Unlike Catalyzing Error-Free Bypass of 8‑OxodGuo, DNA Polymerase λ Is Responsible for a Significant Part of Fapy·dG-Induced G → T Mutations in Human Cells

8-OxodGuo and Fapy·dG induced 10–22% mutations, predominantly G → T transversions, in human embryonic kidney 293T cells in four TG*N sequence contexts, where N = C, G, A, or T. siRNA knockdown of pol λ resulted in 34 and 55% increases in the level of mutations in the progeny from the 8-oxodGuo construct in the TG*T and TG*G sequences, respectively, suggesting that pol λ is involved in error-free bypass of 8-oxodGuo. For Fapy·dG, in contrast, the level of G → T mutations was reduced by 27 and 46% in the TG*T and TG*G sequences, respectively, suggesting that pol λ is responsible for a significant fraction of Fapy·dG-induced G → T mutations

DMF/H₂O Volume Ratio Controls the Syntheses and Transformations of a Series of Cobalt Complexes Constructed Using a Rigid Angular Multitopic Ligand

Through middle-temperature solvothermal reactions of CoCl2·6H2O with the rigid-angled ligand 3-(2′-pyridyl)-5-(4′′-pyridyl)-1,2,4-triazole (Hdpt24), we obtained the three cobalt complexes {[Co(dpt24)2)]3·4DMF·1.5H2O}n (1), {[Co(dpt24)2)]2·H2O}n (2), and Co(dpt24)2(Hdpt24)·H2O] (4) at N,N-dimethylformamide (DMF)/H2O volume ratios of 9:1, 1:1, and 0:1, respectively. Interestingly, 1 underwent transformations into 2, {[Co(dpt24)2]·0.5DMF}n (3), and 4 when treated with DMF/H2O at volume ratios of 1:1, 1:9, and 0:1, respectively. Moreover, 3 and 4 converted back to 1 in 9:1 DMF/H2O and to 2 in 1:1 DMF/H2O; 3 transformed into 4 in H2O and vice versa in 1:9 DMF/H2O. Structurally, 1 is a three-dimensional (3D) 2-fold interpenetrating distorted NbO-type complex, 2 possesses a two-dimensional layer metal−organic framework, 3 is a 3D 2-fold interpenetrating typical NbO-type complex, and 4 is a wheel-shaped mononuclear neutral complex. This approach, using a mixed solvent’s component ratio to direct the syntheses and conversions of four cobalt complexes, provides unprecedented control for crystal engineering

Supplementary Materials and Methods from Isoflavone ME-344 Disrupts Redox Homeostasis and Mitochondrial Function by Targeting Heme Oxygenase 1

Antibodies. Primers. Click Chemistry and Affinity Enrichment Mass Spectrometry. Surface Plasmon Resonance - Biacore 3000 Kinetic Determinations. Co-Immunoprecipitation. Transfections with shRNA and plasmids. Plate colony formation assay. References.</p

Supplementary Tables S11-S14 from Isoflavone ME-344 Disrupts Redox Homeostasis and Mitochondrial Function by Targeting Heme Oxygenase 1

Supplementary Table S11. All Proteins Identified. Supplementary Table S12. The Protein Groups text file from MaxQuant was processed using Perseus. Common contaminants, reversed database hits, and proteins identified by modified peptides were removed. LFQ normalized protein intensities were log2 transformed. Proteins were filtered to retain proteins identified by MS/MS (not matching between runs) in all three ME-344 pull down experiments with at least 2 peptides. Missing values in the control pull downs were imputed in Perseus with a width of 0.6 and downshift of 1.8. The difference in mean log2 protein intensities (ME344 bait - control) and fold change in abundance are provided. Supplementary Table S13. The Protein Groups text file from MaxQuant was processed using Perseus. Common contaminants, reversed database hits, and proteins identified by modified peptides were removed. LFQ normalized protein intensities were log2 transformed. Proteins were filtered to retain proteins identified by MS/MS (not matching between runs) in all three ME-344 pull down experiments with at least 2 peptides. Missing values in the control pull downs were imputed in Perseus with a width of 0.6 and downshift of 1.8. The difference in mean log2 protein intensities (ME344 bait - control) and fold change in abundance are provided. Proteins enriched with ME-344 (Difference in Log2 Protein Intensities >0). Supplementary Table S14. Proteins with at least 2 peptides identified by MS/MS in all three ME-344 pull down experiments that were not identified in the control affinity enrichment.</p

Supplementary Figures S1-S5 and Tables S1-S10, S15-S23 from Isoflavone ME-344 Disrupts Redox Homeostasis and Mitochondrial Function by Targeting Heme Oxygenase 1

Supplementary Figure S1. Effects of HO-1 knockdown in H460 cell lines and HO-1 over-expression in H596 cell lines. Supplementary Figure S2. Affinity Enrichment Mass Spectrometry. Supplementary Figure S3. ME-344 induced apoptosis in sensitive cell lines H460 and SHP-77 through caspase 3 activation. Supplementary Figure S4. NAC attenuated ME-344-induced increases in ROS levels in H460 and H596 cell lines. Supplementary Figure S5. ME-344-induced changes in protein expression of VDAC1 and VDAC2 in drug sensitive (H460 and SHP-77), resistant (H596 and SW900) or normal cell lines (MRC-5). Supplementary Table S1. The immunohistochemistry score system for human lung tissue microarrays (TMAs). Supplementary Table S2. Median fluorescent intensity fold changes of ROS in sensitive and resistant human lung cancer cell lines and human normal lung cell line after treatment of ME-344 (relative to control). Supplementary Table S3. Relative protein basal level of Nrf2, HO-1, GSTP, ALDH in sensitive, resistant and normal cell lines (Protein/β-actin, relative to H460). Supplementary Table S4. Relative mRNA basal level of Nrf2, HO-1, GSTP, ALDH in sensitive, resistant and normal cell lines (mRNA/18S rRNA, relative to H460). Supplementary Table S5. Relative protein fold change of Nrf2, HO-1, GSTP, ALDH in sensitive, resistant and normal cell lines after treatment of ME-344 (Protein/β-actin, relative to control). Supplementary Table S6. Relative mRNA fold change of Nrf2, HO-1, GSTP, ALDH in sensitive, resistant and normal cell lines after treatment of ME-344 (mRNA/18S rRNA, relative to control). Supplementary Table S7. Relative mRNA basal level of UPR markers in sensitive, resistant and normal cell lines (mRNA/18S rRNA, relative to H460). Supplementary Table S8. Relative mRNA fold change of UPR markers in sensitive, resistant and normal cell lines after treatment of ME-344 (mRNA/18S rRNA, relative to control). Supplementary Table S9. Relative protein basal level of UPR markers in sensitive, resistant and normal cell lines (protein/β-actin, relative to H460). Supplementary Table S10. Relative protein fold change of UPR markers in sensitive, resistant and normal cell lines after treatment of ME-344 (protein/β-actin, relative to control). Supplementary Table S15. Immunohistochemistry scores of HO-1 in lung normal and tumor specimens of different histological types. Supplementary Table S16. Immunohistochemistry scores of Nrf2 in lung normal and tumor specimens of different histological types. Supplementary Table S17. Immunohistochemistry scores of HO-1 and Nrf2 in lung normal and tumor specimens of different staging. Supplementary Table S18. GSH (nmol/mg protein) generation of H460 and H596 cell lines with pretreatment of NAC. Supplementary Table S19. IC50 (µM) of H460 and H596 cell lines with and without pretreatment of NAC. Supplementary Table S20. Relative protein basal level of VDAC1 and VDAC2 in sensitive, resistant and normal cell lines (Protein/β-actin, relative to H460). Supplementary Table S21. Relative protein fold change of VDAC1 and VDAC2 in sensitive, resistant and normal cell lines after treatment of ME-344 (Protein/β-actin, relative to control). Supplementary Table S22. Basal and fold change after ME-344 treatment of ROS levels and protein expression of Nrf2 and HO-1. Supplementary Table S23. Basal and fold change after ME-344 treatment of ROS levels in HO-1 knockdown and overexpressing H460 and H596 cell lines.</p