chef dr iii pfge apparatus  (Bio-Rad)

Journal: Therapeutics and Clinical Risk Management

Article Title: Treatment with Saccharomyces boulardii and Escherichia coli Nissle is safe and associated with reduced nosocomial transmission of van B vancomycin-resistant Enterococcus faecium on an early rehabilitation ward in Germany: a retrospective analysis

doi: 10.2147/TCRM.S179208

Figure Lengend Snippet: Observation period and chronological sequence of measures performed at ERWIN probably contributing to the incidence of VRE. Notes: In the winter of 2015 the ward was closed for several weeks (black bar) due to an outbreak of carbapenem-resistant Klebsiella pneumoniae . Afterward ICM were intensified. Application of probiotics was started in September 2015. Abbreviations: ERWIN, early rehabilitation ward of Ingolstadt Hospital; ICM, infection control measures; PFGE, pulsed-field gel electrophoresis; RKI, Robert Koch Institute; VRE, vancomycin-resistant Enterococcus faecium .

Article Snippet: Sma I-digested genomic DNA was resolved in an agarose gel in an alternating electric field provided in a CHEF III PFGE apparatus (Bio-Rad Laboratories Inc., Hercules, CA, USA).

Techniques: Sequencing, Infection, Pulsed-Field Gel, Electrophoresis

Journal: Therapeutics and Clinical Risk Management

Article Title: Treatment with Saccharomyces boulardii and Escherichia coli Nissle is safe and associated with reduced nosocomial transmission of van B vancomycin-resistant Enterococcus faecium on an early rehabilitation ward in Germany: a retrospective analysis

doi: 10.2147/TCRM.S179208

Figure Lengend Snippet: Results of PFGE and PCR analyses of VRE isolated between October 2014 and March 2015 and between October and November 2016. Notes: ( A ) Photograph of PFGE typing, and results of PCR analyses. PCR was performed to identify genetic background of vancomycin resistance ( van A, van B) and genes of pathogenicity factors ( esp and hyl ). PFGE revealed the presence of three van B clusters (clusters 1, 3, 4), a van A cluster (cluster 2), and seven unique band patterns. ( B ) Isolation of van B isolates in chronological order between October 2014 and March 2015. *VRE colonized patients also exhibiting carbapenem-resistant Klebsiella pneumoniae . ( C ) Isolation of van A isolates in chronological order between October and November 2016. S=VRE exhibiting a unique band pattern in PFGE analysis. Abbreviations: PFGE, pulsed-field gel electrophoresis; VRE, vancomycin-resistant Enterococcus faecium .

Article Snippet: Sma I-digested genomic DNA was resolved in an agarose gel in an alternating electric field provided in a CHEF III PFGE apparatus (Bio-Rad Laboratories Inc., Hercules, CA, USA).

Techniques: Isolation, Pulsed-Field Gel, Electrophoresis

Journal: Nucleic Acids Research

Article Title: Fission yeast Stn1 maintains stability of repetitive DNA at subtelomere and ribosomal DNA regions

doi: 10.1093/nar/gkab767

Figure Lengend Snippet: Rearrangements at rDNA and subtelomeres are incurred in stn1-1 . ( A ) Sensitivity to HU of wild-type, reb1 Δ, and stn1-1 reb1 Δ. Five-fold serial dilutions of the indicated strains were spotted onto YES plates containing 4 mM HU or no HU (control), and incubated for 4 days at 30°C. Two independent clones of stn1-1 reb1 Δ were examined. These separated images (top and bottom) were taken from a single photo of the respective plate. ( B ) Pol1-myc localization at rfp4 and gal1 + loci tested by ChIP. gal1 + was used as a control locus. Each symbol indicates independent experiments. Error bar indicates SEM ( n = 3). P -value was calculated by a paired two-tailed Student's t -test (* P < 0.05). Three biological replicates were tested. ( C ) Instability of rDNA repeats in prolonged cultures of stn1-1 . Independent clones were cultured in liquid YES for the indicated days at 25°C, and then genomic DNA was digested by Sfi I endonuclease and analyzed by PFGE followed by Southern hybridization with a radiolabelled rDNA probe (left panel). The position of Sfi I sites, telomeric repeats (blue boxes), rDNA repeats (shaded boxes) and centromeres (oval) are shown at the top right schematic diagram. Signal intensity was quantified along each lane (the quantified range is indicated by a line at the right side of the gel) and normalized to the maximum value for each lane. The density plot for every clone is shown at the right side. Gray and red colors represent Day1 and Day10, respectively. ( D ) The copy number of rDNA repeats relative to that of the ade6 + gene was determined by qPCR. Each dot represents the result from an individual colony ( n = 5). Horizontal lines indicate the median value. A Mann–Whitney test was used for statistical analysis (* P < 0.05; ns, not significance).

Article Snippet: The digested DNA was separated by PFGE with a CHEF-DR-III PFGE apparatus (BioRad) under the following conditions: 1% SEAKEM Gold (LONZA) agarose gel in 0.5× TBE; electrode angle 120°; voltage gradient 6.8 V/cm; initiating switching time 40 s; final switching time 80 s; run time 15 h; temperature 10°C.

Techniques: Incubation, Clone Assay, Two Tailed Test, Cell Culture, Hybridization, MANN-WHITNEY