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The studies showed that protease activated receptor 2 (PAR-2) expression is enhanced in human coronary atherosclerotic lesions from humans with no classic risk factors for atherosclerosis. The pharmacological study establishes whether modulation of PAR-2 represents a possible therapeutic target for controlling the vascular response injury.

Main Conclusion: In the early diverging angiosperm Trithuria submersa TsAG1 and TsAG2 are expressed in different flower organs, including bracts, while TsAG3 is more ovule-specific, probably functioning as a D-type gene. Species of Trithuria, the only genus of the family Hydatellaceae, represent ideal candidates to explore the biology and flower evolution of early diverging angiosperms. The life cycle of T. submersa is generally known, and the "reproductive units" are morphologically well described, but the availability of genetic and developmental data of T. submersa is still scarce. To fill this gap, a transcriptome analysis of the reproductive structures was performed and presented in this work. This analysis provided sequences of MADS-box transcription factors, a gene family known to be involved in flower and fruit development. In situ hybridization experiments on floral buds were performed to describe the spatiotemporal expression patterns of the AGAMOUS genes, revealing the existence of three AG genes with different expression domains in flower organs and in developing ovules. Trithuria may offer important clues to the evolution of reproductive function among early angiosperms and Nymphaeales in particular, and this study aims to broaden relevant knowledge regarding key genes of reproductive development in non-model angiosperms, shaping first flower appearance and evolution., (© 2024. The Author(s).)

In gymnosperms such as Ginkgo biloba, the arrival of pollen plays a key role in ovule development, before fertilization occurs. Accordingly, G. biloba female plants geographically isolated from male plants abort all their ovules after the pollination drop emission, which is the event that allows the ovule to capture pollen grains. To decipher the mechanism induced by pollination required to avoid ovule senescence and then abortion, we compared the transcriptomes of pollinated and unpollinated ovules at three time points after the end of the emission of pollination drop. Transcriptomic and in situ expression analyses revealed that several key genes involved in programmed cell death such as senescence and apoptosis, DNA replication, and cell cycle regulation were differentially expressed in unpollinated ovules compared to pollinated ovules. We provide evidence that the pollen captured by the pollination drop affects auxin local accumulation and might cause deregulation of key genes required for the ovule's programmed cell death, activating both the cell cycle regulation and DNA replication genes., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

The uptake and translocation of four polybrominated diphenyl ethers (PBDEs) and four novel brominated flame retardants (NBFRs) in tomato plants (Solanum lycopersicum L.) were investigated via the RHIZOtest, a standard soil-based biotest, optimized for organic compounds. Tomato plants were exposed to soil samples spiked with 0 (i.e. control), 5.00 or 50.00 ng g -1 dw of each compound. Compared of those of the control, exposure to increasing spiking concentrations resulted in average reductions of 13% and 26% (w/w) in tomato plant biomass. Higher concentrations of NBFRs were analyzed both in roots, ranging from 0.23 to 8.01 ng g -1 dw for PBDEs and from 1.25 to 18.51 ng g -1 dw for NBFRs, and in shoots, ranging from 0.09 to 5.58 ng g -1 dw and from 0.47 to 7.78 ng g -1 dw for PBDEs and NBFRs, respectively. This corresponded to an average soil uptake of 5% for PBDEs and 9% for NBFRs at the lower soil-spiking level, and 3% for PBDEs and 6% for NBFRs at the higher soil spiking level. Consequently, among both initial spiking levels, the soil-root concentration factor (RCF) values were lower on average for PBDEs (0.13 ± 0.05 g dw soil g -1 dw roots) than for NBFRs (0.33 ± 0.16 g dw soil g -1 dw roots). Conversely, nondifferent values of the root-shoot transfer factor (TF) were calculated for both PBDEs (0.54 ± 0.13 g dw roots g -1 dw shoots) and NBFRs (0.49 ± 0.24 g dw roots g -1 dw shoots). The differences and similarities reported in the RCF and TF between and within the two groups of compounds can be explained by their properties. The calculated RCF and TF values of the PBDEs exhibited a decreasing trend as the number of bromine atoms increased. Additionally, a robust negative linear correlation was observed between RCF values and the respective logK ow values for the PBDEs, at both soil-spiking levels. The root uptake of NBFRs exhibited a negative correlation with their hydrophobicity; however, this was not observed in the context of root-to-shoot transfer. The presence of a second aromatic ring appears to be the key factor influencing the observed variations in NBFRs, with biphenyl NBFRs (BTBPE and DBDPE) characterized by lower uptake and reduced translocation potential than monophenyl PBEB and HBB. Understanding the transfer of these compounds to crops, especially near plastic recycling waste sites, is crucial for understanding the risks of their potential inclusion in the human food chain., 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 Ltd.. All rights reserved.)

Background: Glenoid bone loss (GBL) calculation in patients with shoulder instability has a wide variability in methods and their reliability. The purpose of this study was to describe and validate a new semi-automated software developed to improve GBL calculation using a 3D imaging modeling (IODA-shoulder) and to compare the method to the PICO area method., Patients and Methods: A semi-automated software to assess GBL was preliminarily developed and validated on 7 fresh frozen specimens (scapulae with artificially created glenoid defect), using water displacement method. Afterwards, the software was retrospectively used on CT images of 20 patients affected by recurrent shoulder dislocation. Inclusion criteria were: unilateral dislocation, minimum 2 dislocation episodes. Exclusion criteria were bone reconstruction of the glenoid, failed shoulder stabilization, bilateral dislocation, shoulder arthritis. Three-dimensional computed tomography images of bilateral shoulder were retrieved for each patient. Two methods to determine GBL were compared. The PICO surface area method and the new IODA method. We assessed the intra- and inter-rater reliability of the two methods with the Intraclass Correlation Coefficient (ICC), the Bland-Alman analysis, and Lin's concordance correlation coefficient (CCC)., Results: We did not find a statistically significant difference between the mean volumes calculated with PICO and IODA methods, respectively 914 vs. 815 mm 3 , p=0.155. The analysis carried out by using the traditional PICO method showed a lower concordance rate among four observers than the higher concordance found using IODA method, regardless of the size and the location of the defect. The ICC agreement with PICO was significantly lower than with IODA (0.76 vs. 0.97). We found a poor CCC with PICO (from 0.65 to 0.81) and a substantial one with IODA (from 0.96 to 0.98)., Discussion: The intra- and inter-rater reliability using IODA method is significantly better than PICO method. The assessment of GBL using IODA method is time saving, avoiding significant inter- and intra-observer variation, mainly due to individual skill and experience in the method., Level of Evidence: IV, experimental study., (Copyright © 2023 Elsevier Masson SAS. All rights reserved.)

Premise: In Arabidopsis thaliana, the role of the most important key genes that regulate ovule development is widely known. In nonmodel species, and especially in gymnosperms, the ovule developmental processes are still quite obscure. In this study, we describe the putative roles of Ginkgo biloba orthologs of regulatory genes during ovule development. Specifically, we studied AGAMOUS (AG), AGAMOUS-like 6 (AGL6), AINTEGUMENTA (ANT), BELL1 (BEL1), Class III HD-Zip, and YABBY Ginkgo genes., Methods: We analyzed their expression domains through in situ hybridizations on two stages of ovule development: the very early stage that corresponds to the ovule primordium, still within wintering buds, and the late stage at pollination time., Results: GBM5 (Ginkgo ortholog of AG), GbMADS8 (ortholog of AGL6) and GbC3HDZ1-2-3 were expressed in both the stages of ovule development, while GbMADS1, GbAGL6-like genes (orthologs of AGL6), GbBEL1-2 and YABBY Ginkgo orthologs (GbiYAB1B and GbiYABC) seem mostly involved at pollination time. GbANTL1 was not expressed in the studied stages and was different from GbANTL2 and GbBEL1, which seem to be involved at both stages of ovule development. In Ginkgo, the investigated genes display patterns of expression only partially comparable to those of other studied seed plants., Conclusions: The expression of most of these regulatory genes in the female gametophyte region at pollination time leads to suggest a communication between the sporophytic maternal tissue and the developing female gametophyte, as demonstrated for well-studied model angiosperms., (© 2022 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

Generally, in gymnosperms, pollination and fertilization events are temporally separated and the developmental processes leading the switch from ovule integument into seed coat are still unknown. The single ovule integument of Ginkgo biloba acquires the typical characteristics of the seed coat long before the fertilization event. In this study, we investigated whether pollination triggers the transformation of the ovule integument into the seed coat. Transcriptomics and metabolomics analyses performed on ovules just prior and after pollination lead to the identification of changes occurring in Ginkgo ovules during this specific time. A morphological atlas describing the developmental stages of ovule development is presented. The metabolic pathways involved in the lignin biosynthesis and in the production of fatty acids are activated upon pollination, suggesting that the ovule integument starts its differentiation into a seed coat before the fertilization. Omics analyses allowed an accurate description of the main changes that occur in Ginkgo ovules during the pollination time frame, suggesting the crucial role of the pollen arrival on the progression of ovule development., (© 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation.)

Nymphaeaceae are early diverging angiosperms with large flowers characterized by showy petals and stamens not clearly whorled but presenting a gradual morphological transition from the outer elements to the inner stamens. Such flower structure makes these plant species relevant for studying flower evolution. MADS-domain transcription factors are crucial components of the molecular network that controls flower development. We therefore isolated and characterized MADS-box genes from the water lily Nymphaea caerulea . RNA-seq experiments on floral buds have been performed to obtain the transcript sequences of floral organ identity MADS-box genes. Maximum Likelihood phylogenetic analyses confirmed their belonging to specific MADS-box gene subfamilies. Their expression was quantified by RT-qPCR in all floral organs at two stages of development. Protein interactions among these transcription factors were investigated by yeast-two-hybrid assays. We found especially interesting the involvement of two different AGAMOUS-like genes ( NycAG1 and NycAG2 ) in the water lily floral components. They were therefore functionally characterized by complementing Arabidopsis ag and shp1 shp2 mutants. The expression analysis of MADS-box genes across flower development in N. caerulea described a complex scenario made of numerous genes in numerous floral components. Their expression profiles in some cases were in line with what was expected from the ABC model of flower development and its extensions, while in other cases presented new and interesting gene expression patterns, as for instance the involvement of NycAGL6 and NycFL . Although sharing a high level of sequence similarity, the two AGAMOUS-like genes NycAG1 and NycAG2 could have undergone subfunctionalization or neofunctionalization, as only one of them could partially restore the euAG function in Arabidopsis ag-3 mutants. The hereby illustrated N. caerulea MADS-box gene expression pattern might mirror the morphological transition from the outer to the inner floral organs, and the presence of transition organs such as the petaloid stamens. This study is intended to broaden knowledge on the role and evolution of floral organ identity genes and the genetic mechanisms causing biodiversity in angiosperm flowers., Competing Interests: The 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., (Copyright © 2021 Moschin, Nigris, Ezquer, Masiero, Cagnin, Cortese, Colombo, Casadoro and Baldan.)

In order to investigate how high school students and researchers perceive science-related (STEM) subjects, we introduce forma mentis networks. This framework models how people conceptually structure their stance, mindset or forma mentis toward a given topic. In this study, we build forma mentis networks revolving around STEM and based on psycholinguistic data, namely free associations of STEM concepts (i.e., which words are elicited first and associated by students/researchers reading "science"?) and their valence ratings concepts (i.e., is "science" perceived as positive, negative or neutral by students/researchers?). We construct separate networks for (Ns = 159) Italian high school students and (Nr = 59) interdisciplinary professionals and researchers in order to investigate how these groups differ in their conceptual knowledge and emotional perception of STEM. Our analysis of forma mentis networks at various scales indicate that, like researchers, students perceived "science" as a strongly positive entity. However, differently from researchers, students identified STEM subjects like "physics" and "mathematics" as negative and associated them with other negative STEM-related concepts. We call this surrounding of negative associations a negative emotional aura. Cross-validation with external datasets indicated that the negative emotional auras of physics, maths and statistics in the students' forma mentis network related to science anxiety. Furthermore, considering the semantic associates of "mathematics" and "physics" revealed that negative auras may originate from a bleak, dry perception of the technical methodology and mnemonic tools taught in these subjects (e.g., calculus rules). Overall, our results underline the crucial importance of emphasizing nontechnical and applied aspects of STEM disciplines, beyond purely methodological teaching. The quantitative insights achieved through forma mentis networks highlight the necessity of establishing novel pedagogic and interdisciplinary links between science, its real-world complexity, and creativity in science learning in order to enhance the impact of STEM education, learning and outreach activities., Competing Interests: Commercial affiliation with Complex Science Consulting does not alter the authors’ adherence to PLOS ONE policies on sharing data and materials. All the authors declare no competing financial, non-financial, professional or personal competing interests.

Background: Bacillus licheniformis GL174 is a culturable endophytic strain isolated from Vitis vinifera cultivar Glera, the grapevine mainly cultivated for the Prosecco wine production. This strain was previously demonstrated to possess some specific plant growth promoting traits but its endophytic attitude and its role in biocontrol was only partially explored. In this study, the potential biocontrol action of the strain was investigated in vitro and in vivo and, by genome sequence analyses, putative functions involved in biocontrol and plant-bacteria interaction were assessed., Results: Firstly, to confirm the endophytic behavior of the strain, its ability to colonize grapevine tissues was demonstrated and its biocontrol properties were analyzed. Antagonism test results showed that the strain could reduce and inhibit the mycelium growth of diverse plant pathogens in vitro and in vivo. The strain was demonstrated to produce different molecules of the lipopeptide class; moreover, its genome was sequenced, and analysis of the sequences revealed the presence of many protein-coding genes involved in the biocontrol process, such as transporters, plant-cell lytic enzymes, siderophores and other secondary metabolites., Conclusions: This step-by-step analysis shows that Bacillus licheniformis GL174 may be a good biocontrol agent candidate, and describes some distinguished traits and possible key elements involved in this process. The use of this strain could potentially help grapevine plants to cope with pathogen attacks and reduce the amount of chemicals used in the vineyard.

Trichoderma filamentous fungi are increasingly used as biocontrol agents and plant biostimulants. Growing evidence indicates that part of the beneficial effects is mediated by the activity of fungal metabolites on the plant host. We have investigated the mechanism of plant perception of HYTLO1, a hydrophobin abundantly secreted by Trichoderma longibrachiatum , which may play an important role in the early stages of the plant-fungus interaction. Aequorin-expressing Lotus japonicus suspension cell cultures responded to HYTLO1 with a rapid cytosolic Ca 2+ increase that dissipated within 30 min, followed by the activation of the defence-related genes MPK3 , WRK33 , and CP450 . The Ca 2+ -dependence of these gene expression was demonstrated by using the extracellular Ca 2+ chelator EGTA and Ned-19, a potent inhibitor of the nicotinic acid adenine dinucleotide phosphate (NAADP) receptor in animal cells, which effectively blocked the HYTLO1-induced Ca 2+ elevation. Immunocytochemical analyses showed the localization of the fungal hydrophobin at the plant cell surface, where it forms a protein film covering the plant cell wall. Our data demonstrate the Ca 2+ -mediated perception by plant cells of a key metabolite secreted by a biocontrol fungus, and provide the first evidence of the involvement of NAADP-gated Ca 2+ release in a signalling pathway triggered by a biotic stimulus.

There is recent evidence that the XY spin model on complex networks can display three different macroscopic states in response to the topology of the network underpinning the interactions of the spins. In this work we present a way to characterize the macroscopic states of the XY spin model based on the spectral decomposition of time series using topological information about the underlying networks. We use three different classes of networks to generate time series of the spins for the three possible macroscopic states. We then use the temporal Graph Signal Transform technique to decompose the time series of the spins on the eigenbasis of the Laplacian. From this decomposition, we produce spatial power spectra, which summarize the activation of structural modes by the nonlinear dynamics, and thus coherent patterns of activity of the spins. These signatures of the macroscopic states are independent of the underlying network class and can thus be used as robust signatures for the macroscopic states. This work opens avenues to analyze and characterize dynamics on complex networks using temporal Graph Signal Analysis.

Anomalous diffusion processes, in particular superdiffusive ones, are known to be efficient strategies for searching and navigation in animals and also in human mobility. One way to create such regimes are Lévy flights, where the walkers are allowed to perform jumps, the "flights," that can eventually be very long as their length distribution is asymptotically power-law distributed. In our work, we present a model in which walkers are allowed to perform, on a one-dimensional lattice, "cascades" of n unitary steps instead of one jump of a randomly generated length, as in the Lévy case, where n is drawn from a cascade distribution p_{n}. We show that this local mechanism may give rise to superdiffusion or normal diffusion when p_{n} is distributed as a power law. We also introduce waiting times that are power-law distributed as well and therefore the probability distribution scaling is steered by the two local distributions power-law exponents. As a perspective, our approach may engender a possible generalization of anomalous diffusion in context where distances are difficult to define, as in the case of complex networks, and also provide an interesting model for diffusion in temporal networks.

Rationale: The plant endophyte Bacillus licheniformis, isolated from leaves of Vitis vinifera, was studied to individuate and characterize the presence of bioactive lipopeptides having amino acidic structures., Methods: Crude extracts of liquid cultures were analyzed by ultra-high-performance liquid chromatography (UHPLC) coupled to a quadrupole time-of-flight (QTOF) mass analyzer. Chromatographic conditions were optimized in order to obtain an efficient separation of the different isobaric lipopeptides, avoiding merged fragmentations of co-eluted isomeric compounds and reducing possible cross-talk phenomena. Composition of the amino acids was outlined through the interpretation of the fragmentation behavior in tandem high-resolution mass spectrometry (HRMS/MS) mode, which showed both common-class and peculiar fragment ions. Both [M + H](+) and [M + Na](+) precursor ions were fragmented in order to differentiate some isobaric amino acids, i.e. Leu/Ile. Neutral losses characteristic of the iso acyl chain were also evidenced., Results: More than 90 compounds belonging to the classes of surfactins and lichenysins, known as biosurfactant molecules, were detected. Sequential LC/HRMS/MS analysis was used to identify linear and cyclic lipopeptides, and to single out the presence of a large number of isomers not previously reported. Some critical issues related to the simultaneous selection of different compounds by the quadrupole filter were highlighted and partially solved, leading to tentative assignments of several structures. Linear lichenysins are described here for the first time., Conclusions: The approach was proved to be useful for the characterization of non-target lipopeptides, and proposes a rationale MS experimental scheme aimed to investigate the difference in amino acid sequence and/or in the acyl chain of the various congeners, when standards are not available. Results expanded the knowledge about production of linear and cyclic bioactive compounds from Bacillus licheniformis, clarifying the structures of isomeric forms, and enabling the use of selected endophytes to produce fungicides for eco-friendly biocontrol. Copyright © 2016 John Wiley & Sons, Ltd., (Copyright © 2016 John Wiley & Sons, Ltd.)

Persistent homology analysis, a recently developed computational method in algebraic topology, is applied to the study of the phase transitions undergone by the so-called mean-field XY model and by the ϕ^{4} lattice model, respectively. For both models the relationship between phase transitions and the topological properties of certain submanifolds of configuration space are exactly known. It turns out that these a priori known facts are clearly retrieved by persistent homology analysis of dynamically sampled submanifolds of configuration space.

We investigated the potential plant growth-promoting traits of 377 culturable endophytic bacteria, isolated from Vitis vinifera cv. Glera, as good biofertilizer candidates in vineyard management. Endophyte ability in promoting plant growth was assessed in vitro by testing ammonia production, phosphate solubilization, indole-3-acetic acid (IAA) and IAA-like molecule biosynthesis, siderophore and lytic enzyme secretion. Many of the isolates were able to mobilize phosphate (33%), release ammonium (39%), secrete siderophores (38%) and a limited part of them synthetized IAA and IAA-like molecules (5%). Effects of each of the 377 grapevine beneficial bacteria on Arabidopsis thaliana root development were also analyzed to discern plant growth-promoting abilities (PGP) of the different strains, that often exhibit more than one PGP trait. A supervised model-based clustering analysis highlighted six different classes of PGP effects on root architecture. A. thaliana DR5::GUS plantlets, inoculated with IAA-producing endophytes, resulted in altered root growth and enhanced auxin response. Overall, the results indicate that the Glera PGP endospheric culturable microbiome could contribute, by structural root changes, to obtain water and nutrients increasing plant adaptation and survival. From the complete cultivable collection, twelve promising endophytes mainly belonging to the Bacillus but also to Micrococcus and Pantoea genera, were selected for further investigations in the grapevine host plants towards future application in sustainable management of vineyards.

The influence of networks topology on collective properties of dynamical systems defined upon it is studied in the thermodynamic limit. A network model construction scheme is proposed where the number of links and the average eccentricity are controlled. This is done by rewiring links of a regular one-dimensional chain according to a probability p within a specific range r that can depend on the number of vertices N. We compute the thermodynamical behavior of a system defined on the network, the XY-rotors model, and monitor how it is affected by the topological changes. We identify the network effective dimension d as a crucial parameter: topologies with d<2 exhibit no phase transitions, while topologies with d>2 display a second-order phase transition. Topologies with d=2 exhibit states characterized by infinite susceptibility and macroscopic chaotic, turbulent dynamical behavior. These features are also captured by d in the finite size context.

We study the XY rotors model on small networks whose number of links scales with the system size N(links)~N(γ), where 1≤γ≤2. We first focus on regular one-dimensional rings in the microcanonical ensemble. For γ<1.5 the model behaves like a short-range one and no phase transition occurs. For γ>1.5, the system equilibrium properties are found to be identical to the mean field, which displays a second-order phase transition at a critical energy density ε=E/N,ε(c)=0.75. Moreover, for γ(c)~/=1.5 we find that a nontrivial state emerges, characterized by an infinite susceptibility. We then consider small-world networks, using the Watts-Strogatz mechanism on the regular networks parametrized by γ. We first analyze the topology and find that the small-world regime appears for rewiring probabilities which scale as p(SW)[proportionality]1/N(γ). Then considering the XY-rotors model on these networks, we find that a second-order phase transition occurs at a critical energy ε(c) which logarithmically depends on the topological parameters p and γ. We also define a critical probability p(MF), corresponding to the probability beyond which the mean field is quantitatively recovered, and we analyze its dependence on γ.