Improving analysis of meta-omics data with the MOSCA framework

Introduction: Meta-omics is an emergent field of research with many resources available in the form of databases and software. The information stored in databases is not always easily accessible, and software tools for meta-omics are often difficult to utilize. In this work, we present Meta-Omics Software for Community Analysis (MOSCA), a software framework that implements pipelines for the integrated analysis of metagenomics (MG), metatranscriptomics (MT) and metaproteomics (MP) data. This framework integrates tools allowing access to databases, handling of data and a complete workflow for meta-omics data analysis. Methodology and results: MOSCA was developed in Python 3, takes as input raw files obtained from Next-generation sequencing (in FastQ format), and from mass spectrometry (mass spectra in vendor or peak-picked formats), and integrates several tools for MG, MT and MP analysis. These tools are connected through their inputs/outputs by snakemake, in a fully automated workflow. MG analysis starts with preprocessing of sequencing reads, which automatically configures Trimmomatic to remove adapters and low-quality reads based on FastQC quality reports, and SortMeRNA for rRNA reads removal. Assembly can be performed with MetaSPAdes or Megahit and is followed by binning with MaxBin2 and CheckM for quality check. Genes are identified with FragGeneScan and are annotated with both UPIMAPI (homology-based annotation) and reCOGnizer (domain-based annotation), with reference to UniProt KB and eight databases included in the Conserved Domains Database, respectively. Bowtie2 is used to align reads to metagenomes. Protein identification and quantification can be performed with either SearchCLI coupled to PeptideShaker (performing peptide-to-spectrum matching and spectra count) or using MaxQuant (with quantification at the MS1 level). Differential gene expression analysis is performed with DESeq2, and heatmaps, volcano plots and PCA plots are generated. The expressed enzymes are plotted into hundreds of KEGG metabolic maps with the tool KEGGCharter, showing the metabolic functions that are differentially expressed and the taxonomic assignment. Tables, heatmaps and other representations obtained with MOSCA provide an interactive, accessible and comprehensive representation of the information obtained from MG, MT and MP analyses. Conclusions: MOSCA performs automatic analyses of MG, MT and MP datasets, integrating over 20 tools to obtain a comprehensive and easy to understand representation of microbial activity in different processes and conditions.info:eu-repo/semantics/publishedVersio

Understanding intra and inter-archipelago population genetic patterns within a recently evolved insular endemic lineage

The recently evolved genus Tolpis Adans. has its major center of diversity located in Macaronesia. Although recent advances have been made to understand the relationships of Tolpis species within Macaronesia, little is still known about the genetic patterns and genetic diversity of the Azorean and Madeiran Tolpis populations. To achieve this, a set of 8 microsatellite loci (SSR) was applied to 478 individuals of Tolpis azorica and T. suc culenta. Genetic structure analysis, in addition to a spatial analysis, confirmed the existence of geographically cir cumscribed genetic patterns allied to a barrier effect by the sea in the Azorean T. azorica and T. succulenta. A detailed analysis of T. azorica revealed three different genetic groups, each group being particular to a different Azorean sub-archipelago, while the analysis conducted with T. succulenta confirmed the occurrence of a differ ential grouping between individuals from Azores and Madeira populations. The impact of catastrophic volcanic events and intense humanization of the habitats is dis cussed, in view of the present genetic diversity and structure of the species. In general, T. azorica populations showed high Fis values and some populations of T. suc culenta both in Azores and in Madeira also showed signs of putative inbreeding. Conservation actions such as the eradication of invasive plant and animal species are advised but translocations of plants or diaspores between islands or between populations of a same island should not be attempted.info:eu-repo/semantics/publishedVersio

Jatrophane and lathyrane diterpenoids from Euphorbia hyberna L

A new diterpene tetraester, from the jatrophane family, and two new diterpene triesters, with a lathyrane skeleton, have been isolated from the chloroform extract of the roots of Euphorbia hyberna L. The structures of these compounds have been established by spectroscopic methods, including 2D NMR experiments.info:eu-repo/semantics/publishedVersio

Chemical constituents of Euphorbia hyberna L. (Euphorbiaceae)

Chemical investigation of the aerial part and the roots of Euphorbia hyberna L. subs. hyberna. resulted in the isolation and identification of four triterpenoids (3�-O-octadecanoyllupeol (1), glut-5-en-3�-ol (2), 24-methylenecicloartan-3�-ol (3) and cicloart-23-ene-3�,25-diol (6)) along with the phenolic compounds ellagic acid (4) and 3,30 -di-O-methylellagic acid (7). Although these are all known compounds, this is the first report of their isolation from this plant. Their structures were elucidated on the basis of spectral methods, including 2D NMR experiences, and confirmed by comparing with the literature data.info:eu-repo/semantics/publishedVersio

Genome size variation within Crithmum maritimum: Clues on the colonization of insular environments

Angiosperms present an astonishing diversity of genome sizes that can vary intra- or interspecifically. The remarkable new cytogenomic data shed some light on our understanding of evolution, but few studies were performed with insular and mainland populations to test possible correlations with dispersal, speciation, and adaptations to insular environments. Here, patterns of cytogenomic diversity were assessed among geographic samples (ca. 114) of Crithmum maritimum (Apiaceae), collected across the Azores and Madeira archipelagos, as well as in adjacent continental areas of Portugal. Using flow cytometry, the results indicated a significant intraspecific genome size variation, spanning from reduced sizes in the insular populations to larger ones in the mainland populations. Moreover, there was a tendency for an increase in genome size along the mainland populations, associated with lower temperatures, higher precipitation, and lower precipitation seasonality. However, this gradient might be the result of historic phylogeographical events associated with previous dispersal and extinction of local populations. Overall, our findings provided evidence that smaller genome sizes might play a critical role in the colonization of islands, corroborating other studies that argue that organisms with smaller genomes use fewer resources, having a selective advantage under insular environments. Although further studies are needed to improve our understanding of the mechanisms underlying genome size evolution on islands, conservation strategies must be promoted to protect the rich cytogenomic diversity found among C. maritimum populations, which occur in coastal areas that are particularly threatened by human activity, pollution, invasive species, and climate changes.info:eu-repo/semantics/publishedVersio

Diversification of Aeonium Species Across Macaronesian Archipelagos: Correlations Between Genome-Size Variation and Their Conservation Status

The rich endemic flora of the Macaronesian Islands places these oceanic archipelagos among the top biodiversity hotspots worldwide. The radiations that have determined the evolution of many of these insular lineages resulted in a wealth of endemic species, many of which occur in a wide range of ecological niches, but show small distribution areas in each of them. Aeonium (Crassulaceae) is the most speciose lineage in the Canary Islands (ca. 40 taxa), and as such can be considered a good model system to understand the diversification dynamics of oceanic endemic floras. The present study aims to assess the genome size variation within Aeonium distribution, i.e., the Macaronesian archipelagos of Madeira, Canaries and Cabo Verde, and analyse it together with information on distribution (i.e., geography and conservation status), taxonomy (i.e., sections), morphological traits (i.e., growth-form), geological data (i.e., island’s geological age), and environmental variables (i.e., altitude, annual mean temperature, and precipitation). Based on extensive fieldwork, a cytogeographic screening of 24 Aeonium species was performed. The conservation status of these species was assessed based on IUCN criteria. 61% of the taxa were found to be threatened (4% Endangered and 57% Vulnerable). For the first time, the genome size of a comprehensive sample of Aeonium across the Macaronesian archipelagos was estimated, and considerable differences in Cx-values were found, ranging from0.984 pg (A. dodrantale) to 2.768 pg (A. gorgoneum). An overall positive correlation between genome size and conservation status was found, with the more endangered species having the larger genomes on average. However, only slight relationships were found between genome size, morphological traits, and environmental variables. These results underscore the importance of characterizing the cytogenomic diversity and conservation status of endemic plants found in Macaronesian Islands, providing, therefore, new data to establish conservation priorities.info:eu-repo/semantics/publishedVersio

Diversity and Cytogenomic Characterization of Wild Carrots in the Macaronesian Islands

The Macaronesian islands constitute an enormous reservoir of genetic variation of wild carrots (subtribe Daucinae; Apiaceae), including 10 endemic species, but an accurate understanding of the diversification processes within these islands is still lacking. We conducted a review of the morphology, ecology, and conservation status of the Daucinae species and, on the basis of a comprehensive dataset, we estimated the genome size variation for 16 taxa (around 320 samples) occurring in different habitats across the Macaronesian islands in comparison to mainland specimens. Results showed that taxa with larger genomes (e.g., Daucus crinitus: 2.544 pg) were generally found in mainland regions, while the insular endemic taxa from Azores and Cabo Verde have smaller genomes. Melanoselinum decipiens and Monizia edulis, both endemic to Madeira Island, showed intermediate values. Positive correlations were found between mean genome size and some morphological traits (e.g., spiny or winged fruits) and also with habit (herbaceous or woody). Despite the great morphological variation found within the Cabo Verde endemic species, the 2Cvalues obtained were quite homogeneous between these taxa and the subspecies of Daucus carota, supporting the close relationship among these taxa. Overall, this study improved the global knowledge of DNA content for Macaronesian endemics and shed light into the mechanisms underpinning diversity patterns of wild carrots in the western Mediterranean regioninfo:eu-repo/semantics/publishedVersio

Is the chlorophyll derivative Zn(II)e6Me a good photosensitizer to be used in root canal disinfection?

The aim of this study was to assess antimicrobial efficacy and cytotoxic outcomes of a chlorophyll based photosensitizer (PS) Zn(II)chlorin e6 methyl ester (Zn(II)e6Me), when applied to human dentin discs and root blocks infected with 48 h biofilms. The results were compared with the ones obtained with FotoSan® (commercial Toluidine Blue O formulation) and 3% sodium hypochlorite (NaOCl).publishe