Journal: Applied and Environmental Microbiology

Article Title: Bacterial Species Determination from DNA-DNA Hybridization by Using Genome Fragments and DNA Microarrays

doi: 10.1128/aem.67.8.3677-3682.2001

Figure Lengend Snippet: FIG. 5. Similarity dendrogram (UPGMA) of hybridization profiles of 338 genome fragments spotted on the microarray. Clusters F (98.7%), C (94.1%), A (91.8%), P (100%), and Y (100%) comprise genome fragments from the reference strains P. fluorescens ATCC 13525T, P. chlororaphis ATCC 9447, P. aeruginosa ATCC 15692, and P. putida ATCC 12633T. Clusters V to Z comprise genome fragment from different reference strains, except cluster Y.

Article Snippet: The arrays hybridized to P. fluorescens ATCC 13525T (triplicate), P. putida ATCC 12633T (duplicate), and P. aeruginosa ATCC 15692 (duplicate) showed similarity values of .97.5% (r . 0.949, P , 0.0001), 95.3% (r 5 0.906, P , 0.0001), and 94.1% (r 5 0.882, P , 0.0001), respectively.

Techniques: Hybridization, Microarray

Journal: Applied and Environmental Microbiology

Article Title: Bacterial Species Determination from DNA-DNA Hybridization by Using Genome Fragments and DNA Microarrays

doi: 10.1128/aem.67.8.3677-3682.2001

Figure Lengend Snippet: FIG. 6. (a) Evenness value (uE) scatter diagram, with average and SD of log hybridization signal ratio. (b) uE values by genome fragment, ID 1 to 92, 93 to 182, 183 to 278, and 279 to 338 originated from P. fluorescens ATCC 13525T, P. chlororaphis ATCC 9447, P. putida ATCC 12633T, and P. aeruginosa ATCC 15692, respectively. The solid line and dotted lines (horizontal) indicate average and SD, respectively.

Article Snippet: The arrays hybridized to P. fluorescens ATCC 13525T (triplicate), P. putida ATCC 12633T (duplicate), and P. aeruginosa ATCC 15692 (duplicate) showed similarity values of .97.5% (r . 0.949, P , 0.0001), 95.3% (r 5 0.906, P , 0.0001), and 94.1% (r 5 0.882, P , 0.0001), respectively.

Techniques: Hybridization

Journal: Kidney360

Article Title: Arginase-1 Expressing Macrophages Interact with Myofibroblasts to Regulate Insulin-Like Growth Factor-1-Dependent Tubule Repair

doi: 10.34067/KID.0000001150

Figure Lengend Snippet: Igf1 is upregulated in an Arg1 -dependent manner in the outer medulla after kidney injury. Arg1 WT and Arg1mko were subjected to IRI/CL-NX and kidneys harvested and microdissected for analysis on day 2. (A) Igf1 mRNA levels in the outer medulla of healthy kidneys and Arg1mko kidneys, n =8 mice per group (B). Immunofluorescence staining of outer medullary sections of Arg1 WT healthy, Arg1 WT injured, and Arg1mko injured kidneys with phospho-IGF1R (red), LTL (green), and DAPI (blue). (C) MFI of phospho-IGF1R signals as shown in (B) were quantified using ImageJ, with five high power fields/kidney section analyzed/group ( n =4 mice). (D) Analysis of mRNA expression of Igf1 in MACS sorted F4/80 + macrophages; ( n =5 mice). (E) Analysis of mRNA expression of Igf1 by naïve, Arg1 low BMDM (transwell coculture of BMDM with BMDM) versus alternatively activated, Arg1 high BMDM (transwell coculture of BMDM with PCRC+GM-CSF, [ n =3]). (F) IGF1 protein concentrations determined by ELISA in the 24 hours conditioned media collected from the conditions described in (E) showing the secreted IGF1 protein levels in MՓ CM1 (naïve, Arg1 low macrophages) and MՓ CM2 (alternatively activated, Arg1 high macrophages) ( n =3/group). P values are shown, and data are presented as mean±SEM. Arg1, arginase-1; Arg1 mko , macrophage-specific Arg1 null; BMDM, bone marrow-derived macrophages; DAPI, 4′,6-diamidino-2-phenylindole; GM-CSF, granulocyte-monocyte colony stimulating factor; IGF1R, IGF1 receptor; IRI, ischemia-reperfusion kidney injury; IRI-CL/NX, ischemia-reperfusion with contralateral nephrectomy; LTL, Lotus tetragonolobus lectin; MACS, magnetic activated cell sorting; MFI, mean fluorescence intensity; MՓ CM, macrophage-derived conditioned medium; PCRC, primary cultured renal cells; pIGF1R, phosphorylated IGF1R; WT, wild type

Article Snippet: IGF1 ELISA assays were performed using Mouse IGF1 ELISA kit (Cat. # ELM-IGF1-1, RayBiotech), and GH ELISA assays were performed by Human GH ELISA Kit (Cat. # ELH-GH-1, RayBiotech).

Techniques: Immunofluorescence, Staining, Expressing, Enzyme-linked Immunosorbent Assay, Derivative Assay, FACS, Fluorescence, Cell Culture

Journal: Cell reports

Article Title: Local non-pituitary growth hormone is induced with aging and facilitates epithelial damage

doi: 10.1016/j.celrep.2021.110068

Figure Lengend Snippet: (A and B) Western blot of (A) hNCC, hNCF, and HCT116 cells and (B) organoids. Cells were treated with indicated doses of etoposide and analyzed 24 h later. Organoids were treated with 3 μM etoposide (Etop). (C) hNCC nucleofected with GH siRNA (siGH RNA) or scramble RNA (Scr RNA) as control for 24 h was treated with indicated doses of etoposide (Etop) and analyzed 24 h later. ImageJ quantification of western blots is depicted in . (D) Representative image of hNCC treated with 20 μM etoposide for 24 h. GH, red; γH2AX, green; phalloidin, gray; DAPI, blue. Bright green nucleus indicates apoptosis. Scale bar, 20 μm. Control, untreated cells. (E) Western blot of GH in culture medium of hNCC and organoids treated with 20 or 5 μM etoposide, respectively. Medium was collected from hNCC at 8 and 24 h and from organoids at 4–48 h after treatment. Ponceau was used as a loading control. Representative blots from at least 3 independent experiments are shown.

Article Snippet: GH1 siRNA (human) , SCBT , Cat# sc-43803.

Techniques: Western Blot, Control

Journal: Cell reports

Article Title: Local non-pituitary growth hormone is induced with aging and facilitates epithelial damage

doi: 10.1016/j.celrep.2021.110068

Figure Lengend Snippet: (A–C) Human intestinal organoids were cultured for up to 2 months and assessed on (A) western blot for aging markers p16 and β gal, and (B and C) real-time PCR for changes in (B) telomere length with culturing reflecting aging and (C) GH and IGF1 mRNA. PCR results are expressed as fold change versus control taken as 1. Results are shown as means ± SEMs of triplicate measurements. Each dot represents 1 experiment. In (B) and (C), results were analyzed by ANOVA, followed by Tukey’s test to correct for multiple group comparisons. Results are graphed as fold change, but statistical testing was performed on raw numbers. *p < 0.05. (D) Representative confocal image of organoids at 1 week and 2 months of culture. GH, green; phalloidin, red; DAPI, blue. Scale bar, 50 μm. (E) Western blot analysis of GH, p53, and γH2AX and DNA damage pathway proteins. ImageJ quantification of western blots is depicted in . (F and G) Organoids were cultured for 2 months, infected with lenti GH shRNA (shGH) or scramble (shScr), and analyzed 6 days later. (F) Western blot of GH and p53 protein expression. ImageJ quantification of western blots is depicted in . (G) Comet assay. Each dot represents 1 independent experiment. Mixed model regression was used to adjust for random effects across experimental replicates. Results are graphed as percentage of control, but statistical testing was performed on raw numbers. **p < 0.01. In (A), (D), and (E), representative blots from at least 3 independent experiments are shown.

Article Snippet: GH1 siRNA (human) , SCBT , Cat# sc-43803.

Techniques: Cell Culture, Western Blot, Real-time Polymerase Chain Reaction, Control, Infection, shRNA, Expressing, Single Cell Gel Electrophoresis

Journal: Cell reports

Article Title: Local non-pituitary growth hormone is induced with aging and facilitates epithelial damage

doi: 10.1016/j.celrep.2021.110068

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: GH1 siRNA (human) , SCBT , Cat# sc-43803.

Techniques: Virus, shRNA, Control, Clinical Proteomics, Recombinant, Cell Recovery, Cell Attachment Assay, SYBR Green Assay, Enzyme-linked Immunosorbent Assay, Labeling, Staining, Plasmid Preparation, cDNA Synthesis, Single Cell Gel Electrophoresis, RNAscope, Software, Imaging, Real-time Polymerase Chain Reaction, Microscopy