The structural landscape of the immunoglobulin fold by large-scale de novo design

De novo designing immunoglobulin-like frameworks that allow for functional loop diversification shows great potential for crafting antibody-like scaffolds with fully customizable structures and functions. In this work, we combined de novo parametric design with deep-learning methods for protein structure prediction and design to explore the structural landscape of 7-stranded immunoglobulin domains. After screening folding of nearly 4 million designs, we have assembled a structurally diverse library of ~50,000 immunoglobulin domains with high-confidence AlphaFold2 predictions and structures diverging from naturally occurring ones. The designed dataset enabled us to identify structural requirements for the correct folding of immunoglobulin domains, shed light on β-sheet-β-sheet rotational preferences and how these are linked to functional properties. Our approach eliminates the need for preset loop conformations and opens the route to large-scale de novo design of immunoglobulin-like frameworks.

Conduction system pacing and atrioventricular node ablation in heart failure: The PACE-FIB study design

AIMS

Atrial fibrillation (AF) worsens the prognosis of patients with heart failure (HF). Successful treatments are still very scarce for those with permanent AF and preserved (HFpEF) or mildly reduced (HFmrEF) ejection fraction. In this study, the long-term benefits and safety profile of heart rate regularization through left-bundle branch pacing (LBBP) and atrioventricular node ablation (AVNA) will be explored in comparison with pharmacological rate-control strategy.

METHODS AND RESULTS

The PACE-FIB trial is a multicentre, prospective, open-label, randomized (1:1) clinical study that will take place between March 2022 and February 2027. A total of 334 patients with HFpEF/HFmrEF and permanent AF will receive either LBBP followed by AVNA (intervention arm) or optimal pharmacological treatment for heart rate control according to European guideline recommendations (control arm). All patients will be followed up for a minimum of 36 months. The primary outcome measure will be the composite of all-cause mortality, HF hospitalization, and worsening HF at 36 months. Other secondary efficacy and safety outcome measures such as echocardiographic parameters, functional status, and treatment-related adverse events, among others, will be analysed too.

CONCLUSION

LBBP is a promising stimulation mode that may foster the clinical benefit of heart rate regularization through AV node ablation compared with pharmacological rate control. This is the first randomized trial specifically addressing the long-term efficacy and safety of this pace-and-ablate strategy in patients with HFpEF/HFmrEF and permanent AF.

New microbial tools to boost restoration and soil organic matter

Anthropogenic activities are causing unprecedented rates of soil and ecosystem degradation, and the current restoration practices take decades and are prone to high rates of failure. Here we propose, the development and application of emerging microbiome tools that can potentially improve the contents and diversity of soil organic matters, enhancing the efficacy and consistency of restoration outcomes.

In Vivo Intra-Uterine Delivery of TAT-Fused Cre Recombinase and CRISPR/Cas9 Editing System in Mice Unveil Histopathology of Pten/p53-Deficient Endometrial Cancers

Phosphatase and TENsin homolog (Pten) and p53 are two of the most frequently mutated tumor suppressor genes in endometrial cancer. However, the functional consequences and histopathological manifestation of concomitant p53 and Pten loss of function alterations in the development of endometrial cancer is still controversial. Here, it is demonstrated that simultaneous Pten and p53 deletion is sufficient to cause epithelial to mesenchymal transition phenotype in endometrial organoids. By a novel intravaginal delivery method using HIV1 trans-activator of transcription cell penetrating peptide fused with a Cre recombinase protein (TAT-Cre), local ablation of both p53 and Pten is achieved specifically in the uterus. These mice developed high-grade endometrial carcinomas and a high percentage of uterine carcinosarcomas resembling those found in humans. To further demonstrate that carcinosarcomas arise from epithelium, double Pten/p53 deficient epithelial cells are mixed with wild type stromal and myometrial cells and subcutaneously transplanted to Scid mice. All xenotransplants resulted in the development of uterine carcinosarcomas displaying high nuclear pleomorphism and metastatic potential. Accordingly, in vivo CRISPR/Cas9 disruption of Pten and p53 also triggered the development of metastatic carcinosarcomas. The results unfadingly demonstrate that simultaneous deletion of p53 and Pten in endometrial epithelial cells is enough to trigger epithelial to mesenchymal transition that is consistently translated to the formation of uterine carcinosarcomas in vivo.

The Histone Chaperones SET/TAF-1β and NPM1 Exhibit Conserved Functionality in Nucleosome Remodeling and Histone Eviction in a Cytochrome c-Dependent Manner

Chromatin homeostasis mediates essential processes in eukaryotes, where histone chaperones have emerged as major regulatory factors during DNA replication, repair, and transcription. The dynamic nature of these processes, however, has severely impeded their characterization at the molecular level. Here, fluorescence optical tweezers are applied to follow histone chaperone dynamics in real time. The molecular action of SET/template-activating factor-Iβ and nucleophosmin 1-representing the two most common histone chaperone folds-are examined using both nucleosomes and isolated histones. It is shown that these chaperones present binding specificity for fully dismantled nucleosomes and are able to recognize and disrupt non-native histone-DNA interactions. Furthermore, the histone eviction process and its modulation by cytochrome c are scrutinized. This approach shows that despite the different structures of these chaperones, they present conserved modes of action mediating nucleosome remodeling.

Insularity determines nestling sex ratio variation in Egyptian vulture populations

Variation in offspring sex ratio, particularly in birds, has been frequently studied over the last century, although seldom using long-term monitoring data. In raptors, the cost of raising males and females is not equal, and several variables have been found to have significant effects on sex ratio, including food availability, parental age, and hatching order. Sex ratio differences between island populations and their mainland counterparts have been poorly documented, despite broad scientific literature on the island syndrome reporting substantial differences in population demography and ecology. Here, we assessed individual and environmental factors potentially affecting the secondary sex ratio of the long-lived Egyptian vulture Neophron percnopterus. We used data collected from Spanish mainland and island populations over a ca. 30-year period (1995-2021) to assess the effects of insularity, parental age, breeding phenology, brood size, hatching order, type of breeding unit (pairs vs. trios), and spatial and temporal variability on offspring sex ratio. No sex bias was found at the population level, but two opposite trends were observed between mainland and island populations consistent with the island syndrome. Offspring sex ratio was nonsignificantly female-biased in mainland Spain (0.47, n = 1112) but significantly male-biased in the Canary Islands (0.55, n = 499), where a male-biased mortality among immatures could be compensating for offspring biases and maintaining a paired adult sex ratio. Temporal and spatial variation in food availability might also have some influence on sex ratio, although the difficulties in quantifying them preclude us from determining the magnitude of such influence. This study shows that insularity influences the offspring sex ratio of the Egyptian vulture through several processes that can affect island and mainland populations differentially. Our research contributes to improving our understanding of sex allocation theory by investigating whether sex ratio deviations from parity are possible as a response to changing environments comprised by multiple and complexly interrelated factors.

Motor potentials evoked by transcranial magnetic stimulation: interpreting a simple measure of a complex system

Transcranial magnetic stimulation (TMS) is a non-invasive technique that is increasingly used to study the human brain. One of the principal outcome measures is the motor-evoked potential (MEP) elicited in a muscle following TMS over the primary motor cortex (M1), where it is used to estimate changes in corticospinal excitability. However, multiple elements play a role in MEP generation, so even apparently simple measures such as peak-to-peak amplitude have a complex interpretation. Here, we summarize what is currently known regarding the neural pathways and circuits that contribute to the MEP and discuss the factors that should be considered when interpreting MEP amplitude measured at rest in the context of motor processing and patients with neurological conditions. In the last part of this work, we also discuss how emerging technological approaches can be combined with TMS to improve our understanding of neural substrates that can influence MEPs. Overall, this review aims to highlight the capabilities and limitations of TMS that are important to recognize when attempting to disentangle sources that contribute to the physiological state-related changes in corticomotor excitability.

Identification of Mechanisms by Which Genetic Susceptibility Loci Influence Systemic Sclerosis Risk Using Functional Genomics in Primary T Cells and Monocytes

OBJECTIVE

Systemic sclerosis (SSc) is a complex autoimmune disease with a strong genetic component. However, most of the genes associated with the disease are still unknown because associated variants affect mostly noncoding intergenic elements of the genome. We used functional genomics to translate the genetic findings into a better understanding of the disease.

METHODS

Promoter capture Hi-C and RNA-sequencing experiments were performed in CD4+ T cells and CD14+ monocytes from 10 SSc patients and 5 healthy controls to link SSc-associated variants with their target genes, followed by differential expression and differential interaction analyses between cell types.

RESULTS

We linked SSc-associated loci to 39 new potential target genes and confirmed 7 previously known SSc-associated genes. We highlight novel causal genes, such as CXCR5, as the most probable candidate gene for the DDX6 locus. Some previously known SSc-associated genes, such as IRF8, STAT4, and CD247, showed cell type-specific interactions. We also identified 15 potential drug targets already in use in other similar immune-mediated diseases that could be repurposed for SSc treatment. Furthermore, we observed that interactions were directly correlated with the expression of important genes implicated in cell type-specific pathways and found evidence that chromatin conformation is associated with genotype.

CONCLUSION

Our study revealed potential causal genes for SSc-associated loci, some of them acting in a cell type-specific manner, suggesting novel biologic mechanisms that might mediate SSc pathogenesis.

Common pathophysiology for ANXA11 disorders caused by aspartate 40 variants

OBJECTIVE

Mutations in ANXA11 cause amyotrophic lateral sclerosis (ALS) and have recently been identified as a cause of multisystem proteinopathy and adult-onset muscular dystrophy. These conditions are adult-onset diseases and result from the substitution of Aspartate 40 (Asp40) for an apolar residue in the intrinsically disordered domain (IDD) of ANXA11. Some ALS-related variants are known to affect ANXA11 IDD; however, the mechanism by which the myopathy occurs is unknown.

METHODS

Genetic analysis was performed using WES-trio. For the study of variant pathogenicity, we used recombinant proteins, muscle biopsy, and fibroblasts.

RESULTS

Here we describe an individual with severe and rapidly progressive childhood-onset oculopharyngeal muscular dystrophy who carries a new ANXA11 variant at position Asp40 (p.Asp40Ile; c.118_119delGAinsAT). p.Asp40Ile is predicted to enhance the aggregation propensity of ANXA11 to a greater extent than other changes affecting this residue. In vitro studies using recombinant ANXA11p.Asp40Ile showed abnormal phase separation and confirmed this variant is more aggregation-prone than the ALS-associated variant ANXA11p.Asp40Gly . The study of the patient's fibroblasts revealed defects in stress granules dynamics and clearance, and muscle histopathology showed a myopathic pattern with ANXA11 protein aggregates. Super-resolution imaging showed aggregates expressed as pearl strips or large complex structures in the sarcoplasm, and as layered subsarcolemmal chains probably reflecting ANXA11 multifunctionality.

INTERPRETATION

We demonstrate common pathophysiology for disorders associated with ANXA11 Asp40 allelic variants. Clinical phenotypes may result from different deleterious impacts of variants upon ANXA11 stability against aggregation, and differential muscle or motor neuron dysfunction expressed as a temporal and tissue-specific continuum.

MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations

We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic-structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage-gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch case.

Role of Dipolar Interactions on the Determination of the Effective Magnetic Anisotropy in Iron Oxide Nanoparticles

Challenging magnetic hyperthermia (MH) applications of immobilized magnetic nanoparticles require detailed knowledge of the effective anisotropy constant (K_eff ) to maximize heat release. Designing optimal MH experiments entails the precise determination of magnetic properties, which are, however, affected by the unavoidable concurrence of magnetic interactions in common experimental conditions. In this work, a mean-field energy barrier model (ΔE), accounting for anisotropy (E_A ) and magnetic dipolar (E_D ) energy, is proposed and used in combination with AC measurements to a specifically developed model system of spherical magnetic nanoparticles with well-controlled silica shells, acting as a spacer between the magnetic cores. This approach makes it possible to experimentally demonstrate the mean field dipolar interaction energy prediction with the interparticle distance, d_ij , E_D ≈ 1/d_ij ³ and obtain the E_A as the asymptotic limit for very large d_ij . In doing so, K_eff uncoupled from interaction contributions is obtained for the model system (iron oxide cores with average sizes of 8.1, 10.2, and 15.3 nm) revealing to be 48, 23, and 11 kJ m^-3 , respectively, close to bulk magnetite/maghemite values and independent from the specific spacing shell thicknesses selected for the study.

Synthesis of [60]Fullerene Hybrids Endowed with Steroids and Monosaccharides: Theoretical Underpinning as Promising anti-SARS-CoV-2 Agents

Cyclopropanation reactions between C60 and different malonates decorated with monosaccharides and steroids using the Bingel-Hirsch methodology have allowed the obtention of a new family of hybrid compounds in good yields. A complete set of instrumental techniques has allowed us to fully characterize the hybrid derivatives and to determine the chemical structure of monocycloadducts. Besides, the proposed structures were investigated by cyclic voltammetry, which evidenced the exclusive reductive pattern of fullerene Bingel-type monoadducts. Theoretical calculations at the DFT-D3(BJ)/PBE 6-311G(d,p) level of the synthesized conjugates predict the most stable conformation and determine the factors that control the hybrid molecules' geometry. Some parameters such as polarity, lipophilicity, polar surface area, hydrophilicity index, and solvent-accessible surface area were also estimated, predicting its potential permeability and capability as cell membrane penetrators. Additionally, a molecular docking simulation has been carried out using the main protease of SARS-CoV-2 (Mpro) as the receptor, thus paving the way to study the potential application of these hybrids in biomedicine.

Analysis of the evolution of ultra-filtered water quality in a drinking water distribution system by particle size distribution: Influence of pre-ozonation

An experimental drinking water distribution system (DWDS) was used to evaluate the evolution of particle size distribution (PSD) and basic quality parameters of ultrafiltered water with or without pre-ozonation. An ultrafiltration (UF) module was set up, associated with a pre-ozonation system (3.7 g O₃ /m³ ). The permeate was circulated in the DWDS (300 m; 0.9 m/s) with 0.4 mg/L of chlorine, and the analysis of the PSD was performed using a β-variable mathematical model. A better control of membrane fouling was obtained with pre-ozonation, and PSD was necessary to observe water quality differences between permeates and in the DWDS. A decrease in particle concentration of 1.8 logarithms was obtained with the application of UF membranes, while a decrease of only 1.2 logarithms was obtained with pre-ozonation. The system without pre-ozonation showed a higher efficiency at removing smaller particles (around 2 μm), with the absence of particles larger than 23 μm during both stages. The PSD revealed a worsening of water quality in the DWDS with an increase of particles smaller than 5 μm during the application of UF membranes, while with pre-ozonation, all particle sizes analyzed increased their concentration. PRACTITIONER POINTS: Pre-ozonation led to a better control of membrane fouling, but a worsening of permeate quality according to particle size distribution. Pre-ozonation does not improve the turbidity, dissolved organic carbon or UV254 removal capacity of ultrafiltration during drinking water treatment. Particles size distribution reveals the deterioration of water quality in a drinking water distribution system better than turbidity or DOC. Ozone prior to ultrafiltration membranes led to a worsening of permeate quality, more significant in the drinking water distribution system.

Ecological relevance of non-perennial rivers for the conservation of terrestrial and aquatic communities

River conservation efforts traditionally focus on perennial watercourses (i.e., those that do not dry) and their associated aquatic biodiversity. However, most of the global river network is not perennial and thus supports both aquatic and terrestrial biodiversity. We assessed the conservation value of nonperennial rivers and streams (NPRS) in one of Europe's driest regions based on aquatic (macroinvertebrates, diatoms) and terrestrial (riparian plants, birds, and carabid beetles) community data. We mapped the distribution of taxa at 90 locations and across wide environmental gradients. Using the systematic planning tool Marxan, we identified priority conservation sites under 2 scenarios: aquatic taxa alone or aquatic and terrestrial taxa together. We explored how environmental factors (runoff, flow intermittence, elevation, salinity, anthropogenic impact) influenced Marxan's site selection frequency. The NPRS were selected more frequently (over 13% on average) than perennial rivers when both aquatic and terrestrial taxa were considered, suggesting that NPRS have a high conservation value at the catchment scale. We detected an underrepresentation of terrestrial taxa (8.4-10.6% terrestrial vs. 0.5-1.1% aquatic taxa were unrepresented in most Marxan solutions) when priority sites were identified based exclusively on aquatic biodiversity, which points to a low surrogacy value of aquatic taxa for terrestrial taxa. Runoff explained site selection when focusing on aquatic taxa (all best-fitting models included runoff, r²  = 0.26-0.27), whereas elevation, salinity, and flow intermittence were more important when considering both groups. In both cases, site selection frequency declined as anthropogenic impact increased. Our results highlight the need to integrate terrestrial and aquatic communities when identifying priority areas for conservation in catchments with NPRS. This is key to overcoming drawbacks of traditional assessments based only on aquatic taxa and to ensure the conservation of NPRS, especially as NPRS become more prevalent worldwide due to climate change and increasing water demands.

Complexed Semiconductor Cores Activate Hexaniobate Ligands as Nucleophilic Sites for Solar‐Light Reduction of CO 2 by Water

Although pure and functionalized solid-state polyniobates such as layered perovskites and niobate nanosheets are photocatalysts for renewable-energy processes, analogous reactions by molecular polyoxoniobate cluster-anions are nearly absent from the literature. We now report that under simulated solar light, hexaniobate cluster-anion encapsulated 30-Ni^II -ion "fragments" of surface-protonated cubic-phase-like NiO cores activate the hexaniobate ligands towards CO₂ reduction by water. Photoexcitation of the NiO cores promotes charge-transfer reduction of Nb^V to Nb^IV , increasing electron density at bridging oxo atoms of Nb-μ-O-Nb linkages that bind and convert CO₂ to CO. Photogenerated NiO "holes" simultaneously oxidize water to dioxygen. The findings point to molecular complexation of suitable semiconductor "fragments" as a general method for utilizing electron-dense polyoxoniobate anions as nucleophilic photocatalysts for solar-light driven activation and reduction of small molecules.

Transcriptome analyses unveiled differential regulation of AGO and DCL genes by pepino mosaic virus strains

Pepino mosaic virus (PepMV) is a single-stranded (ss), positive-sense (+) RNA potexvirus that affects tomato crops worldwide. We have described an in planta antagonistic interaction between PepMV isolates of two strains in which the EU isolate represses the accumulation of the CH2 isolate during mixed infections. Reports describing transcriptomic responses to mixed infections are scant. We carried out transcriptomic analyses of tomato plants singly and mixed-infected with two PepMV isolates of both strains. Comparison of the transcriptomes of singly infected plants showed that deeper transcriptomic alterations occurred at early infection times, and also that each of the viral strains modulated the host transcriptome differentially. Mixed infections caused transcriptomic alterations similar to those for the sum of single infections at early infection times, but clearly differing at later times postinfection. We next tested the hypothesis that PepMV-EU, in either single or mixed infections, deregulates host gene expression differentially so that virus accumulation of both strains gets repressed. That seemed to be the case for the genes AGO1a, DCL2d, AGO2a, and DCL2b, which are involved in the antiviral silencing pathway and were upregulated by PepMV-EU but not by PepMV-CH2 at early times postinfection. The pattern of AGO2a expression was validated by reverse transcription-quantitative PCR in tomato and Nicotiana benthamiana plants. Using an N. benthamiana ago2 mutant line, we showed that AGO2 indeed plays an important role in the antiviral defence against PepMV, but it is not the primary determinant of the outcome of the antagonistic interaction between the two PepMV strains.

Kinetic Control of Ultrafast Transient Liquid Assisted Growth of Solution-Derived YBa2 Cu3 O7 -x Superconducting Films

Transient liquid assisted growth (TLAG) is an ultrafast non-equilibrium growth process mainly governed by kinetic parameters, which are only accessible through fast in situ characterizations. In situ synchrotron X-ray diffraction (XRD) analysis and in situ electrical resistivity measurements are used to derive kinetic diagrams of YBa₂ Cu₃ O_{7- x} (YBCO) superconducting films prepared via TLAG and to reveal the unique peculiarities of the process. In particular, diagrams for the phase evolution and the YBCO growth rates have been built for the two TLAG routes. It is shown that TLAG transient liquids can be obtained upon the melting of two barium cuprate phases (and not just one), differentiated by their copper oxidation state. This knowledge serves as a guide to determine the processing conditions to reach high performance films at high growth rates. With proper control of these kinetic parameters, films with critical current densities of 2-2.6 MA cm^-2 at 77 K and growth rates between 100-2000 nm s^-1 are reached. These growth rates are 1.5-3 orders of magnitude higher than those of conventional methods.

Mechanical strain stimulates COPII-dependent secretory trafficking via Rac1

Cells are constantly exposed to various chemical and physical stimuli. While much has been learned about the biochemical factors that regulate secretory trafficking from the endoplasmic reticulum (ER), much less is known about whether and how this trafficking is subject to regulation by mechanical signals. Here, we show that subjecting cells to mechanical strain both induces the formation of ER exit sites (ERES) and accelerates ER-to-Golgi trafficking. We found that cells with impaired ERES function were less capable of expanding their surface area when placed under mechanical stress and were more prone to develop plasma membrane defects when subjected to stretching. Thus, coupling of ERES function to mechanotransduction appears to confer resistance of cells to mechanical stress. Furthermore, we show that the coupling of mechanotransduction to ERES formation was mediated via a previously unappreciated ER-localized pool of the small GTPase Rac1. Mechanistically, we show that Rac1 interacts with the small GTPase Sar1 to drive budding of COPII carriers and stimulates ER-to-Golgi transport. This interaction therefore represents an unprecedented link between mechanical strain and export from the ER.

Using machine learning to link the influence of transferred Agrobacterium rhizogenes genes to the hormone profile and morphological traits in Centella asiatica hairy roots

Hairy roots are made after the integration of a small set of genes from Agrobacterium rhizogenes in the plant genome. Little is known about how this small set is linked to their hormone profile, which determines development, morphology, and levels of secondary metabolite production. We used C. asiatica hairy root line cultures to determine the putative links between the rol and aux gene expressions with morphological traits, a hormone profile, and centelloside production. The results obtained after 14 and 28 days of culture were processed via multivariate analysis and machine-learning processes such as random forest, supported vector machines, linear discriminant analysis, and neural networks. This allowed us to obtain models capable of discriminating highly productive root lines from their levels of genetic expression (rol and aux genes) or from their hormone profile. In total, 12 hormones were evaluated, resulting in 10 being satisfactorily detected. Within this set of hormones, abscisic acid (ABA) and cytokinin isopentenyl adenosine (IPA) were found to be critical in defining the morphological traits and centelloside content. The results showed that IPA brings more benefits to the biotechnological platform. Additionally, we determined the degree of influence of each of the evaluated genes on the individual hormone profile, finding that aux1 has a significant influence on the IPA profile, while the rol genes are closely linked to the ABA profile. Finally, we effectively verified the gene influence on these two specific hormones through feeding experiments that aimed to reverse the effect on root morphology and centelloside content.

Potato virus X-delivered CRISPR activation programs lead to strong endogenous gene induction and transient metabolic reprogramming in Nicotiana benthamiana

Programmable transcriptional regulators based on CRISPR architecture are promising tools for the induction of plant gene expression. In plants, CRISPR gene activation is effective with respect to modulating development processes, such as the flowering time or customizing biochemical composition. The most widely used method for delivering CRISPR components into the plant is Agrobacterium tumefaciens-mediated genetic transformation, either transient or stable. However, as a result of their versatility and their ability to move, virus-derived systems have emerged as an interesting alternative for supplying the CRISPR components to the plant, in particular guide RNA (gRNA), which represents the variable component in CRISPR strategies. In the present study, we describe a Potato virus X-derived vector that, upon agroinfection in Nicotiana benthamiana, serves as a vehicle for delivery of gRNAs, producing highly specific virus-induced gene activation. The system works in combination with a N. benthamiana transgenic line carrying the remaining complementary CRISPR gene activation components, specifically the dCasEV2.1 cassette, which has been shown previously to mediate strong programmable transcriptional activation in plants. Using an easily scalable, non-invasive spraying method, we show that gRNA-mediated activation programs move locally and systemically, generating a strong activation response in different target genes. Furthermore, by activating three different endogenous MYB transcription factors, we demonstrate that this Potato virus X-based virus-induced gene reprogramming strategy results in program-specific metabolic fingerprints in N. benthamiana leaves characterized by distinctive phenylpropanoid-enriched metabolite profiles.

Semantic Representation of Context for Description of Named Rivers in a Terminological Knowledge Base

The description of named entities in terminological knowledge bases has never been addressed in any depth in terminology. Firm preconceptions, rooted in philosophy, about the only referential function of proper names have presumably led to disparage their inclusion in terminology resources, despite the relevance of named entities having been highlighted by prominent figures in the discipline of terminology. Scholars from different branches of linguistics depart from the conservative stance on proper names and have foregrounded the need for a novel approach, more linguistic than philosophical, to describing proper names. Therefore, this paper proposed a linguistic and terminological approach to the study of named entities when used in scientific discourse, with the purpose of representing them in EcoLexicon, an environmental knowledge base designed according to the premises of Frame-based Terminology. We focused more specifically on named rivers (or potamonyms) mentioned in a coastal engineering corpus. Inclusion of named entities in terminological knowledge bases requires analyzing the context that surrounds them in specialized texts because these contexts convey specialized knowledge about named entities. For the semantic representation of context, this paper thus analyzed the local syntactic and semantic contexts that surrounded potamonyms in coastal engineering texts and described the semantic annotation of the predicate-argument structure of sentences where a potamonym was mentioned. The semantic variables annotated were the following: (1) semantic category of the arguments; (2) semantic role of the arguments; (3) semantic relation between the arguments; and (4) lexical domain of the verbs. This method yielded valuable insight into the different semantic roles that named rivers played, the entities and processes that participated in the events educed by potamonyms through verbs, and how they all interacted. Furthermore, since arguments are specialized terms and verbs are relational constructs, the analysis of argument structure led to the construction of semantic networks that depicted specialized knowledge about named rivers. These conceptual networks were then used to craft the thematic description of potamonyms. Accordingly, the semantic network and the thematic description not only constituted the representation of a potamonym in EcoLexicon, but also allowed the geographic contextualization of specialized concepts in the terminological resource.

Custom-made design of metabolite composition in N. benthamiana leaves using CRISPR activators

Transcriptional regulators based on CRISPR architecture expand our ability to reprogramme endogenous gene expression in plants. One of their potential applications is the customization of plant metabolome through the activation of selected enzymes in a given metabolic pathway. Using the previously described multiplexable CRISPR activator dCasEV2.1, we assayed the selective enrichment in Nicotiana benthamiana leaves of four different flavonoids, namely, naringenin, eriodictyol, kaempferol, and quercetin. After careful selection of target genes and guide RNAs combinations, we created successful activation programmes for each of the four metabolites, each programme activating between three and seven genes, and with individual gene activation levels ranging from 4- to 1500-fold. Metabolic analysis of the flavonoid profiles of each multigene activation programme showed a sharp and selective enrichment of the intended metabolites and their glycosylated derivatives. Remarkably, principal component analysis of untargeted metabolic profiles clearly separated samples according to their activation treatment, and hierarchical clustering separated the samples into five groups, corresponding to the expected four highly enriched metabolite groups, plus an un-activated control. These results demonstrate that dCasEV2.1 is a powerful tool for re-routing metabolic fluxes towards the accumulation of metabolites of interest, opening the door for the custom-made design of metabolic contents in plants.

Temperature and Rainfall Patterns Constrain the Multidimensional Rewilding of Global Forests

The long-term contribution of global forest restoration to support multiple dimensions of biodiversity and ecosystem function remains largely illusive across contrasting climates and forest types. This hampers the capacity to predict the future of forest rewilding under changing global climates. Here, 120 studies are synthesized across five continents, and it is found that forest restoration promotes multiple dimensions of biodiversity and ecosystem function such as soil fertility, plant biomass, microbial habitat, and carbon sequestration across contrasting climates and forest types. Based on global relationship between stand age and soil organic carbon stock, planting 350 million hectares of forest under the UN Bonn Challenge can sequester >30 Gt soil C in the surface 20 cm over the next century. However, these findings also indicate that predicted increases in temperature and reductions in precipitation can constrain the positive effects of forest rewilding on biodiversity and ecosystem function. Further, important tradeoffs are found in very old forests, with considerable disconnection between biodiversity and ecosystem function. Together, these findings provide evidence of the importance of the multidimensional rewilding of forests, suggesting that on-going climatic changes may dampen the expectations of the positive effects of forest restoration on biodiversity and ecosystem function.

Do Religiosity and Ethnocentrism Influence Indian Consumers’ Unwillingness to Buy Halal-Made Products? The Role of Animosity Toward Halal Products

The purpose of this research is to assess the relationship between Indian (non-muslims) consumers’ animosity toward halal products and their unwillingness to buy halal products. Moreover, we seek to investigate boycott attitudes, religiosity, ethnocentrism, and patriotism as drivers of consumer animosity and reluctance to purchase halal products. Consumer animosity toward halal products has received some attention in marketing research, and we aim to further explore animosity regarding the halal label. We collect online survey responses from 512 Indian consumers and analyze the data using SmartPLS3 software. Findings show a positive impact of boycott attitude, religiosity, and ethnocentrism on Indian consumers’ level of animosity and thus their unwillingness to purchase halal products. Furthermore, consumer animosity acts as a mediator of the relationship between boycott attitude, religiosity, ethnocentrism, patriotism, and reluctance to buy halal products. Notably, the findings provide a menu of potential managerial actions to reduce or enhance consumer animosity.

High-Throughput Screening of Blade-Coated Polymer:Polymer Solar Cells: Solvent Determines Achievable Performance

Optimization of a new system for organic solar cells is a multiparametric analysis problem that requires substantial efforts in terms of time and resources. The strong microstructure-dependent performance of polymer:polymer cells makes them particularly difficult to optimize, or to translate previous knowledge from spin coating into more scalable techniques. In this work, the photovoltaic performance of blade-coated devices was studied based on the promising polymer:polymer system PBDB-T and PF5-Y5 as donor and acceptor, respectively. Using the recently developed high-throughput methodology, the system was optimized for multiple variables, including solvent system, active layer composition, ratio, and thickness, among others, by fabricating more than 500 devices with less than 24 mg of each component. As a result, the power conversion efficiency of the blade-coated devices varied from 0.08 to 6.43 % in the best device. The performed statistical analysis of the large experimental data obtained showed that solvent selection had the major impact on the final device performance due to its influence on the active layer microstructure. As a conclusion, the use of the plot of the device efficiency in the Hansen space was proposed as a powerful tool to guide solvent selection in organic photovoltaics.

Microfluidic devices for studying bacterial taxis, drug testing and biofilm formation

Some bacteria have coevolved to establish symbiotic or pathogenic relationships with plants, animals or humans. With human association, the bacteria can cause a variety of diseases. Thus, understanding bacterial phenotypes at the single-cell level is essential to develop beneficial applications. Traditional microbiological techniques have provided great knowledge about these organisms; however, they have also shown limitations, such as difficulties in culturing some bacteria, the heterogeneity of bacterial populations or difficulties in recreating some physical or biological conditions. Microfluidics is an emerging technique that complements current biological assays. Since microfluidics works with micrometric volumes, it allows fine-tuning control of the test conditions. Moreover, it allows the recruitment of three-dimensional (3D) conditions, in which several processes can be integrated and gradients can be generated, thus imitating physiological 3D environments. Here, we review some key microfluidic-based studies describing the effects of different microenvironmental conditions on bacterial response, biofilm formation and antimicrobial resistance. For this aim, we present different studies classified into six groups according to the design of the microfluidic device: (i) linear channels, (ii) mixing channels, (iii) multiple floors, (iv) porous devices, (v) topographic devices and (vi) droplet microfluidics. Hence, we highlight the potential and possibilities of using microfluidic-based technology to study bacterial phenotypes in comparison with traditional methodologies.

Resilience of seagrass populations to thermal stress does not reflect regional differences in ocean climate

The prevalence of local adaptation and phenotypic plasticity among populations is critical to accurately predicting when and where climate change impacts will occur. Currently, comparisons of thermal performance between populations are untested for most marine species or overlooked by models predicting the thermal sensitivity of species to extirpation. Here we compared the ecological response and recovery of seagrass populations (Posidonia oceanica) to thermal stress throughout a year-long translocation experiment across a 2800-km gradient in ocean climate. Transplants in central and warm-edge locations experienced temperatures > 29°C, representing thermal anomalies > 5°C above long-term maxima for cool-edge populations, 1.5°C for central and < 1°C for warm-edge populations. Cool-edge, central and warm-edge populations differed in thermal performance when grown under common conditions, but patterns contrasted with expectations based on thermal geography. Cool-edge populations did not differ from warm-edge populations under common conditions and performed significantly better than central populations in growth and survival. Our findings reveal that thermal performance does not necessarily reflect the thermal geography of a species. We demonstrate that warm-edge populations can be less sensitive to thermal stress than cooler, central populations suggesting that Mediterranean seagrasses have greater resilience to warming than current paradigms suggest.

The Economics Spectrum Drives Root Trait Strategies in Mediterranean Vegetation

Extensive research efforts are devoted to understand fine root trait variation and to confirm the existence of a belowground root economics spectrum (RES) from acquisitive to conservative root strategies that is analogous to the leaf economics spectrum (LES). The economics spectrum implies a trade-off between maximizing resource acquisition and productivity or maximizing resource conservation and longevity; however, this theoretical framework still remains controversial for roots. We compiled a database of 320 Mediterranean woody and herbaceous species to critically assess if the classic economics spectrum theory can be broadly extended to roots. Fine roots displayed a wide diversity of forms and properties in Mediterranean vegetation, resulting in a multidimensional trait space. The main trend of variation in this multidimensional root space is analogous to the main axis of LES, while the second trend of variation is partially determined by an anatomical trade-off between tissue density and diameter. Specific root area (SRA) is the main trait explaining species distribution along the RES, regardless of the selected traits. We advocate for the need to unify and standardize the criteria and approaches used within the economics framework between leaves and roots, for the sake of theoretical consistency.

Fine-scale coexistence between Mediterranean mesocarnivores is mediated by spatial, temporal, and trophic resource partitioning

The partition of the ecological niche can enhance the coexistence of predators due to differences in how they exploit three main resources: food, space, and time, the latter being an axis that often remains unexplored.We studied niche segregation in a Mediterranean mesocarnivore community composed by Vulpes vulpes, Genetta genetta, Meles meles, and Herpestes ichneumon, addressing simultaneously different niche axes: the temporal, trophic, and spatial axes.We assessed temporal segregation between mesopredators and prey and between potential competitors, using camera trap data between 2018 and 2020 in a Mediterranean landscape in Southern Spain. We deployed camera traps in 35 stations in three sites with varying vegetation cover within Doñana National Park. We further examined the spatial overlap in activity centers and trophic preferences between potential competitors using diet information from studies performed in the study area.We found an overall temporal segregation between trophic generalist species, with species showing higher temporal overlap differing in their trophic preferences and/or showing limited spatial overlap. Furthermore, we observed an overall high overlap between the activity patterns of predators and their major prey in the area (the common genet vs. small mammals and the red fox vs. European rabbit).Our study suggests that coexistence of the different species that compose the mesocarnivore assemblage in Mediterranean landscapes can be facilitated by subtle differences along the three main niche axes, with temporal segregation being a most pronounced mechanism. Our findings reinforce the idea that the coexistence mechanisms underlying community structure are multidimensional.

Microvesicles carrying LRP5 induce macrophage polarization to an anti-inflammatory phenotype

Microvesicles (MV) contribute to cell-to-cell communication through their transported proteins and nucleic acids. MV, released into the extracellular space, exert paracrine regulation by modulating cellular responses after interaction with near and far target cells. MV are released at high concentrations by activated inflammatory cells. Different subtypes of human macrophages have been characterized based on surface epitopes being CD16+ macrophages associated with anti-inflammatory phenotypes. We have previously shown that low-density lipoprotein receptor-related protein 5 (LRP5), a member of the LDLR family that participates in lipid homeostasis, is expressed in macrophage CD16+ with repair and survival functions. The goal of our study was to characterize the cargo and tentative function of macrophage-derived MV, whether LRP5 is delivered into MV and whether these MV are able to induce inflammatory cell differentiation to a specific CD16- or CD16+ phenotype. We show, for the first time, that lipid-loaded macrophages release MV containing LRP5. LDL loading induces increased expression of macrophage pro-inflammatory markers and increased release of MV containing pro-inflammatory markers. Conditioning of fresh macrophages with MV released by Lrp5-silenced macrophages induced the transcription of inflammatory genes and reduced the transcription of anti-inflammatory genes. Thus, MV containing LRP5 induce anti-inflammatory phenotypes in macrophages.

Control of Brain State Transitions with a Photoswitchable Muscarinic Agonist

The ability to control neural activity is essential for research not only in basic neuroscience, as spatiotemporal control of activity is a fundamental experimental tool, but also in clinical neurology for therapeutic brain interventions. Transcranial-magnetic, ultrasound, and alternating/direct current (AC/DC) stimulation are some available means of spatiotemporal controlled neuromodulation. There is also light-mediated control, such as optogenetics, which has revolutionized neuroscience research, yet its clinical translation is hampered by the need for gene manipulation. As a drug-based light-mediated control, the effect of a photoswitchable muscarinic agonist (Phthalimide-Azo-Iper (PAI)) on a brain network is evaluated in this study. First, the conditions to manipulate M2 muscarinic receptors with light in the experimental setup are determined. Next, physiological synchronous emergent cortical activity consisting of slow oscillations-as in slow wave sleep-is transformed into a higher frequency pattern in the cerebral cortex, both in vitro and in vivo, as a consequence of PAI activation with light. These results open the way to study cholinergic neuromodulation and to control spatiotemporal patterns of activity in different brain states, their transitions, and their links to cognition and behavior. The approach can be applied to different organisms and does not require genetic manipulation, which would make it translational to humans.

Perceptions of people with intellectual and developmental disabilities about COVID-19 in Spain: a cross-sectional study

BACKGROUND

As the world battles COVID-19, there is a need to study the perceptions of people with intellectual and developmental disabilities (IDD) about the effects of the pandemic and associated lockdown on their lives. This work explores the perceptions of Spaniards with IDD during the lockdown with respect to four topics: access to information, emotional experiences, effects on living conditions and access to support.

METHODS

The topics were explored using a subset of 16 closed-ended questions from an online survey. In total, 582 participants with IDD completed the survey. The frequencies and percentages of responses to the questions were calculated, and chi-square tests performed to explore the relationship between participants' sociodemographic characteristics and responses. Given that people differed in the way in which they completed the survey, the relationship between participants' responses and completion method was also analysed.

RESULTS

Participants reported that the pandemic and subsequent lockdown have had a deleterious effect on their emotional well-being (around 60.0% of participants) and occupations (48.0% of students and 72.7% of workers). Although access to information and support was reportedly good overall, being under the age of 21 years and studying were associated with perceptions reflecting poorer access to information (V = .20 and V = .13, respectively) and well-being support (V = .15 and V = .13, respectively). Being supported by a third party to complete the survey was consistently related to perceptions of worse outcomes.

CONCLUSIONS

The study yielded data on the perceptions of people with IDD regarding the effects that COVID-19 and the subsequent lockdown have had on their lives. Suggestions on how to overcome the difficulties reported and future lines of research are discussed.

Metabolic Profiling of Resistant and Susceptible Tobaccos Response Incited by Ralstonia pseudosolanacearum Causing Bacterial Wilt

The causal agent of bacterial wilt, Ralstonia pseudosolanacearum, can cause significant economic losses during tobacco production. Metabolic analyses are a useful tool for the comprehensive identification of plant defense response metabolites. In this study, a gas chromatography-mass spectrometry (GC-MS) approach was used to identify metabolites differences in tobacco xylem sap in response to R. pseudosolanacearum CQPS-1 in two tobacco cultivars: Yunyan87 (susceptible to R. pseudosolanacearum) and K326 (quantitatively resistant). Metabolite profiling 7 days post inoculation with R. pseudosolanacearum identified 88 known compounds, 42 of them enriched and 6 depleted in the susceptible cultivar Yunyan87, while almost no changes occurred in quantitatively resistant cultivar K326. Putrescine was the most enriched compound (12-fold) in infected susceptible tobacco xylem, followed by methyl-alpha-d-glucopyranoside (9-fold) and arabinitol (6-fold). Other sugars, amino acids, and organic acids were also enriched upon infection. Collectively, these metabolites can promote R. pseudosolanacearum growth, as shown by the increased growth of bacterial cultures supplemented with xylem sap from infected tobacco plants. Comparison with previous metabolic data showed that beta-alanine, phenylalanine, and leucine were enriched during bacterial wilt in both tobacco and tomato xylem.

C1 esterase inhibitor and the contact system in COVID-19

Coronavirus disease 2019 (COVID-19) is frequently associated with severe systemic consequences, including vasculitis, a hyperinflammatory state and hypercoagulation. The mechanisms leading to these life-threatening abnormalities are multifactorial. Based on the analysis of publicly available interactomes, we propose that severe acute respiratory syndrome coronavirus-2 infection directly causes a deficiency in C1 esterase inhibitor, a pathogen-specific mechanism that may help explain significant systemic abnormalities in patients with COVID-19.