Journal: Synthetic and Systems Biotechnology

Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress

doi: 10.1016/j.synbio.2026.01.020

Figure Lengend Snippet: Improving the tolerance to formaldehyde via ALE. (A) Growth of FM-1 in minimal medium with 10 g/L glucose and different formaldehyde concentrations. 0 mM (square), 0.5 mM (triangle), 0.8 mM (circle), and 1 mM (inverted triangle). (B) ALE procedure of culture-1 in CGXII minimal medium supplemented with different formaldehyde concentrations and 10 g/L glucose. (C) Growth curve of the evolved mutants in CGXII minimal medium supplemented with 10 g/L glucose and 0.8 mM formaldehyde. (D) Growth curve of evolved mutant in CGXII minimal medium supplemented with 10 g/L glucose and 1.6 mM formaldehyde. (E) Growth curve of evolved mutant in CGXII minimal medium supplemented with 10 g/L glucose. (F) Formaldehyde degradation during cell growth of wild-type C. glutamicum ATCC 13032, FM-1 and FM-3. Values and error bars reflect the mean ± s.d. of three biological replicates (N = 3).

Article Snippet: To assess the toxicity of formaldehyde in C. glutamicum ATCC 13032 lacking the formaldehyde dissimilation pathway, we cultivated a previously developed C. glutamicum FM-1 strain ( C. glutamicum ATCC 13032 Δ adhE Δ ald ), which was referred to as MX-1 in our previous study [ ], in CGXII medium supplemented with various concentrations of formaldehyde ( A).

Techniques: Mutagenesis

Journal: Synthetic and Systems Biotechnology

Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress

doi: 10.1016/j.synbio.2026.01.020

Figure Lengend Snippet: Effects of single-site mutations on formaldehyde tolerance. (A) Frequency of mutations of four bases in evolved strain FM-3. (B) Growth of strain FM-1 and its derivatives harboring single-site mutations on CGXII minimal agar medium supplemented with 10 g/L glucose and 1 mM formaldehyde. (C) Growth curves of strain FM-1 and its derivatives in CGXII medium supplemented with 10 g/L glucose and 0.8 mM formaldehyde. Values and error bars reflect the mean ± s.d. of three biological replicates (N = 3). Statistical significance at 31 h between FM-1- cgl1199 1015−1032del and FM-1 was determined by unpaired two-tailed Student's t -test: ∗∗∗P < 0.001.

Article Snippet: To assess the toxicity of formaldehyde in C. glutamicum ATCC 13032 lacking the formaldehyde dissimilation pathway, we cultivated a previously developed C. glutamicum FM-1 strain ( C. glutamicum ATCC 13032 Δ adhE Δ ald ), which was referred to as MX-1 in our previous study [ ], in CGXII medium supplemented with various concentrations of formaldehyde ( A).

Techniques: Two Tailed Test

Journal: Synthetic and Systems Biotechnology

Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress

doi: 10.1016/j.synbio.2026.01.020

Figure Lengend Snippet: Transcriptome analysis of FM-3 and FM-1 cultivated with or without formaldehyde stress. (A) Volcano plots of differential transcription levels in 1F vs. 1N, 3F vs. 3N, 3N vs. 1N, and 3F vs. 1F. (B) Changes in mRNA levels of genes involved in central metabolism and the respiratory chain between FM-3 and FM-1. Only significant changes (log 2 (fold change) ≥1 or ≤ −1, FDR≤0.05) are shown. Upregulated and downregulated genes are indicated with red and blue, respectively. 1F, FM-1 cultivated with formaldehyde stress. 1N, FM-1 cultivated without formaldehyde stress. 3F, FM-3 cultivated with formaldehyde stress. 3N, FM-3 cultivated without formaldehyde stress.

Article Snippet: To assess the toxicity of formaldehyde in C. glutamicum ATCC 13032 lacking the formaldehyde dissimilation pathway, we cultivated a previously developed C. glutamicum FM-1 strain ( C. glutamicum ATCC 13032 Δ adhE Δ ald ), which was referred to as MX-1 in our previous study [ ], in CGXII medium supplemented with various concentrations of formaldehyde ( A).

Techniques:

Journal: Synthetic and Systems Biotechnology

Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress

doi: 10.1016/j.synbio.2026.01.020

Figure Lengend Snippet: Comparison of proteomes between FM-3 and FM-1 cultivated with formaldehyde or without formaldehyde stress. Functional classification of transcriptome differences based on KEGG_small_class annotation in 3N vs. 1N (A), 3F vs. 1F (B). Proteins with differentially expression in 1F vs. 1N (C) and 3F vs. 3N (D). Only significant changes (log 2 (fold change) ≥1 or ≤ −1, FDR≤0.05) are shown. Proteins exhibiting increased or decreased abundance are highlighted in red and blue, respectively. 1F, FM-1 cultivated with formaldehyde stress. 1N, FM-1 cultivated without formaldehyde stress. 3F, FM-3 cultivated with formaldehyde stress. 3N, FM-3 cultivated without formaldehyde stress.

Article Snippet: To assess the toxicity of formaldehyde in C. glutamicum ATCC 13032 lacking the formaldehyde dissimilation pathway, we cultivated a previously developed C. glutamicum FM-1 strain ( C. glutamicum ATCC 13032 Δ adhE Δ ald ), which was referred to as MX-1 in our previous study [ ], in CGXII medium supplemented with various concentrations of formaldehyde ( A).

Techniques: Comparison, Functional Assay, Expressing

Journal: Synthetic and Systems Biotechnology

Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress

doi: 10.1016/j.synbio.2026.01.020

Figure Lengend Snippet: Effects of Cgl1590 mutations on formaldehyde tolerance. (A) Amino acid sequence alignment between Cgl1590 and its derivatives. (B) Effects of cgl1590 truncation on formaldehyde tolerance. (C) Effects of cgl1590 knock-out on formaldehyde tolerance. (D) Effects of cgl1590 overexpression on formaldehyde tolerance. Cells were treated with 0.8 mM formaldehyde as stress condition. Values and error bars reflect the mean ± s.d. of three biological replicates (N = 3). Analysis of cell length and morphology of FM-1 without formaldehyde stress (E), FM-1 containing cgl1590 750insG mutation without formaldehyde stress (F), FM-1 with formaldehyde stress (G), and FM-1 strain containing cgl1590 750insG mutation with formaldehyde stress (H). All strains were grown in CGXII minimal medium supplemented with 10 g/L glucose, with or without 0.8 mM formaldehyde, and examined by SEM. Cell length was determined by measuring 70 cells of each strain and analyzed using ImageJ software. Statistical significance at 36 h between FM-1-△ cgl1590 and FM-1 was determined by two-tailed Student's t -test: ∗∗∗P < 0.001.

Article Snippet: To assess the toxicity of formaldehyde in C. glutamicum ATCC 13032 lacking the formaldehyde dissimilation pathway, we cultivated a previously developed C. glutamicum FM-1 strain ( C. glutamicum ATCC 13032 Δ adhE Δ ald ), which was referred to as MX-1 in our previous study [ ], in CGXII medium supplemented with various concentrations of formaldehyde ( A).

Techniques: Sequencing, Knock-Out, Over Expression, Mutagenesis, Software, Two Tailed Test

Journal: bioRxiv

Article Title: Computationally guided design of a metastasis-on-a-chip platform for quantitative evaluation of chemotactic cues in developmental cancers

doi: 10.64898/2026.07.25.740695

Figure Lengend Snippet: (A) Expression of KDR, encoding VEGFR2, and (B) FLT4, encoding VEGFR3, across publicly available pediatric solid tumor datasets included in the R2 MegaSampler platform. Expression values are presented as log2-transformed signal intensity. The distributions illustrate inter-dataset and inter-tumor heterogeneity in the expression of receptors associated predominantly with VEGF-A and VEGF-C signaling, respectively. M, metastasis; T, primary tumor; ES, Ewing sarcoma; NB, neuroblastoma; OS, osteosarcoma.

Article Snippet: VEGF-A165 and VEGF-C concentrations were quantified using commercially available human ELISA kits (RayBiotech, Peachtree Corners, GA, USA; Catalog Nos.

Techniques: Expressing, Transformation Assay

Journal: bioRxiv

Article Title: Computationally guided design of a metastasis-on-a-chip platform for quantitative evaluation of chemotactic cues in developmental cancers

doi: 10.64898/2026.07.25.740695

Figure Lengend Snippet: VEGF-C transport was simulated using initial concentrations of 0.1 or 5 µg/mL in Chamber 2. Predicted VEGF-C concentrations over time are shown in (A) Channel 2, adjacent to the source, (B) at the microchannel array separating Reservoirs 2 and 1, and (C) in Channel 1, on the Chamber 1 side of the device. An initial concentration of 5 µg/mL generated measurable exposure at the microchannel array within the experimental time window, whereas 0.1 µg/mL produced substantially lower concentrations and negligible predicted exposure at the microchannel array and in Channel 1. Different concentration units and y-axis ranges were used for the individual device regions.

Article Snippet: VEGF-A165 and VEGF-C concentrations were quantified using commercially available human ELISA kits (RayBiotech, Peachtree Corners, GA, USA; Catalog Nos.

Techniques: Concentration Assay, Generated, Produced

Journal: bioRxiv

Article Title: Computationally guided design of a metastasis-on-a-chip platform for quantitative evaluation of chemotactic cues in developmental cancers

doi: 10.64898/2026.07.25.740695

Figure Lengend Snippet:

Article Snippet: VEGF-A165 and VEGF-C concentrations were quantified using commercially available human ELISA kits (RayBiotech, Peachtree Corners, GA, USA; Catalog Nos.

Techniques: Incubation, Cell Culture, Enzyme-linked Immunosorbent Assay

Journal: bioRxiv

Article Title: Computationally guided design of a metastasis-on-a-chip platform for quantitative evaluation of chemotactic cues in developmental cancers

doi: 10.64898/2026.07.25.740695

Figure Lengend Snippet: (A) Representative merged bright-field and fluorescence images of neuroblastoma, Ewing sarcoma, and osteosarcoma cells detected within the microchannel array under control, VEGF-A165, and VEGF-C conditions. Images were processed using a custom Fiji macro that automatically identified the microchannel region, detected fluorescent cells, and retained cells located within the microchannels according to predefined size, circularity, intensity, and channel-overlap criteria. Scale bars =50µm. (B) Quantification of the number of cells detected within the microchannels for neuroblastoma, Ewing sarcoma, and osteosarcoma. Individual data points represent independent microfluidic devices, and bars show mean ± SD. Statistical significance was assessed using ordinary one-way ANOVA followed by Dunnett’s multiple-comparisons test against the corresponding control. *p < 0.05; ns, not significant.

Article Snippet: VEGF-A165 and VEGF-C concentrations were quantified using commercially available human ELISA kits (RayBiotech, Peachtree Corners, GA, USA; Catalog Nos.

Techniques: Fluorescence, Control