The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti

<p>Abstract</p> <p>Background</p> <p><it>Rhizobium</it>-Legume symbiosis is an attractive biological process that has been studied for decades because of its importance in agriculture. However, this system has undergone extensive study and although many of the major factors underpinning the process have been discovered using traditional methods, much remains to be discovered.</p> <p>Results</p> <p>Here we present an analysis of the 'Symbiosis Interactome' using novel computational methods in order to address the complex dynamic interactions between proteins involved in the symbiosis of the model bacteria <it>Sinorhizobium meliloti </it>with its plant hosts. Our study constitutes the first large-scale analysis attempting to reconstruct this complex biological process, and to identify novel proteins involved in establishing symbiosis. We identified 263 novel proteins potentially associated with the Symbiosis Interactome. The topology of the Symbiosis Interactome was used to guide experimental techniques attempting to validate novel proteins involved in different stages of symbiosis. The contribution of a set of novel proteins was tested analyzing the symbiotic properties of several <it>S. meliloti </it>mutants. We found mutants with altered symbiotic phenotypes suggesting novel proteins that provide key complementary roles for symbiosis.</p> <p>Conclusion</p> <p>Our 'systems-based model' represents a novel framework for studying host-microbe interactions, provides a theoretical basis for further experimental validations, and can also be applied to the study of other complex processes such as diseases.</p

Treatment of type 2 diabetes by patient profile in the clinical practice of endocrinology in Spain: Delphi study results from the think twice program

Introduction: The aim of this Delphi study is to unveil the management of patients with type 2 diabetes (T2D) and different levels of complexity in the clinical practice in Spain. Methods: Based on the common management practices of T2D profiles reported by Spanish endocrinologists, a Delphi questionnaire of 55 statements was developed and responded to by a national panel (n = 101). Results: A consensus was reached for 30 of the 55 statements. Regarding overweight patients inadequately controlled with metformin, treatment with a sodium-glucose transport protein 2 inhibitor (SGLT2-I) is preferred over treatment with a dipeptidyl peptidase-4 inhibitor (DPP4-I). If the patient is already being treated with a DPP4-I, an SGLT2-I is added on to the treatment regimen rather than replacing the DPP4-I. Conversely, if the treatment regimen includes a sulfonylurea, it is usually replaced by other antihyperglycemic agents. Current treatment trends in uncontrolled obese patients include the addition of an SGLT2-I or a glucagon-like peptide-1 receptor agonist (GLP1-RA) to background therapy. When the glycated hemoglobin target is not reached, triple therapy with metformin ? GLP1-RA ? SGLT2-I is initiated. Although SGLT2-Is are the treatment of choice in patients with T2D and heart failure or uncontrolled hypertension, no consensus was reached regarding the preferential use of SGLT2- Is or GLP1-RAs in patients with established cardiovascular disease. Conclusion: Consensus has been reached for a variety of statements regarding the management of several T2D profiles. Achieving a more homogeneous management of complex patients with T2D may require further evidence and a better understanding of the key drivers for treatment choice

Zeolites functionalised with essential oils as new fungicidal materials for citrus fruits

Postharvest diseases produced by fungi are one of the main problems affecting the quality of agricultural products during storage. In citrus fruits, the largest economic losses are caused by wound pathogens, in particular, by Penicillium digitatum (PD), Penicillium italicum (PI) and Geotrichum citri-aurantii (GC), causing citrus green mould, blue mould and sour rot, respectively

Atomic surface segregation and structural characterization of PdPt bimetallic nanoparticles

"Bimetallic nanoparticles are of interest since they lead to many interesting electrical, chemical, catalytic, and optical properties. They are particularly important in the field of catalysis since they show superior catalytic properties than their monometallic counterparts. The structures of bimetallic nanoparticles depend mainly on the synthesis conditions and the miscibility of the two components. In this work, PdPt alloyed-bimetallic nanoparticles (NPs) were synthesized through the polyol method, and characterized using spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM). High-angle annular dark-field (HAADF)-STEM images of bimetallic nanoparticles were obtained. The contrast of images shows that nanoparticles have an alloy structure with an average size of 8.2 nm. Together with the characterization of nanoparticles, a systematic molecular dynamics simulations study focused on the structural stability and atomic surface segregation trends in 923-atom PdPt alloyed-bimetallic NPs was carried out.

Micro and mesoporous materials with essential oils as sustainable biocide materials

Over the last few years policy is shifting towards more sustainable models, and agriculture is changing together. Legislative changes in the use of pesticides lead to the search for new materials that guarantee the needs of the present without compromising future generations. Consequently, there is an increasing necessity to develop new sustainable materials with fungicidal properties to preserve the quality of fresh horticultural produce during storage. Postharvest diseases of citrus fruits, mainly caused by wound pathogens such as Penicillium digitatum (PD), Penicillium italicum (PI) and Geotrichum citri-aurantii (GC), can produce large economic losses [1]. Many studies have been conducted to find biocide materials that may control the development of these fungi. It has been reported that silver-functionalised zeolitic materials are effective to reduce decay on oranges infected by these fungi [2], but the release of silver may be a problem due to strict regulations associated with food products. An alternative can be the use natural substances as thyme and cinnamon essential oils supported on zeolites as biocidal agents against PD, PI and GC. In vitro studies using Faujasite zeolites impregnated with essential oils at different concentrations showed a significant fungal growth inhibition, obtaining the best results with thyme essential oil. In subsequent in vivo studies, LTA and MCM-22 zeolites synthesized from silica extracted from rice husks, SiO2 and a pillared clay with 20% by weight of thyme essential oil were applied to oranges artificially inoculated with each fungus. Results showed that the antifungal activity highly depended on the fungus and the material used. LTA zeolite with 20% thyme essential oil was the most active antifungal material. As another alternative, silica mesoporous materials were synthetised and impregnated with pomegranate peel extract (PPE) in aqueous or methanolic medium. In in vitro studies, these materials inhibited the growth of PD by 80% compared to the control without functionalised silica. Furthermore, in vivo studies with oranges artificially inoculated with each fungus showed the biocidal activity of the PPE-functionalised materials, especially against PD and PI. Nevertheless, optimization of these materials is still necessary to improve their disease control and general performance

Methylation changes induced by a glycodendropeptide immunotherapy and associated to tolerance in mice

IntroductionAllergen-specific immunotherapy (AIT) is applied as treatment to rise tolerance in patients with food allergies. Although AIT is thoroughly used, the underlying epigenetic events related to tolerant induction are still unknown. Thus, we aim to investigate epigenetic changes that could be related to tolerance in dendritic cells (DCs) from anaphylactic mice to lipid transfer proteins, Pru p 3, in the context of a sublingual immunotherapy (SLIT) with a glycodendropeptide (D1ManPrup3) that has demonstrated tolerant or desensitization responses depending on the treatment dose.MethodsChanges in DNA methylation in CpG context were determined comparing Sensitized (Antigen-only) animals and two groups receiving SLIT with the D1ManPrup3 nanostructure (D1ManPrup3-SLIT): Tolerant (2nM D1ManPrup3) and Desensitized (5nM D1ManPrup3), against anaphylactic animals. DNA from lymph nodes-DCs were isolated and then, Whole Genome Bisulphite Sequencing was performed to analyze methylation.ResultsMost differentially methylated regions were found on the area of influence of gene promoters (DMPRs). Compared to the Anaphylactic group, the highest value was found in Desensitized mice (n = 7,713 DMPRs), followed by Tolerant (n = 4,091 DMPRs) and Sensitized (n = 3,931 DMPRs) mice. Moreover, many of these epigenetic changes were found in genes involved in immune and tolerance responses (Il1b, Il12b, Il1a, Ifng, and Tnf) as shown by functional enrichment (DCs regulation, B cell-mediated immunity, and effector mechanisms).DiscussionIn conclusion, different doses of D1ManPrup3-SLIT induce different DNA methylation changes, which are reflected in the induction of distinct responses, tolerance, or desensitization

Extracellular vesicles from pristane-treated CD38-deficient mice express an antiinflammatory neutrophil protein signature, which reflects the mild lupus severity elicited in these mice

In CD38-deficient (Cd38-/-) mice intraperitoneal injection of pristane induces a lupus-like disease, which is milder than that induced in WT mice, showing significant differences in the inflammatory and autoimmune processes triggered by pristane. Extracellular vesicles (EV) are present in all body fluids. Shed by cells, their molecular make-up reflects that of their cell of origin and/or tissue pathological situation. The aim of this study was to analyze the protein composition, protein abundance, and functional clustering of EV released by peritoneal exudate cells (PECs) in the pristane experimental lupus model, to identify predictive or diagnostic biomarkers that might discriminate the autoimmune process in lupus from inflammatory reactions and/or normal physiological processes. In this study, thanks to an extensive proteomic analysis and powerful bioinformatics software, distinct EV subtypes were identified in the peritoneal exudates of pristane-treated mice: 1) small EV enriched in the tetraspanin CD63 and CD9, which are likely of exosomal origin; 2) small EV enriched in CD47 and CD9, which are also enriched in plasma-membrane, membrane-associated proteins, with an ectosomal origin; 3) small EV enriched in keratins, ECM proteins, complement/coagulation proteins, fibrin clot formation proteins, and endopetidase inhibitor proteins. This enrichment may have an inflammation-mediated mesothelial-tomesenchymal transition origin, representing a protein corona on the surface of peritoneal exudate EV; 4) HDL-enriched lipoprotein particles. Quantitative proteomic analysis allowed us to identify an anti-inflammatory, Annexin A1- enriched pro-resolving, neutrophil protein signature, which was more prominent in EV from pristane-treated Cd38-/- mice, and quantitative differences in the protein cargo of the ECM-enriched EV from Cd38-/- vs WT mice. These differences are likely to be related with the distinct inflammatory outcome shown by Cd38-/- vs WT mice in response to pristane treatment. Our results demonstrate the power of a hypothesis-free and data-driven approach to transform the heterogeneity of the peritoneal exudate EV from pristanetreated mice in valuable information about the relative proportion of different EV in a given sample and to identify potential protein markers specific for the different small EV subtypes, in particular those proteins defining EV involved in the resolution phase of chronic inflammation.Proyecto del plan estatal, Ministerio de Ciencia e Innovacion PT13/0001/011CSIC PT17/0019/0010 PID2020-119567RB-I0