Journal: Nature Structural & Molecular Biology

Article Title: Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD

doi: 10.1038/s41594-023-01095-4

Figure Lengend Snippet: Genomic locations of the (a) Tbx3 and (b) Nanog genes annotated with the locations to which dCas9-GFP was targeted using either CARGO vectors or a single gRNA that targets nearby genomic repeats (red lines). Locations of bacterial artificial chromosome (BAC) DNA FISH probes for the Tbx3 and Nanog enhancers are also indicated as are the targeted enhancers themselves (green). The corresponding ChIP-seq profiles indicate the binding of the NuRD complex subunits CHD4 and MBD3 as well as the location of active enhancers (determined from the ChIP-seq profiles for H3K27ac, H3K4me1 and p300). (c) Representative confocal images showing co-localisation of dCas9-GFP (labelled using a AF488-tagged anti-GFP nanobody) and AF647-BAC DNA FISH probes targeting the Nanog enhancer. Images are representative of two independent replicates. (d) Representative confocal images of Cy3-labelled BAC DNA FISH probes targeting the Tbx3 promoter and AF647-labelled BAC DNA FISH probes targeting the Tbx3 enhancer. Images are representative of two independent replicates. (e) Boxplots showing the enhancer-promoter distances in MBD3-inducible mESCs with and without tamoxifen: +MBD3 (blue) and -MBD3 (orange) respectively. There is a significant increase in enhancer-promoter distance in the presence of intact NuRD for Tbx3 (+MBD3, n = 70; -MBD3, n = 101), Bmp4 (+MBD3, n = 172; -MBD3, n = 71) and Sox2 (+MBD3, n = 42; -MBD3, n = 50) (** p < 0.01, *** p < 10 −6 , two-sided t-test). (Center line, median; box limits, upper and lower quartiles; whiskers, 95 % confidence interval.) To estimate the precision limit of the experiment, control samples were generated in which the distance was measured for the Sox2 enhancer labelled with both Cy3 and AF647 (grey, n = 32).

Article Snippet: BAC DNA was labeled using Cy3 and Alexa Fluor 647 Nick Translation Labeling Kits (Jena Bioscience, catalog nos.

Techniques: ChIP-sequencing, Binding Assay, Confocal, Control, Generated, FISH, Immunofluorescence, In Situ Hybridization, CRISPR

Journal: Journal of Cellular Biotechnology

Article Title: Protein spectrum of blood plasma in patients with diabetes mellitus type II

doi: 10.3233/jcb-179009

Figure Lengend Snippet: Fig. 8. The scanned image of the gel, obtained by two-dimensional electrophoresis and differential fluorescent staining with Cy3 Protein Labeling Kit and Cy5 Protein Labeling Kit (Jena Bioscience). The results from the comparison of the groups I – III. [Group I: blood plasma of patients with D2TM with complications. Group III: blood plasma of clinically healthy individuals (healthy controls)].

Article Snippet: The samples of the compared groups were mixed with fluorescent dyes Cy3 Protein Labeling Kit and Cy5 Protein Labeling Kit (Jena Bioscience) in equal proportions and separated using two-dimensional electrophoresis.

Techniques: Electrophoresis, Staining, Labeling, Comparison, Clinical Proteomics

Journal: Journal of Cellular Biotechnology

Article Title: Protein spectrum of blood plasma in patients with diabetes mellitus type II

doi: 10.3233/jcb-179009

Figure Lengend Snippet: Fig. 7. The scanned image of the gel, obtained by two-dimensional electrophoresis and differential fluorescent staining with Cy3 Protein Labeling Kit and Cy5 Protein Labeling Kit (Jena Bioscience). The results of the comparison of the groups I – II. (Group I: blood plasma of D2TM patients with complications. Group II: blood plasma of diabetic patients without complications.)

Article Snippet: The samples of the compared groups were mixed with fluorescent dyes Cy3 Protein Labeling Kit and Cy5 Protein Labeling Kit (Jena Bioscience) in equal proportions and separated using two-dimensional electrophoresis.

Techniques: Electrophoresis, Staining, Labeling, Comparison, Clinical Proteomics

Journal: Molecular Pharmaceutics

Article Title: Optimizing the Delivery of mRNA to Mesenchymal Stem Cells for Tissue Engineering Applications

doi: 10.1021/acs.molpharmaceut.3c00898

Figure Lengend Snippet: Distribution of mRNA nanoparticles in a collagen-nHA scaffold. (A) Representative confocal scanning micrograph of Cy3-labeled mRNA nanoparticles (jetPEI-modRNA 5 μg 2:1 v/w) in a cross section of a collagen-nHA scaffold. mRNA nanoparticles are fluorescently tagged (red), and the collagen-nHA scaffold structure autofluoresces (blue). mRNA nanoparticles remained close to both scaffold surfaces, where they had initially been soak-loaded. Scale bar = 500 μm. (B) Higher-magnification confocal scanning micrograph of (i) Cy3-labeled mRNA nanoparticles within the nanoparticle-rich area of the scaffold demonstrating even distribution of nanoparticles throughout the scaffold pores. (ii) A blank collagen-nHA scaffold was imaged as a control. Scale bar = 100 μm.

Article Snippet: To assess the distribution of mRNA nanoparticles within a collagen-nHA scaffold, modRNA was tagged with Cy3 using a Mirus Label IT Cy3 nucleic acid labeling kit (Medical Supply Company, Ireland) according to the manufacturer’s instructions.

Techniques: Labeling