Journal: bioRxiv

Article Title: TCA cycle entry point, growth variability and amino acid utilization in Alteromonas macleodii ATCC 27126

doi: 10.64898/2026.03.04.709670

Figure Lengend Snippet: From left to right: The growth (OD and cell count) of ATCC 27126 on various amino acids (blue background), in comparison with the pyruvate positive control and the equimolar positive control (green background), and the carbon free negative control (red background). The top row shows growth on plates, in comparison with the OD and cell counts in tubes (Lower three rows).

Article Snippet: Here, we use growth assays in 96 well plates on individual amino acids and their combinations to directly measure the ability of a model marine bacterium, Alteromonas macleodii ATCC 27126, to utilize these resources for growth.

Techniques: Cell Characterization, Comparison, Positive Control, Negative Control

Journal: eLife

Article Title: A conserved mycobacterial nucleomodulin hijacks the host COMPASS complex to reprogram pro-inflammatory transcription and promote intracellular survival

doi: 10.7554/eLife.107677

Figure Lengend Snippet: ( A ) Y2H assay identifying interactions between MgdE mutants and COMPASS complex subunits. Yeast cells were co-transformed with bait (pGBKT7) and prey (pGADT7) plasmids expressing wild-type or mutant MgdE and human COMPASS subunits (ASH2L, WDR5, RbBP5, and DPY30). Growth was assessed on non-selective (-Leu/-Trp, left) and selective (-Leu/-Trp/-Ade/-His+200 ng/μL aureobasidin A, right) media. Controls: CK− (pGBKT7- lam +pGADT7 T, negative) and CK+ (pGBKT7- p53 +pGADT7 T, positive). ( B ) Co-IP analysis of MgdE mutants with WDR5. HEK293T cells were co-transfected with Flag-tagged MgdE mutants and HA-tagged WDR5 (1:1 molar ratio). Complexes were immunoprecipitated using anti-HA antibody and protein A/G beads, followed by immunoblotting with anti-Flag and anti-HA antibodies. ( C ) Nuclear distribution of wild-type and mutants MgdE. Confocal microscopy of HEK293T cells expressing wild-type or D224AH247A MgdE-EGFP at 12 and 24 hr post-transfection (hpt). Nuclear foci were visualized by enhanced green fluorescent protein (EGFP) (green) and DAPI (blue) staining. Scale bar, 10 µm. Images were acquired with a 100x oil immersion objective (NA = 1.4). ( D ) Immunoblot analysis of H3K4me3 levels. HEK293T cells expressing wild-type or D224AH247A mutant MgdE were analyzed for changes in H3K4me3 levels over 0-24 hr post-transfection. Histone H3 was used as a loading control. Data represent mean ± SD of three independent biological replicates. Statistical significance was determined using two-tailed unpaired Student’s t -tests, * p <0.05, ** p <0.01, *** p <0.001. Figure 5—source data 1. Original files for western blot analysis displayed in panel B. Figure 5—source data 2. Original western blots for panel B, indicating the relevant bands. Figure 5—source data 3. Original files for western blot analysis displayed in panel D. Figure 5—source data 4. Original western blots for panel D, indicating the relevant bands.

Article Snippet: The Y2H Gold yeast strain (Takara Bio) was maintained in YPDA (yeast extract, peptone, dextrose, and adenine sulfate) medium.

Techniques: Y2H Assay, Transformation Assay, Expressing, Mutagenesis, Co-Immunoprecipitation Assay, Transfection, Immunoprecipitation, Western Blot, Confocal Microscopy, Staining, Control, Two Tailed Test

Journal: Frontiers in Microbiology

Article Title: Comparative Analyses of the Transcriptome and Proteome of Escherichia coli C321.△A and Further Improving Its Noncanonical Amino Acids Containing Protein Expression Ability by Integration of T7 RNA Polymerase

doi: 10.3389/fmicb.2021.744284

Figure Lengend Snippet: Bacterial strains and plasmids used in this study.

Article Snippet: E. coli C321.ΔA , E. coli MG1655Δ ( ybhB-bioAB )::[λcI857 N( croea59 ):: tetR-bla ] Δ prfA Δ mutS :: zeoR ; all 321 TAG codons changed to TAA , Addgene (ID: 48998).

Techniques: Plasmid Preparation, CRISPR, Sequencing, Mutagenesis