dna dsdna  (Cusabio)

Journal: Virus Research

Article Title: Mycoviruses diversity in the black kōji mold, Aspergillus luchuensis (section Nigri ) isolated from liquor-production environments in Japan

doi: 10.1016/j.virusres.2026.199724

Figure Lengend Snippet: Identification of mycoviruses in A. luchuensis strains. (A) Origin of Aspergillus strains for dsRNA screening and the results of analysis. The number in parentheses indicates the number of dsRNA positive and tested Aspergillus spp. strains (Nanaji and Fujimori, unpublished data, see also the text). The map is provided by the Geospatial Information Authority of Japan ( https://www.gsi.go.jp ). The dsRNA-sequencing strains are shown on the right with an additional Okinawa strain (JCM22320, ). (B) Colony morphologies of selected A. luchuensis strains carrying virus-like dsRNA elements. (C) dsRNA profiles of the selected A. luchuensis strains. Each dsRNA fraction was analyzed by 1.0% agarose gel electrophoresis. Fungal strains subjected to dsRNA-seq analysis are indicated in red. Expected dsRNA bands for an alternavirus (AlAV1) and a partitivirus (AlPV1) genome, as well as AlPV1 satellite-like elements, were shown on the right (see ). The asterisks indicate the expected dsRNA bands for two other partitiviruses, AlPV2 and AlPV3. A 1 kb dsDNA ladder size marker (GeneRuler 1 kb DNA ladder, Thermo Fisher Scientific, Waltham, MA, USA) was used as a size standard.

Article Snippet: A 1 kb dsDNA ladder size marker (GeneRuler 1 kb DNA ladder, Thermo Fisher Scientific, Waltham, MA, USA) was used as a size standard.

Techniques: Sequencing, Virus, Agarose Gel Electrophoresis, Marker

Journal: Nucleic Acids Research

Article Title: Genome-wide CRISPR screens identify the EXO1-CAF-1 pathway suppressing R-loop-associated DNA damage

doi: 10.1093/nar/gkag226

Figure Lengend Snippet: EXO1 and CHAF1A are recruited to R-loops and synergistically suppress R-loop accumulation. ( A ) BrdU alkaline comet assay showing that CHAF1A depletion causes increased accumulation of replication-associated single stranded DNA lesions in both EXO1-knockout lines compared to WT HeLa cells. At least 100 nuclei were quantified for each condition. The median values are marked on the graph and listed at the top. Asterisks indicate statistical significance (Mann–Whitney, two-tailed). Schematic representations of the assay conditions are shown at the top. ( B, C ) S9.6 PLA experiments showing increased EXO1 ( B ) and CHAF1A ( C ) recruitment to R-loops in HeLa cells. At least 100 cells were quantified for each condition. Bars indicate the mean values, error bars represent standard errors of the mean, and asterisks indicate statistical significance ( t -test, two-tailed, unpaired). ( D, E ) S9.6-dsDNA PLA experiments showing increased R-loops in HeLa cells with concomitant inactivation of EXO1 and CHAF1A. RNAseH1 overexpression suppresses the PLA signal, indicating that it derives from R-loops. At least 100 cells were quantified for each condition. Bars indicate the mean values, error bars represent standard errors of the mean, and asterisks indicate statistical significance ( t -test, two-tailed, unpaired).

Article Snippet: Antibodies used were: S9.6 (Kerafast ENH001), double-stranded DNA (dsDNA; Novus NBP3-07302), γH2AX (Abcam ab2893), EXO1 (Novus NBP2-16391), and CHAF1A (Cell Signaling Technology 5480s).

Techniques: Alkaline Single Cell Gel Electrophoresis, Knock-Out, MANN-WHITNEY, Two Tailed Test, Over Expression

Journal: Nucleic Acids Research

Article Title: Genome-wide CRISPR screens identify the EXO1-CAF-1 pathway suppressing R-loop-associated DNA damage

doi: 10.1093/nar/gkag226

Figure Lengend Snippet: Concomitant depletion of EXO1 and CHAF1A causes the accumulation of R-loop-associated DNA damage. ( A ) S9.6-γH2AX PLA experiments showing increased R-loop-associated DNA damage in HeLa cells with concomitant inactivation of EXO1 and CHAF1A. RNAseH1 overexpression suppresses the PLA signal, indicating that it derives from R-loops. At least 100 cells were quantified for each condition. Bars indicate the mean values, error bars represent standard errors of the mean, and asterisks indicate statistical significance ( t -test, two-tailed, unpaired). The siCHAF1A/siControl mean ratios are also presented. ( B–D ) γH2AX immunofluorescence showing that CHAF1A depletion causes increased DNA damage in both EXO1-knockout lines compared to WT HeLa cells, which is suppressed by RNaseH1 overexpression. Quantifications ( B, D ) and representative micrographs with scale bars representing 10 µm ( C ) are shown. At least 100 cells were quantified for each condition. Bars indicate the mean values, error bars represent standard errors of the mean, and asterisks indicate statistical significance ( t -test, two-tailed, unpaired). ( E–G ) Neutral comet assays showing that CHAF1A depletion causes increased DSB formation in both EXO1-knockout lines compared to WT HeLa cells, which is suppressed by RNaseH1 overexpression. Quantifications ( E, G ) and representative micrographs with scale bars representing 10 µm ( F ) are shown. At least 100 comets were quantified for each sample. The median values are marked on the graph, and asterisks indicate statistical significance (Mann–Whitney, two-tailed).

Article Snippet: Antibodies used were: S9.6 (Kerafast ENH001), double-stranded DNA (dsDNA; Novus NBP3-07302), γH2AX (Abcam ab2893), EXO1 (Novus NBP2-16391), and CHAF1A (Cell Signaling Technology 5480s).

Techniques: Over Expression, Two Tailed Test, Immunofluorescence, Knock-Out, MANN-WHITNEY

Journal: PLOS One

Article Title: GBP2 promotes podocyte pyroptosis and contributes to the pathogenesis of pediatric lupus nephritis

doi: 10.1371/journal.pone.0344601

Figure Lengend Snippet: A Evaluation of urinary protein-creatinine ratio, kidney-to-body weight ratio, blood urea nitrogen and anti-dsDNA antibody levels in control and Lupus nephritis (LN) mice. B Representative immunohistochemical staining of renal tissues in control and LN mice (400 × magnification; scale bar, 50 μm). C Evaluation of pyroptosis-related mRNA levels by RT-qPCR. D Evaluation of pyroptosis-related protein levels by western blotting. Data were expressed as the mean ± SD (n = 6 per group). * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: Following the manufacturer’s protocol, the concentrations of double-stranded DNA (dsDNA) (Cusabio Technology, Wuhan, China; CSB-E11194m) in mouse serum and the levels of IL-1β (ELK Biotechnology, Wuhan, China; ELK1271) and IL-18 (ELK Biotechnology; ELK2269) in the culture supernatant of MPC-5 cells were quantified using ELISA.

Techniques: Control, Immunohistochemical staining, Staining, Quantitative RT-PCR, Western Blot