Journal: The EMBO Journal

Article Title: Mitotic checkpoint gene expression is tuned by codon usage bias

doi: 10.15252/embj.2021107896

Figure Lengend Snippet: A Cellular protein noise (coefficient of variation, CV = std / mean) in live‐cell microscopy images of S. pombe ; n = 7 images (Nmt1‐GFP), 11 (Mad1‐GFP), 19 (Mad2‐GFP), 10 (Mad3‐GFP); single images had 16–79 GFP‐positive and 6–94 GFP‐negative (control) cells. Boxplots show median and interquartile range (IQR); whiskers extend to values no further than 1.5 times the IQR from the first and third quartile, respectively. Mad1, Mad2, and Mad3 all showed significantly lower noise than Nmt1 (Wilcoxon rank sum test; all P < 0.001). B Simulations of stochastic gene expression noise from selected mRNA/protein half‐life combinations assuming a constantly active promoter (see Methods). Synthesis rates were set to obtain a mean mRNA number of 4 per cell, and a mean protein number of 6,000 per cell. The x‐axis of each graph shows time, the y‐axis shows mRNA number per cell (blue) or protein number per cell (black). C Theoretical prediction for the coefficient of variation (CV = std/mean) of the protein number per cell, assuming different mRNA and protein half‐lives, using the same underlying model as in B. Synthesis rates were adjusted to maintain a mean mRNA number per cell of 3.5, and a mean protein number per cell of 6,000 (approx. 100 nM). D mRNA abundances by qPCR following metabolic labeling and removal of the labeled pool (two independent experiments). Lines are regression curves from generalized linear mixed model fits, excluding the measurements at t = 0 in order to accommodate for noninstantaneous labeling by 4tU. Act1 + and ecm33 + were used as long and short half‐life controls, respectively; qPCR was performed for the endogenous mRNAs. Half‐lives (95% confidence interval): mad1 + 5.6 min (4.3–8.4), mad2 + 7.7 min (6.2–10.4), mad3 + 5.2 min (4.3–6.9), act1 + 61.8 min (37.2–172.3), ecm33 + 5.0 min (4.5–5.7). E Protein abundances after translation shut‐off with cycloheximide (CHX); n = 3 experiments, error bars = std. Lines indicate fit to a one‐phase exponential decay. Cdc2 and Cdc13 were used as long and short half‐life controls, respectively. Immunoblots for the endogenous proteins (no tag). A representative experiment shown in Appendix Fig . Source data are available online for this figure.

Article Snippet: Cycloheximide (from Streptomyces griseus) , Chem Impex , Cat # 00083.

Techniques: Microscopy, Negative Control, Expressing, Labeling, Western Blot

Journal: The EMBO Journal

Article Title: Mitotic checkpoint gene expression is tuned by codon usage bias

doi: 10.15252/embj.2021107896

Figure Lengend Snippet:

Article Snippet: Cycloheximide (from Streptomyces griseus) , Chem Impex , Cat # 00083.

Techniques: Recombinant, In Vitro, Sequencing, Labeling, Protease Inhibitor, Isolation, Magnetic Beads, Bicinchoninic Acid Protein Assay, Software, Membrane

Journal: Cellular and Molecular Bioengineering

Article Title: Re-engineering Antimicrobial Peptides into Oncolytics Targeting Drug-Resistant Ovarian Cancers

doi: 10.1007/s12195-020-00626-z

Figure Lengend Snippet: Chemotherapeutic synergy. (a) Isobolograms of MAD1 and Doxorubicin (Dox), Paclitaxel (Ptx) or Cisplatin (Cis) combinatorial synergy in OVCAR-3 (left) and NCI/ADR-RES (right) cells. Fractional inhibitory concentration (FIC) < 1 and < 0.5 represent additive and synergistic effects, respectively. (b) Comparison of Dox and Cis IC50 towards NCI/ADR-RES as either a monotherapy (ADR-RES, black) or in combination with 20 μM MAD1 (ADR-RES + MAD1, grey). Activity of each drug as a monotherapy in pre-resistant OVCAR-3 (OVCAR-3, white) cells shown for comparison. (c–f) Indicated ovarian cancer cell line or patient-derived ovarian carcinoma cells were cultured in ultra-low attachment conditions and treated for 48 h with 2 μM cisplatin or 4 μM MAD1 alone and in combination. Data represent volume in arbitrary units (a.u.) and median.

Article Snippet: 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT), Fmoc-protected amino acids, N,N 0 -diisopropylcarbodiimide (DIC), O-(7-Azabenzotriazol-1-yl)-N,N,N’,N’-tetramethyluronium hexafluorophosphate (HATU), N,N -dimethylformamide (DMF), and Paclitaxel were purchased from Chem-Impex International, Inc. RPMI-1640, M199, trypsin and EDTA solution, Antibiotic-Antimycotic Solution, ultra-low attachment (ULA) plates, and 1× phosphate buffered saline (PBS) were purchased from Corning.

Techniques: Concentration Assay, Comparison, Activity Assay, Derivative Assay, Cell Culture

Journal: Journal of Bone and Joint Infection

Article Title: Determination of Tobramycin and Vancomycin Exposure Required to Eradicate Biofilms on Muscle and Bone Tissue In Vitro

doi: 10.7150/jbji.29711

Figure Lengend Snippet: Minimum inhibitory concentration (MIC) and fractional inhibitory concentration (FIC) index for musculoskeletal associated biofilms. FIC index values indicate synergistic (≤0.5), indifferent (0.5-4), or antagonistic (≥4) drug interactions.

Article Snippet: Three antimicrobial regimens were investigated: tobramycin alone (TOB; tobramycin sulfate USP, Spectrum Chemical), vancomycin alone (VANC; vancomycin hydrochloride USP, Chem-Impex International Inc.), and tobramycin/vancomycin 1:1 combination by mass (TOB+VANC).

Techniques: Concentration Assay

Journal: Journal of Bone and Joint Infection

Article Title: Determination of Tobramycin and Vancomycin Exposure Required to Eradicate Biofilms on Muscle and Bone Tissue In Vitro

doi: 10.7150/jbji.29711

Figure Lengend Snippet: MBEC for 10 musculoskeletal biofilms on bone (left column) and muscle (right column) tissue treated with (A) tobramycin, (B) vancomycin, or (C) tobramycin/vancomycin combination for 6 to 72 hr (see also Table ).

Article Snippet: Three antimicrobial regimens were investigated: tobramycin alone (TOB; tobramycin sulfate USP, Spectrum Chemical), vancomycin alone (VANC; vancomycin hydrochloride USP, Chem-Impex International Inc.), and tobramycin/vancomycin 1:1 combination by mass (TOB+VANC).

Techniques:

Journal: Journal of Bone and Joint Infection

Article Title: Determination of Tobramycin and Vancomycin Exposure Required to Eradicate Biofilms on Muscle and Bone Tissue In Vitro

doi: 10.7150/jbji.29711

Figure Lengend Snippet: Strains with extreme minimum biofilm eradication concentration (MBEC) for musculoskeletal biofilms on bone and muscle tissue.

Article Snippet: Three antimicrobial regimens were investigated: tobramycin alone (TOB; tobramycin sulfate USP, Spectrum Chemical), vancomycin alone (VANC; vancomycin hydrochloride USP, Chem-Impex International Inc.), and tobramycin/vancomycin 1:1 combination by mass (TOB+VANC).

Techniques: Concentration Assay

Journal: Journal of Bone and Joint Infection

Article Title: Determination of Tobramycin and Vancomycin Exposure Required to Eradicate Biofilms on Muscle and Bone Tissue In Vitro

doi: 10.7150/jbji.29711

Figure Lengend Snippet: Fold change in MBEC for musculoskeletal biofilms on muscle or bone treated with tobramycin/vancomycin compared to MBEC on polystyrene.

Article Snippet: Three antimicrobial regimens were investigated: tobramycin alone (TOB; tobramycin sulfate USP, Spectrum Chemical), vancomycin alone (VANC; vancomycin hydrochloride USP, Chem-Impex International Inc.), and tobramycin/vancomycin 1:1 combination by mass (TOB+VANC).

Techniques: