Journal: Frontiers in Plant Science

Article Title: Habitat-adapted heterologous symbiont Salinispora arenicola promotes growth and alleviates salt stress in tomato crop plants

doi: 10.3389/fpls.2022.920881

Figure Lengend Snippet: Salinispora arenicola enhances the growth of tomato plants under normal and salt stress conditions. Phenotype measurements of 39 DAG plants grown with either NaCl-free irrigation or saline irrigation that were either inoculated with a habitat-adapted heterologous symbiont (HAHS) bacterium or not (control; Ctrl). Statistical significance was determined using a permutational ANOVA (PERMANOVA; p = 0.001 ). Lowercase letters denote statistical differences (pairwise test) among conditions.

Article Snippet: All statistical analyses were conducted in Sigma Plot v. 12 (Systat Software, Inc., Chicago, IL, United States) and PRIMER + PERMANOVA software (Version 7.0.13; PRIMER-e, Plymouth, United Kingdom).

Techniques:

Journal: PLoS genetics

Article Title: Disease-related growth factor and embryonic signaling pathways modulate an enhancer of TCF21 expression at the 6q23.2 coronary heart disease locus.

doi: 10.1371/journal.pgen.1003652

Figure Lengend Snippet: Figure 3. AP-1 dependent transcriptional regulation at rs12190287 in vitro. (a) Dual-luciferase assay of rs12190287-C and G variants determined in A7r5 cells transfected with rs12190287 enhancer (C-Luc and G-Luc), consensus AP-1 reporter (AP1-Luc) or empty reporter (pLuc), along with human c-JUN, JUND, or ATF3 expression vectors and measured after 24 hours. *P,0.0001 versus C-Luc, G-Luc or 21-Luc+Empty where indicated. (b) Dual-luciferase assay of rs12190287 enhancer in A7r5 cells transfected with empty vector (Empty) or dominant negative expression constructs for human CREB (CREBD), c-JUN (JunD), or ATF3 (ATF3D). *P,0.01 versus C-Luc+Empty. (c) Dual-luciferase assay of rs12192087 enhancer in heterozygous HCASMC transfected with small interfering RNA duplexes (siRNA) against c-JUN, JUND, ATF3 or a negative control (Neg si). *P,0.01 versus C-Luc or G-Luc+Neg si. (d) EMSA of rs12190287 C/G enhancer showing specific shifted complexes (arrow) and JunD and c-Jun super-shifted complexes (bold arrows). Bar-head line denotes non-specific shifted complexes. Values are normalized mean 6 SD from triplicates. Similar results were observed from three independent experiments. doi:10.1371/journal.pgen.1003652.g003

Article Snippet: Protein concentrations were determined using a BCA assay (Pierce) and 50–100 mg nuclear protein for each condition was loaded on a pre-cast NuPAGE 4–12% Bis-Tris polyacrylamide gel (Invitrogen/Life Technologies), with gel run at 150 v for 1 h using MES buffer (Invitrogen/Life Technologies), and transferred to PVDF membrane at 35 v for 1 h. Membranes were blocked in 5% non-fat dry milk in 16 TBST for 1 h and PLOS Genetics | www.plosgenetics.org 14 July 2013 | Volume 9 | Issue 7 | e1003652 incubated overnight with rabbit polyclonal antibodies against TCF21 (Sigma; 0.25 mg/ml), cJUN (Santa Cruz; 1.0 mg/ml), JUND (Santa Cruz; 1.0 mg/ml), ATF3 (Santa Cruz; 1.0 mg/ml), or WT1 (Santa Cruz; 1.0 mg/ml), followed by incubation in a secondary anti-rabbit HRP-conjugated antibody (Invitrogen/Life Technologies; 0.2 mg/ml) and detection by standard ECL (Pierce).

Techniques: In Vitro, Luciferase, Transfection, Expressing, Plasmid Preparation, Dominant Negative Mutation, Construct, Small Interfering RNA, Negative Control

Journal: PLoS genetics

Article Title: Disease-related growth factor and embryonic signaling pathways modulate an enhancer of TCF21 expression at the 6q23.2 coronary heart disease locus.

doi: 10.1371/journal.pgen.1003652

Figure Lengend Snippet: Figure 4. PDGFRb is upstream of TCF21 at rs12190287 in HCASMC. (a) TaqMan based qRT-PCR results showing relative mRNA expression levels of total TCF21 in heterozygous HCASMC treated with TGF-b1, PDGF-BB or PMA for indicated times. Expression levels were normalized to 18S and expressed as fold change from 0 h. *P,0.0001 versus 0 h. (b) TaqMan qRT-PCR expression results of c-JUN, JUND, and ATF3 in heterozygous HCASMC treated TGF-b1 or PDGF-BB for the indicated times. (c) Allele-specific TaqMan qRT-PCR based expression of TCF21 at rs12190287 shown as normalized allelic ratio C/G in heterozygous HCASMC treated with either TGF-b1 or PDGF-BB for the indicated times. *P,0.01 versus 0 h. Values are mean 6 SD of triplicates. Similar results were observed from three independent experiments. doi:10.1371/journal.pgen.1003652.g004

Article Snippet: Protein concentrations were determined using a BCA assay (Pierce) and 50–100 mg nuclear protein for each condition was loaded on a pre-cast NuPAGE 4–12% Bis-Tris polyacrylamide gel (Invitrogen/Life Technologies), with gel run at 150 v for 1 h using MES buffer (Invitrogen/Life Technologies), and transferred to PVDF membrane at 35 v for 1 h. Membranes were blocked in 5% non-fat dry milk in 16 TBST for 1 h and PLOS Genetics | www.plosgenetics.org 14 July 2013 | Volume 9 | Issue 7 | e1003652 incubated overnight with rabbit polyclonal antibodies against TCF21 (Sigma; 0.25 mg/ml), cJUN (Santa Cruz; 1.0 mg/ml), JUND (Santa Cruz; 1.0 mg/ml), ATF3 (Santa Cruz; 1.0 mg/ml), or WT1 (Santa Cruz; 1.0 mg/ml), followed by incubation in a secondary anti-rabbit HRP-conjugated antibody (Invitrogen/Life Technologies; 0.2 mg/ml) and detection by standard ECL (Pierce).

Techniques: Quantitative RT-PCR, Expressing

Journal: PLoS genetics

Article Title: Disease-related growth factor and embryonic signaling pathways modulate an enhancer of TCF21 expression at the 6q23.2 coronary heart disease locus.

doi: 10.1371/journal.pgen.1003652

Figure Lengend Snippet: Figure 7. AP-1 regulation at rs12524865 and haplotype structure in East Asians. (a) Linkage disequilibrium (LD) plot from ,2400 Metabochip genotyped East Asian samples from the TAICHI study (HALST cohort) with imputation from HapMap Phase II and III Han Chinese (CHB), showing eSNPs for TCF21 and distinct haplotype blocks containing rs12524865 and rs12190287. White to black squares represent increasing r2 values, also shown in blocks. (b) Dual-luciferase assay of rs12524865 C/A enhancer transfected in A7r5 and treated with adenylyl cyclase activator, forskolin (Fsk) or PKC activator, phorbol-12-myristate-13-acetate (PMA) for 4 hours. Relative luciferase activities measured after 24 hours. *P,0.01 versus C- Luc+Veh. (c) Total enrichment of c-Jun, JunB, JunD, and ATF3 at rs12524865 determined by chromatin immunoprecipitation (ChIP) in HCASMC treated with PDGF-BB or vehicle (Control) for 6 hours. *P,0.005 versus Control for each condition. (d) Total enrichment of histone modifications H3K4me1, H3K4me3, H3K27ac, and H3K27me1 at rs12524865 determined by ChIP in HCASMC treated with PDGF-BB. *P,0.001 versus Control for each condition. Values are mean 6 SD from triplicates. Similar results were observed from three independent experiments. doi:10.1371/journal.pgen.1003652.g007

Article Snippet: Protein concentrations were determined using a BCA assay (Pierce) and 50–100 mg nuclear protein for each condition was loaded on a pre-cast NuPAGE 4–12% Bis-Tris polyacrylamide gel (Invitrogen/Life Technologies), with gel run at 150 v for 1 h using MES buffer (Invitrogen/Life Technologies), and transferred to PVDF membrane at 35 v for 1 h. Membranes were blocked in 5% non-fat dry milk in 16 TBST for 1 h and PLOS Genetics | www.plosgenetics.org 14 July 2013 | Volume 9 | Issue 7 | e1003652 incubated overnight with rabbit polyclonal antibodies against TCF21 (Sigma; 0.25 mg/ml), cJUN (Santa Cruz; 1.0 mg/ml), JUND (Santa Cruz; 1.0 mg/ml), ATF3 (Santa Cruz; 1.0 mg/ml), or WT1 (Santa Cruz; 1.0 mg/ml), followed by incubation in a secondary anti-rabbit HRP-conjugated antibody (Invitrogen/Life Technologies; 0.2 mg/ml) and detection by standard ECL (Pierce).

Techniques: Luciferase, Transfection, Chromatin Immunoprecipitation, Control

Journal: PLoS genetics

Article Title: Disease-related growth factor and embryonic signaling pathways modulate an enhancer of TCF21 expression at the 6q23.2 coronary heart disease locus.

doi: 10.1371/journal.pgen.1003652

Figure Lengend Snippet: Figure 8. Predicted model of AP-1 dependent regulation of TCF21 at rs12190287 and rs12524865. Individuals carrying risk alleles for rs12190287 or rs12524865 at 6q23.2 are expected to have increased TCF21 expression upon stimulation of PDGFR-b by PDGF-BB in coronary artery smooth muscle cells, due to increased enrichment of active histone modifications (represented by closed and open diamonds) leading to an open chromatin conformation, allowing binding of an active AP-1 TF complex containing various combinations of c-Jun, JunD, and ATF3. WT1 functions as a transrepressor of this active complex at rs12190287, whereby WT1 may fine-tune the spatial and temporal activation of TCF21 expression. Multiple kinases other than mitogen-activated kinase (MEKK) may be involved in the activation and recruitment of AP-1 complexes to these binding sites. doi:10.1371/journal.pgen.1003652.g008

Article Snippet: Protein concentrations were determined using a BCA assay (Pierce) and 50–100 mg nuclear protein for each condition was loaded on a pre-cast NuPAGE 4–12% Bis-Tris polyacrylamide gel (Invitrogen/Life Technologies), with gel run at 150 v for 1 h using MES buffer (Invitrogen/Life Technologies), and transferred to PVDF membrane at 35 v for 1 h. Membranes were blocked in 5% non-fat dry milk in 16 TBST for 1 h and PLOS Genetics | www.plosgenetics.org 14 July 2013 | Volume 9 | Issue 7 | e1003652 incubated overnight with rabbit polyclonal antibodies against TCF21 (Sigma; 0.25 mg/ml), cJUN (Santa Cruz; 1.0 mg/ml), JUND (Santa Cruz; 1.0 mg/ml), ATF3 (Santa Cruz; 1.0 mg/ml), or WT1 (Santa Cruz; 1.0 mg/ml), followed by incubation in a secondary anti-rabbit HRP-conjugated antibody (Invitrogen/Life Technologies; 0.2 mg/ml) and detection by standard ECL (Pierce).

Techniques: Expressing, Binding Assay, Activation Assay