Journal: Neoplasia (New York, N.Y.)

Article Title: Liver fluke granulin promotes extracellular vesicle-mediated crosstalk and cellular microenvironment conducive to cholangiocarcinoma

doi: 10.1016/j.neo.2020.02.004

Figure Lengend Snippet: Programmed CRISPR/Cas9 mutation of the human progranulin gene. Panel A, linear map of a pre-designed lentiviral CRISPR/Cas9 vector containing fused codon-optimized puromycin resistance marker (dark gray bar)-Cas9 (yellow bar) and green fluorescent protein (green bar) driven by the mammalian elongation factor alpha-1 promoter (dark blue arrow); guide RNA (gRNA) targeting human granulin exon 2 (red bar) is expressed from a single vector. The human U6 promoter (blue arrow) drove the gRNA. The vector backbone includes the 5′- and 3′-long terminal repeats (LTR) of the HIV-1 provirus (light gray blocks). Panel B, schematic representation of the partial human granulin gene precursor, huPGRN on chromosome 17: NC_000017.11 regions 44,345,086–44,353,106 (8021 bp) and protein structure. Nucleotide sequence in exon 2 encodes the N-terminus and part of the granulin/epithelin module (GEM) of progranulin; indicating locations of gRNA (4417–4438 nt; red colored-letter) predicted double-stranded break (DSB) (red arrow). Panels C–E, on target INDEL mutations in ΔPGRN-H69 analysis by NGS libraries and CRISPResso bioinformatic platform. Frequency distribution of position-dependent insertions (red bars) (C) and deletion (magenta) (D) the major INDELs; 6 and 2 bp deletions at the programmed CRISPR/Cas9 cleavage site. Other minor mutations including 1 bp insertion (red square) or base substitution (bold) were observed further (>10 bp) predicted cleavage site (E). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: Total RNA and evRNA either from H69 or ΔhuPGRN-H69 cells were isolated using RNAzol (Molecular Research Center, Inc.) or total exosome RNA isolation kit (ThermoFisher) following the manufacturer’s instructions.

Techniques: CRISPR, Mutagenesis, Plasmid Preparation, Marker, Sequencing

Journal: Journal of controlled release : official journal of the Controlled Release Society

Article Title: Bolaamphiphiles as Carriers for siRNA Delivery: From Chemical Syntheses to Practical Applications

doi: 10.1016/j.jconrel.2015.06.041

Figure Lengend Snippet: Biophysical characterization of bola/nucleic acid complexes. The nucleic acids used to obtain the above results were designed against GFP. (a) Binding affinity of GLH-58 and GLH-60 to Alexa-488 labeled RNA/DNA hybrid duplexes. The fitting (dashed lines) is described in Methods. (b) Size analysis graphs for bola micelles alone and bola/DS RNA complexes, (c) Cryo-EM images of the GLH-58 and GLH-60 micelles alone and in complexation with DS RNAs, (d) Ability of 5 ug /mL of GLH-58 and GLH-60 to protect quenched DNA duplexes (50 nM) upon DNase digestion. All the concentrations mentioned are final.

Article Snippet: The fitting (dashed lines) is described in Methods. (b) Size analysis graphs for bola micelles alone and bola/DS RNA complexes, (c) Cryo-EM images of the GLH-58 and GLH-60 micelles alone and in complexation with DS RNAs, (d) Ability of 5 ug /mL of GLH-58 and GLH-60 to protect quenched DNA duplexes (50 nM) upon DNase digestion.

Techniques: Binding Assay, Labeling, Cryo-EM Sample Prep

Journal: Journal of controlled release : official journal of the Controlled Release Society

Article Title: Bolaamphiphiles as Carriers for siRNA Delivery: From Chemical Syntheses to Practical Applications

doi: 10.1016/j.jconrel.2015.06.041

Figure Lengend Snippet: Cellular characterization of bola/nucleic acid complexes in human breast cancer cells (MDA-MB-231) (a) Uptake of Alexa-488 labeled RNA/DNA hybrid duplexes (50 nM) mediated by GLH-58 and GLH-60 bolas (at 10 ug/ml), (b) Endosomal co-localization of Alexa-546 labeled RNA/DNA hybrid duplexes delivered by GLH-58, (c) Silencing of GFP mediated by the release of DS RNA designed against GFP by GLH-58 and GLH-60 in GFP expressing MDA-MB-231 cells, (d) Effect of addition of GLH-58/DS RNA and GLH-60/DS RNA complexes on viability of cells. All the concentrations mentioned are final.

Article Snippet: The fitting (dashed lines) is described in Methods. (b) Size analysis graphs for bola micelles alone and bola/DS RNA complexes, (c) Cryo-EM images of the GLH-58 and GLH-60 micelles alone and in complexation with DS RNAs, (d) Ability of 5 ug /mL of GLH-58 and GLH-60 to protect quenched DNA duplexes (50 nM) upon DNase digestion.

Techniques: Labeling, Expressing

Journal: Journal of controlled release : official journal of the Controlled Release Society

Article Title: Bolaamphiphiles as Carriers for siRNA Delivery: From Chemical Syntheses to Practical Applications

doi: 10.1016/j.jconrel.2015.06.041

Figure Lengend Snippet: Complex formation of (a) GLH-58/RNA and (b) GLH-60/RNA in Molecular Dynamics simulations; bola hydrophobic skeleton (gray) its head groups (blue spheres). RNA (tan) its P atoms of the backbone phosphate groups (red). Solvent Accessible Surface Area (SASA) plots for the Molecular Dynamics (MD) simulations of (c) 19 GLH-58 and (d) 14 GLH-60 bolas complexed with an RNA. Plots shown in black correspond to the SASA of the RNA alone. Plots shown in color indicate SASA variations of the RNA surface exposed to the solvent in the bola/RNA complex. Red boxes indicate time intervals of stable complex states over which the median SASA values shown above them were calculated. 12 mer RNA used in these studies is one-half the DS RNA designed against GFP.

Article Snippet: The fitting (dashed lines) is described in Methods. (b) Size analysis graphs for bola micelles alone and bola/DS RNA complexes, (c) Cryo-EM images of the GLH-58 and GLH-60 micelles alone and in complexation with DS RNAs, (d) Ability of 5 ug /mL of GLH-58 and GLH-60 to protect quenched DNA duplexes (50 nM) upon DNase digestion.

Techniques:

Journal: Cell Chemical Biology

Article Title: Resistance of Mycobacterium tuberculosis to indole 4-carboxamides occurs through alterations in drug metabolism and tryptophan biosynthesis

doi: 10.1016/j.chembiol.2021.02.023

Figure Lengend Snippet:

Article Snippet: The concentration of the complex was measured spectrophotometrically using the Pierce BCA Assay kit (ThermoFisher) and the accompanying BSA standards.

Techniques: Recombinant, Bicinchoninic Acid Protein Assay, Software

Journal: Ecotoxicology and environmental safety

Article Title: Benzophenone-3 exposure induced apoptosis via impairing mitochondrial function in human chondrocytes.

doi: 10.1016/j.ecoenv.2024.117286

Figure Lengend Snippet: Fig. 3. Effects of BP-3 exposure on mitochondrial function in chondrocytes. C28/I2 human chondrocytes were treated with 0 μM, 4.4 μM, 22 μM and 44 μM BP-3 for 48 h. Representative images (A) and quantitative analysis (C) of intracellular ROS levels after BP-3 treatment (n=3 per group). Representative images (B) and quantitative analysis (D) of the mitochondrial membrane potential after BP-3 treatment analyzed by flow cytometry (n=3 per group). (E) ATP levels in the mito chondria after BP-3 treatment (n=3 per group). (F) The activities of mitochondrial respiratory enzyme complex I, II, III and IV in C28/I2 human chondrocytes after BP-3 treatment (n=3 per group). Values represent mean ± SEM for at least three independent experiments. *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: Activities of mitochondrial respiratory enzyme complex I, II, III and IV were determined by using commercial mitochondrial respiratory chain complex Assay Kit (Solarbio, Beijing, China).

Techniques: Membrane, Flow Cytometry