Rhizogenic Agrobacterium protein RolB interacts with the TOPLESS repressor proteins to reprogram plant immunity and development.

Rhizogenic Agrobacterium strains comprise biotrophic pathogens that cause hairy root disease (HRD) on hydroponically grown Solanaceae and Cucurbitaceae crops, besides being widely explored agents for the creation of hairy root cultures for the sustainable production of plant-specialized metabolites. Hairy root formation is mediated through the expression of genes encoded on the T-DNA of the root-inducing (Ri) plasmid, of which several, including root oncogenic locus B (rolB), play a major role in hairy root development. Despite decades of research, the exact molecular function of the proteins encoded by the rol genes remains enigmatic. Here, by means of TurboID-mediated proximity labeling in tomato (Solanum lycopersicum) hairy roots, we identified the repressor proteins TOPLESS (TPL) and Novel Interactor of JAZ (NINJA) as direct interactors of RolB. Although these interactions allow RolB to act as a transcriptional repressor, our data hint at another in planta function of the RolB oncoprotein. Hence, by a series of plant bioassays, transcriptomic and DNA-binding site enrichment analyses, we conclude that RolB can mitigate the TPL functioning so that it leads to a specific and partial reprogramming of phytohormone signaling, immunity, growth, and developmental processes. Our data support a model in which RolB manipulates host transcription, at least in part, through interaction with TPL, to facilitate hairy root development. Thereby, we provide important mechanistic insights into this renowned oncoprotein in HRD.

MINI-AC: inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles.

Gene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. Plant GRNs control transcriptional programs involved in growth, development, and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context-specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI-AC (Motif-Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single-cell experiments with TF binding site (TFBS) information to learn GRNs in plants. We benchmarked MINI-AC using bulk AC datasets from different Arabidopsis thaliana tissues and showed that it outperforms other methods to identify correct TFBS. In maize, a crop with a complex genome and abundant distal AC regions, MINI-AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF-target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC-based GRNs with MINI-AC. Finally, we combined MINI-AC predictions from bulk and single-cell AC datasets to identify general and cell-type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI-AC represents a powerful tool for inferring accurate AC-derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.

Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots.

Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs have been characterized as important regulators in different biological processes, little is known about the transcriptional regulation for most plant lincRNAs. Through the integration of 8 annotation resources, we defined 6,599 high-confidence lincRNA loci in Arabidopsis (Arabidopsis thaliana). For lincRNAs belonging to different evolutionary age categories, we identified major differences in sequence and chromatin features, as well as in the level of conservation and purifying selection acting during evolution. Spatiotemporal gene expression profiles combined with transcription factor (TF) chromatin immunoprecipitation (ChIP) data were used to construct a TF-lincRNA regulatory network containing 2,659 lincRNAs and 15,686 interactions. We found that properties characterizing lincRNA expression, conservation, and regulation differ between plants and animals. Experimental validation confirmed the role of 3 TFs, KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4, as key regulators controlling root-specific lincRNA expression, demonstrating the predictive power of our network. Furthermore, we identified 58 lincRNAs, regulated by these TFs, showing strong root cell type-specific expression or chromatin accessibility, which are linked with genome-wide association studies genetic associations related to root system development and growth. The multilevel genome-wide characterization covering chromatin state information, promoter conservation, and chromatin immunoprecipitation-based TF binding, for all detectable lincRNAs across 769 expression samples, permits rapidly defining the biological context and relevance of Arabidopsis lincRNAs through regulatory networks.

Enhanced optical vector bottle beams with obscured nodal surfaces.

Optical bottle beams, characterized by their unique three-dimensional dark core, have garnered substantial interest due to their potential applications across multiple domains of science and technology. This paper delves into the current methods used to create these beams and provides a method to obscure their nodal planes through coaxial non-interfering orthogonally polarized beams to generate bottle beams with enhanced uniformity. Experimental and theoretical results show the enhanced vector bottle beam maintains a smaller, more spherically uniform potential well and interesting quasi-particle polarization characteristics.

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles.

JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.

Density-Dependence of Surface Transport in Tellurium-Enriched Nanograined Bulk Bi2 Te3.

Three-dimensional topological insulators (3D TI) exhibit conventional parabolic bulk bands and protected Dirac surface states. A thorough investigation of the different transport channels provided by the bulk and surface carriers using macroscopic samples may provide a path toward accessing superior surface transport properties. Bi2 Te3 materials make promising 3D TI models; however, due to their complicated defect chemistry, these materials have a high number of charge carriers in the bulk that dominate the transport, even as nanograined structures. To partially control the bulk charge carrier density, herein the synthesis of Te-enriched Bi2 Te3 nanoparticles is reported. The resulting nanoparticles are compacted into nanograined pellets of varying porosity to tailor the surface-to-volume ratio, thereby emphasizing the surface transport channels. The nanograined pellets are characterized by a combination of resistivity, Hall- and magneto-conductance measurements together with (THz) time-domain reflectivity measurements. Using the Hikami-Larkin-Nagaoka (HLN) model, a characteristic coherence length of ≈200 nm is reported that is considerably larger than the diameter of the nanograins. The different contributions from the bulk and surface carriers are disentangled by THz spectroscopy, thus emphasizing the dominant role of the surface carriers. The results strongly suggest that the surface transport carriers have overcome the hindrance imposed by nanoparticle boundaries.

Activation of T cell checkpoint pathways during ß-cell antigen presentation by engineered dendritic cells promotes protection from type 1 diabetes.

Defective immune regulation has been recognized in type 1 diabetes (T1D). Immune regulatory T cell check-point receptors, which are generally upregulated on activated T cells, have been the molecules of attention as therapeutic targets for enhancing immune response in tumour therapy. Here, we show that pancreatic ß-cell antigen (BcAg) presentation by engineered tolerogenic dendritic cells (tDCs) that express CTLA4 selective ligand (B7.1wa) or a combination of CTLA4, PD1 and BTLA selective ligands (B7.1wa, PD-L1 and HVEM-CRD1 respectively; multiligand-DCs) causes an increase in regulatory cytokine and T cell (Treg) responses and suppression of the effector T cell function as compared with engineered control-DCs. Non-obese diabetic mice treated with BcAg-pulsed CTLA4-ligand-DCs and multiligand-DCs at pre-diabetic and early-hyperglycaemic stages showed significantly lower degree of insulitis, higher frequencies of insulin-positive islets, profound delay in and reversal of hyperglycaemia for a significant duration. Immune cells from the tDC-treated mice not only produced lower amounts of IFNγ and higher amounts of IL10 and TGFß1 upon BcAg challenge, but also failed to induce hyperglycaemia upon adoptive transfer. While both CTLA4-ligand-DCs and multiligand-DCs were effective in inducing tolerance, multiligand-DC treatment produced an overall higher suppressive effect on effector T cell function and disease outcome. These studies show that enhanced engagement of T cell checkpoint receptors during BcAg presentation can modulate T cell function and suppress autoimmunity and progression of the disease in T1D.

Unidirectional Modes Induced by Nontraditional Coriolis Force in Stratified Fluids.

Using topology, we unveil the existence of new unidirectional modes in compressible rotating stratified fluids. We relate their emergence to the breaking of time-reversal symmetry by rotation and vertical mirror symmetry by stratification and gravity. We stress the role of the Coriolis force's nontraditional part, induced by a rotation field tangent to the surface. In contrast with horizontally trapped equatorial waves induced by the traditional component of the Coriolis force perpendicular to the surface, we find vertically trapped modes that propagate along interfaces between regions with distinct stratification properties. We show that such modes are generalized atmospheric Lamb waves whose direction of propagation can be selected by the nontraditional component of the Coriolis force.

Position statement on the use of albumin in liver cirrhosis.

Cirrhosis is characterised by a prolonged asymptomatic period in which the inflammation persists, increasing as the disease progresses. Characteristic of this is the increase in pro-inflammatory cytokines and pro-oxidant molecules which are determining factors in the development of multiple organ dysfunction. In the early development of cirrhosis, splanchnic arterial vasodilation, activation of vasoconstrictor systems (renin-angiotensin-aldosterone) and the sympathetic nervous system (noradrenaline) bring about bacterial translocation and systemic dissemination via portal circulation of bacterial products, and molecular patterns associated with damage, which exacerbate the systemic inflammation present in the patient with cirrhosis. Albumin is a molecule that undergoes structural and functional changes as liver damage progresses, affecting its antioxidant, immunomodulatory, oncotic and endothelial stabilising properties. Our knowledge of the properties of albumin reveals a molecule with multiple treatment options in patients with cirrhosis, from the compensated then decompensated phases to multiple organ dysfunction. Its recognised uses in spontaneous bacterial peritonitis, post-paracentesis circulatory dysfunction, acute kidney injury and hepatorenal syndrome are fully validated, and a treatment option has opened up in decompensated cirrhosis and in acute-on-chronic liver disease.

Widefield SERS for High-Throughput Nanoparticle Screening.

Surface-enhanced Raman scattering (SERS) imaging is a powerful technology with unprecedent potential for ultrasensitive chemical analysis. Point-by-point scanning and often excessively long spectral acquisition-times hamper the broad exploitation of the full analytical potential of SERS. Here, we introduce large-scale SERS particle screening (LSSPS), a multiplexed widefield screening approach to particle characterization, which is 500-1000 times faster than typical confocal Raman implementations. Beyond its higher throughput, LSSPS simultaneously quantifies both the sample's Raman and Rayleigh scattering to directly quantify the fraction of SERS-active particles which allows for an unprecedented correlation of SERS activity with particle size. .

Interface-Dominated Topological Transport in Nanograined Bulk Bi2 Te3.

3D topological insulators (TI) host surface carriers with extremely high mobility. However, their transport properties are typically dominated by bulk carriers that outnumber the surface carriers by orders of magnitude. A strategy is herein presented to overcome the problem of bulk carrier domination by using 3D TI nanoparticles, which are compacted by hot pressing to macroscopic nanograined bulk samples. Bi2 Te3 nanoparticles well known for their excellent thermoelectric and 3D TI properties serve as the model system. As key enabler for this approach, a specific synthesis is applied that creates nanoparticles with a low level of impurities and surface contamination. The compacted nanograined bulk contains a high number of interfaces and grain boundaries. Here it is shown that these samples exhibit metallic-like electrical transport properties and a distinct weak antilocalization. A downward trend in the electrical resistivity at temperatures below 5 K is attributed to an increase in the coherence length by applying the Hikami-Larkin-Nagaoka model. THz time-domain spectroscopy reveals a dominance of the surface transport at low frequencies with a mobility of above 103 cm2 V-1 s-1 even at room temperature. These findings clearly demonstrate that nanograined bulk Bi2 Te3 features surface carrier properties that are of importance for technical applications.

Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors.

Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.

Nonlinear self-trapping and guiding of light at different wavelengths with sheep blood.

We demonstrate the formation of waveguides, a few centimeters long, in colloidal suspensions of sheep red blood cells for a wide range of wavelengths due to nonlinear self-trapping and self-guiding of a laser beam. The near infrared (NIR) light experiences a weaker nonlinear self-action and thus requires much higher power to obtain self-trapping as compared to visible light. To examine the waveguiding of light at different wavelengths, we utilize a pump-probe-type setting for beam coupling: a pump beam at a 532 nm wavelength is used to create a waveguide first, and then a probe beam with various wavelengths is sent through the waveguide channel. Effective guidance for both visible and NIR wavelengths is observed through such otherwise highly scattering bio-soft-matter.

A longitudinal multiethnic study of biomarkers in systemic lupus erythematosus: Launching the GLADEL 2.0 Study Group.

Introduction: After more than 20 years of sustained work, the Latin American Group for the Study of Lupus (GLADEL) has made a significant number of contributions to the field of lupus, not only in the differential role that race/ethnicity plays in its course and outcome but also in several other studies including the beneficial effects of using antimalarials in lupus patients and the development of consensus guidelines for the treatment of lupus in our region. Methods: A new generation of "Lupus Investigators" in more than 40 centers throughout Latin America has been constituted in order to continue the legacy of the investigators of the original cohort and to launch a novel study of serum and urinary biomarkers in patients with systemic lupus erythematosus. Results: So far, we have recruited 807 patients and 631 controls from 42 Latin-American centers including 339 patients with SLE without renal involvement, 202 patients with SLE with prevalent but inactive renal disease, 176 patients with prevalent and active renal disease and 90 patients with incident lupus nephritis. Conclusions: The different methodological aspects of the GLADEL 2.0 cohort are discussed in this manuscript, including the challenges and difficulties of conducting such an ambitious project.

Water Content Monitoring in Water-in-Crude-Oil Emulsions Using an Ultrasonic Multiple-Backscattering Sensor.

This work shows the application of an ultrasonic multiple-scattering sensor for monitoring water-in-petroleum emulsions. The sensor consists of a commercial ultrasonic transducer with an array of cylindrical scatterers placed in the near field. The scatterers are thin metal bars arranged in rows in front of the transducer. The backscattering signals were analyzed by calculating the wave energy and by a cross-correlation between signal segments; they were also used to determine the propagation velocity in the emulsions. The tests performed used emulsions with water volume concentrations from 0% to 50%. The results showed that both the signal energy and propagation velocity strongly depended on the concentration of water in the emulsion. Therefore, the ultrasonic multiple-scattering sensor can be used for on-line and real-time monitoring of the water content in water-in-crude-oil emulsions.

Three-Dimensional Surface-Enhanced Raman Scattering Platforms: Large-Scale Plasmonic Hotspots for New Applications in Sensing, Microreaction, and Data Storage.

Surface-enhanced Raman scattering (SERS) is a molecular-specific spectroscopic technique that provides up to 1010-fold enhancement of signature Raman fingerprints using nanometer-scale 0D to 2D platforms. Over the past decades, 3D SERS platforms with additional plasmonic materials in the z-axis have been fabricated at sub-micrometer to centimeter scale, achieving higher hotspot density in all x, y, and z spatial directions and higher tolerance to laser misalignment. Moreover, the flexibility to construct platforms in arbitrary sizes and 3D shapes creates attractive applications besides traditional SERS sensing. In this Account, we introduce our library of substrate-based and substrate-less 3D plasmonic platforms, with an emphasis on their non-sensing applications as microlaboratories and data storage labels. We aim to provide a scientific synopsis on these high-potential yet currently overlooked applications of SERS and ignite new scientific discoveries and technology development in 3D SERS platforms to tackle real-world issues. One highlight of our substrate-based SERS platforms is multilayered platforms built from micrometer-thick assemblies of plasmonic particles, which can achieve up to 1011 enhancement factor. As an alternative, constructing 3D hotspots on non-plasmonic supports significantly reduces waste of plasmonic materials while allowing high flexibility in structural design. We then introduce our emerging substrate-less plasmonic capsules including liquid marbles and colloidosomes, which we further incorporate the latter within an aerosol to form centimeter-scale SERS-active plasmonic cloud, the world's largest 3D SERS platform to date. We then discuss the various emerging applications arising only from these 3D platforms, in the fields of sensing, microreactions, and data storage. An important novel sensing application is the stand-off detection of airborne analytes that are several meters away, made feasible with aerosolized plasmonic clouds. We also describe plasmonic capsules as excellent miniature lab-in-droplets that can simultaneously provide in situ monitoring at the molecular level during reaction, owing to their ultrasensitive 3D plasmonic shells. We highlight the emergence of 3D SERS-based data storage platforms with 10-100-fold higher storage density than 2D platforms, featuring a new approach in the development of level 3 security (L3S) anti-counterfeiting labels. Ultimately, we recognize that 3D SERS research can only be developed further when its sensing capabilities are concurrently strengthened. With this vision, we foresee the creation of highly applicable 3D SERS platforms that excel in both sensing and non-sensing areas, providing modern solutions in the ongoing Fourth Industrial Revolution.

Ionic Liquid-Based Low-Temperature Synthesis of Phase-Pure Tetradymite-Type Materials and Their Thermoelectric Properties.

Phase-pure crystalline Bi2Se3 and Bi2Te3 nanoparticles are formed in reactions of [C4C1Im]3[Bi3I12] (C4C1Im = 1-butyl-3-methylimidazolium) with [C4C1Pyr][ESiMe3] (E = Se or Te; C4C1Pyr = 1-butyl-1-methylpyrrolidinium) in the ionic liquid (IL) [C4C1Im]I. The resulting crystalline tetradymite-type nanoparticles exhibit stoichiometric Bi:E (E = Se or Te) molar ratios (2:3). Because all synthetic steps were performed under strict inert gas conditions, the surfaces of the Bi2Se3 and Bi2Te3 nanoparticles are free of metal oxide species. As proven by infrared and X-ray photoelectron spectroscopy analyses, the nanoparticle surfaces reveal only minor organic contamination from solvent residues ([C4C1Im]I). The nanomaterials show high Seebeck coefficients of -124 µV K-1 (Bi2Se3) and -155 µV K-1 (Bi2Te3) and feature high electrical conductivities (328 and 946 S cm-1, respectively) at the highest tested temperature (240 °C). The corresponding thermal conductivities (0.8 and 2.3 W m-1 K-1, respectively, at 30 °C) are comparable to those of single crystals and recently reported ab initio calculations, which is in remarkable contrast to typical findings of nanograined bulk materials obtained from compacted nanoparticles. These findings emphasize the low level of impurities, surface contamination, and, in general, defects produced by the synthetic approach reported here. The figure of merit in the in-plane direction of the compacted pellets reached peak values 0.45 for Bi2Se3 and 0.4 for Bi2Te3.

Entropy of Conduction Electrons from Transport Experiments.

The entropy of conduction electrons was evaluated utilizing the thermodynamic definition of the Seebeck coefficient as a tool. This analysis was applied to two different kinds of scientific questions that can-if at all-be only partially addressed by other methods. These are the field-dependence of meta-magnetic phase transitions and the electronic structure in strongly disordered materials, such as alloys. We showed that the electronic entropy change in meta-magnetic transitions is not constant with the applied magnetic field, as is usually assumed. Furthermore, we traced the evolution of the electronic entropy with respect to the chemical composition of an alloy series. Insights about the strength and kind of interactions appearing in the exemplary materials can be identified in the experiments.

Complex dietary polysaccharide modulates gut immune function and microbiota, and promotes protection from autoimmune diabetes.

The dietary supplement and prebiotic values of ß-glucan-rich products have been widely recognized and dietary approaches for modulating autoimmunity have been increasingly explored, we assess the impact of oral administration of high-purity yeast ß-glucan (YBG) on gut immune function, microbiota and type 1 diabetes (T1D) using mouse models. Oral administration of this non-digestible complex polysaccharide caused a dectin-1-dependent immune response involving increased expression of interleukin-10 (IL-10), retinaldehyde dehydrogenase (Raldh) and pro-inflammatory cytokines in the gut mucosa. YBG-exposed intestinal dendritic cells induced/expanded primarily Foxp3+ , IL-10+ and IL-17+ T cells, ex vivo. Importantly, prolonged oral administration of low-dose YBG at pre-diabetic stage suppressed insulitis and significantly delayed the appearance of T1D in non-obese diabetic (NOD) mice. Further, prolonged treatment with YBG showed increased Foxp3+ T-cell frequencies, and a significant change in the gut microbiota, particularly an increase in the abundance of Bacteroidetes and a decrease in the Firmicute members. Oral administration of YBG, together with Raldh-substrate and ß-cell antigen, resulted in better protection of NOD mice from T1D. These observations suggest that YBG not only has a prebiotic property, but also an oral tolerogenic-adjuvant-like effect, and these features could be exploited for modulating autoimmunity in T1D.

Normative data for static balance testing in healthy individuals using open source computerized posturography.

PURPOSE: Computerized posturography is the gold standard for balance assessment. Because of the great cost and dimensions of commercial equipments, low-cost and portable devices have been developed and validated, such as RombergLab, a software in open source term which works connected with a low-cost force platform. The objective of this study was to obtain normative posturography data using this software. METHODS: A multicentric prospective and descriptive study, with 350 healthy participants, was designed. Static postural stability (measured using the modified clinical test of sensory interaction on balance) was evaluated using the software connected to the force platform. Using the confidence ellipse area (CEA) in each condition, global equilibrium score (GES) was calculated and adjusted for significant variable factors using cluster analysis. RESULTS: Mean (SD) GES was 0.72 (0.22). Age (p < 0.01), height (p < 0.01) and recruitment center (p < 0.05) were found as influence factors for GES. Cluster analysis obtained 16 groups stratified by age and height. GES decreases with age and height (p < 0.005). No significant interaction of age nor height was found with GES in these clusters (p > 0.05). After correction for height and age, GES was no longer influenced by the recruitment center (p > 0.05). CONCLUSIONS: With the introduction of the global equilibrium score values of the present study into the software, we consider RombergLab v1.3 a reference posturography tool for healthy individuals. Further studies are needed for validating it as a suitable instrumented test for screening between healthy and pathologic subjects and its reliability over time for the follow-up of patients.