Khayat, A. S. | Search bioRxiv

bioRxiv2020

A small interfering RNA (siRNA) database for SARS-CoV-2

Coronavirus disease 2019 (COVID-19) rapidly transformed into a global pandemic, for which a demand for developing antivirals capable of targeting the SARS-CoV-2 RNA genome and blocking the activity of its genes has emerged. In this work, we propose a database of SARS-CoV-2 targets for siRNA approaches, aiming to speed the design process by providing a broad set of possible targets and siRNA sequences. Beyond target sequences, it also displays more than 170 features, including thermodynamic information, base context, target genes and alignment information of sequences against the human genome, and diverse SARS-CoV-2 strains, to assess whether siRNAs targets bind or not off-target sequences. This dataset is available as a set of four tables in a single spreadsheet file, each table corresponding to sequences of 18, 19, 20, and 21 nucleotides length, respectively, aiming to meet the diversity of technology and expertise among labs around the world concerning siRNAs design of varied sizes, more specifically between 18 and 21nt length. We hope that this database helps to speed the development of new target antivirals for SARS-CoV-2, contributing to more rapid and effective responses to the COVID-19 pandemic.

bioinformatics↗

bioRxiv2020

Biosynthesis and chemical characterization of an intracellular red pigment of Talaromyces islandicus T101

The interest in red colorants by the food industry has been increasing recently due to its wide application in many foods and beverages, and also to the carcinogenic and teratogenic effects of some synthetic dyes. Many ascomycetous fungi are able to synthesize and produce pigments, rendering them as alternative sources of natural dyes that are independent of environmental conditions. Talaromyces islandicus TI01 was isolated from a marine-influenced environment that has been suffering for decades from anthropogenic actions in its body of water. Broth microdilution technique was performed to analyze the antimicrobial activity. For analysis of the cytotoxic activity, the MTT [3-(4,5-dimethylthiazol-2-yl) -2,5-diphenyltetrazolium bromide] assay was conducted. The chemical analysis of the extract was performed by LC/MS (liquid chromatography coupled to mass spectrometry). The minimum bactericidal concentration (MBC) of T. islandicus intracellular red pigmented extract (IRPE) for E. coli ATCC 25922 and S. aureus ATCC 25923 was 1000 g/ml. The minimum inhibitory concentration (MIC) for E. coli was 250 g/mL and for S. aureus 500 g/mL, respectively, whereas for C. tropicalis ATCC 1369 was 62.5 g/mL. IC50 for breast cancer cell line (MCF-7) was 45.43 {+/-} 1.657 g / mL. The major compounds present in the extract were: Luteoskyrin (1) and N-GABA-PP-V (6-[(Z)-2-Carboxyvinyl]-N-GABA-PP-V) (2). The results show that IRPE from T. islandicus TI01 has a prominent antibacterial activity against E. coli and S. aureus, making this pigment interesting for development of new food colorants and/or conservative agents, since these bacteria are food-borne pathogens.

microbiology↗