Journal: ACS Environmental Au

Article Title: Bacterial Concentrations and Water Turbulence Influence the Importance of Conjugation Versus Phage-Mediated Antibiotic Resistance Gene Transfer in Suspended Growth Systems

doi: 10.1021/acsenvironau.1c00027

Figure Lengend Snippet: Lower frequency but higher relative importance of genR transfer via phage delivery (relative to conjugation) occurs at lower bacterial concentration. (a) Transfer frequency was determined after 1 h of conjugation and phage delivery assays in minimal medium with 3.0 g/L glucose and shaken at an Re of 5 × 10 4 . The genR donor ( E. coli DH5α harboring plasmid RP4 for conjugation assays or λ phage for phage delivery assays) and recipient ( E. coli MG1655) were mixed at a 1:1 ratio. Frequency determined by the plate counting method is presented as bars with the detection limit (10 –6 ) indicated by the horizontal dashed line; orange dots represent the frequency determined by qPCR analysis. Asterisks (*) indicate significant differences ( p < 0.05) between conjugation and phage delivery frequency based on Student’s t -test. “N.D.” refers to “not detected”. (b) Upregulation of conjugation-related genes ( tra I, tra J, and trb Ap) and phage delivery-related genes ( lamB and mal T) at lower bacterial concentration (twofold gene expression change). The top X -axis depicts decreasing bacterial concentration (CFU/mL). The expression level at a bacterial concentration of 10 8 CFU/mL was used as the control. Error bars depict ± one standard deviation from the mean of at least three independent replicates.

Article Snippet: Conjugative plasmid RP4 was obtained from Addgene (plasmid 79813).

Techniques: Conjugation Assay, Concentration Assay, Plasmid Preparation, Gene Expression, Expressing, Control, Standard Deviation

Journal: ACS Environmental Au

Article Title: Bacterial Concentrations and Water Turbulence Influence the Importance of Conjugation Versus Phage-Mediated Antibiotic Resistance Gene Transfer in Suspended Growth Systems

doi: 10.1021/acsenvironau.1c00027

Figure Lengend Snippet: Turbulence (represented by Reynolds number) significantly impacts the relative frequency of conjugation vs phage delivery for the horizontal transfer of genR in a bell-shaped fashion. The transfer frequency was determined after 1 h of conjugation and phage delivery assays in minimal medium containing 3.0 g/L glucose with bacterial concentration at 10 7 CFU/mL. The genR donor ( E. coli DH5α harboring plasmid RP4 for conjugation assays or λ phage for phage delivery assays) and recipient ( E. coli MG1655) were mixed at a 1:1 ratio. Asterisks (*) indicate significant differences ( p < 0.05) between conjugation and phage delivery frequency based on Student’s t -test. Error bars depict ± one standard deviation from the mean of at least three independent replicates.

Article Snippet: Conjugative plasmid RP4 was obtained from Addgene (plasmid 79813).

Techniques: Conjugation Assay, Concentration Assay, Plasmid Preparation, Standard Deviation

Journal: ACS Environmental Au

Article Title: Bacterial Concentrations and Water Turbulence Influence the Importance of Conjugation Versus Phage-Mediated Antibiotic Resistance Gene Transfer in Suspended Growth Systems

doi: 10.1021/acsenvironau.1c00027

Figure Lengend Snippet: Plasmid, Phage, and Bacterial Strains Used in This Study

Article Snippet: Conjugative plasmid RP4 was obtained from Addgene (plasmid 79813).

Techniques: Plasmid Preparation, Marker, Conjugation Assay

Journal: bioRxiv

Article Title: Perturbation of ubiquitin homeostasis promotes macrophage oxidative defenses

doi: 10.1101/276964

Figure Lengend Snippet: A). Structures of compounds DUB inh -Biotin and ΔCN-biotin. The arrow highlights the key cyano group. B). RAW264. 7 whole cell lysates were incubated with DUB inh -Biotin or ΔCN-biotin before immunoprecipitation using streptavidin-coated beads. The retained proteins were analyzed by SDS-PAGE and revealed by silver stain. C). Pull downs and corresponding inputs were immunoblotted for MYSM1, DUBA, Ataxin3, USP14, YOD1 and USP25. Data are representative of three independent experiments.

Article Snippet: The primary antibodies used for immunoblotting were anti-ubiquitin, clone P4D1 (sc-8017), anti-USP14 (sc-100630), anti-USP25 (sc-398414) and anti-gp91 phox (sc-130543) from Santa Cruz, anti-YOD1 (ARP67915) from Aviva Systems Biology, anti-Otud5 (DUBA, 21002-1-AP) from ProteinTech, anti-MYSM1 (ab193081) and anti-Ataxin3 (ab175262) from Abcam, anti-ubiquitin lys48-specific (05-1307) and anti-linear ubiquitin clone LUB9 (MABS451) from EDM Millipore, anti-ubiquitin k63-specific (5621) and anti-CHOP (2895) from Cell Signaling, anti-actin clone ACTN05 (MS-1295) and anti-p97/VCP (MA3-004) from TermoFisher.

Techniques: Incubation, Immunoprecipitation, SDS Page, Silver Staining

Journal: Biology Direct

Article Title: MIR194-2HG, a miRNA host gene activated by HNF4A, inhibits gastric cancer by regulating microRNA biogenesis

doi: 10.1186/s13062-024-00549-z

Figure Lengend Snippet: BTF3L4 was the common target gene of miR-192 and miR-194 in GC. ( A ) The common differentially expressed genes of miR-192 and miR-194 were listed in the heat map. ( B ) RNA-seq analysis showed that BTF3L4 expression was downregulated by either miR-194 or miR-192 in GC cell lines. ( C ) Bioinformatics prediction showed that the 3’UTR of BTF3L4 contains the binding sites of miR-194 and miR-192. ( D ) Overexpression of miR-194 or miR-192, or both, significantly decreased the expression level of BTF3L4 in GC cell lines. ( E ) Western blotting assays showed that the overexpression of miR-194 or miR-192 significantly decreased the expression level of BTF3L4 in GC cell lines. ( F - H ) Luciferase reporter assays showed that BTF3L4 was directly targeted by miR-194 or miR-192. ( I ) Overall survival analysis showed that low expression levels of miR-194 or miR-192 predicted a poor prognosis in GC tissues. ( J ) BTF3L4 expression showed a significant negative correlation with miR-194/192 and MIR194-2HG in GC tissues. **, P < 0.01

Article Snippet: The antibodies used in this study are listed as follows: BTF3L4 (Proteintech, 16500-1-AP), HNF4A (Santa Cruz, sc-374229), β-Actin (Proteintech, 20536-1-AP).

Techniques: RNA Sequencing, Expressing, Binding Assay, Over Expression, Western Blot, Luciferase

Journal: Biology Direct

Article Title: MIR194-2HG, a miRNA host gene activated by HNF4A, inhibits gastric cancer by regulating microRNA biogenesis

doi: 10.1186/s13062-024-00549-z

Figure Lengend Snippet: MIR194-2HG inhibited GC progression via the miR-194/miR-192-BTF3L4 axis. ( A ) BTF3L4 expression was significantly upregulated in GC according to the RNA-seq data in the TCGA_STAD cohort. ( B ) BTF3L4 expression was significantly upregulated in GC according to the RNA-seq data in the GSE122401 cohort. ( C , D ) BTF3L4 expression was positively correlated with poor differentiation (G-stages) and malignant progression (T-stages) of GC. ( E ) BTF3L4 overexpression predicted a poor relapse-free survival in the TCGA_STAD cohort. ( F ) BTF3L4 overexpression predicted poor prognosis in GSE62254 cohort. ( G , H ) Knockdown of MIR194-2HG significantly upregulated mRNA and protein levels of BTF3L4 in GC cell lines. ( I , J ) Knockdown of BTF3L4 restored the promoting effect of MIR194-2HG depletion on the proliferation of GC cell lines. ( K , L ) Knockdown of BTF3L4 partially restored the promoting effect of MIR194-2HG depletion on the invasion of GC cell lines

Article Snippet: The antibodies used in this study are listed as follows: BTF3L4 (Proteintech, 16500-1-AP), HNF4A (Santa Cruz, sc-374229), β-Actin (Proteintech, 20536-1-AP).

Techniques: Expressing, RNA Sequencing, Over Expression, Knockdown

Journal: Biology Direct

Article Title: MIR194-2HG, a miRNA host gene activated by HNF4A, inhibits gastric cancer by regulating microRNA biogenesis

doi: 10.1186/s13062-024-00549-z

Figure Lengend Snippet: Hypothetical working model of MIR194-2HG in GC. Briefly, MIR194-2HG expression is clinically associated with favorable prognosis and plays tumor suppressive roles in GC. Mechanically, MIR194-2HG expression was transcriptionally induced by the hepatocyte nuclear factor HNF4A. Meanwhile, MIR194-2HG positively regulates the expression of its derived miR-194 and miR-192. The oncogene BTF3L4 has been confirmed to be a common target gene of miR-192 and miR-194. MIR194-2HG knockdown promotes GC progression by maintaining BTF3L4 overexpression through regulating microRNA biogenesis if miR-194/192

Article Snippet: The antibodies used in this study are listed as follows: BTF3L4 (Proteintech, 16500-1-AP), HNF4A (Santa Cruz, sc-374229), β-Actin (Proteintech, 20536-1-AP).

Techniques: Expressing, Derivative Assay, Knockdown, Over Expression