Journal: Computational and Structural Biotechnology Journal

Article Title: BioCAT: Search for biosynthetic gene clusters producing nonribosomal peptides with known structure

doi: 10.1016/j.csbj.2022.02.013

Figure Lengend Snippet: Principal scheme of the BioCAT pipeline. First, the input genome is processed by antiSMASH and the NRP structure is processed by rBAN. Next, all potential biosynthesis gene clusters (BGCs) are aligned against all possible core peptide chains (CPCs) built from the monomeric graph generated by rBAN. Alignment is performed using eight different variants of the alignment score definition (Sln, Mln, Sdn, etc). Finally, for each successful matching, these scores are processed by the Random Forest Classifier, which generates the final matching score distributed from 0 to 1 and the binary matching score.

Article Snippet: In the BioCAT pipeline, the genome sequence is analyzed by antiSMASH and the structure is characterized by rBAN, so, these programs are required to be installed.

Techniques: Generated

Journal: bioRxiv

Article Title: Spatio-temporal analysis of the innate immune response to cytoplasmic dsDNA using a novel cGAMP biosensor

doi: 10.1101/2024.06.10.598238

Figure Lengend Snippet: A , B , Live cell imaging analyses of HEK293T and HFF-1 cGAMP-biosensor cells treated with 2 μM diABZI. C , IFNb-Luc reporter assays in HEK293T cells transfected with empty plasmid or wt STING, or HEK293T cGAMP-biosensor cells, and treated with the indicated concentrations of the STING agonist diABZI. Note that HEK293T do not express endogenous cGAS or STING.

Article Snippet: To generate the HeLa and HEK293T cGAMP biosensor cells, the cGAMP biosensor was cloned into the PiggyBAC backbone plasmid (Biocat PB510B-1-SBI).

Techniques: Live Cell Imaging, Transfection, Plasmid Preparation