Journal: Frontiers in Plant Science

Article Title: Re-examination of the APETALA2/Ethylene-Responsive Factor Gene Family in Barley ( Hordeum vulgare L.) Indicates a Role in the Regulation of Starch Synthesis

doi: 10.3389/fpls.2021.791584

Figure Lengend Snippet: Co-expression and interaction analyses of HvAP2/ERF candidate genes involved in starch synthesis. (A) Relative expression levels of key starch synthase genes. DPA: days post anthesis. (B) Relative expression levels of 12 HvAP2/ERF genes. (C) Characterization of the interaction between the HvAP2-18 protein and the promoter of starch synthase genes via LUC assay. (D) Characterization of the interaction between the HvAP2-18 protein and the promoter of HvAGP-S , HvSBE1 , and HvSS2a via yeast one-hybrid assay. Statistically significant differences are indicated: *, P < 0.05; **, P < 0.01 (Student’s t -test).

Article Snippet: The yeast one-hybrid (Y1H) assay was conducted following the protocol of the Matchmaker Gold Yeast One-Hybrid Library Screening System (Clontech, Palo Alto, CA, United States).

Techniques: Expressing, Starch, Y1H Assay

Journal: Briefings in Bioinformatics

Article Title: RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method

doi: 10.1093/bib/bbae166

Figure Lengend Snippet: Poses of the top 20 ligand selected by RmsdXNA and rDock from Chembridge and Life Chemicals screening libraries docked on 4PLX using rDock. Top-scored ligand poses selected by RmsdXNA tend to intercalate between the RNA residues. This is not observed for the top-scored ligands selected by rDock.

Article Snippet: In this VS example, rDock is utilized to generate 20 poses within a 20 Å target search box on the 3’ end of MALAT1 [ , ] (PDB ID: 4PLX) against two screening compound libraries, Hit2Lead (provided by Chembridge Corp. in San Diego, CA, USA, http://www.hit2lead.com ) and Life Chemicals RNA screening library ( https://www.lifechemicals.com ).

Techniques:

Journal: iScience

Article Title: A dual SHOX2:GFP; MYH6:mCherry knockin hESC reporter line for derivation of human SAN-like cells

doi: 10.1016/j.isci.2022.104153

Figure Lengend Snippet: Generation of human SAN-like cells from hESCs (A) Schematic representation of the differentiation protocols 1–8. The protocol involves three stages (S1, S2, and S3) during the first 9 days of directed differentiation. (B–D) Quantitative PCR (B), live fluorescence images (C), and FACS plots (D) of the day 30 cells derived from the SHOX2:GFP;MYH6:mCherry H9 line using the corresponding differentiation protocols (n = at least 3 biological replicates for each condition). For quantitative PCR data, fold changes were normalized to protocol #1. p values calculated using ordinary one-way ANOVA with Fisher’s test (∗∗p < 0.01, ∗∗∗p < 0.001 ). Data are represented as mean ± SEM. The x axis in panel D is side scatter. (E) Quantitative PCR analysis for SHOX2 transcriptional expression of GFP + cells purified after sorting. n = 3 biological replicates. p value calculated by unpaired two-tailed Student’s t-test ∗∗∗p < 0.001. Data are represented as mean ± SEM, and normalized to GFP-negative population. (F) Schematic and results of the epigenetic library chemical screen. (G) Schematic of the final differentiation protocol. (H) Immunofluorescence image and FACS plot of day 30 cells derived using the protocol described in (G), Scale bar = 100 μm. AA: Activin A, B: BMP4, Ch: CHIR99021, Wi: Wnt inhibitor, RA: Retinoic Acid, Fi: FGF inhibitor, Cu: cucurbitacin, Tyr490: tyrphostin AG 490. See also Figures S1 and .

Article Snippet: Cayman Epigenetic Chemical library , Cayman , #11076.

Techniques: Real-time Polymerase Chain Reaction, Fluorescence, Derivative Assay, Expressing, Purification, Two Tailed Test, Immunofluorescence

Journal: iScience

Article Title: A dual SHOX2:GFP; MYH6:mCherry knockin hESC reporter line for derivation of human SAN-like cells

doi: 10.1016/j.isci.2022.104153

Figure Lengend Snippet:

Article Snippet: Cayman Epigenetic Chemical library , Cayman , #11076.

Techniques: Recombinant, Software