Genomic analysis of the first european bacteriophages with depolymerase activity and biocontrol efficacy against the phytopathogen Ralstonia solanacearum

Ralstonia solanacearum is the causative agent of bacterial wilt, one of the most destructive plant diseases. While chemical control has an environmental impact, biological control strategies can allow sustainable agrosystems. Three lytic bacteriophages (phages) of R. solanacearum with biocontrol capacity in environmental water and plants were isolated from river water in Europe but not fully analysed, their genomic characterization being fundamental to understand their biology. In this work, the phage genomes were sequenced and subjected to bioinformatic analysis. The morphology was also observed by electron microscopy. Phylogenetic analyses were performed with a selection of phages able to infect R. solanacearum and the closely related phytopathogenic species R. pseudosolanacearum. The results indicated that the genomes of vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 range from 40,688 to 41,158 bp with almost 59% GC-contents, 52 ORFs in vRsoP-WF2 and vRsoP-WM2, and 53 in vRsoP-WR2 but, with only 22 or 23 predicted proteins with functional homologs in databases. Among them, two lysins and one exopolysaccharide (EPS) depolymerase, this type of depolymerase being identified in R. solanacearum phages for the first time. These three European phages belong to the same novel species within the Gyeongsanvirus, Autographiviridae family (formerly Podoviridae). These genomic data will contribute to a better understanding of the abilities of these phages to damage host cells and, consequently, to an improvement in the biological control of R. solanacearum

Lipidomic landscape of circulating extracellular vesicles isolated from adolescents exposed to ethanol intoxication: a sex difference study

Abstract Background Lipids represent essential components of extracellular vesicles (EVs), playing structural and regulatory functions during EV biogenesis, release, targeting, and cell uptake. Importantly, lipidic dysregulation has been linked to several disorders, including metabolic syndrome, inflammation, and neurological dysfunction. Our recent results demonstrated the involvement of plasma EV microRNAs as possible amplifiers and biomarkers of neuroinflammation and brain damage induced by ethanol intoxication during adolescence. Considering the possible role of plasma EV lipids as regulatory molecules and biomarkers, we evaluated how acute ethanol intoxication differentially affected the lipid composition of plasma EVs in male and female adolescents and explored the participation of the immune response. Methods Plasma EVs were extracted from humans and wild-type (WT) and Toll-like receptor 4 deficient (TLR4-KO) mice. Preprocessing and exploratory analyses were conducted after the extraction of EV lipids and data acquisition by mass spectrometry. Comparisons between ethanol-intoxicated and control human female and male individuals and ethanol-treated and untreated WT and TLR4-KO female and male mice were used to analyze the differential abundance of lipids. Annotation of lipids into their corresponding classes and a lipid set enrichment analysis were carried out to evaluate biological functions. Results We demonstrated, for the first time, that acute ethanol intoxication induced a higher enrichment of distinct plasma EV lipid species in human female adolescents than in males. We observed a higher content of the PA, LPC, unsaturated FA, and FAHFA lipid classes in females, whereas males showed enrichment in PI. These lipid classes participate in the formation, release, and uptake of EVs and the activation of the immune response. Moreover, we observed changes in EV lipid composition between ethanol-treated WT and TLR4-KO mice (e.g., enrichment of glycerophosphoinositols in ethanol-treated WT males), and the sex-based differences in lipid abundance are more notable in WT mice than in TLR4-KO mice. All data and results generated have been made openly available on a web-based platform ( http://bioinfo.cipf.es/sal ). Conclusions Our results suggest that binge ethanol drinking in human female adolescents leads to a higher content of plasma EV lipid species associated with EV biogenesis and the propagation of neuroinflammatory responses than in males. In addition, we discovered greater differences in lipid abundance between sexes in WT mice compared to TLR4-KO mice. Our findings also support the potential use of EV-enriched lipids as biomarkers of ethanol-induced neuroinflammation during adolescence

Ethanol-induced sex-based differences in the extracellular vesicles lipidome.

Lipids represent essential components of extracellular vesicles (EVs), playing structural and regulatory functions. Importantly, lipidic dysregulation has been linked to several inflammatory and neurological disorders. Thus, exosome lipidomics is emerging as an innovative field for discovering novel lipid species with biomedical applications. Likewise, EVs isolated from adolescents exposed to alcohol intoxication demonstrated a sex-based difference in their microRNA profiles. Accordingly, we applied a lipidomics computational strategy using R language programming in order to examine how acute ethanol intoxication affects the lipid composition of plasma EVs, differently by sex in adolescents and the involvement of the immune response. After an exploratory analysis experimental groups (ethanol and control groups of females and males) were compared with a differential abundance analysis. Annotation of the lipids in their corresponding classes and class enrichment were carried out to evaluate the biological function. This strategy was performed in human subjects and WT and TLR4-KO mice. The latter to explore the role of the toll-like receptor 4 (TLR4) in the response. We identified a higher enrichment of specific EV lipid species in human female adolescents (e.g., PA, LPC, unsaturated FA and FAHFA) than in males (e.g., PI). These lipid species participate in the formation, release, and uptake of EVs and the activation of the immune response; therefore, results suggest that female adolescents who binge drink alcohol also display increased levels of EV biogenesis and neuroinflammatory spread than males. Our findings also support the potential use of EV-enriched lipids as biomarkers of ethanol-induced neuroinflammation during adolescence.</p

A deep transcriptome meta-analysis reveals sex differences in multiple sclerosis

Background: Multiple sclerosis (MS), a chronic auto-immune, inflammatory, and degenerative disease of the central nervous system, affects both males and females; however, females suffer from a higher risk of developing MS (2–3:1 ratio relative to males). The precise sex-based factors influencing risk of MS are currently unknown. Here, we explore the role of sex in MS to identify molecular mechanisms underlying observed MS sex differences that may guide novel therapeutic approaches tailored for males or females. Methods: We performed a rigorous and systematic review of genome-wide transcriptome studies of MS that included patient sex data in the Gene Expression Omnibus and ArrayExpress databases following PRISMA statement guidelines. For each selected study, we analyzed differential gene expression to explore the impact of the disease in females (IDF), in males (IDM) and our main goal: the sex differential impact of the disease (SDID). Then, for each scenario (IDF, IDM and SDID) we performed 2 meta-analyses in the main tissues involved in the disease (brain and blood). Finally, we performed a gene set analysis in brain tissue, in which a higher number of genes were dysregulated, to characterize sex differences in biological pathways. Results: After screening 122 publications, the systematic review provided a selection of 9 studies (5 in blood and 4 in brain tissue) with a total of 474 samples (189 females with MS and 109 control females; 82 males with MS and 94 control males). Blood and brain tissue meta-analyses identified, respectively, 1 (KIR2DL3) and 13 (ARL17B, CECR7, CEP78, IFFO2, LOC401127, NUDT18, RNF10, SLC17A5, STMP1, TRAF3IP2-AS1, UBXN2B, ZNF117, ZNF488) MS-associated genes that differed between males and females (SDID comparison). Functional analyses in the brain revealed different altered immune patterns in females and males (IDF and IDM comparisons). The pro-inflammatory environment and innate immune responses related to myeloid lineage appear to be more affected in females, while adaptive responses associated with the lymphocyte lineage in males. Additionally, females with MS displayed alterations in mitochondrial respiratory chain complexes, purine, and glutamate metabolism, while MS males displayed alterations in stress response to metal ion, amine, and amino acid transport. Conclusion: We found transcriptomic and functional differences between MS males and MS females (especially in the immune system), which may support the development of new sex-based research of this disease. Our study highlights the importance of understanding the role of biological sex in MS to guide a more personalized medicine

Sex differences in the molecular basis of multiple sclerosis: meta-analysis of transcriptomic data

Multiple sclerosis (MS), an auto-immune, inflammatory, and degenerative disorder of the central nervous system, affects both males and females; however, females are at an increased risk of developing MS (2-3:1 ratio compared to males). The factors behind these sex differences are not still clear. Therefore, the aim of this work has been to explore the role of sex in MS to identify potential molecular mechanisms underlying sex-based differences. To this end, we performed a systematic review in public databases of transcriptomic studies, in nervous tissue and blood. Next, we performed 3 meta-analyses that allowed us to detect MS alterations in females, in males and between both sexes. As a result of our work, we selected 9 studies (4 of nerve tissue and 5 of blood) containing 474 individuals. Our meta-analyses identified some genes and functions altered on a sex-specific or between-sex basis. Among them, highlight 15 genes that showed a significantly different expression pattern between sexes in some of the tissues analyzed: (KIR2DL3 in blood; ARL17B, CECR7, CEP78, IFFO2, LOC401127, NUDT18, RNF10, SLC17A5, STEMP1, TRAF3IP2-AS1, UBXN2B, ZNF117, ZNF488 in nervous tissue; LOC 102723701 in both tissues). This work evidences the existence of sex differences in MS at the transcriptomic level and, moreover, open the door to future applications leading to more sex-specific treatments.</p

Molecular and functional atlas of sex-differences in multiple sclerosis subtypes analising single cell and single nucleus transcriptomic data

Multiple sclerosis (MS) is the commonest cause of non-traumatic disability among young adults. MS hallmark underlies myelin damage induced by defective autoimmune responses, leading to the neurodegeneration of the central nervous system. Sex differences in MS have been reported at several epidemiological and clinical levels as prevalence, progression and response to treatment. However, the molecular mechanisms underneath those differences remain poorly understood.  To exhaustively characterise sex bias in MS by cell type, we performed an in silico analysis of scRNA-seq and snRNA-seq data using R programming language. Firstly, we performed a systematic review implementing PRISMA guidelines [PMID:33780438] in public repositories. Then, we processed each selected dataset through quality control filtering, normalisation, high variable genes selection, dimensionality reduction, clustering and cell type annotation. Finally, we characterise each cell type by differential gene expression and functional profiling analyses, evaluating for the latter biological functions from the Gene Ontology [PMID:10802651] and pathways from the KEGG [PMID:10592173] databases. Three datasets, each representing a different subtype of MS, were spotted. Nervous tissue dataset (n=1) stored astrocytes, microglia, neurons, oligodendrocytes, and oligodendrocyte precursor cells, whilst blood datasets (n=2) included diverse types of lymphocytes, dendritic cells and monocytes. We found significant sex-differential and sex-specific gene expression patterns, biological functions, and pathways for almost all cell types in each dataset. Some significant features were shared among cell types with similar or opposite patterns, whilst others were cell type exclusive. Therefore, this atlas enhances personalised medicine by unveiling molecular and functional sex-dependent prospective biomarkers.</p