Journal: Genome Biology

Article Title: Functional correction and genome integrity with duplex base editing of β-thalassemic hematopoietic stem cells

doi: 10.1186/s13059-026-03974-7

Figure Lengend Snippet: Functional correction after duplex base editing. A – D Chromatograms and quantification of HPLC analysis results after each corresponding treatment on D6 of erythropoiesis. A Chromatograms with peaks presenting HbF, HbA and HbA2 hemoglobin. B Quantification of hemoglobin levels expressed as percentage (%). The % of each hemoglobin type was calculated over the total hemoglobin tetramers, ** P= 0.0079, * P= 0.0180. C Chromatograms with peaks representing β, δ, α and γ ( G γ + Α γ) globin. D Quantification of total γ-globin but also separate G γ and A γ expression presented as ratios over α-globin, * P =0.0118 for γ-globin, * P =0.0106 for G γ and * P =0.0265 for Α γ. E – H Quantification of HPLC analysis of ( E ) γ-globin relative to all β-like globins, ( F ) γ-globin relative to β-globin, ( G ) β-globin relative to α-globin and ( H ) δ-globin relative to α-globin, ** P =0.0089, * P =0.0106. I Quantification of HBG protein after immunoblotting on D6 of differentiation normalized to HBA protein and expressed as fold change to the mock, * P =0.0405. Both proteins were first normalized to β-actin protein. J Relative γ-globin mRNA expression after RT-qPCR analysis on D3 of erythroid differentiation, normalized to α-globin and expressed as fold change relative to mock, * P =0.0471. K Quantification of BCL11A protein after immunoblotting on D0 of differentiation, normalized to β-actin protein and expressed as fold change relative to mock. L Relative BCL11A mRNA expression after RT-qPCR analysis on D0 of erythroid differentiation, normalized to endogenous β-actin and expressed as fold change relative to the mock, ** P =0.0035, * P =0.0379. All data are presented as mean±S.D. (n=3, data are based on biological replicates from three independent donors) using ordinary one-way ANOVA with Dunnett’s multiple comparisons test for P -value

Article Snippet: For the synthesis of BE (pCMV_BE4max, Addgene #112093) [ ] as mRNA, the in vitro transcription protocol was performed using the HiScribeTM T7 ARCA mRNA Kit (with tailing) (New England Biolabs) according to our published procedures [ ].

Techniques: Functional Assay, Expressing, Western Blot, Quantitative RT-PCR

Journal: Genome Biology

Article Title: Functional correction and genome integrity with duplex base editing of β-thalassemic hematopoietic stem cells

doi: 10.1186/s13059-026-03974-7

Figure Lengend Snippet: RNA-seq analysis of BFU-E colonies. A Schematic diagram of the study design for RNA-seq analysis. B Flow cytometry analysis for the detection of dead and apoptotic cells after each treatment. Data are presented as % ( n =1). C BFU-E and CFU-GM colony scoring on day 14 for each treatment. Data are presented as % ( n =1). D Left: charts showing the percentage frequency of specific edits detected by Sanger Sequencing for each treatment. Y-axis labels indicate the edit in each allele, where N represents no editing in the one allele (monoallelic). Right: charts showing genotypes for the three colonies selected for further analysis. X-axis indicates the specific edits, with values representing editing status: 100=biallelic, 50=monoallelic, 0=no edit. E Relative HBG mRNA expression after RNA-seq analysis, normalized to HBA and expressed as log 2 fold change relative to mock, * P =0.0325. Data are presented as mean±S.D. ( n =3, data are based on biological replicates from three different BFU-E colonies) using Kruskal-Wallis test with Dunn’s multiple comparison test

Article Snippet: For the synthesis of BE (pCMV_BE4max, Addgene #112093) [ ] as mRNA, the in vitro transcription protocol was performed using the HiScribeTM T7 ARCA mRNA Kit (with tailing) (New England Biolabs) according to our published procedures [ ].

Techniques: RNA Sequencing, Flow Cytometry, Sequencing, Expressing, Comparison

Journal: Genome Biology

Article Title: Functional correction and genome integrity with duplex base editing of β-thalassemic hematopoietic stem cells

doi: 10.1186/s13059-026-03974-7

Figure Lengend Snippet: mRNA expression of apoptotic and immune response genes after RNA-seq analysis. Normalized mRNA expression is shown as log 2 fold change of statistically significant ( A-D ) apoptotic and ( E-H ) immune response genes after each treatment. Data are presented as mean±S.D. ( n =3, data are based on biological replicates from three different BFU-E colonies). DESeq2 analysis was performed and adjusted P -values are indicated as follows: *<0.05, **<0.01, ***<0.001, ****<0.0001

Article Snippet: For the synthesis of BE (pCMV_BE4max, Addgene #112093) [ ] as mRNA, the in vitro transcription protocol was performed using the HiScribeTM T7 ARCA mRNA Kit (with tailing) (New England Biolabs) according to our published procedures [ ].

Techniques: Expressing, RNA Sequencing

Journal: Cell

Article Title: SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses

doi: 10.1016/j.cell.2020.10.004

Figure Lengend Snippet:

Article Snippet: HiScribe T7 ARCA mRNA Kit , NEB , Cat. # E2060S.

Techniques: Virus, Recombinant, Transfection, RNA Sequencing Assay, Software

Journal: Microbiology Spectrum

Article Title: Iron limitation indirectly reduces the Escherichia coli torCAD operon expression by a reduction of molybdenum cofactor availability

doi: 10.1128/spectrum.03480-23

Figure Lengend Snippet: Expression of a PiscR-lacZ fusion TorA activity and Moco content in E. coli mutant strains. ( A ) β-galactosidase activities expressed in Miller units were determined for iscR-lacZ fusion in E. coli BW25113 wild-type strain and Δ nac , Δ fur , Δ torI , Δ arcA , Δ ccmA , Δ IscU , Δ fnr , and Δ iscR strains. The strains were cultivated anaerobically in the presence of 20 mM TMAO for 4 h. β-galactosidase activities were normalized to the OD 600 nm values. Standard deviation was calculated from three biological replicates. ( B ) Quantification of relative amounts of Moco in the E. coli BW25113 wild-type strain and the mutant Δ fnr , Δ arcA , Δ fur , and Δ iscU strains. The strains were grown anaerobically in the presence of 20 mM TMAO for 8 h in the LB medium. Total Moco in crude extracts was oxidized overnight with acidic iodine into its fluorescence derivative, FormA. FormA was separated and quantified by its fluorescence monitored at λ ex = 383 nm and λ em = 450 nm. The black, white, and gray bars represent without the isc operon, with iscRSUAhscABfdx iscX , and with iscSUAhscABfdx-iscX , respectively. ( C ) TMAO reductase activity in the E. coli BW25113 wild-type strain and the mutant Δ fnr , Δ arcA , Δ fur , and Δ iscU strains. The strains were cultivated anaerobically in the presence of 20 mM TMAO. TMAO reductase activities (in units) were normalized to the OD 600 nm values. Standard deviation was calculated from three biological replicates. The black, white, and gray bars represent with either the vector only, or with a plasmid carrying the iscRSUAhscABfdx-iscX or iscSUAhscABfdx-iscX genes, respectively.

Article Snippet: BW25113 (referred to as parental strain) and the isogenic mutant strains Δ torA, Δ fnr, Δ fur, Δ nac, Δ torI, Δ narL, Δ ccmA, Δ arcA, Δ iscR, Δ modE, Δ moaA, Δ moaC, Δ moaD, Δ moaE, Δ moeA, Δ moeB, Δ mogA, Δ mobA, Δ mocA, and Δ iscU were obtained from the Keio collection from the National BioResource Project (National Institute of Genomics, Japan) ( , ).

Techniques: Expressing, Activity Assay, Mutagenesis, Standard Deviation, Fluorescence, Plasmid Preparation

Journal: Arteriosclerosis, thrombosis, and vascular biology

Article Title: Modulation of the coagulation cascade using aptamers

doi: 10.1161/ATVBAHA.115.300131

Figure Lengend Snippet: Clinical trials of aptamers targeting proteins involved in coagulation Data from www.clinicaltrials.gov . TTP = thrombotic thrombocytopenic purpura, VWD = von Willebrand Disease

Article Snippet: NU172 (ARCA Biopharma, Inc.) Thrombin , Heart Disease , Phase 2 Recruitment Status Unknown (June 2011) , NCT00808964.

Techniques: Clinical Proteomics, Coagulation