate with age in brain neurons. Thus, EDTP, and presumably MTMR14, promotes brain ageing by increasingly suppressing autophagy throughout adulthood. We propose that EDTP and MTMR14 phosphatases operate as endogenous pro-ageing factors setting the rate at which neurons age largely independently of environmental factors, and that autophagy is influenced by DNA N6-methyladenine levels in insects.

Huntington’s Disease (HD) is a fatal neurodegenerative disorder caused by the expansion of a polyglutamine-coding CAG repeat in the Huntingtin gene. One of the main causes of neurodegeneration in HD is transcriptional dysregulation that, in part, is caused by the inhibition of histone acetyltransferase (HAT) enzymes. HD pathology can be alleviated by increasing the activity of specific HATs or by inhibiting histone deacetylase (HDAC) enzymes. To determine which histone’s post-translational modifications (PTMs) might play crucial roles in HD pathology, we investigated the phenotype-modifying effects of PTM mimetic mutations of variant histone H3.3 in a Drosophila model of HD. Specifically, we studied the mutations (K→Q: acetylated; K→R: non-modified; and K→M: methylated) of lysine residues K9, K14, and K27 of transgenic H3.3. In the case of H3.3K14Q modification, we observed the amelioration of all tested phenotypes (viability, longevity, neurodegeneration, motor activity, and circadian rhythm defects), while H3.3K14R had the opposite effect. H3.3K14Q expression prevented the negative effects of reduced Gcn5 (a HAT acting on H3K14) on HD pathology, while it only partially hindered the positive effects of heterozygous Sirt1 (an HDAC acting on H3K14). Thus, we conclude that the Gcn5-dependent acetylation of H3.3K14 might be an important epigenetic contributor to HD pathology.

Chlamydia trachomatis (C. trachomatis) is an obligate intracellular bacterium linked to ocular and urogenital infections with potentially serious sequelae, including blindness and infertility. First-line antibiotics, such as azithromycin (AZT) and doxycycline, are effective, but treatment failures have also been reported. Encapsulation of antibiotics in liposomes is considered an effective approach for improving their local effects, bioavailability, biocompatibility and antimicrobial activity. To test whether liposomes could enhance the antichlamydial action of AZT, we encapsulated AZT in different surface-charged elastic liposomes (neutral, cationic and anionic elastic liposomes) and assessed their antibacterial potential against the C. trachomatis serovar D laboratory strain as well as the clinical isolate C. trachomatis serovar F. A direct quantitative polymerase chain reaction (qPCR) method was used to measure chlamydial genome content 48 h post infection and to determine the recoverable chlamydial growth. All the liposomes efficiently delivered AZT to HeLa 229 cells infected with the laboratory Chlamydia strain, exhibiting the minimal inhibitory concentrations (MIC) and the minimal bactericidal concentrations (MBC) of AZT even 4–8-fold lower than those achieved with the free AZT. The tested AZT-liposomes were also effective against the clinical Chlamydia strain by decreasing MIC values by 2-fold relative to the free AZT. Interestingly, the neutral AZT-liposomes had no effect on the MBC against the clinical strain, while cationic and anionic AZT-liposomes decreased the MBC 2-fold, hence proving the potential of the surface-charged elastic liposomes to improve the effectiveness of AZT against C. trachomatis.

The ability to relocalize proteins to defined subcellular locations presents a powerful tool to examine protein-protein interactions that can overcome a tendency of non-targeted exogenous proteins to form inaccessible aggregates. Here, we show that a 24-amino-acid sequence from the Drosophila proapoptotic protein Hid's tail anchor (HTA) domain can target exogenous proteins to the mitochondria in Drosophila cells. We use this HTA tag to target the Drosophila centriole cartwheel protein Sas6 to the mitochondria, and show that both exogenous and endogenous Gorab can be co-recruited from the Golgi to the new mitochondrial site. This accords with our previous observation that monomeric Drosophila Gorab binds Sas6 to become centriole associated with a 50-fold greater affinity than dimeric Gorab binds Rab6 to become localized at the Golgi. Strikingly, Drosophila Sas6 can bind both Drosophila Gorab and its human GORAB ortholog, whereas human SAS6 is unable to bind either GORAB or Gorab. We discuss these findings in relation to the evolutionary conservation of Gorab and the divergence of Sas6, possibly reflecting known differences in persistence of the cartwheel in the centriole duplication cycle of fly and human cells.

The macromorphological examination of identified human osteological collections from the pre-antibiotic era (e.g., Terry Collection) can provide invaluable information about the skeletal manifestations of tuberculosis (TB) in individuals who did not receive pharmaceutical therapy. With analysis of such collections, new diagnostic criteria for TB can be recognised which can be used in palaeopathological interpretation. The aim of our paper is to provide a reference and aid for the identification of TB in past populations by demonstrating and discussing in detail the vertebral alterations indicative of one of its rare skeletal manifestations, lumbosacral TB. These changes were detected in two individuals from the Terry Collection (Terry No. 760 and Terry No. 1093). These two case studies furnish palaeopathologists with a stronger basis for diagnosing lumbosacral TB in skeletons which exhibit similar vertebral lesions from osteoarchaeological series. To illustrate this, an archaeological case from Hungary (KK146) is also presented, displaying vertebral alterations resembling that of the two cases from the Terry Collection. Through the demonstrated case studies, we can derive a better insight into the disease experience of people who lived in the past and suffered from TB.

Plant defense responses against Fusarium infection can be controlled by light. In this study, the effects of nocturnal red light were investigated on glutathione transferases (GSTs) in the leaves of the moderate- and high-Fusarium resistant wheat cultivars, GK Ígéret and GK Arató, respectively. GST activity increased in the light phase during the day, while it decreased after midnight. Since GST activity was lowest at midnight, we examined whether red light application at midnight could prevent the night-time drop in enzyme activity. We found that 15-min-long nocturnal red light application was effective to increase GST activity at dawn. The effects of red light pretreatments on GST expression and activity, as well as the oxidative stress induced by fumonisin B1 (FB1), were investigated. FB1 exposure increased GST activity and the expression of GST genes at dawn but nocturnal red light application in combination with the mycotoxin also increased GST activity and the transcript levels of the selected GSTs in the resistant GK Arató. In addition to its effects on GSTs, it was discovered that, depending on the degree of tolerance, nocturnal red light increased the activity of the major antioxidant enzymes at dawn in both of the chosen wheat genotypes. These decreased FB1’s oxidative stress-causing actions, resulting in lower lipid peroxidation and less cell viability loss when exposed to the mycotoxin. Pretreatment with nocturnal red light enhanced the activity of GST and antioxidant enzymes in wheat plant leaves, contributing to FB1 detoxification and reducing oxidative stress.