Journal: bioRxiv

Article Title: Gene Therapy Mediated Partial Reprogramming Extends Lifespan and Reverses Age-Related Changes in Aged Mice

doi: 10.1101/2023.01.04.522507

Figure Lengend Snippet: a . Measurement of DNA methylation age acceleration in liver ( left panel) and heart ( right panel) from control doxycycline treated mice (Control-Dox) or TRE- OSK mice using LUC epigenetic clocks trained on the indicated tissues. b . Human keratinocytes transduced with lentivirus at 2 different MOIs (0.5 and 1.0) expressing OSK showed epigenetic age reversal as compared to control GFP transduced or non-transduced (WT) cells. n=2 technical repeats for each group. One-Way ANOVA with Holm-Šídák’s multiple comparisons test. ns - not significant; *** p <0.001.

Article Snippet: Lentivirus encoding GFP was purchased by VectorBuilder (Chicago, IL).

Techniques: DNA Methylation Assay, Control, Transduction, Expressing

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Nano-graphene oxide improved the antibacterial property of antisense yycG RNA on Staphylococcus aureus

doi: 10.1186/s13018-019-1356-x

Figure Lengend Snippet: GO-PEI-AS yycG increased AS yycG transformation and inhibited virulence gene expressions. a AS yycG plasmids were labeled with gene encoding enhanced green fluorescent protein (AS yycG -eGFP) and CLSM was applied to determine the expression level of eGFP. b The transfection efficiency was determined by comparing the green fluorescent intensities ( n = 10, * p < 0.05). c Quantitative RT-PCR analysis showed gene transcription in untreated S. aureus and AS yycG -, GO-, and GO-PEI-AS yycG -treated strains; S. aureus gene expression was quantified relatively using 16sR as an internal control and calculated based on untreated S. aureus ATCC29213 expression, which was set as 1.0. ( n = 10, * p < 0.05)

Article Snippet: The sequences of AS yycG and eGFP were synthesized by Sangon Biotech (Shanghai, China) and are listed in the Additional file .

Techniques: Transformation Assay, Labeling, Expressing, Transfection, Quantitative RT-PCR, Gene Expression, Control

Journal: Nucleic Acids Research

Article Title: A deep learning model trained on expressed transcripts across different tissue types reveals cell-type codon-optimization preferences

doi: 10.1093/nar/gkaf233

Figure Lengend Snippet: Comparative analyses of reporter gene sequences following codon optimization. ( A and B ) Heatmap display of DNA sequence similarity between codon-optimized Egfp (A) or FLuc (B) reporter gene sequences through DL models, wild-type/original sequences, and codon-optimized by the GenScript (GS) tool. ( C and D ) Histograms of CAI values, GC content, and CpG dinucleotides for codon-optimized FLuc (C) or Egfp (D) sequences. ( E and F ) Heatmap of codon preferences between optimized FLuc (E) or Egfp (F).

Article Snippet: Similarly, the expression conferred by the liver-optimized Egfp sequence in AML12s was higher than the expression levels generated by the original or GenScript-optimized sequences (Fig. ).

Techniques: Sequencing

Journal: Nucleic Acids Research

Article Title: A deep learning model trained on expressed transcripts across different tissue types reveals cell-type codon-optimization preferences

doi: 10.1093/nar/gkaf233

Figure Lengend Snippet: Quantification of codon-optimized reporter genes. ( A–D ) Histograms showing relative luciferase activity from Neuro-2a (neuroblasts) (A), AML12 (hepatocytes) (B), C2C12 (myoblasts) (C), and differentiated C2C12 (dC2C12, myotubes) (D) transfected with the wild-type FLuc construct, codon-optimized constructs obtained from DL models trained with brain, liver, and muscle genes, or optimized by the GenScript (GS) algorithm. Values represent normalized luciferase activities scaled to wild-type levels set to 100. ( E ) Representative epifluorescence microscopy images of transfected cells (scale bar: 10 μm). Neuro-2a (top row), AML12 (middle row), or C2C12 (bottom row) cells were transfected with the original Egfp construct, DL-based codon-optimized constructs, or optimized by the GenScript algorithm. ( F – H ) Cells were subjected to flow cytometry analyses and evaluated for MFI. Histograms showing the detection of EGFP fluorescence for Neuro2a (F), AML12 (G), and C2C12 (H). n = 3; >10 000 events counted. All histograms show mean values ± SD; * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: Similarly, the expression conferred by the liver-optimized Egfp sequence in AML12s was higher than the expression levels generated by the original or GenScript-optimized sequences (Fig. ).

Techniques: Luciferase, Activity Assay, Transfection, Construct, Epifluorescence Microscopy, Flow Cytometry, Fluorescence