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Limited data are available about the coastal ecology of the Calabria region, in the southern Italy. As well, data about the levels of biodiversity and the structure of food webs in these environments are totally missing. However, considering the wide range of physical and ecological conditions distinguishing these ecosystems, a remarkable spread of biodiversity is expected. This review represents a first attempt to describe and estimate the structure of the food webs in a range of shallow stations along the south-western coasts of southern Italy, in the Ionian Sea. They comprise a Special Area of Conservation (Amendolara shoal), an urbanized area (Sibari), a sandy area impacted by industrial installations (Corigliano) and a seagrass meadow (Calopezzati). For each of these stations, we produced ecological simulation models based on the available information in order to estimate the structure of food webs. In particular, the patterns of distribution of trophic resources resulting from literature data were statistically compared to a theoretical model based on the physical and ecological features of coastal ecosystems. The model was responsive and predicted remarkable differences in the compartmentalization of trophic resources among stations, due to the diversity of substrates and the anthropic activities impacting each area. Large availability of resources for omnivores and detritivores characterized most stations. A noteworthy richness of trophic resources for herbivores was forecasted off Amendolara and Calopezzati. In parallel, the model obtained for the urbanized area of Sibari predicted a higher abundance of trophic resources for filter feeders, especially in the deepest station., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Gadolinium (Gd), commonly used in contrast agents for medical imaging, has been detected in hospital wastewater and aquatic environments, raising environmental concerns. This study examined the accumulation and cellular impacts of Gd in the clam species Donax trunculus, commonly used as bioindicator of contamination. Gadolinium accumulation in clams increased with exposure and over time. Biological responses varied with Gd levels: low concentrations (10 and 50 µg/L) led to low metabolic activity and glycogen content, but high antioxidant activities and lipid peroxidation levels (LPO); high concentrations (250 and 500 µg/L) resulted in increased metabolic activity, while antioxidant enzyme activity was inhibited and LPO levels were the lowest. Metabolic activity decreased after two weeks, suggesting limited long-term metabolic resilience. The study underscores D. trunculus as an effective early warning species for Gd pollution and highlights the ecological risks of rising Gd levels, emphasizing the need for environmental monitoring and regulation., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

The extensive use of antibiotics in human and veterinary medicine has led to the emergence of antibiotic contaminants in the environment, posing significant risks to ecosystems and public health. This contamination arises from the persistence of antibiotics in aquatic environments, particularly in aquifer systems, where they contribute to the growing threat of antibiotic resistance. Despite increasing research, the understanding of the ecological and human health implications of these contaminants remains incomplete. Since these compounds are only partially removed by conventional wastewater treatment plants (WWTPs), they are continuously released into the environment. Antibiotics enter the environment mainly through human and animal excretions, improper drug disposal, wastewater treatment plants, and waste streams from antibiotic production. Recent research has focused on antibiotic metabolites and transformation products, which can affect aquatic ecosystems and the food chain, posing long-term risks to human health. This critical review provides a comprehensive analysis of the risk assessment of veterinary antibiotics (VAs) in European aquatic environments, where VAs concentrations ranging from micrograms to milligrams per liter. By examining toxicity data from freshwater and saltwater species, the study evaluates acute and chronic effects across different antibiotic classes. The review also assesses the sensitivity of various taxonomic groups and species to different antibiotics, providing insights into potential ecological risks. Species sensitivity distributions and hazard concentrations affecting a given percentage of species are calculated to assess the overall ecological risk. The findings reveal varying proportions of toxicity data across antibiotic classes, with Aminoglycosides, β-lactams, Fluoroquinolones, Macrolides, and Tetracyclines classes demonstrating higher toxicity levels than others towards certain cyanobacteria and chlorophyta species. Macrolides and Fluoroquinolones emerge as particularly concerning due to their high toxicological risks across various aquatic environments. The analysis underscores the urgent need for further research to fill knowledge gaps and develop effective strategies to mitigate the harmful effects of VAs on aquatic ecosystems and human health., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Vanadium compounds (VCs) exhibit a broad range of pharmacological properties, with their most significant medical applications being in the treatment of cancer and diabetes. The therapeutic effects and mode of action of VCs may be associated with their ability to bind proteins and, consequently, understanding the VC-protein interaction is of paramount importance. Among the promising VCs, the V V O 2 complex with the aroylhydrazone furan-2-carboxylic acid ((3-ethoxy-2-hydroxybenzylidene)hydrazide, hereafter denoted as VC1), deserves attention, since it exhibits cytotoxicity against various cancer cell lines, including HeLa. The interaction between VC1 and its analogue, denoted as VC2 (the dioxidovanadium(V) complex with (E)-N'-(1-(2-hydroxy-5-methoxyphenyl)ethylidene)furan-2-carbohydrazide), and hen egg white lysozyme (HEWL) was examined by UV-vis spectroscopy, fluorescence, circular dichroism, and X-ray crystallography. The interaction of VC1 and VC2 with HEWL does not alter the protein secondary and tertiary structure. Crystallographic studies indicate that the two metal complexes or V-containing fragments originating from VC1 and VC2 bind the protein via non-covalent interactions. Furthermore, when bound to HEWL, two VC1 molecules and two VC2 molecules form a supramolecular association stabilized by stacking interactions. This type of interaction could favour the binding of similar compounds to proteins and affect their biological activity., Competing Interests: Declaration of competing interest There are no conflicts to declare., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The spatial organization of chromatin within the eukaryotic nucleus is critical in regulating key cellular functions, such as gene expression, and its disruption can lead to disease. Advances in experimental techniques, such as Hi-C and microscopy, have significantly enhanced our understanding of chromatin's intricate and dynamic architecture, revealing complex patterns of interaction at multiple scales. Along with experimental methods, physics-based computational models, including polymer phase separation and loop-extrusion mechanisms, have been developed to explain chromatin structure in a principled manner. Here, we illustrate genome-wide applications of these models, highlighting their ability to predict chromatin contacts across different scales and to spread light on the underlying molecular determinants. Additionally, we discuss how these models provide a framework for understanding alterations in chromosome folding associated with disease states, such as SARS-CoV-2 infection and pathogenic structural variants, providing valuable insights into the role of chromatin architecture in health and disease.

Plastic pollution is a notable environmental issue, being plastic widespread and characterized by long lifetime. Serious environmental problems are caused by the improper management of plastic end-of-life. In fact, plastic litter is currently detected in any environment. Biodegradable Polymers (BPs) are promising materials if correctly applied and managed at their end of life, to minimize environmental problems. However, poor data on the fate and toxicity of BPs on marine organisms still limit their applicability. In this work we tested the effects of five biodegradable polymers (polybutylene succinate, PBS; polybutylene succinate-co-butylene adipate, PBSA; polycaprolactone, PCL; poly (3-hydroxybutyrates, PHB; polylactic acid, PLA) widely used for several purposes. Adult individuals of the isopod Idotea balthica basteri were fed on these polymers for twenty-seven days by adding biodegradable microplastic polymers (BMPs) to formulated feeds at two concentrations, viz. 0.84 and 8.4 g/kg feed. The plastic fragments affected the mortality rates of the isopods, as well as the expression levels of eighteen genes (tested by Real Time qPCR) involved in stress response and detoxification processes. Our findings confirmed that I. balthica basteri is a convenient model organism to study the response to environmental pollution and emerging contaminants in the aquatic environment, and highlighted the need for the correct use of BMPs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Fungicides are used to control phytopathogens but all these fungicides have deleterious effects. Allelopathic interactions can be harnessed as a natural way to control the pathogens but there are no reports that show the allelopathic interactions of donor plant, recipient crop, as well as the target plant pathogen and the material used for inoculum production. So, in the present study, the suitability of Carthamus oxyacantha M. Bieb. was assessed against Macrophomina phaseolina, the cause of charcoal rot in maize. Among the various treatments in pot experiment, a negative control, 3 concentrations of inoculum (1.2×105, 2.4×105, and 3.6×105 colony forming units (CFU) mL-1, 3 concentrations (0.5, 1.0, and 1.5% w/w) of C. oxyacantha along with an autoclaved M. phaseolina (Mp) and C. oxyacantha alone were included to investigate their allelopathic effects on maize, not investigated earlier. Maximum suppression of the disease was observed by 1.5% (w/w) concentration of C. oxyacantha. Soil amendment with C. oxyacantha significantly suppressed the disease incidence (DI) and disease severity index (DSI) in charcoal rot of maize up to 40 and 55%, respectively over the strongest level of inoculum (Mp3). C. oxyacantha not only reduced area under disease incidence progress curve (AUDIPC) and area under disease severity progress curve (AUDSPC), but also improved the morphological, biochemical and physiological parameters of maize. The maximum increase of 48, 65, and 75% in values of shoot length (SL), shoot dry mass (SDM), and root dry mass (RDM), respectively was observed by application of the highest concentration of C. oxyacantha in the treatment Mp1+Co3, over infested control (Mp1). Photosynthetic pigments, such as chlorophyll a, chlorophyll b and carotenoids were increased to 58, 64, and 46%, respectively over Mp1, by the application of C. oxyacantha. Carbon assimilation rate (A), stomatal conductance (gs), rate of transpiration (E), and internal carbon dioxide concentration (Ci) were significantly increased to 58, 48, 48, and 20%, respectively over infested control (Mp3), by application of C. oxyacantha concentration 1.5 (w/w). Moreover, defense enzymes like superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities were boosted up to 27, 28, and 28% over Mp3, respectively. Positive allelopathy of C. oxyacantha towards maize and negative allelopathy towards M. phaseolina makes C. oxyacantha a suitable candidate for charcoal rot disease control in maize., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Aslam et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Secondary metabolites play important physiological roles being bioactive as defences against other organisms, or attractive signals used for various purposes, including reproduction. Their production and the emission in the environment may be viewed as an adaptive feature subjected to evolutionary selection. They were demonstrated to be useful for applications in various biotechnological fields, such as pharmaceutical, nutraceutical and cosmeceutical. Sponges and microalgae, including diatoms, are the most promising sources of bioactive compounds from the sea. We aimed at detecting the ecotoxicological effects of crude extracts and fractions obtained from three marine sponges, Geodia cydonium, Haliclona (Halichoclona) vansoesti and Agelas oroides and two benthic diatoms, Nanofrustulum shiloi and Cylindrotheca closterium on model marine organisms. We tested their effects on the Mediterranean purple sea urchin, Paracentrotus lividus, and on two diatoms, Phaeodactylum tricornutum and Cylindrotheca closterium, chosen because they are considered standard indicators for assessment of ecological impacts. Our results showed that extracts and fractions from both sponges and diatoms may be harmful for model invertebrates. However, eggs appeared "protected" from sponge allelochemicals when still unfertilized. The majority of sponge fractions exhibited noticeable impacts during the post-fertilization treatments. In contrast, fractions from diatoms notably increased the rate of malformations compared to the control, both in pre- and post-fertilization treatments., (© 2024. The Author(s).)

Regenerative life support systems for space crews recycle waste into water, food, and oxygen using different organisms. The European Space Agency's MELiSSA program uses the cyanobacterium Limnospira indica PCC8005 for air revitalization and food production. Before space use, components' compatibility with reduced gravity was tested. This study introduced a ground analog for microgravity experiments with oxygenic cyanobacteria under continuous illumination, using a random positioning machine (RPM) setup. L. indica PCC8005 grew slower under low-shear simulated microgravity, with proteome analysis revealing downregulation of ribosomal proteins, glutamine synthase, and nitrate uptake transporters, and upregulation of gas vesicle, photosystem I and II, and carboxysome proteins. Results suggested inhibition due to high oxygen partial pressure, causing carbon limitation when cultivated in low-shear simulated microgravity. A thicker stagnant fluid boundary layer reducing oxygen release in simulated microgravity was observed. These findings validate this RPM setup for testing the effects of non-terrestrial gravity on photosynthetic microorganisms., (© 2024. The Author(s).)

The binding of the potential drug [V IV O(8-HQ) 2 ], where 8-HQ is 8-hydroxyquinolinato, with hen egg white lysozyme (HEWL) was evaluated through spectroscopic (electron paramagnetic resonance, EPR, and UV-visible), spectrometric (electrospray ionization-mass spectrometry, ESI-MS), crystallographic (X-ray diffraction, XRD), and computational (DFT and docking) studies. ESI-MS indicates the interaction of [V IV O(8-HQ)(H 2 O)] + and [V IV O(8-HQ) 2 (H 2 O)] species with HEWL. Room temperature EPR spectra suggest both covalent and non-covalent binding of the two different V-containing fragments. XRD analyses confirm these findings, showing that [V IV O(8-HQ)(H 2 O)] + interacts covalently with the solvent exposed Asp119, while cis-[V IV O(8-HQ) 2 (H 2 O)] non-covalently with Arg128 and Lys96 from a symmetry mate. The covalent binding of [V IV O(8-HQ)(H 2 O)] + to Asp119 is favored by a π-π contact with Trp62 and a H-bond with Asn103 of a symmetry-related molecule. Additionally, the covalent binding of V V O 2 + to Asp48 and non-covalent binding of other V-containing fragments to Arg5, Cys6, and Glu7 are revealed. Molecular docking indicates that, in the absence of the interactions occurring at the protein-protein interface close to Asp119, the covalent binding to Glu35 or Asp52 should be preferred. Such a protein-protein stabilization could be more common than what believed up today, at least in the solid state, and should be considered in the characterization of metal-protein adducts., (© 2024 Wiley-VCH GmbH.)

Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2 Mb wide genomic region encompassing the human LTN1 gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in silico the ensemble of single-molecule LTN1 3D structures, which we benchmark against recent in situ Hi-C 2.0 data. The model-derived single molecules are then used to predict structural folding features at the single-cell level, providing testable predictions for super-resolution microscopy experiments.

Ferritin (Ft) is a protein with a peculiar three-dimensional architecture. It is characterized by a hollow cage structure and is responsible for iron storage and detoxification in almost all living organisms. It has attracted the interest of the scientific community thanks to its appealing features, such as its nano size, thermal and pH stability, ease of functionalization, and low cost for large-scale production. Together with high storage capacity, these properties qualify Ft as a promising nanocarrier for the development of delivery systems for numerous types of biologically active molecules. In this paper, we introduce the basic structural and functional aspects of the protein, and summarize the methods employed to load bioactive molecules within the ferritin nanocage.

Since the discovery of G-quadruplex (G4) participation in vital cellular processes, the regulation of the interaction of naturally occurring G4s with the relative target proteins has emerged as a promising approach for therapeutic development. Additionally, a synthetic strategy has produced several oligonucleotide aptamers, embodying a G4 module, which exhibit relevant biological activity by binding selectively to a target protein. In this context, the G4-protein structures available in the Protein Data Bank represent a valuable molecular view of the different G4 topologies involved in protein interaction. Interestingly, recent results have shown the co-existence of G4s with other structural domains such as duplexes. Overall, these findings allow a better understanding of the mechanisms that regulate intricate biological functions and suggest new design for innovative medical treatments., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The short-chain fatty acids (SCFAs) acetate, propionate and butyrate, the major products of intestinal microbial fermentation of dietary fibres, are involved in fine-tuning brain functions via the gut-brain axis. However, the effects of SCFAs in the hypothalamic neuronal network regulating several autonomic-brain functions are still unknown. Using NMR spectroscopy, we detected a reduction in brain acetate concentrations in the hypothalamus of obese leptin knockout ob/ob mice compared to lean wild-type littermates. Therefore, we investigated the effect of acetate on orexin/hypocretin neurons (hereafter referred as OX or OX-A neurons), a subset of hypothalamic neurons regulating energy homeostasis, which we have characterized in previous studies to be over-activated by the lack of leptin and enhancement of endocannabinoid tone in the hypothalamus of ob/ob mice. We found that acetate reduces food-intake in concomitance with a reduction of orexin neuronal activity in ob/ob mice. This was demonstrated by evaluating food-intake behaviour and orexin-A/c-FOS immunoreactivity coupled with patch-clamp recordings in Hcrt-eGFP neurons, quantification of prepro-orexin mRNA, and immunolabeling of GPR-43, the main acetate receptor. Our data provide new insights into the mechanisms of the effects of chronic dietary supplementation with acetate, or complex carbohydrates, on energy intake and body weight, which may be partly mediated by inhibition of orexinergic neuron activity., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The high-resolution X-ray structures of the model protein lysozyme in the presence of the potential drug [V IV O(acetylacetonato) 2 ] from crystals grown in 1.1 M NaCl, 0.1 M sodium acetate at pH 4.0 reveal the binding to the protein of different and unexpected mixed-valence cage-like polyoxidovanadates (POVs): [V 15 O 36 (OH 2 )] 5- , which non-covalently interacts with the lysozyme surface, [V 15 O 33 (OH 2 )] + and [V 20 O 51 (OH 2 )] n- (this latter based on an unusual {V 18 O 43 } cage) which covalently bind the protein. EPR spectroscopy confirms the partial oxidation of V IV to V V and the formation of mixed-valence species. The results indicate that the interaction with proteins can stabilize the structure of unexpected - both for dimension and architecture - POVs, not observed in aqueous solution., (© 2024 Wiley-VCH GmbH.)

Marine microplastics, categorized as primary and secondary, including synthetic microfibers like polyethylene terephthalate (PET), polypropylene (PP) and acrylic (PC), represent a potential environmental concern. The complex classification of these fibers, originating from diverse sources such as textiles and many others commercial goods, prompts a need for understanding their impact on aquatic organisms. This study assesses the ecological risks associated with both natural and synthetic fibers in aquatic ecosystems, focusing on toxicity data and their effects on taxonomic groups like Mollusca, Arthropoda, Echinodermata, Cnidaria, and Chordata. To carry out species sensitivity distribution (SSD) curves, a comprehensive analysis of scientific literature was conducted, collecting toxicity data related to various fibers. The resulting SSDs provide insights into the relative sensitivity of different taxonomic groups. The potential ecological risks were evaluated by comparing measured concentrations in diverse aquatic environments with Predicted No-Effect Concentration (PNEC) values. The calculation of Risk Quotient (RQ) allowed to indicate areas where fibers abundance poses a potential threat to aquatic organisms. The study reveals that nylon fibers can pose the highest toxicity risk, especially in Atlantic and Pacific Ocean, Arabian Gulf and VietNam river. Mollusca emerged as particularly sensitive to different fiber types, likely due to their body structure facilitating the accumulation of microfibers. The research emphasizes the urgent need for further studies to get data to human health risk analysis and to address comprehensive environmental management strategies to address the global issue of microfiber pollution., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

The generation of terahertz radiation via laser-induced plasma from two-color femtosecond pulses in air has been extensively studied due to its broad emission spectrum and significant pulse energy. However, precise control over the temporal properties of these ultra-broadband terahertz pulses, as well as the measurement of their polarization state, remain challenging. In this study, we review our latest findings on these topics and present additional results not previously reported in our earlier works. First, we investigate the impact of chirping on the fundamental wave and the effect of manipulating the phase difference between the fundamental wave and the second-harmonic wave on the properties of generated terahertz pulses. We demonstrate that we can tune the time shape of terahertz pulses, causing them to reverse polarity or become bipolar by carefully selecting the correct combination of chirp and phase. Additionally, we introduce a novel technique for polarization characterization, termed terahertz unipolar polarimetry, which utilizes a weak probe beam and avoids the systematic errors associated with traditional methods. This technique is effective for detecting polarization-structured terahertz beams and the longitudinal component of focused terahertz beams. Our findings contribute to the improved control and characterization of terahertz radiation, enhancing its application in fields such as nonlinear optics, spectroscopy, and microscopy.

The production of cementitious formulations involves the addition of chemical additives essential for the optimization of many properties. Superplasticizers are considered additives of great interest but when mixed with concrete they lead to an undesirable increase of air content, with the consequent development of foam. This can adversely affect both mechanical properties and workability, therefore, the use of an antifoam agent is also necessary which should be able to prevent or destroy the foam. This work aims to synthesize esters derived from the reaction of glycine betaine with saturated and unsaturated fatty alcohols of different chain lengths. The reaction products were analyzed by 1 H NMR analysis, and the stability of antifoam agents in a superplasticizer solution was studied through foaming tests according to the Ross-Miles method. At the same time, their effectiveness in the cementitious systems was evaluated through flow Table tests. Finally, the effectiveness of the antifoam agents was quantified through an image analysis software, Image J , which allowed the investigation of the contents of the bubble in concrete samples. All synthesized antifoams showed properties superior to the commercial product, especially defoamers containing saturated fatty alcohols. It has been found that alcohols with too small or too long carbon chains were not effective. In particular, it was verified the optimal range of carbon atoms number contained in the antifoam chain which included between 12 and 14., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 Published by Elsevier Ltd.)

There is a growing interest in the search for metal-based therapeutics for protein misfolding disorders such as Alzheimer's disease (AD). A novel and largely unexplored class of metallodrugs is constituted by paddlewheel diruthenium complexes, which exhibit unusual water solubility and stability and unique coordination modes to proteins. Here, we investigate the ability of the complexes [Ru 2 Cl(DPhF)(O 2 CCH 3 ) 3 ]·H 2 O ( 1 ), [Ru 2 Cl(DPhF) 2 (O 2 CCH 3 ) 2 ]·H 2 O ( 2 ), and K 2 [Ru 2 (DPhF)(CO 3 ) 3 ]·3H 2 O ( 3 ) (DPhF - = N , N '-diphenylformamidinate) to interfere with the amyloid aggregation of the Aβ 1-42 peptide. These compounds differ in charge and steric hindrance due to the coordination of a different number of bulky ligands. The mechanisms of action of the three complexes were studied by employing a plethora of physicochemical and biophysical techniques as well as cellular assays. All these studies converge on different mechanisms of inhibition of amyloid fibrillation: complexes 1 and 2 show a clear inhibitory effect due to an exchange ligand process in the Ru 2 unit aided by aromatic interactions. Complex 3 shows no inhibition of aggregation, probably due to its negative charge in solution. This study demonstrates that slight variations in the ligands surrounding the bimetallic core can modulate the amyloid aggregation inhibition and supports the use of paddlewheel diruthenium complexes as promising therapeutics for Alzheimer's disease.

The reactivity of the anticancer drug picoplatin ( cis -amminedichlorido(2-methylpyridine)platinum(II) complex) with the model proteins hen egg white lysozyme (HEWL) and bovine pancreatic ribonuclease (RNase A) was investigated by electrospray ionisation mass spectrometry (ESI MS) and X-ray crystallography. The data were compared with those previously obtained for the adducts of these proteins with cisplatin, carboplatin and oxaliplatin under the same experimental conditions. ESI-MS data show binding of Pt to both proteins, with fragments retaining the 2-methylpyridine ligand and, possibly, a chloride ion. X-ray crystallography identifies different binding sites on the two proteins, highlighting a different behaviour of picoplatin in the absence or presence of dimethyl sulfoxide (DMSO). Metal-containing fragments bind to HEWL close to the side chains of His15, Asp18, Asp119 and both Lys1 and Glu7, whereas they bind to RNase A on the side chain of His12, Met29, His48, Asp53, Met79, His105 and His119. The data suggest that the presence of DMSO favours the loss of 2-methylpyridine and alters the ability of the Pt compound to bind to the two proteins. With both proteins, picoplatin appears to behave similarly to cisplatin and carboplatin when dissolved in DMSO, whereas it behaves more like oxaliplatin in the absence of the coordinating solvent. This study provides important insights into the pharmacological profile of picoplatin and supports the conclusion that coordinating solvents should not be used to evaluate the biological activities of Pt-based drugs.

As the demand for rare earth elements (REEs) continues to surge in diverse industrial and medical domains, the ecological consequences of their ubiquitous presence have garnered heightened attention. Among the REEs, gadolinium (Gd), commonly used in medical imaging contrast agents, has emerged as a pivotal concern due to its inadvertent introduction into marine ecosystems via wastewater release. This study delves into the complex ecotoxicological implications of Gd contamination, focusing on its impact on the embryonic development and sperm functionality of Mytilus galloprovincialis . The findings from this study underscore the potential hazards posed by this rare element, offering a critical perspective on the ecological risks associated with Gd. Notably, this exploratory work reveals that Gd exerts a significant embryotoxic effect at elevated concentrations, with an observed half maximal effective concentration (EC50) value of 0.026 mg/L. Additionally, Gd exposure leads to a considerable reduction in sperm motility and alters sperm morfo-kinetic parameters, especially at a concentration of 5.6 mg/L. The results highlight a dose-dependent relationship between Gd exposure and the prevalence of specific malformation types in Mytilus embryos, further providing crucial insights into the potential risks imposed by this rare earth element., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

SARS-CoV-2 can re-structure chromatin organization and alter the epigenomic landscape of the host genome, but the mechanisms that produce such changes remain unclear. Here, we use polymer physics to investigate how the chromatin of the host genome is re-organized upon infection with SARS-CoV-2. We show that re-structuring of A/B compartments can be explained by a re-modulation of intra-compartment homo-typic affinities, which leads to the weakening of A-A interactions and the enhancement of A-B mixing. At the TAD level, re-arrangements are physically described by a reduction in the loop extrusion activity coupled with an alteration of chromatin phase-separation properties, resulting in more intermingling between different TADs and a spread in space of the TADs themselves. In addition, the architecture of loci relevant to the antiviral interferon response, such as DDX58 or IFIT, becomes more variable within the 3D single-molecule population of the infected model, suggesting that viral infection leads to a loss of chromatin structural specificity. Analysing the time trajectories of pairwise gene-enhancer and higher-order contacts reveals that this variability derives from increased fluctuations in the chromatin dynamics of infected cells. This suggests that SARS-CoV-2 alters gene regulation by impacting the stability of the contact network in time., (© 2024. The Author(s).)

Many organic reactions are characterized by a complex mechanism with a variety of transition states and intermediates of different chemical natures. Their correct and accurate theoretical characterization critically depends on the accuracy of the computational method used. In this work, we study a complex ambimodal cycloaddition with five transition states, two intermediates, and three products, and we ask whether density functional theory (DFT) can provide a correct description of this type of complex and multifaceted reaction. Our work fills a gap in that most systematic benchmarks of DFT for chemical reactions have considered much simpler reactions. Our results show that many density functionals not only lead to seriously large errors but also differ from one another in predicting whether the reaction is ambimodal. Only a few of the available functionals provide a balanced description of the complex and multifaceted reactions. The parameters varied in the tested functionals are the ingredients, the treatment of medium-range and nonlocal correlation energy, and the inclusion of Hartree-Fock exchange. These results show a clear need for more benchmarks on the mechanisms of large molecules in complex reactions.

Coronaviruses are highly transmissible and pathogenic viruses for humans and animals. The vast quantity of information collected about SARS-CoV-2 during the pandemic helped to unveil details of the mechanisms behind the infection, which are still largely elusive. Recent research demonstrated that different class I/II human leukocyte antigen (HLA) alleles might define an individual susceptibility to SARS-CoV-2 spreading, contributing to the differences in the distribution of the infection through different populations; additional studies suggested that the homolog of the HLA in cats, the feline leukocyte antigen (FLA), plays a pivotal role in the transmission of viruses. With these premises, this study aimed to exploit a bioinformatic approach for the prediction of the transmissibility potential of two distinct feline coronaviruses (FCoVs) in domestic cats (feline enteric coronavirus (FeCV) and feline infectious peritonitis virus (FIPV)) using SARS-CoV-2 as the reference model. We performed an epitope mapping of nonapeptides deriving from SARS-CoV-2, FeCV, and FIPV glycoproteins and predicted their affinities for different alleles included in the three main loci in class I FLAs (E, H, and K). The predicted complexes with the most promising affinities were then subjected to molecular docking and molecular dynamics simulations to provide insights into the stability and binding energies in the cleft. Results showed the FLA proteins encoded by alleles in the FLA-I H (H*00501 and H*00401) and E (E*01001 and E*00701) loci are largely responsive to several epitopes deriving from replicase and spike proteins of the analyzed coronaviruses. The analysis of the most affine epitope sequences resulting from the prediction can stimulate the development of anti-FCoV immunomodulatory strategies based on peptide drugs.

The reaction of Pt-based anticancer agents with arsenic trioxide affords robust complexes known as arsenoplatins. The prototype of this family of anticancer compounds is arsenoplatin-1 (AP-1) that contains an As(OH) 2 fragment linked to a Pt(II) moiety derived from cisplatin. Crystallographic and spectrometric studies of AP-1 binding to a B-DNA double helix dodecamer are presented here, in comparison with cisplatin and transplatin. Results reveal that AP-1, cisplatin and transplatin react differently with the DNA model system. Notably, in the AP-1/DNA systems, the Pt-As bond can break down with time and As-containing fragments can be released. These results have implications for the understanding of the mechanism of action of arsenoplatins.

The combination of plasmonic nanoparticles and hydrogels results in nanocomposite materials with unprecedented properties that give rise to powerful platforms for optical biosensing. Herein, we propose a physicochemical characterization of plasmonic hydrogel nanocomposites made of polyethylene glycol diacrylate (PEGDA) hydrogels with increasing molecular weights (700-10000 Da) and gold nanoparticles (AuNPs, ∼60 nm). The swelling capability, mechanical properties, and thermal responses of the nanocomposites are analyzed and the combination with the resulting optical properties is elucidated. The different optomechanical properties of the proposed nanocomposites result in different transduction mechanisms, which can be exploited for several biosensing applications. A correlation between the polymer molecular weight, the effective refractive index of the material, and the optical response is found by combining experimental data and numerical simulations. In particular, the localized surface plasmon resonance (LSPR) position of the AuNPs was found to follow a parabolic profile as a function of the monomer molecular weight (MW), while its absorbance intensity was found as inversely proportional to the monomer MW. Low MW PEGDA nanocomposites were found to be responsive to refractive index variations for small molecule sensing. Differently, high MW PEGDA nanocomposites exhibited absorbance intensity increase/decrease as a function of the hydrophobicity/hydrophilicity of the targeted small molecule. The proposed optomechanical model paves the way to the design of innovative platforms for real-life applications, such as wearable sensing, point-of-care testing, and food monitoring via smart packaging devices., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

The oceans cover over 70% of our planet, hosting a biodiversity of tremendous wealth. Sponges are one of the major ecosystem engineers on the seafloor, providing a habitat for a wide variety of species to be considered a good source of bioactive compounds. In this study, a metataxonomic approach was employed to describe the bacterial communities of the sponges collected from Faro Lake (Sicily) and Porto Paone (Gulf of Naples). Morphological analysis and amplification of the conserved molecular markers, including 18S and 28S (RNA ribosomal genes), CO1 (mitochondrial cytochrome oxidase subunit 1), and ITS (internal transcribed spacer), allowed the identification of four sponges. Metataxonomic analysis of sponges revealed a large number of amplicon sequence variants (ASVs) belonging to the phyla Proteobacteria, Cloroflexi, Dadabacteria, and Poribacteria. In particular, Myxilla ( Myxilla ) rosacea and Clathria ( Clathria ) toxivaria displayed several classes such as Alphaproteobacteria, Dehalococcoidia, Gammaproteobacteria, Cyanobacteria, and Bacteroidia. On the other hand, the sponges Ircinia oros and Cacospongia mollior hosted bacteria belonging to the classes Dadabacteriia, Anaerolineae, Acidimicrobiia, Nitrospiria, and Poribacteria. Moreover, for the first time, the presence of Rhizobiaceae bacteria was revealed in the sponge M . ( Myxilla ) rosacea , which was mainly associated with soil and plants and involved in biological nitrogen fixation., Competing Interests: MS and SR were employed by Bio-Fab Research Srl. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Esposito, Federico, Sonnessa, Reddel, Bertolino, Ruocco, Zagami, Giovine, Pozzolini, Guida, Zupo and Costantini.)

Photo-induced isomerization of azobenzene molecules drives mass migrations in azopolymer samples. The resulting macroscopic directional photo-deformation of the material morphology has found many applications in literature, although the fundamental mechanisms behind this mass transfer are still under debate. Hence, it is of paramount importance to find quantitative observables that could drive the community toward a better understanding of this phenomenon. In this regard, azopolymer mechanical properties have been intensively studied, but the lack of a nanoscale technique capable of quantitative viscoelastic measurements has delayed the progress in the field. Here, we use bimodal atomic force microscopy (AFM) as a powerful technique for nanomechanical characterizations of azopolymers. With this multifrequency AFM approach, we map the azopolymer local elasticity and viscosity, with high resolution, after irradiation. We find that, while in the (previously) illuminated region, a general photo-softening is measured; locally, the Young modulus and the viscosity depend upon the inner structuring of the illuminating light spot. We then propose a possible interpretation based on a light-induced expansion plus a local alignment of the polymer chains (directional hole-burning effect), which explains the experimental observations. The possibility to access, in a reliable and quantitative way, both Young modulus and viscosity could trigger new theoretical-numerical investigations on the azopolymer mass migration dynamics since, as we show, both parameters can be considered measurable. Furthermore, our results provide a route for engineering the nanomechanical properties of azopolymers, which could find interesting applications in cell mechanobiology research., Competing Interests: Conflict of interest: Authors state no conflicts of interest., (© 2023 the author(s), published by De Gruyter, Berlin/Boston.)

Protein fibrillation is commonly associated with pathologic amyloidosis. However, under appropriate conditions several proteins form fibrillar structures in vitro that can be used for biotechnological applications. MNEI and its variants, firstly designed as single chain derivatives of the sweet protein monellin, are also useful models for protein fibrillary aggregation studies. In this work, we have drawn attention to a protein dubbed Mut9, already characterized as a "super stable" MNEI variant. Comparative analysis of the respective X-ray structures revealed how the substitutions present in Mut9 eliminate several unfavorable interactions and stabilize the global structure. Molecular dynamic predictions confirmed the presence of a hydrogen-bonds network in Mut9 which increases its stability, especially at neutral pH. Thioflavin-T (ThT) binding assays and Fourier transform infrared (FTIR) spectroscopy indicated that the aggregation process occurs both at acidic and neutral pH, with and without addition of NaCl, even if with a different kinetics. Accordingly, Transmission Electron Microscopy (TEM) showed a fibrillar organization of the aggregates in all the tested conditions, albeit with some differences in the quantity and in the morphology of the fibrils. Our data underline the great potential of Mut9, which combines great stability in solution with the versatile conversion into nanostructured biomaterials., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Paddlewheel diruthenium complexes are being used as metal-based drugs. It has been proposed that their charge and steric properties determine their selectivity towards proteins. Here, we explore these parameters using the first water-soluble diruthenium complex bearing two formamidinate ligands, [Ru 2 Cl(DPhF) 2 (O 2 CCH 3 ) 2 ], and two derivatives, [Ru 2 Cl(DPhF)(O 2 CCH 3 ) 3 ] and K 2 [Ru 2 (DPhF)(CO 3 ) 3 ] (DPhF -  = N,N'-diphenylformamidinate), with one formamidinate. Their protein binding properties have been assessed employing hen egg white lysozyme (HEWL). The results confirm the relationship between the type of interaction (coordinate/non-coordinate bonds) and the charge of diruthenium complexes. The crystallization medium is also a key factor. In all cases, diruthenium species maintain the M-M bond and produce stable adducts. The antiproliferative properties of these diruthenium complexes have been evaluated on an eukaryotic cell-based model. Our data show a correlation between the number of the formamidinate ligands and the anticancer activity of the diruthenium derivatives against human epithelial carcinoma cells. Increased cytotoxicity may be related to increased steric hindrance and Ru 2 5+ core electronic density. However, the effect of increasing the lipophilicity of diruthenium species by introducing a second N,N'-diphenylformamidinate must be also considered. This work illustrates a systematic approach to shed light on the relevant properties of diruthenium compounds to design metal-based metallodrugs and diruthenium metalloenzymes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

High-resolution crystal structures of lysozyme in the presence of the potential drug V IV O(acetylacetonato) 2 under two different experimental conditions have been solved. The crystallographic study reveals the loss of the ligands, the oxidation of V IV to V V and the subsequent formation of adducts of the protein with two different polyoxidovanadates: [V 4 O 12 ] 4- , which interacts with lysozyme non-covalently, and the unprecedented [V 20 O 54 (NO 3 )] n- , which is covalenty bound to the side chain of an aspartate residue of symmetry related molecules., (© 2023 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Calcium (Ca) represents about 40% of the total mineral mass, mainly in the bone, providing mechanical strength to the skeleton and teeth. An adequate Ca intake is necessary for bone growth and development in children and adolescents and for maintaining bone mineral loss in elderly age. Ca deficiency predisposes to osteopenia and osteoporosis. Healthy nutrition, including an adequate intake of Ca-rich food, is paramount to prevent and cure osteoporosis. Recently, several clinical studies have demonstrated that, in conditions of Ca dysmetabolism, Ca-rich mineral water is beneficial as a valuable source of Ca to be used as an alternative to caloric Ca-rich dairy products. Although promising, these data have been collected from small groups of participants. Moreover, they mainly regard the effect of Ca-rich mineral water on bone metabolism. In contrast, an investigation of the effect of Ca supplementation on systemic metabolism is needed to address the spreading of systemic metabolic dysfunction often associated with Ca dysmetabolism. In the present study, we analyzed urine and blood sera of 120 women in perimenopausal condition who were subjected for six months to 2l daily consumption of bicarbonate-calcium mineral water marketed under ® Lete. Remarkably, this water, in addition to being rich in calcium and bicarbonate, is also low in sodium. A complete set of laboratory tests was carried out to investigate whether the specific water composition was such to confirm the known therapeutic effects on bone metabolism. Second, but not least, urine and blood sera were analyzed using NMR-based metabolomic procedures to investigate, other than the action on Ca metabolism, potential system-wide metabolic effects. Our data show that Lete water is a valid supplement for compensating for Ca dysmetabolism and preserving bone health and integrity.

Platinum complexes are ubiquitous in chemistry and largely used as catalysts or as precursors in drug chemistry, thus a deep knowledge of their electronic properties may help in planning new synthetic strategies or exploring new potential applications. Herein, the electronic structure of many octahedral platinum complexes is drastically revised especially when they feature electronegative elements such as halogens and chalcogens. The investigation revealed that in most cases the five d platinum orbitals are invariably full, thus the empty antibonding orbitals, usually localized on the metal, are mainly centered on the ligands, suggesting a questionable assignment of formal oxidation state IV. The analysis supports the occurrence of the inverted ligand field theory in all cases with the only exceptions of the Pt-F and Pt-O bonding. The trends for the molecular complexes are mirrored also by the density of states plots of extended structures featuring octahedral platinum moieties in association with chalcogens atoms. Finally, the oxidative addition of a Se-Cl linkage to a square platinum complex to achieve an octahedral moiety has been revised in the framework of the inverted ligand field., (© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Polycyclic aromatic hydrocarbons (PAHs) are widespread across the globe and can be highly toxic for the marine environment. This research investigated the short-term (48 h of exposure) effects of PAHs mixtures on the nauplii and adult of crustacean Artemia franciscana considering the impact in term of toxicity and changes in gene expression. Results showed that all combinations caused additive or synergic effects with the exception of naphthalene + phenanthrene (NAP + PHE; Combination Index (CI) = 22.3), while naphthalene + benzo(k)fluoranthene (NAP + BkF; CI = 7.8) mixture evidenced an antagonistic effect. Real-time qPCR showed that all mixtures impacted the expression level of the five known genes involved in Artemia stress response. The effects of PAHs at environmental concentrations on both adult and nauplii suggested the need for further investigations about the impact of such contaminants on the marine biota considering that crustaceans can accumulate PAHs at concentrations comparable to those assessed in the present study., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

N-oleoylglycine (OlGly), a lipid derived from the basic component of olive oil, oleic acid, and N-oleoylalanine (OlAla) are endocannabinoid-like mediators. We report that OlGly and OlAla, by activating the peroxisome proliferator-activated receptor alpha (PPARα), reduce the rewarding properties of a highly palatable food, dopamine neuron firing in the ventral tegmental area, and the obesogenic effect of a high-fat diet rich in lard (HFD-L). An isocaloric olive oil HFD (HFD-O) reduced body weight gain compared to the HFD-L, in a manner reversed by PPARα antagonism, and enhanced brain and intestinal OlGly levels and gut microbial diversity. OlGly or OlAla treatment of HFD-L mice resulted in gut microbiota taxonomic changes partly similar to those induced by HFD-O. We suggest that OlGly and OlAla control body weight by counteracting highly palatable food overconsumption, and possibly rebalancing the gut microbiota, and provide a potential new mechanism of action for the obeso-preventive effects of olive oil-rich diets., (© 2023. Springer Nature Limited.)

For many years, there has been a debate on the polluting loads affecting the Gulf of Naples, one of Italy's most spectacular and iconic landscape. The wide territory bordering the Gulf includes the Sarno river basin (SRB) managed by the Southern Apennines River Basin District Authority in the framework of Unit of Management Sarno (UoM-Sarno). The paper investigated the anthropogenic pressures and their spatial distribution in the UoM-Sarno, revealing as SRB represents a hotspot of pollution mainly due to the high population density and widespread hydro-demanding activities which are responsible of high organic and eutrophication loads. The pollution sources, variably distributed on the area, and potentially conveyed to the wastewater treatment plants (WWTPs) located into SRB, were estimated considering the WWTPs treatment capacity as well. Results revealed a holistic picture of UoM-Sarno area allowing to establish the priorities of the interventions aimed at safeguarding the coastal marine resources. In particular, 2590 tons BOD/year were directly discharged into the Gulf of Naples due to the missing of sewers, and other 10,600 tons BOD/year are potentially discharged in the Sarno river reaching the sea, considering the contribution of population, industrial activity, and livestock., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

This paper presents a detailed review of the use of 87 Sr/ 86 Sr isotope systematics for wine provenance studies. The method is based on the principle that the Sr isotope ratio in wine reflects that of the labile fraction of the vineyard soil from which the wine is produced. The review encompasses 87 Sr/ 86 Sr data from wine samples published between 1993 and 2021 from terroirs in 22 different countries. The analytical procedures and techniques adopted by the different authors and the range of isotope ratios obtained in the different studies are discussed and evaluated. This study provides a bibliometric analysis of the 87 Sr/ 86 Sr isotope approach for wine authentication at different scales. Although limitations are evident when implemented at large (global) scales, we demonstrate that the 87 Sr/ 86 Sr isotope tracing technique remains a powerful and reliable tool for determining the geographical origin of wine when combined with detailed knowledge of the geological and soil characteristics of the substrata. For example, this combination of data allows the wines grown in the volcanic soils of Central and Southern Italy to be unambiguously fingerprinted. We present a detailed protocol for the application of the Sr isotope technique to wine authentication.

The coagulation process relies on an intricate network of three-dimensional structural interactions and subtle biological regulations. In the present review, we illustrate the state of the art of the structural biology of the coagulation cascade by surveying the Protein Data Bank and the EBI AlphaFold databases. Investigations performed in the last decade have provided structural information on essentially all players involved in the process. Indeed, the initial characterization of specific and rather canonical domains has been progressively extended to complicated multidomain proteins. Recently, the application of cryogenic electron microscopy techniques has unraveled the structural features of highly complex coagulation factors, which has led to enhanced understanding. This review initially focuses on the structure of the individual factors as a function of their involvement in intrinsic, extrinsic, and common pathways. A specific emphasis is given to what is known or unknown on the structural basis of each step of the cascade. Available data providing clues on the structural recognition of the factors involved in the functional partnerships of the pathways are illustrated. Recent structures of important complexes formed by these proteins with regulators are described, focusing on the drugs used as anticoagulants and on their reversal agents. Finally, we highlight the different roles that innovative biomolecules such as aptamers may have in the regulation of the cascade., (© 2023 The Author(s).)

Aerobic organisms use molecular oxygen in several reactions, including those in which the oxidation of substrate molecules is coupled to oxygen reduction to produce large amounts of metabolic energy. The utilization of oxygen is associated with the production of ROS, which can damage biological macromolecules but also act as signaling molecules, regulating numerous cellular processes. Mitochondria are the cellular sites where most of the metabolic energy is produced and perform numerous physiological functions by acting as regulatory hubs of cellular metabolism. They retain the remnants of their bacterial ancestors, including an independent genome that encodes part of their protein equipment; they have an accurate quality control system; and control of cellular functions also depends on communication with the nucleus. During aging, mitochondria can undergo dysfunctions, some of which are mediated by ROS. In this review, after a description of how aging affects the mitochondrial quality and quality control system and the involvement of mitochondria in inflammation, we report information on how vitamin E, the main fat-soluble antioxidant, can protect mitochondria from age-related changes. The information in this regard is scarce and limited to some tissues and some aspects of mitochondrial alterations in aging. Improving knowledge of the effects of vitamin E on aging is essential to defining an optimal strategy for healthy aging.

The correct assessment of body composition is essential for an accurate diagnostic evaluation of nutritional status. The body mass index (BMI) is the most widely adopted indicator for evaluating undernutrition, overweight, and obesity, but it is unsuitable for differentiating changes in body composition. In recent times, bioelectrical impedance analyses (BIA) have been proven as a more accurate procedure for the assessment of body composition. Furthermore, the efficiency of bioelectrical impedance vector analyses, as an indicator of nutritional status and hydration, has been demonstrated. By applying a bioimpedance analysis, it is possible to detect fat mass (FM), fat free mass (FFM), phase angle, and body cell mass (BCM). It is important to point out that phase angle and BCM are strongly associated with health status. The aim of this research was to examine body composition and the association between the phase angle and BCM in 87 subjects (14 males and 73 females), aged between 23 and 54 years, with BMIs ranging from 17.0 to 32.0 kg/m 2 , according to sex. The BMI results revealed that the majority of the assessed subjects were within the normal range and had a normal percentage of FM. Our data indicate that a direct relation exists between phase angle and cellular health and that these values increase almost linearly. Consequently, a high phase angle may be related to increased BCM values.

Theoretical characterization of reactions of complex molecules depends on providing consistent accuracy for the relative energies of intermediates and transition states. Here we employ the DLPNO-CCSD(T) method with core-valence correlation, large basis sets, and extrapolation to the CBS limit to provide benchmark values for Diels-Alder transition states leading to competitive strained pentacyclic adducts. We then used those benchmarks to test a diverse set of wave function and density functional methods for the absolute and relative barrier heights of these transition states. Our results show that only a few of the tested density functionals can predict the absolute barrier heights satisfactorily, although relative barrier heights are more accurate. The most accurate functionals tested are ωB97M-V, M11plus, ωB97X-V, PBE-D3(0), M11, and MN15 with MUDs from best estimates less than 3.0 kcal. These findings can guide selection of density functionals for future studies of crowded, strained transition states of large molecules.

Environmental pollution, particularly in the marine environment, has become a significant concern due to the increasing presence of pollutants and their adverse effects on ecosystems and human health. This study focuses on the bioaccumulation of trace elements in the muscle tissue of the blackmouth catshark ( Galeus melastomus ) from different areas in the Mediterranean Sea. Trace elements are of interest due to their persistence, toxicity, and potential for bioaccumulation. This research aims to assess the distribution and accumulation of trace elements in the muscle tissue of G. melastomus and investigate their potential impact on the deep-sea environment of the Mediterranean. The focused areas include the Ligurian Sea, the northern and central Tyrrhenian Sea, the southern Tyrrhenian Sea, the Ionian Sea, the Pantelleria Waters, and the Gela Waters. Samples were collected following established protocols, and trace element analysis was conducted using inductively coupled plasma mass spectrometry. The study provides data on the concentrations of 17 trace elements, namely aluminum, arsenic, cadmium, cobalt, copper, manganese, molybdenum, nickel, zinc, selenium, strontium, lead, chromium, iron, barium, bismuth, and uranium. The findings contribute to a better understanding of trace element bioaccumulation patterns in elasmobranch species, specifically G. melastomus , and highlight the potential risks associated with chemical contamination in the Mediterranean Sea. This research emphasizes the importance of studying the impacts of pollutants on marine organisms, particularly those occupying key ecological roles, like sharks, to support effective conservation and management strategies.

Technology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of genome architecture mapping (GAM), a ligation-free technique that maps chromatin contacts genome-wide. We perform a detailed comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. When examining the strongest contacts detected by either method, we find that only one-third of these are shared. The strongest contacts specifically found in GAM often involve 'active' regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain 'inactive' regions. Our work shows that active genomic regions are involved in extensive complex contacts that are currently underestimated in ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies., (© 2023. The Author(s).)

Orchids depend on mycorrhizal fungi to germinate from seed. While multiple orchid mycorrhizal (OrM) taxa are often found associated with adult orchids, the relative contribution of particular OrM taxa to germination and early orchid development is poorly understood. We isolated 28 OrM fungi associated with the Mediterranean orchid Anacamptis papilionacea and tested the efficiency of five isolates on germination and early development, four belonging to the Tulasnella calospora species complex and one belonging to Ceratobasidium. Co-cultures of varying two-way and three-way combinations of OrM isolates were used in vitro to compare the simultaneous effect on seed germination rate with monocultures. We then tested whether, when given initial priority over other fungi, particular OrM taxa were more effective during the early stages of development. Seedlings germinated with different isolates were transferred to a growth chamber, and either the same or different isolate was added 45 days later. After 3 months, the number of roots, length of the longest root, and tuber area were measured. All OrM fungi resulted in seed germination; however, lower germination rates were associated with the Ceratobasidium isolate compared to the tulasnelloid isolates. There was significant decreased germination in co-culture experiments when the Ceratobasidium isolate was added. Despite being associated with reduced germination rates, the addition of the Ceratobasidium isolate to the seedlings germinated with tulasnelloid strains resulted in significant increased tuber size. Although A. papilionacea associates with many OrM taxa, these results show that OrM fungi may play different roles during orchid germination and early development. Even when given initial priority, other fungi may colonize developing orchids and interact to influence early orchid development., (© 2023. The Author(s).)

In the last decades, the interest in bioactive compounds derived from natural sources including bacteria, fungi, plants, and algae has significantly increased. It is well-known that aquatic or terrestrial organisms can produce, in special conditions, secondary metabolites with a wide range of biological properties, such as anticancer, antioxidant, anti-inflammatory, and antimicrobial activities. In this study, we focused on the extremophilic microalga Galdieria sulphuraria as a possible producer of bioactive compounds with antiviral activity. The algal culture was subjected to organic extraction with acetone. The cytotoxicity effect of the extract was evaluated by the 2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. The antiviral activity was assessed through a plaque assay against herpesviruses and coronaviruses as enveloped viruses and poliovirus as a naked one. The monolayer was treated with different concentrations of extract, ranging from 1 µg/mL to 200 µg/mL, and infected with viruses. The algal extract displayed strong antiviral activity at non-toxic concentrations against all tested enveloped viruses, in particular in the virus pre-treatment against HSV-2 and HCoV-229E, with IC 50 values of 1.7 µg/mL and IC 90 of 1.8 µg/mL, respectively. However, no activity against the non-enveloped poliovirus has been detected. The inhibitory effect of the algal extract was confirmed by the quantitative RT-PCR of viral genes. Preliminary chemical profiling of the extract was performed using ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS), revealing the enrichment in primary fatty acid amides (PFAA), such as oleamide, palmitamide, and pheophorbide A. These promising results pave the way for the further purification of the mixture to explore its potential role as an antiviral agent.