Tritium and deuterium labelling of a kainate receptor antagonist and evaluation as a radioligand

Kainate receptors play a crucial role in mediating synaptic transmission within the central nervous system. However, the lack of selective pharmacological tool compounds for the GluK3 subunit represents a significant challenge in studying these receptors. Recently presented compound 1 stands out as a potent antagonist of GluK3 receptors, exhibiting nanomolar affinity at GluK3 receptors and strongly inhibiting glutamate-induced currents at homomeric GluK1 and GluK3 receptors in HEK293 cells with Kb values of 65 and 39 nM, respectively. This study presents the synthesis of two potent GluK3-preferring iodine derivatives of compound 1, serving as precursors for radiolabelling. Furthermore, we demonstrate the optimisation of dehalogenation conditions using hydrogen and deuterium, resulting in [2H]-1, and demonstrate the efficient synthesis of the radioligand [3H]-1 with a specific activity of 1.48 TBq/mmol (40.1 Ci/mmol). Radioligand binding studies conducted with [3H]-1 as a radiotracer at GluK1, GluK2, and GluK3 receptors expressed in Sf9 and rat P2 membranes demonstrated its potential applicability for selectively studying native GluK3 receptors in the presence of GluK1 and 2-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor-blocking ligands.

Ecology explains anhydrobiotic performance across tardigrades, but the shared evolutionary history matters more

Desiccation stress is lethal to most animals. However, some microinvertebrate groups have evolved coping strategies, such as the ability to undergo anhydrobiosis (i.e. survival despite the loss of almost all body water). Tardigrades are one such group, where the molecular mechanisms of anhydrobiosis have been more thoroughly studied. Despite the ecological, evolutionary and biotechnological importance of anhydrobiosis, little is known about its inter- and intra-specific variability nor its relationship with natural habitat conditions or phylogenetic history. We developed a new index-anhydrobiotic recovery index (ARI)-to evaluate the anhydrobiotic performance of tardigrade populations from the family Macrobiotidae. Moreover, we compared the explanatory role of habitat humidity and phylogenetic history on this trait using a variance partitioning approach. We found that ARI is correlated with both microhabitat humidity and yearly rainfall, but it is mostly driven by phylogenetic niche conservatism (i.e. a high portion of ARI variation is explained by phylogeny alone). Finally, we showed that anhydrobiotic performance is highly variable, even between closely related species, and that their response to local ecological conditions is tightly linked to their phylogenetic history. This study not only presents key insights into an emerging model system, but also provides a new methodological approach for wider scale studies of the ecological and evolutionary implications of anhydrobiosis.

Changes in plasma PLAC-1 concentration and its expression during early-mid pregnancy in bovine placental tissues - a pilot study

BACKGROUND

Placenta-specific protein 1 (PLAC1) is a small secreted protein considered to be a molecule with a significant role in the development of the placenta and the establishment of the mother-foetus interface. This study aimed to confirm the presence of bovine PLAC1 and to examine its profile in the placenta and plasma in the first six months of pregnancy. The expression pattern of PLAC1 was analysed by RT-qPCR and Western Blotting. Quantitative evaluation was carried out using ELISA.

RESULTS

PLAC1 concentrations in the plasma of pregnant cows were significantly higher (p < 0.05) than those obtained from non-pregnant animals. PLAC1 protein concentrations in the placental tissues of the foetal part were significantly (p < 0.05) higher than in the tissues of the maternal part of the placenta. PLAC1 transcripts were detected in both placental tissue samples and epithelial cell cultures.

CONCLUSIONS

In conclusion, the results of the present preliminary study suggest that PLAC1 is involved in the development of bovine placenta. The presence of this protein in the plasma of pregnant animals as early as the first month may make it a potential candidate as a pregnancy marker in cows. Further studies on exact mechanisms of action of PLAC1 in bovine placenta are necessary.

Construction of Hierarchical Films via Layer-by-Layer Assembly of Exfoliated Unilamellar Zeolite Nanosheets

Zeolites have been widely applied as versatile catalysts, sorbents, and ion exchangers with unique porous structures showing molecular sieving capability. In these years, it is reported that some layered zeolites can be delaminated into molecularly thin 2-dimensional (2D) nanosheets characterized by inherent porous structures and highly exposed active sites. In the present study, two types of zeolite nanosheets with distinct porous structures with MWW topology (denoted mww) and ferrierite-related structure (denoted bifer) are deposited on a substrate through the solution process via electrostatic self-assembly. Alternate deposition of zeolite nanosheets with polycation under optimized conditions allows the layer-by-layer growth of their multilayer films with a stacking distance of 2-3 nm. Furthermore, various hierarchical structures defined at the unit-cell dimensions can be constructed simply by conducting the deposition of mww and bifer nanosheets in a designed sequence. Adsorption of a dye, Rhodamine B, in these films, is examined to show that adsorption is dependent on constituent zeolite nanosheets and their assembled nanostructures. This work has provided fundamental advancements in the fabrication of artificial zeolite-related hierarchical structures, which may be extended to other zeolite nanosheets, broadening their functionalities, applications, and benefits.

Modulating Stress Susceptibility and Resilience: Insights from miRNA Manipulation and Neural Mechanisms in Mice

This study explored the impact of microRNAs, specifically mmu-miR-1a-3p and mmu-miR-155-5p, on stress susceptibility and resilience in mice of different strains. Previous research had established that C57BL/6J mice were stress-susceptible, while NET-KO and SWR/J mice displayed stress resilience. These strains also exhibited variations in the serum levels of mmu-miR-1a-3p and mmu-miR-155-5p. To investigate this further, we administered antagonistic sequences (Antagomirs) targeting these microRNAs to C57/BL/6J mice and their analogs (Agomirs) to NET-KO and SWR/J mice via intracerebroventricular (i.c.v) injection. The impact of this treatment was assessed using the forced swim test. The results showed that the stress-susceptible C57/BL/6J mice could be transformed into a stress-resilient phenotype through infusion of Antagomirs. Conversely, stress-resilient mice displayed altered behavior when treated with Ago-mmu-miR-1a-3p. The study also examined the expression of mmu-miR-1a-3p in various brain regions, revealing that changes in its expression in the cerebellum (CER) were associated with the stress response. In vitro experiments with the Neuro2a cell line indicated that the Antago/Ago-miR-1a-3p and Antago/Ago-miR-155-5p treatments affected mRNAs encoding genes related to cAMP and Ca2+ signaling, diacylglycerol kinases, and phosphodiesterases. The expression changes of genes such as Dgkq, Bdnf, Ntrk2, and Pde4b in the mouse cerebellum suggested a link between cerebellar function, synaptic plasticity, and the differential stress responses observed in susceptible and resilient mice. In summary, this research highlights the role of mmu-miR-1a-3p and mmu-miR-155-5p in regulating stress susceptibility and resilience in mice and suggests a connection between these microRNAs, cerebellar function, and synaptic plasticity in the context of stress response.

The Impact of Various Poly(vinylpyrrolidone) Polymers on the Crystallization Process of Metronidazole

In this paper, we propose one-step synthetic strategies for obtaining well-defined linear and star-shaped polyvinylpyrrolidone (linPVP and starPVP). The produced macromolecules and a commercial PVP K30 with linear topology were investigated as potential matrices for suppressing metronidazole (MTZ) crystallization. Interestingly, during the formation of binary mixtures (BMs) containing different polymers and MTZ, we found that linear PVPs exhibit maximum miscibility with the drug at a 50:50 weight ratio (w/w), while the star-shaped polymer mixes with MTZ even at a 30:70 w/w. To explain these observations, comprehensive studies of MTZ-PVP formulations with various contents of both components were performed using Fourier-transform infrared spectroscopy, differential scanning calorimetry, and X-ray diffraction. The obtained results clearly showed that the polymer's topology plays a significant role in the type of interactions occurring between the matrix and MTZ. Additionally, we established that for MTZ-PVP 50:50 and 75:25 w/w BMs, linear polymers have the most substantial impact on inhibiting the crystallization of API. The star-shaped macromolecule turned out to be the least effective in stabilizing amorphous MTZ at these polymer concentrations. Nevertheless, long-term structural investigations of the MTZ-starPVP 30:70 w/w system (which is not achievable for linear PVPs) demonstrated its complete amorphousness for over one month.

The HINT1 Gene rs2526303 Polymorphism and Its Association with Personality Traits in Cigarette Smokers

The development of a substance use disorder (SUD) is a multifaceted process influenced by both genetic and environmental factors. Recent research has suggested the potential involvement of the HINT1 gene in various aspects of plasticity, mood regulation, anxiety-like behaviour, and stress-coping mechanisms. Moreover, personality traits are also recognised to be instrumental in developing substance dependency. Given these considerations, our study investigated the associations among cigarette smoking, personality traits, and the rs2526303 polymorphism. Additionally, we investigated the interactions between personality traits and rs2526303 in the HINT1 gene. The study group comprised 531 volunteers: 375 cigarette users (mean age = 29.42 ± 10.72; F = 49%, M = 51%) and 156 never-smokers (mean age = 26.93 ± 10.09; F = 79%, M = 21%). Genotyping was conducted using the real-time PCR method, and the NEO Five-Factor Personality Inventory and State-Trait Anxiety Inventory were administered. There were no statistically significant differences in the frequency of rs2526303 genotypes and alleles in the cigarette user group compared to the control group. Compared to the control group, the cigarette users obtained higher scores in the assessment of the NEO-FFI Extraversion scale and lower results for the NEO-FFI Openness, Agreeableness, and Conscientiousness scales. Additionally, there was a statistically significant effect of rs2526303 genotype interaction and cigarette-using status on the conscientiousness scale. These outcomes collectively suggest a notable association between cigarette smoking and specific dimensions of personality, particularly highlighting differences in extraversion, openness, agreeableness, and conscientiousness. Furthermore, the detected interaction effect involving rs2526303 concerning conscientiousness signifies a complex interplay between genetic factors and smoking behaviour.

Deposition of NiAl/Al3Ni2(CrB2) Coatings from Ni, Al and CrB2 Powders Using Mechanical Synthesis in Planetary Ball Mill

Interest in composite thick coatings with an intermetallic matrix stimulates the development of new deposition techniques like the co-milling of pre-alloyed NiAl powder with platelet-shaped substrates. Obtained coatings were up to several micrometers thick as cold-welding of intermetallic particles was effective only at the start of this process, while later, chipping prevailed over added material. The present experiment covered the co-milling in the planetary ball mill of Ni and Al elemental powders (1:1 molar ratio) with AISI 304 steel platelets for 32 h at 300 rpm. Next, this process was repeated with an admixture of 15 wt.% of CrB2 powder. In both cases, their milling succeeded in producing up to a 200 μm coating after 4 h. The use of light, scanning and transmission electron microscopy (LM/SEM/TEM) helped to establish that the coatings had gradient microstructures with more refined crystallites of NiAl, Al3Ni2 and CrB2 closer to the surface. With the addition of a ceramic phase, the coatings presented higher hardness and lower friction during dry wear tests both at RT and at 500 °C.

Artificial intelligence in detecting left atrial appendage thrombus by transthoracic echocardiography and clinical features: the Left Atrial Thrombus on Transoesophageal Echocardiography (LATTEE) registry

AIMS

Transoesophageal echocardiography (TOE) is often performed before catheter ablation or cardioversion to rule out the presence of left atrial appendage thrombus (LAT) in patients on chronic oral anticoagulation (OAC), despite associated discomfort. A machine learning model [LAT-artificial intelligence (AI)] was developed to predict the presence of LAT based on clinical and transthoracic echocardiography (TTE) features.

METHODS AND RESULTS

Data from a 13-site prospective registry of patients who underwent TOE before cardioversion or catheter ablation were used. LAT-AI was trained to predict LAT using data from 12 sites (n = 2827) and tested externally in patients on chronic OAC from two sites (n = 1284). Areas under the receiver operating characteristic curve (AUC) of LAT-AI were compared with that of left ventricular ejection fraction (LVEF) and CHA2DS2-VASc score. A decision threshold allowing for a 99% negative predictive value was defined in the development cohort. A protocol where TOE in patients on chronic OAC is performed depending on the LAT-AI score was validated in the external cohort. In the external testing cohort, LAT was found in 5.5% of patients. LAT-AI achieved an AUC of 0.85 [95% confidence interval (CI): 0.82-0.89], outperforming LVEF (0.81, 95% CI 0.76-0.86, P < .0001) and CHA2DS2-VASc score (0.69, 95% CI: 0.63-0.7, P < .0001) in the entire external cohort. Based on the proposed protocol, 40% of patients on chronic OAC from the external cohort would safely avoid TOE.

CONCLUSION

LAT-AI allows accurate prediction of LAT. A LAT-AI-based protocol could be used to guide the decision to perform TOE despite chronic OAC.

Bronze Age Raw Material Hoard from Greater Poland: Archaeometallurgical Study Based on Material Research, Thermodynamic Analysis, and Experiments

Hoard finds from the Bronze Age have appeared all over Europe, prompting questions about their functions (either as raw materials for recycling or votive objects). The hoard trove of raw materials from Przybysław in Greater Poland is an interesting example of a discovery that is related to the foundry activities of Late Bronze Age and Early Iron Age communities (c. 600 BC). The deposit consists of fragments of raw materials that were damaged end products intended for smelting. The research included the characterisation of the material in terms of the variety of the raw materials that were used. The individual elements of the hoard were characterised in terms of their chemical compositions, microstructures, and properties. A range of modern instrumental research methods were used: metallographic macroscopic and microscopic observations by optical microscopy (OM), scanning electron microscopy (SEM), chemical-composition analysis by X-ray fluorescence spectroscopy (ED-XRF), X-ray microanalysis (EDS), and detailed crystallisation analysis by electron microscopy with an emphasis on electron backscatter diffraction (EBSD). As part of this study, model alloys were also prepared for two of the selected chemical compositions, (i.e., CuPbSn and CuPb). These alloys were analysed for their mechanical and technological properties. This research of the hoard from Przybysław (Jarocin district, Greater Poland) has contributed to the recognition and interpretation of the function and nature of the hoard by using modern research and modelling methods as a cultic raw material deposit.

Molecular and Medical Aspects of Psychedelics

Psychedelics belong to the oldest psychoactive drugs. They arouse recent interest due to their therapeutic applications in the treatment of major depressive disorder, substance use disorder, end-of-life anxiety,= and anxiety symptoms, and obsessive-compulsive disorder. In this review, the current state of preclinical research on the mechanism of action, neurotoxicity, and behavioral impact of psychedelics is summarized. The effect of selective 5-HT2A receptor agonists, 25I- and 25B-NBOMe, after acute and repeated administration is characterized and compared with the effects of a less selective drug, psilocybin. The data show a significant effect of NBOMes on glutamatergic, dopaminergic, serotonergic, and cholinergic neurotransmission in the frontal cortex, striatum, and nucleus accumbens. The increases in extracellular levels of neurotransmitters were not dose-dependent, which most likely resulted from the stimulation of the 5-HT2A receptor and subsequent activation of the 5-HT2C receptors. This effect was also observed in the wet dog shake test and locomotor activity. Chronic administration of NBOMes elicited rapid development of tolerance, genotoxicity, and activation of microglia. Acute treatment with psilocybin affected monoaminergic and aminoacidic neurotransmitters in the frontal cortex, nucleus accumbens, and hippocampus but not in the amygdala. Psilocybin exhibited anxiolytic properties resulting from intensification of GABAergic neurotransmission. The data indicate that NBOMes as selective 5-HT2A agonists exert a significant effect on neurotransmission and behavior of rats while also inducing oxidative DNA damage. In contrast to NBOMes, the effects induced by psilocybin suggest a broader therapeutic index of this drug.

Limbic System Response to Psilocybin and Ketamine Administration in Rats: A Neurochemical and Behavioral Study

The pathophysiology of depression is related to the reduced volume of the hippocampus and amygdala and hypertrophy of the nucleus accumbens. The mechanism of these changes is not well understood; however, clinical studies have shown that the administration of the fast-acting antidepressant ketamine reversed the decrease in hippocampus and amygdala volume in depressed patients, and the magnitude of this effect correlated with the reduction in depressive symptoms. In the present study, we attempted to find out whether the psychedelic substance psilocybin affects neurotransmission in the limbic system in comparison to ketamine. Psilocybin and ketamine increased the release of dopamine (DA) and serotonin (5-HT) in the nucleus accumbens of naive rats as demonstrated using microdialysis. Both drugs influenced glutamate and GABA release in the nucleus accumbens, hippocampus and amygdala and increased ACh levels in the hippocampus. The changes in D2, 5-HT1A and 5-HT2A receptor density in the nucleus accumbens and hippocampus were observed as a long-lasting effect. A marked anxiolytic effect of psilocybin in the acute phase and 24 h post-treatment was shown in the open field test. These data provide the neurobiological background for psilocybin's effect on stress, anxiety and structural changes in the limbic system and translate into the antidepressant effect of psilocybin in depressed patients.

Manifestation of Health Denialism in Attitudes toward COVID-19 Vaccination: A Qualitative Study

Science denialism is characterized by the refusal to accept existing consensus and available evidence. Typical strategies denialists employ include spreading conspiracies, selective use of information, relying on fake experts, or general fallacies in logic. A flood of misinformation, fake news, and conspiracy theories accompanied the COVID-19 pandemic. Simultaneously, it was a subject of many denialistic opinions, from denying the existence of the epidemic challenge to claims that questioned the safety and effectiveness of the COVID-19 vaccines. This study's main aim was to assess the manifestations of denialism in attitudes toward the preventive measures recommended during the pandemic, with a special focus on vaccination. In-depth interviews were conducted with fifty representatives of the general population, demonstrating diversified opinions about COVID-19 vaccines and other preventive behaviors. The interviews were performed face to face in participants' houses or at other places they identified as convenient. Some of the interviewees preferred to do the interview via teleconference. The interviews were carried out from November 2022 to March 2023. The interviewees were recruited initially by convenience, and in further stages, the snowball technique was used. The interviewees were residents of four main administrative districts in Poland. Out of 50 participants, 26 were males, 29 were between 18-40, 16 were inhabitants of rural areas, and 28 had a university level of education. The interviews were based on a semi-structured guide that addressed, in addition to views about the origin of the new coronavirus, respondents' attitudes toward vaccination and sanitary recommendation, the health status of interviewees, their use of healthcare services, and their health behaviors. The interviews were transcribed and analyzed with MAXQDA Analytics Pro 2022 software (Release 22.7.0). Thematic analysis (TA) was applied to the content generated from the interviews. Based on the uptake of the COVID-19 vaccine, the participants were divided into three groups: unvaccinated, hesitant, and vaccinated (18, 4, and 28 interviewees, respectively). The main themes were established based on the TA of the interviews: attitudes toward COVID-19 vaccination, perception of sources of information, and the origin of the new coronavirus. The first theme decidedly drew the greatest attention of the interviewees. There was also a clear relationship between vaccination status and the presence of denialist thinking among interviewees. Interestingly, the role of experts as a key source of information about the pandemic was underlined by study participants. However, the criteria for being an expert differed. The subject of the origin of a new coronavirus was not interesting to interviewees. The analysis of the adherence to preventive measures revealed an interplay of diversified attitudes and motivations. Individuals presenting denialist views most frequently abstained from COVID-19 vaccination. However, such views were also present among those who hesitated or even among those who had been vaccinated. Furthermore, denialism was only one of the determinants of adherence to preventive measures.

When will RNA get its AlphaFold moment?

The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches. We believe that there are challenges preventing the successful development of deep learning-based methods like AlphaFold for RNA in the short term. Broadly speaking, the challenges are the limited number of structures and alignments making data-hungry deep learning methods unlikely to succeed. Additionally, there are several issues with the existing structure and sequence data, as they are often of insufficient quality, highly biased and missing key information. Here, we discuss these challenges in detail and suggest some steps to remedy the situation. We believe that it is possible to create an accurate RNA structure prediction method, but it will require solving several data quality and volume issues, usage of data beyond simple sequence alignments, or the development of new less data-hungry machine learning methods.

Polyhydroxylated Fullerene C60(OH)40 Nanofilms Promote the Mesenchymal-Epithelial Transition of Human Liver Cancer Cells via the TGF-β1/Smad Pathway

Background

The various growth factors change the phenotype of neoplastic cells from sedentary (epithelial) to invasive (mesenchymal), which weaken intercellular connections and promote chemotaxis. It can be assumed that the use of anti-inflammatory polyhydroxyfull nanofilms will restore the sedentary phenotype of neoplastic cells in the primary site of the tumor and, consequently, increase the effectiveness of the therapy.

Methods

The studies were carried out on liver cancer cells HepG2, C3A and SNU-449, and non-cancer hepatic cell line THLE-3. Transforming growth factor (TGF), epidermal growth factor and tumor necrosis factor were used to induce the epithelial-mesenchymal transition. C60(OH)40 nanofilm was used to induce the mesenchymal-epithelial transition. Obtaining an invasive phenotype was confirmed on the basis of changes in the morphology using inverted light microscopy. RT-PCR was used to confirm mesenchymal or epithelial phenotype based on e-cadherin, snail, vimentin expression or others. Water colloids at a concentration of 100 mg/L were used to create nanofilms of fullerene, fullerenol, diamond and graphene oxide. The ELISA test for the determination of TGF expression and growth factor antibody array were used to select the most anti-inflammatory carbon nanofilm. Mitochondrial activity and proliferation of cells were measured by XTT and BrdU tests.

Results

Cells lost their natural morphology of cells growing in clusters and resembled fibroblast cells after adding a cocktail of factors. Among the four allotropic forms of carbon tested, only the C60(OH)40 nanofilm inhibited the secretion of TGF in all the cell lines used and inhibited the secretion of other factors, including insulin-like growth factor system. Nanofilm C60(OH)40 was non-toxic to liver cells and inhibited the TGF-β1/Smad pathway of invasive cells treated with the growth factor cocktail.

Conclusion

The introduction of an anti-inflammatory, nontoxic component that can induce the mesenchymal-epithelial transition of cancer cells may represent a future adjuvant therapy after tumor resection.

Food Insecurity: Is Leagility a Potential Remedy?

In the wake of the COVID-19 pandemic, and Ukraine-Russian conflict, both significant geo-political and socio-economic shocks to the global food system and food insecurity has risen across the world. One potential remedy to reduce the level of food insecurity is to move from a lean just-in-time food system to one where there is more resilience through greater agility both in routine supply operations and also in the event of an emergency situation. The aim of this critical perspectives paper was to firstly reflect on the concepts of lean, agility, and 'leagility'. Then, this study considered the ability of individual organisations and the whole food system to be resilient, adaptive, enable the elimination of waste, reduce inefficiency, and assure the consistent delivery to market requirements in terms of both volume, safety, and quality. Promoting the concept of leagility together with advocating resilient, sustainable practices that embed buffer and adaptive capacity, this paper positions that increasing digitalisation and improving business continuity planning can ensure effective operationalisation of supply chains under both normal and crisis situations, ultimately reducing the risk of food insecurity at personal, household, and community levels.

Nanoparticle Tracking Analysis of Urinary Extracellular Vesicle Proteins as a New Challenge in Laboratory Medicine

Urinary extracellular vesicle (uEV) proteins may be used as specific markers of kidney damage in various pathophysiological conditions. The nanoparticle-tracking analysis (NTA) appears to be the most useful method for the analysis of uEVs due to its ability to analyze particles below 300 nm. The NTA method has been used to measure the size and concentration of uEVs and also allows for a deeper analysis of uEVs based on their protein composition using fluorescence measurements. However, despite much interest in the clinical application of uEVs, their analysis using the NTA method is poorly described and requires meticulous sample preparation, experimental adjustment of instrument settings, and above all, an understanding of the limitations of the method. In the present work, we demonstrate the usefulness of an NTA. We also present problems encountered during analysis with possible solutions: the choice of sample dilution, the method of the presentation and comparison of results, photobleaching, and the adjustment of instrument settings for a specific analysis. We show that the NTA method appears to be a promising method for the determination of uEVs. However, it is important to be aware of potential problems that may affect the results.

Receptor for the Advanced Glycation End Products (RAGE) Pathway in Adipose Tissue Metabolism

Advanced glycation end products (AGEs) are mediators in the process of cellular dysfunction in response to hyperglycemia. Numerous data indicate that the accumulation of AGEs in the extracellular matrix plays a key role in the development of obesity-related adipose tissue dysfunction. Through binding of their membrane receptor (RAGE), AGEs affect numerous intracellular pathways and impair adipocyte differentiation, metabolism, and secretory activity. Therefore, inhibiting the production and accumulation of AGEs, as well as interfering with the metabolic pathways they activate, may be a promising therapeutic strategy for restoring normal adipose tissue function and, thus, combating obesity-related comorbidities. This narrative review summarizes data on the involvement of the RAGE pathway in adipose tissue dysfunction in obesity and the development of its metabolic complications. The paper begins with a brief review of AGE synthesis and the RAGE signaling pathway. The effect of the RAGE pathway on adipose tissue development and activity is then presented. Next, data from animal and human studies on the involvement of the RAGE pathway in obesity, diabetes, and cardiovascular diseases are summarized. Finally, therapeutic perspectives based on interference with the RAGE pathway are discussed.

Antimicrobial action and chemical and physical properties of CuO-doped engineered cementitious composites

CuO nanoparticles (NPs) were added to cement matrices in quantities of 0.25, 0.50 and 1.00 wt% to inhibit the growth of Gram-positive (Bacillus cereus, Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa, Escherichia coli) bacteria. It was shown that CuO NPs, in all tested concentrations, improved the antibacterial properties of the cement matrix. Nevertheless, the best mechanical, structural and durability properties were obtained for cement composites doped with CuO NPs at 0.25 wt%. Larger amounts of NPs caused a decrease in all parameters relative to the reference mortar, which may be the result of a slight change in the porosity of the composite microstructure. For 0.50 wt% CuO NPs, a slight increase in the volume of micropores in the cement matrix was observed, and an increased number of larger pores was confirmed by non-invasive computed tomography (CT). The reduction in the mechanical parameters of composites with 0.50 and 1.00 wt% CuO NPs may also be due to the slower hydration of the cement binder, as confirmed by changes in the heat of hydration for these configurations, or agglomeration of NPs, especially for the 1.00 wt% concentration, which was manifested in a decrease in the plasticity of the mortars.

Association of the rs3864283 Polymorphism Located in the HINT1 Gene with Cigarette Use and Personality Traits

Nicotine is the major reinforcing component of tobacco and it is believed that the pharmacological effects of nicotine motivate the initiation and maintenance of a smoking habit. HINT1 appears to play a role in the modulation of the effects of drug abuse. Hence, the aim of this study was the analysis of the association between the rs3864283 polymorphism of the HINT1 gene and cigarette use; the analysis of personality traits assessed by the means of the NEO-FFI Inventory; the analysis of anxiety measured by the STAI questionnaire; and the analysis of the interactions between the rs3864283 and both personality traits and anxiety. The study group consisted of 522 volunteers. Of these, 371 were cigarette users and 151 were never-smokers. The genomic DNA was isolated from venous blood using standard procedures. The results of both inventories, i.e., NEO-FFI and STAI., were reported as the sten scores. Genotyping was conducted with the real-time PCR method. Statistically significant differences were found in the frequency of rs3864283 genotypes and alleles in the tested sample of Cigarette Users when compared to the control group. The Cigarette Users compared to the control group obtained higher scores in the assessment of NEO-FFI extraversion scale, and significantly lower results were obtained for the NEO-FFI openness scale, the agreeableness scale, and the conscientiousness scale. There was a statistically significant effect of rs3864283 genotype interaction and Cigarette Use or not using (control group) on the extraversion scale. There was also a statistically significant effect of Cigarette Users or the control group on the extraversion scale score. The results obtained in the presented study indicated a significant association between the HINT1 rs3864283 variant and smoking status. Moreover, this is the first study incorporating genetic association of above-mentioned polymorphic site with interaction analysis of personality traits and anxiety. Overall, the results of this study suggest that HINT1 is an important genetic component associated with nicotine usage mechanisms.

Somatostatin-expressing interneurons modulate neocortical network through GABAb receptors in a synapse-specific manner

The firing activity of somatostatin-expressing inhibitory neurons (SST-INs) can suppress network activity via both GABAa and GABAb receptors (Rs). Although SST-INs do not receive GABAaR input from other SST-INs, it is possible that SST-IN-released GABA could suppress the activity of SST-INs themselves via GABAbRs, providing a negative feedback loop. Here we characterized the influence of GABAbR modulation on SST-IN activity in layer 2/3 of the somatosensory cortex in mice. We compared this to the effects of GABAbR activation on parvalbumin-expressing interneurons (PV-INs). Using in vitro whole-cell patch clamp recordings, pharmacological and optogenetic manipulations, we found that the firing activity of SST-INs suppresses excitatory drive to themselves via presynaptic GABAbRs. Postsynaptic GABAbRs did not influence SST-IN spontaneous activity or intrinsic excitability. Although GABAbRs at pre- and postsynaptic inputs to PV-INs are modestly activated during cortical network activity in vitro, the spontaneous firing of SST-INs was not the source of GABA driving this GABAbR activation. Thus, SST-IN firing regulates excitatory synaptic strength through presynaptic GABAbRs at connections between pyramidal neurons (Pyr-Pyr) and synapses between pyramidal neurons and SST-INs (Pyr-SST), but not Pyr-PV and PV-Pyr synapses. Our study indicates that two main types of neocortical inhibitory interneurons are differentially modulated by SST-IN-mediated GABA release.

The Evaluation of Activity of Selected Lactic Acid Bacteria for Bioconversion of Milk and Whey from Goat Milk to Release Biomolecules with Antibacterial Activity

The aim of the study was to assess the antibacterial features of functional macromolecules released during the fermentation of goat milk and whey from goat milk by selected lactic acid bacteria strains that are components of kefir grain microflora. Two milk sources were used: goat milk and whey from goat milk. The lactic acid bacteria (LAB) and indicator microorganisms used were Lactobacillus plantarum PCM 1386, Lactobacillus fermentum PCM 491, Lactobacillus rhamnosus PCM 2677, Lactobacillus acidophilus PCM 2499, Escherichia coli PCM 2793, Salmonella enteritidis PCM 2548, Micrococcus luteus PCM 525, and Proteus mirabilis PCM 1361. The metabolic activity of LAB was described by the Gompertz model, and the parameters proposed for this experiment were the maximum rate of change of electrical impedance and potential biodegradability. Antibacterial activity was examined using the culture method in a liquid medium, determination of the reduction in indicator microorganisms, and optical density changes. Results show that the selective LAB produced certain active biomolecules with antibacterial activity from whey, a by-product that is sometimes troublesome for goat milk processors to manage. Lactobacillus acidophilus is a microorganism that is characterized by the highest metabolic activity in goat milk and whey from goat milk. It has the possibility to produce macromolecules with antibacterial activity.

Quantum phase transition dynamics in the two-dimensional transverse-field Ising model

The quantum Kibble-Zurek mechanism (QKZM) predicts universal dynamical behavior near the quantum phase transitions (QPTs). It is now well understood for the one-dimensional quantum matter. Higher-dimensional systems, however, remain a challenge, complicated by the fundamentally different character of the associated QPTs and their underlying conformal field theories. In this work, we take the first steps toward theoretical exploration of the QKZM in two dimensions for interacting quantum matter. We study the dynamical crossing of the QPT in the paradigmatic Ising model by a joint effort of modern state-of-the-art numerical methods, including artificial neural networks and tensor networks. As a central result, we quantify universal QKZM behavior close to the QPT. We also note that, upon traversing further into the ferromagnetic regime, deviations from the QKZM prediction appear. We explain the observed behavior by proposing an extended QKZM taking into account spectral information as well as phase ordering. Our work provides a testing platform for higher-dimensional quantum simulators.

Nanotechnology-Assisted RNA Delivery: From Nucleic Acid Therapeutics to COVID-19 Vaccines

In recent years, the main quest of science has been the pioneering of the groundbreaking biomedical strategies needed for achieving a personalized medicine. Ribonucleic acids (RNAs) are outstanding bioactive macromolecules identified as pivotal actors in regulating a wide range of biochemical pathways. The ability to intimately control the cell fate and tissue activities makes RNA-based drugs the most fascinating family of bioactive agents. However, achieving a widespread application of RNA therapeutics in humans is still a challenging feat, due to both the instability of naked RNA and the presence of biological barriers aimed at hindering the entrance of RNA into cells. Recently, material scientists' enormous efforts have led to the development of various classes of nanostructured carriers customized to overcome these limitations. This work systematically reviews the current advances in developing the next generation of drugs based on nanotechnology-assisted RNA delivery. The features of the most used RNA molecules are presented, together with the development strategies and properties of nanostructured vehicles. Also provided is an in-depth overview of various therapeutic applications of the presented systems, including coronavirus disease vaccines and the newest trends in the field. Lastly, emerging challenges and future perspectives for nanotechnology-mediated RNA therapies are discussed.

Identification and Structural Aspects of G-Quadruplex-Forming Sequences from the Influenza A Virus Genome

Influenza A virus (IAV) causes seasonal epidemics and sporadic pandemics, therefore is an important research subject for scientists around the world. Despite the high variability of its genome, the structure of viral RNA (vRNA) possesses features that remain constant between strains and are biologically important for virus replication. Therefore, conserved structural motifs of vRNA can represent a novel therapeutic target. Here, we focused on the presence of G-rich sequences within the influenza A/California/07/2009(H1N1) genome and their ability to form RNA G-quadruplex structures (G4s). We identified 12 potential quadruplex-forming sequences (PQS) and determined their conservation among the IAV strains using bioinformatics tools. Then we examined the propensity of PQS to fold into G4s by various biophysical methods. Our results revealed that six PQS oligomers could form RNA G-quadruplexes. However, three of them were confirmed to adopt G4 structures by all utilized methods. Moreover, we showed that these PQS motifs are present within segments encoding polymerase complex proteins indicating their possible role in the virus biology.

Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

Design and Evaluation of 223Ra-Labeled and Anti-PSMA Targeted NaA Nanozeolites for Prostate Cancer Therapy-Part II. Toxicity, Pharmacokinetics and Biodistribution

Metastatic castration-resistant prostate cancer (mCRPC) is a progressive and incurable disease with poor prognosis for patients. Despite introduction of novel therapies, the mortality rate remains high. An attractive alternative for extension of the life of mCRPC patients is PSMA-based targeted radioimmunotherapy. In this paper, we extended our in vitro study of 223Ra-labeled and PSMA-targeted NaA nanozeolites [223RaA-silane-PEG-D2B] by undertaking comprehensive preclinical in vitro and in vivo research. The toxicity of the new compound was evaluated in LNCaP C4-2, DU-145, RWPE-1 and HPrEC prostate cells and in BALB/c mice. The tissue distribution of 133Ba- and 223Ra-labeled conjugates was studied at different time points after injection in BALB/c and LNCaP C4-2 tumor-bearing BALB/c Nude mice. No obvious symptoms of antibody-free and antibody-functionalized nanocarriers cytotoxicity and immunotoxicity was found, while exposure to 223Ra-labeled conjugates resulted in bone marrow fibrosis, decreased the number of WBC and platelets and elevated serum concentrations of ALT and AST enzymes. Biodistribution studies revealed high accumulation of 223Ra-labeled conjugates in the liver, lungs, spleen and bone tissue. Nontargeted and PSMA-targeted radioconjugates exhibited a similar, marginal uptake in tumour lesions. In conclusion, despite the fact that NaA nanozeolites are safe carriers, the intravenous administration of NaA nanozeolite-based radioconjugates is dubious due to its high accumulation in the lungs, liver, spleen and bones.

Surface-enhanced Raman scattering of water in aqueous dispersions of silver nanoparticles

The resonance Raman effect (RRE) is a phenomenon which results in a strong selective enhancement of Raman signals from the samples. Previous studies showed that the RRE in liquid water directly corresponds to its supramolecular structure. It was also reported that the electric-field-induced orientation of water molecules on the electrode surface results in the surface-enhanced Raman scattering (SERS) effect. In this work, we show the SERS effect for water molecules in the dispersion of silver nanoparticles (AgNPs) without any external electrical field. An enhancement factor was estimated to be (4.8 ± 0.8) × 10⁶ for an excitation wavelength of 514.5 nm and for AgNPs with an average size of 34 ± 14 nm. The temperature experiment results showed a higher enhancement with temperature increase. Performed simulation studies revealed a slowdown of the mobility of the water molecules close to the surface of AgNPs.

Rapid recycling of glutamate transporters on the astroglial surface

Glutamate uptake by astroglial transporters confines excitatory transmission to the synaptic cleft. The efficiency of this mechanism depends on the transporter dynamics in the astrocyte membrane, which remains poorly understood. Here, we visualise the main glial glutamate transporter GLT1 by generating its pH-sensitive fluorescent analogue, GLT1-SEP. Fluorescence recovery after photobleaching-based imaging shows that 70-75% of GLT1-SEP dwell on the surface of rat brain astroglia, recycling with a lifetime of ~22 s. Genetic deletion of the C-terminus accelerates GLT1-SEP membrane turnover while disrupting its surface pattern, as revealed by single-molecule localisation microscopy. Excitatory activity boosts surface mobility of GLT1-SEP, involving its C-terminus, metabotropic glutamate receptors, intracellular Ca2+, and calcineurin-phosphatase activity, but not the broad-range kinase activity. The results suggest that membrane turnover, rather than lateral diffusion, is the main 'redeployment' route for the immobile fraction (20-30%) of surface-expressed GLT1. This finding reveals an important mechanism helping to control extrasynaptic escape of glutamate.

Low-Temperature Hydrothermal Treatment Surface Functionalization of the Ultrafine-Grained TiMo Alloys for Medical Applications

Hydroxyapatite (HAp) is the most widely used material for bio coating. The functional layer can be produced by many methods, however, the most perspective by its utility, easy to scale up, and simplicity aspects remains a hydrothermal treatment approach. In this work, an HAp coating was produced by low-temperature hydrothermal treatment on the ultrafine-grain beta Ti-xMo (x = 23, 27, 35 wt.%) alloys. The proposed surface treatment procedure combines acid etching, alkaline treatment (AT), and finally hydrothermal treatment (HT). The uniqueness of the approach relies on the recognition of the influence of the molar concentration of NaOH (5 M, 7 M, 10 M, 12 M) during the alkaline treatment on the growth of hydroxyapatite crystals. Obtained and modified specimens were examined structurally and microstructurally at every stage of the process. The results show that the layer after AT consist of titanium oxide and phases based on sodium with various phase relations dependent on NaOH concentration and base composition. The AT in 7 M and 10 M enables to obtain the HAp layer, which can be characterized as the most developed in terms of thickness and porosity. Finally, selected coated samples were investigated in terms of surface wettability test managed in time relation, which for the results confirm high hydrophilicity of the surfaces. Conducted research shows that the low-temperature hydrothermal processing could be considered for a possible adaptation in the drug encapsulation and delivery systems.

Titanium Dioxide Thin Films Obtained by Atomic Layer Deposition Promotes Osteoblasts' Viability and Differentiation Potential While Inhibiting Osteoclast Activity-Potential Application for Osteoporotic Bone Regeneration

Atomic layer deposition (ALD) technology has started to attract attention as an efficient method for obtaining bioactive, ultrathin oxide coatings. In this study, using ALD, we have created titanium dioxide (TiO2) layers. The coatings were characterised in terms of physicochemical and biological properties. The chemical composition of coatings, as well as thickness, roughness, wettability, was determined using XPS, XRD, XRR. Cytocompatibillity of ALD TiO2 coatings was accessed applying model of mouse pre-osteoblast cell line MC3T3-E1. The accumulation of transcripts essential for bone metabolism (both mRNA and miRNA) was determined using RT-qPCR. Obtained ALD TiO2 coatings were characterised as amorphous and homogeneous. Cytocompatibility of the layers was expressed by proper morphology and growth pattern of the osteoblasts, as well as their increased viability, proliferative and metabolic activity. Simultaneously, we observed decreased activity of osteoclasts. Obtained coatings promoted expression of Opn, Coll-1, miR-17 and miR-21 in MC3T3-E1 cells. The results are promising in terms of the potential application of TiO2 coatings obtained by ALD in the field of orthopaedics, especially in terms of metabolic- and age-related bone diseases, including osteoporosis.

The Response of Pseudomonas aeruginosa PAO1 to UV-activated Titanium Dioxide/Silica Nanotubes

Pseudomonas aeruginosa is a bacterium of high clinical and biotechnological importance thanks to its high adaptability to environmental conditions. The increasing incidence of antibiotic-resistant strains has created a need for alternative methods to increase the chance of recovery in infected patients. Various nanomaterials have the potential to be used for this purpose. Therefore, we aimed to study the physiological response of P. aeruginosa PAO1 to titanium dioxide/silica nanotubes. The results suggest that UV light-irradiated nanomaterial triggers strong agglomeration in the studied bacteria that was confirmed by microscopy, spectrophotometry, and flow cytometry. The effect was diminished when the nanomaterial was applied without initial irradiation, with UV light indicating that the creation of reactive oxygen species could play a role in this phenomenon. The nanocomposite also affected biofilm formation ability. Even though the biomass of biofilms was comparable, the viability of cells in biofilms was upregulated in 48-hour biofilms. Furthermore, from six selected genes, the mexA coding efflux pump was upregulated, which could be associated with an interaction with TiO2. The results show that titanium dioxide/silica nanotubes may alter the physiological and metabolic functions of P. aeruginosa PAO1.

Non-Coding RNAs in Cancer Radiosensitivity: MicroRNAs and lncRNAs as Regulators of Radiation-Induced Signaling Pathways

Radiotherapy is a cancer treatment that applies high doses of ionizing radiation to induce cell death, mainly by triggering DNA double-strand breaks. The outcome of radiotherapy greatly depends on radiosensitivity of cancer cells, which is determined by multiple proteins and cellular processes. In this review, we summarize current knowledge on the role of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), in determining the response to radiation. Non-coding RNAs modulate ionizing radiation response by targeting key signaling pathways, including DNA damage repair, apoptosis, glycolysis, cell cycle arrest, and autophagy. Additionally, we indicate miRNAs and lncRNAs that upon overexpression or inhibition alter cellular radiosensitivity. Current data indicate the potential of using specific non-coding RNAs as modulators of cellular radiosensitivity to improve outcome of radiotherapy.

The miR-26b-5p/KPNA2 Axis Is an Important Regulator of Burkitt Lymphoma Cell Growth

The expression of several microRNAs (miRNAs) is known to be changed in Burkitt lymphoma (BL), compared to its normal counterparts. Although for some miRNAs, a role in BL was demonstrated, for most of them, their function is unclear. In this study, we aimed to identify miRNAs that control BL cell growth. Two BL cell lines were infected with lentiviral pools containing either 58 miRNA inhibitors or 44 miRNA overexpression constructs. Eighteen constructs showed significant changes in abundance over time, indicating that they affected BL growth. The screening results were validated by individual green fluorescent protein (GFP) growth competition assays for fifteen of the eighteen constructs. For functional follow-up studies, we focused on miR-26b-5p, whose overexpression inhibited BL cell growth. Argonaute 2 RNA immunoprecipitation (Ago2-IP) in two BL cell lines revealed 47 potential target genes of miR-26b-5p. Overlapping the list of putative targets with genes showing a growth repression phenotype in a genome-wide CRISPR/Cas9 knockout screen, revealed eight genes. The top-5 candidates included EZH2, COPS2, KPNA2, MRPL15, and NOL12. EZH2 is a known target of miR-26b-5p, with oncogenic properties in BL. The relevance of the latter four targets was confirmed using sgRNAs targeting these genes in individual GFP growth competition assays. Luciferase reporter assay confirmed binding of miR-26b-5p to the predicted target site for KPNA2, but not to the other genes. In summary, we identified 18 miRNAs that affected BL cell growth in a loss- or gain-of-function screening. A tumor suppressor role was confirmed for miR-26b-5p, and this effect could at least in part be attributed to KPNA2, a known regulator of OCT4, c-jun, and MYC.

Behavioral response of naïve and non-naïve deer to wolf urine

Large carnivores are recolonizing many regions in Europe, where their ungulate prey have lived without them for >150 years. Whether the returning large carnivores will modify ungulate behavior and indirectly affect lower trophic levels, depends on the ability of ungulates to recognize risk based on past encounters and cues indicating carnivore presence. In two case studies, we tested, by means of camera trapping, the behavioral response of deer to wolf urine. The first case study was in the Netherlands where deer (still) live in absence of wolves, and the second in Poland with long-term wolf presence. As controls we used water (no scent) and all-purpose soap (unfamiliar scent). Deer vigilance level on control plots was 20% in both case studies indicating that wolf occupancy per se does not lead to a consistent difference in behavior. Placing wolf urine did not significantly affect deer behavior in either the wolf-absent or the wolf-present area. More intense cues, or a combination of cues, are likely needed to affect deer behavior. Moreover, we found an unexpected reaction of deer towards all-purpose soap of reduced foraging (and tendency for increased vigilance) in the wolf-present area, whereas it did not affect deer behavior in the wolf-absent area. We hypothesize that deer associate all-purpose soap with human presence, causing no response in human-dominated landscapes (the Netherlands), but triggering a behavioral reaction in more remote areas (Poland). This illustrates attention should be paid to controls used in scent experiments as they may be associated differently than intended.

Farmers' preferences for nutrient and climate-related agri-environmental schemes: A cross-country comparison

We use data from a survey of 2439 farmers in 5 countries around the Baltic Sea (Denmark, Estonia, Finland, Poland and Sweden) to investigate their preferences for adopting agricultural practices aimed at reducing nutrient leaching and greenhouse gas emissions. The measures considered are set-aside, catch crops and reduced fertilization. Contracts vary with respect to the area enrolled, contract length, possibility of premature termination, availability of professional advice and compensation. We quantitatively describe farmers' preferences in terms of their willingness-to-accept compensation for specific attributes of these contracts, if implemented. The results vary substantially between farm types (farmers' characteristics) and between the 5 countries, and support differentiation of contract obligations and payments to improve the uptake of Agri-Environmental Schemes. The results can be readily used to improve the design of country-specific nutrient reduction policies, in accordance with the next Common Agricultural Policy.

Early pre- and postsynaptic decrease in glutamatergic and cholinergic signaling after spinalization is not modified when stimulating proprioceptive input to the ankle extensor α-motoneurons: Anatomical and neurochemical study

Alpha-motoneurons (MNs) innervating ankle extensor muscles show reduced peripheral inputs from Ia proprioceptive afferents and cholinergic afferents after chronic spinalization (SCT). That phenomenon is not observed on ankle flexor MNs, indicating a smaller vulnerability of the latter MNs circuit to SCT. Locomotor training of spinal rats which partially restored those inputs to extensor MNs tended to hyper innervate flexor MNs, disclosing a need for selective approaches. In rats with intact spinal cord 7-days of low-threshold proprioceptive stimulation of the tibial nerve enriched glutamatergic Ia and cholinergic innervation of lateral gastrocnemius (LG) MNs, suggesting usefulness of selective stimulation for restoration of inputs to extensor MNs after SCT. Accordingly, to examine its effectiveness after SCT, tibial nerves and soleus muscles were implanted bilaterally, and for MN identification fluorescence tracers to LG and tibialis anterior (TA) muscles were injected two weeks prior to spinalization. Stimulation of tibial nerve, controlled by H-reflex recorded in the soleus muscle, started on the third post-SCT day and continued for 7 days. Nine days post-SCT the number and volume of glutamatergic Ia and of cholinergic C-boutons on LG MNs was decreased, but stimulation affected neither of them. Postsynaptically, a threefold decrease of NMDAR NR1 subunit and thirtyfold decrease of M2 muscarinic receptor transcripts caused by SCT were not counteracted by stimulation, whereas a threefold decrease of AMPAR GluR2 subunit tended to deepen after stimulation. We conclude that LG MNs, supported with proprioceptive stimuli after SCT, do not transcribe the perceived cues into compensatory response at the transcriptional level in the early post-SCT period.

Benchmarking of alignment-free sequence comparison methods

BACKGROUND

Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment.

RESULTS

Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events.

CONCLUSION

The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.

Ants Response to Human-Induced Disturbance in a Rain Tropical Forest

A high rate of human-induced disturbance of tropical ecosystems results in enormous loss of biodiversity due to local extinctions. Yet, mechanisms at the population level that lead to the extinction are still poorly understood. Here we tested the hypothesis that human-induced disturbance results in smaller amount of nesting sites for wood-dwelling arthropods that leads to smaller population size and diminished reproduction, and therefore, may promote local extinctions. We completed censuses in less-disturbed and human-disturbed secondary rain forest plots in Puerto Rico. We measured population size and brood production in wood-nesting ants and examined whether these parameters differ between less-disturbed and more-disturbed habitats. In addition, we measured volume of wood parts of all inhabited and potential nesting sites to assess nest site availability. We found that more human-disturbed forests furnish smaller nest sites, resulting in diminished population size and lowered brood production. Our study shows that human-induced disturbance decreases volume of available nesting sites that leads to decreased population size and lowered reproduction. Thus, in addition to the well-documented loss of species richness in human-disturbed tropical habitats, we demonstrated the direct effect of the disturbance that may promote vulnerability of local populations.

Association of variants in BAFF (rs9514828 and rs1041569) and BAFF-R (rs61756766) genes with the risk of chronic lymphocytic leukemia

The B-cell activator factor (BAFF)/BAFF receptor (BAFF-R) axis seems to play an important role in the development and progression of chronic lymphocytic leukemia (CLL). Here, we investigated the association of eight single nucleotide polymorphisms (SNPs) in the BAFF (TNFSF13B) and BAFF-R (TNFRSF13C) genes with risk of sporadic CLL in a group of 439 CLL patients and 477 controls. We also examined the correlation between selected SNPs and CLL clinical parameters as well as BAFF plasma levels and intracellular BAFF expression. Our results point to a possible association between the rs9514828 (CT vs. CC + TT; OR = 0.74; CI 95 % = 0.57; 0.97; p = 0.022) and rs1041569 (AT vs. AA + TT; OR = 0.72; CI 95 % = 0.54; 0.95; p = 0.021) of BAFF gene and rs61756766 (CC vs. CT; OR = 2.03; CI 95 % = 1.03; 3.99; p = 0.03) of BAFF-R gene and CLL risk. Additionally, we observed that homozygotes rs1041569 AA and TT had a slightly higher risk (HR = 1.12) for the need of treatment in comparison to AT heterozygotes. In conclusion, our results indicate that SNPs in BAFF and BAFF-R genes may be considered as potential CLL risk factors.

Sound Wave Energy Resulting from the Impact of Water Drops on the Soil Surface

The splashing of water drops on a soil surface is the first step of water erosion. There have been many investigations into splashing-most are based on recording and analysing images taken with high-speed cameras, or measuring the mass of the soil moved by splashing. Here, we present a new aspect of the splash phenomenon's characterization the measurement of the sound pressure level and the sound energy of the wave that propagates in the air. The measurements were carried out for 10 consecutive water drop impacts on the soil surface. Three soils were tested (Endogleyic Umbrisol, Fluvic Endogleyic Cambisol and Haplic Chernozem) with four initial moisture levels (pressure heads: 0.1 kPa, 1 kPa, 3.16 kPa and 16 kPa). We found that the values of the sound pressure and sound wave energy were dependent on the particle size distribution of the soil, less dependent on the initial pressure head, and practically the same for subsequent water drops (from the first to the tenth drop). The highest sound pressure level (and the greatest variability) was for Endogleyic Umbrisol, which had the highest sand fraction content. The sound pressure for this soil increased from 29 dB to 42 dB with the next incidence of drops falling on the sample The smallest (and the lowest variability) was for Fluvic Endogleyic Cambisol which had the highest clay fraction. For all experiments the sound pressure level ranged from ~27 to ~42 dB and the energy emitted in the form of sound waves was within the range of 0.14 μJ to 5.26 μJ. This was from 0.03 to 1.07% of the energy of the incident drops.

The Comparison of MTT and CVS Assays for the Assessment of Anticancer Agent Interactions

Multiple in vitro tests are widely applied to assess the anticancer activity of new compounds, including their combinations and interactions with other drugs. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay is one of the most commonly used assays to assess the efficacy and interactions of anticancer agents. However, it can be significantly influenced by compounds that modify cell metabolism and reaction conditions. Therefore, several assays are sometimes used to screen for potential anticancer drugs. However, the majority of drug interactions are evaluated only with this single method. The aim of our studies was to verify whether the choice of an assay has an impact on determining the type of interaction and to identify the source of discrepancies. We compared the accuracy of MTT and CVS (crystal violet staining) assays in the interaction of two compounds characterized by similar anticancer activity: isothiocyanates (ITCs) and Selol. Confocal microscopy studies were carried out to assess the influence of these compounds on the reactive oxygen species (ROS) level, mitochondrial membrane potential, dead-to-live cell ratio and MTT-tetrazolium salt reduction rate. The MTT assay was less reliable than CVS. The MTT test of Selol and 2-oxoheptyl ITC, which affected the ROS level and MTT reduction rate, gave false negative (2-oxoheptyl ITC) or false positive (Selol) results. As a consequence, the MTT assay identified an antagonistic interaction between Selol and ITC, while the metabolism-independent CVS test identified an additive or synergistic interaction. In this paper, we show for the first time that the test assay may change the interpretation of the compound interaction. Therefore, the test method should be chosen with caution, considering the mechanism of action of the compound.