Biology subjects

Sorokina, M.

Publications and source records attributed to Sorokina, M..

3 recordsLinked to original sources

bioRxiv2021

Open Natural Products Research: Curation and Dissemination of Biological Occurrences of Chemical Structures through Wikidata

Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC="FIGDIR/small/433265v3_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@184136borg.highwire.dtl.DTLVardef@16e0d6org.highwire.dtl.DTLVardef@30ae1org.highwire.dtl.DTLVardef@1bf4825_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2021

Description and analysis of glycosidic residues in the largest open natural products database

Natural products (NP), biomolecules produced by living organisms, inspire the pharmaceutical industry and research due to their structural characteristics and the substituents from which they derive their activities. Glycosidic residues are frequently present in NP structures and have particular pharmacokinetic and pharmacodynamic importance as they improve their solubility and are often involved in molecular transport, target specificity, ligand-target interactions and receptor binding. The COlleCtion of Open Natural prodUcTs (COCONUT) is currently the largest open database of NP and therefore a suitable starting point for the detection and analysis of the diversity of glycosidic residues in NP. In this work, we report and describe the presence of circular, linear, terminal and non-terminal glycosidic units in NP, together with their importance in drug discovery.

bioinformatics↗

bioRxiv2019

Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools

The rise of antibiotic resistance (AR) in clinical settings is one of the biggest modern global public health concerns. Therefore, the understanding of AR mechanisms, evolution and global distribution is a priority due to its impact on the treatment course and patient survivability. Besides all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental uncultivable microorganisms. In this study, 293 metagenomic from the TARA Oceans project were used to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools. After extensive manual curation, we show the global ocean ARG abundance, distribution, taxonomy, phylogeny and their potential to be horizontally transferred by plasmids or viruses and their correlation with environmental and geographical parameters. A total of 99,205 environmental ORFs were identified as potential ARGs. These ORFs belong to 560 ARG families that confer resistance to 26 antibiotic classes. 24,567 ORFs were found in contigs classified as plasmidial sequences, suggesting the importance of mobile genetic elements in the dynamics of ARGs transmission. Moreover, 4,804 contigs with more than 2 ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. This also raises the possibility of horizontal gene transfer (HGT) between clinical and natural environments. The abundance of ARGs showed different patterns of distribution, with some classes being significantly more abundant in coastal biomes. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs from the recently discovered MCR-1 family with high abundance on Polar Biomes. Of these, 5 were assigned to the genus Psychrobacter, an opportunistic pathogen that can cause fatal infections in humans. Our results are available on Zenodo in MySQL database dump format and all the code used for the analyses, including a Jupyter notebook can be accessed on GitHub (https://github.com/rcuadrat/ocean_resistome).

bioinformatics↗