Journal: Nature Structural & Molecular Biology

Article Title: Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis

doi: 10.1038/s41594-023-00943-7

Figure Lengend Snippet: a , Volcano plots as in Fig. , highlighting pluripotency-associated factors that are enriched (red) or not significantly changed (black) on WT (left plot) or Suv39h dn (right plot) ESC mitotic chromosomes. b , Esrrb immunolabeling (red) of WT and Suv39h dn flow-sorted chromosomes 19 (left panel) and X (right panel), where DAPI counterstain is shown in light gray. Scale bar, 5 μm. Esrrb mean intensities were measured across individual chromosomes; the mean ± s.d. is shown ( n = minimum 50 chromosomes analyzed over 3 independent experiments). P values of statistically significant changes, measured by unpaired, two-tailed Student’s t -tests, are indicated. c , Esrrb ChIP–qPCR analysis in WT versus Suv39h dn mitotic and asynchronous ESCs. Enrichment (immunoprecipitated as a percentage of input (% IP)) was measured at Esrrb bookmarked sites ( Capn2 , Esrrb , Jam2-s1 , Jam2-s2 , Tbx3 and Tet2 ), Esrrb lost sites (bound only in interphase ; Mgat3 and Twistnb ) or control sites that do not bind Esrrb ( Esrrb-3 ′ and Actb ). The mean + s.d. results are shown. For interphase cells n = 3 biological replicates, for mitotic cells n = 4 biological replicates (except Capn2 , Esrrb , Rex1 and Jam2-s1 , where n = 5). d , Live-cell imaging of Esrrb–tdTomato mouse ESCs pretreated with DMSO (upper panel) or 100 nM of chaetocin (lower panel) cultured with SiR-DNA (red). Arrows show Esrrb localization to mitotic chromatin. Scale bar, 5 μm. Esrrb–tdTomato mean intensities on mitotic DNA (gated based on SiR-DNA signal) and in interphase nuclei were quantified for each condition; the mean ± s.d. is shown. For mitotic chromosomes: n = 25 (DMSO) or n = 35 (chaetocin) cells analyzed; for interphase nuclei: n = 46 cells analyzed for both DMSO and chaetocin treatments, representing 3 independent experiments. b – d , P values of statistically significant changes, measured by unpaired, two-tailed Student’s t -tests, are indicated. and precise n numbers are provided.

Article Snippet: Real-time qPCR (BioRad, CFX96 system with CFX manager software) was performed in technical triplicate for each biological replicate, using SYBR Green PCR Master Mix (QIAGEN) and the primers listed in Supplementary Table .

Techniques: Immunolabeling, Two Tailed Test, ChIP-qPCR, Immunoprecipitation, Control, Live Cell Imaging, Cell Culture

Journal: Cell host & microbe

Article Title: Reshaping of the Dendritic Cell Chromatin Landscape and Interferon Pathways During HIV Infection

doi: 10.1016/j.chom.2018.01.012

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: CFX96 thermal cycler , Biorad , Model T100.

Techniques: Virus, Recombinant, Saline, High Molecular Weight, Electron Microscopy, SYBR Green Assay, Staining, Library Quantification, Next-Generation Sequencing, Fractionation, Plasmid Preparation, DNA Purification, Bicinchoninic Acid Protein Assay, Enzyme-linked Immunosorbent Assay, Luciferase, Infection, Sequencing, Cloning, Control, shRNA, Software, Flow Cytometry, Gene Expression, Microarray

Journal: Journal of Translational Medicine

Article Title: A novel small molecule inhibitor of p32 mitochondrial protein overexpressed in glioma

doi: 10.1186/s12967-017-1312-7

Figure Lengend Snippet: Protein thermal shift induced by M36 binding p32. Human recombinant protein p32 was incubated with 100 µM M36 or DMSO control and protein thermal shift determined with BioRad CFX96 real-time PCR

Article Snippet: The thermal shift reaction was performed with a BioRad CFX96 real-time PCR machine, and analysis for binding induced shifts in thermal transition was performed with Precision Melt Analysis Software provided by the manufacturer (BioRad).

Techniques: Binding Assay, Recombinant, Incubation, Control, Real-time Polymerase Chain Reaction

Journal: Microorganisms

Article Title: The Global Trends and Advances in Oral Microbiome Research on Oral Squamous Cell Carcinoma: A Systematic Review

doi: 10.3390/microorganisms13020373

Figure Lengend Snippet: Key biomarkers and diagnostic advancements in oral squamous cell carcinoma: a review of current evidence.

Article Snippet: Cheng, Y.-S.L. et al. [ ] , 2017 , Metabolism, biomarkers, carcinoma, reverse transcriptase polymerase chain reaction , 105 human subjects , Observational study , Bio-Rad CFX96 Real-Time System , Mann–Whitney U test with Bonferroni corrections , Only S100P showed significantly higher levels in patients with OSCC compared to both patients with CPNS ( p = 0.003) and CPS ( p = 0.007).

Techniques: Diagnostic Assay, Sequencing, Spectrophotometry, Biomarker Discovery, Isolation, Control, Real-time Polymerase Chain Reaction, Concentration Assay, Mann-Whitney U-Test, Chromatography, Software, Marker, Clinical Proteomics, Enzyme-linked Immunosorbent Assay, Next-Generation Sequencing, Expressing, Amplification, Immunohistochemistry, Reverse Transcription, Polymerase Chain Reaction, Electrophoresis, Activity Assay, Comparison, Blocking Assay, Quantitation Assay, Multiplex sample analysis, Western Blot, Histopathology, Migration, Multiplex Assay, Gene Expression, Genome Wide, DNA Methylation Assay, Immunofluorescence, Sampling, Luminex, Illumina Sequencing, Infection, Fluorescence, In Situ Hybridization, Quantitative Proteomics, Extraction, Flow Cytometry, Gas Chromatography-Mass Spectrometry, DNA Sequencing