Journal: Cell Reports Medicine

Article Title: Ancestral library identifies conserved reprogrammable liver motif on AAV capsid

doi: 10.1016/j.xcrm.2022.100803

Figure Lengend Snippet: Library production and in vitro infectivity (A) A barcoded AAV vector library was produced either with (N = 5) or without (N = 3) addition of an exogenous assembly-activating protein (AAP). Individual dots in MA plots represent distinct barcodes, colors represent the amino acid identity at position 5. To the right of MA plots, eCDF plots with SEM depicted as horizontal error bars. (B) Results of an independent sites linear elastic net regularization approach show that addition of AAP modifies the impact of certain sites on production of vector. (C) Huh7 cells were transduced with the barcoded AAV library and DNA/RNA were isolated from those transduced cells (N = 5 per condition). Individual barcodes in MA plots are colored by identity at position 3 within the library. Extant barcoded vectors were also spiked into this transduction mixture. Fold change is plotted as bar graphs (error bars determined by bootstrapping, 1,000 replicates). (D) Regularization and linear modeling approach reveal potential similarities and differences among our positions of variation with respect to transduction and gene expression in vitro .

Article Snippet: Huh7 Cell Line , ATCC , PTA-4583.

Techniques: In Vitro, Infection, Plasmid Preparation, Produced, Transduction, Isolation, Gene Expression

Journal: Cell Reports Medicine

Article Title: Ancestral library identifies conserved reprogrammable liver motif on AAV capsid

doi: 10.1016/j.xcrm.2022.100803

Figure Lengend Snippet:

Article Snippet: Huh7 Cell Line , ATCC , PTA-4583.

Techniques: Virus, Plasmid Preparation, Recombinant, Imaging, RNA Sequencing, Software, Microscopy

Journal: Antimicrobial Agents and Chemotherapy

Article Title: In Vitro Resistance Profile of the Hepatitis C Virus NS3/4A Protease Inhibitor TMC435 ▿ †

doi: 10.1128/AAC.01452-09

Figure Lengend Snippet: Summary of results from in vitro selection experiments. (A) Frequency of changes in the protease domain of NS3 (amino acids 1 to 181) observed in experiments conducted with different replicon-containing cell lines in the presence or the absence of TMC435. NS3 sequences from 120 control replicon colonies or cell pools (21 of genotype 1a and 99 of genotype 1b) and 109 TMC435-treated replicon colonies or cell pools (46 of genotype 1a and 63 of genotype 1b) were assessed. Positions at which mutations were present in more than three sequences are shown. Dark gray bars, TMC435-treated cells; white bars, control cells. (B) Frequency of mutations at one or more of NS3 positions 43, 80, 155, 156, and 168 in cells selected with TMC435. Experiments were performed with genotype 1a (Huh7-SG1a H77) or genotype 1b (Huh7-Luc and Huh7-con1b) replicon-containing cells. Mutations containing a mixture of the wild-type residue with a mutated residue are counted as containing the mutated residue only. The frequency was calculated for each subtype. Black bars, genotype 1a; light gray bars, genotype 1b.

Article Snippet: Huh7-con1b cells (i.e., a genotype 1b [con1-based] subgenomic replicon clone with cell culture-adaptive mutation S2204I in NS5A) and Huh7-SG1a H77 cells (i.e., a genotype 1a [H77-based] subgenomic replicon clone with cell culture-adaptive mutations P1496L and S2204I in NS3 and NS5A) were obtained from Apath LLC (Brooklyn, NY) ( 1 , 2 ).

Techniques: In Vitro, Selection, Control, Residue