Journal:

Article Title: Potato Dextrose Agar Antifungal Susceptibility Testing for Yeasts and Molds: Evaluation of Phosphate Effect on Antifungal Activity of CMT-3

doi: 10.1128/AAC.46.5.1455-1461.2002

Figure Lengend Snippet: Comparison of the MICs of fluconazole, ketoconazole, and CMT-3 determined by the BMM and the PDA method

Article Snippet: Four yeast strains, i.e., Candida parapsilosis ATCC 22019, Candida tropicalis ATCC 750, Candida krusei ATCC 6258, and Candida albicans ATCC 24433, and strains of four filamentous fungi, i.e., a Penicillium sp, Aspergillus flavus , Aspergillus fumigatus ATCC 1022, and a Rhizopus sp, were used to evaluate the reproducibility of the PDA method and its accuracy by comparing the MIC ranges obtained by this method and the NCCLS model. Other fungal isolates, such as Pseudallescheria boydii , Paecilomyces variotii ATCC 22319, Yarrowia lipolytica , and Candida glabrata , were also used to test the feasibility of the PDA method.

Techniques:

Journal: Nucleic Acids Research

Article Title: HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs

doi: 10.1093/nar/gkab1221

Figure Lengend Snippet: Defect of HIRA complex results in H2A.Z decrease on genome wide. ( A ) Schematic diagram of genome editing in defective cell lines. Hira-, Ubn2- and H3.3-knockout cell lines and Ubn1/2 double mutants were generated using CRISPR-Cas9 system. For subsequent experiments, 6 × HA tag was added to the N-terminus of Srcap in R1 wild type and above defective cell lines. ( B ) Western blot respectively shows the proteins levels of Hira (a), Ubn1&Ubn2 (b), and H3.3 (c) in the defective cell lines. ( C ) Meta-analysis (left) and heatmap (right) show H2A.Z reads density around summit (upper) and TSS (below) in R1 WT , Hira-KO , Ubn2-KO/Ubn1-KD , Ubn1/2-DM and H3.3-KO cells within a ±3 kb window. ( D ) Venn diagram shows the overlap of H2A.Z down-regulated peaks between the above defective cell lines. ( E ) The reduced H2A.Z peaks in either Hira-KO or Ubn2-KO/Ubn1-KD cell lines are defined as HIRA complex regulated (HR) peaks (23 530 peaks). The 5426 HR peaks overlapping with Ubn1/2-DM cell line is defined as HIRA-regulated and H3.3-dependent (HIRA-H3.3D). The other 18 104 HR peaks are HIRA-regulated and H3.3-independent (HIRA-H3.3ID).

Article Snippet: Antibodies and beads used for immunoprecipitation and western blot were as follows: H2A.Z antibody (1:5,000, Active Motif, 39113); Ubn1 antibody (1:3,000, Abcam, ab84953); H2B antibody (1:10,000, Abcam, ab1790); Hira antibody (1:500, Millipore, WC119); HA antibody (1:2,000, CWBIO, CW01245); Ubn1 antibody (1:3,000, Santacruz, SC-515340); Ubn1 antibody (in-house antibody); Ubn2 antibody (1:3,000, in-house antibody); Ino80 antibody (1:2,000, Proteintech, 18810-1-AP); Daxx antibody (1:3,000, Santa cruz, sc-7152); mouse IgG antibody (Santa cruz, sc-2025); Srcap antibody (1:750, Kerafast, ESL103); Flag-M2 (1:3,000, Sigma, F3165); anti-HA agarose beads (Sigma, 104M4753V); Flag antibody (1:5,000, rabbit, huaxingbio, HX1819); GAPDH antibody (1:10,000, Abclonal, AC033).

Techniques: Genome Wide, Knock-Out, Generated, CRISPR, Western Blot

Journal: Nucleic Acids Research

Article Title: HIRA complex presets transcriptional potential through coordinating depositions of the histone variants H3.3 and H2A.Z on the poised genes in mESCs

doi: 10.1093/nar/gkab1221

Figure Lengend Snippet: HIRA collaborates with SRCAP to deposit H2A.Z on genome. ( A ) Meta-analysis (left) and heatmap (right) show Srcap reads density around summit (upper) and TSS (below) within a ±3 kb window. ( B ) Representative loci on Slc25a42 gene show the enrichment of H2A.Z and Srcap. ( C ) ChIP-qPCR validation of H2A.Z and Srcap enrichment at promoter of Slc35a42 gene. Error bars represent data from three independent experiments. ( D ) Venn diagram shows the overlap between H2A.Z, Hira and Srcap peaks. ( E ) Western blot shows the interaction among endogenous HA-Srcap, Hira and Ubn1 from nuclear lysates. Ino80, Daxx, H2A.Z and H3.3 are also detected. ( F ) Top panel showed schematic presentation of full length and truncation mutants of Hira subunit. Bottom panel showed the biochemical interactions between Hira truncations and SRCAP complex are analyzed by GST pull-down coupled with western blot analyses. ( G ) Heatmaps (upper) show H2A.Z reads density around H2A.Z peak summits (upper) in R1 WT , Hira-KO and Hira-truncation mutant expressing cells within a ±3 kb window. Representative loci (bottom) show the enrichment of H2A.Z. (H) ChIP-qPCR of H2A.Z, Srcap and Flag at representative genes Nrg2 and Spata4 in the rescued overexpressed cell lines. Error bars represent data from three independent experiments.

Article Snippet: Antibodies and beads used for immunoprecipitation and western blot were as follows: H2A.Z antibody (1:5,000, Active Motif, 39113); Ubn1 antibody (1:3,000, Abcam, ab84953); H2B antibody (1:10,000, Abcam, ab1790); Hira antibody (1:500, Millipore, WC119); HA antibody (1:2,000, CWBIO, CW01245); Ubn1 antibody (1:3,000, Santacruz, SC-515340); Ubn1 antibody (in-house antibody); Ubn2 antibody (1:3,000, in-house antibody); Ino80 antibody (1:2,000, Proteintech, 18810-1-AP); Daxx antibody (1:3,000, Santa cruz, sc-7152); mouse IgG antibody (Santa cruz, sc-2025); Srcap antibody (1:750, Kerafast, ESL103); Flag-M2 (1:3,000, Sigma, F3165); anti-HA agarose beads (Sigma, 104M4753V); Flag antibody (1:5,000, rabbit, huaxingbio, HX1819); GAPDH antibody (1:10,000, Abclonal, AC033).

Techniques: Western Blot, Mutagenesis, Expressing

Journal: Cell reports

Article Title: Functional genome-wide short hairpin RNA library screening identifies key molecules for extracellular vesicle secretion from microglia

doi: 10.1016/j.celrep.2022.110791

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Accell Mouse Selenop (20363) siRNA - SMARTpool , Horizon Discovery Ltd. , E-041618-00-0020.

Techniques: Virus, Plasmid Preparation, shRNA, Selection, Recombinant, Enzyme-linked Immunosorbent Assay, Synthesized, Software, Functional Assay, Saline, Gel Extraction, Expressing, SYBR Green Assay, Bicinchoninic Acid Protein Assay, Next-Generation Sequencing