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New England Biolabs low range pfge markers

Pulsed-field gel electrophoresis <t>(PFGE)</t> and Southern analysis of cellular DNAs of wild-type and mutant strains. A , PFGE of cellular DNAs of wt , Δ recCBD and Δ rnr cells grown at 22 °C and 4 °C. M1 and M2 are the yeast chromosomal and low-range PFGE markers from New England Biolabs (USA). Ethidium bromide (EtBr)-stained gel showing intact (circular) chromosomal DNA in the well, linearized chromosomal DNA of >2 mb in size, and the broken DNA fragments of sizes around 50 kb are also indicated. Note that the discrete DNA fragments of various sizes are observed only in Δ rnr cells incubated at 4 °C. B , Southern analysis of PFGE resolved cellular DNAs of wt , Δ recCBD, and Δ rnr cells at 4 °C. Southern hybridization using probes specific to the chromosomal DNA, 16S RNA, and the indigenous plasmid pLz4W. A probe specific to pLz4W hybridizes to the discrete DNA fragments of Δ rnr cells incubated at 4 °C. C , time-dependent accumulation of discrete DNA fragments in Δ rnr cells at 4 °C and the Southern analysis using a probe specific to pLz4W. Δrnr cells show a time-dependent accumulation of various forms of pLz4W at 4 °C. pLz4W, plasmid of P. syringae Lz4W.

Low Range Pfge Markers, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "A type II toxin–antitoxin system is responsible for the cell death at low temperature in Pseudomonas syringae Lz4W lacking RNase R"

Article Title: A type II toxin–antitoxin system is responsible for the cell death at low temperature in Pseudomonas syringae Lz4W lacking RNase R

Journal: The Journal of Biological Chemistry

doi: 10.1016/j.jbc.2024.107600

Pulsed-field gel electrophoresis (PFGE) and Southern analysis of cellular DNAs of wild-type and mutant strains. A , PFGE of cellular DNAs of wt , Δ recCBD and Δ rnr cells grown at 22 °C and 4 °C. M1 and M2 are the yeast chromosomal and low-range PFGE markers from New England Biolabs (USA). Ethidium bromide (EtBr)-stained gel showing intact (circular) chromosomal DNA in the well, linearized chromosomal DNA of >2 mb in size, and the broken DNA fragments of sizes around 50 kb are also indicated. Note that the discrete DNA fragments of various sizes are observed only in Δ rnr cells incubated at 4 °C. B , Southern analysis of PFGE resolved cellular DNAs of wt , Δ recCBD, and Δ rnr cells at 4 °C. Southern hybridization using probes specific to the chromosomal DNA, 16S RNA, and the indigenous plasmid pLz4W. A probe specific to pLz4W hybridizes to the discrete DNA fragments of Δ rnr cells incubated at 4 °C. C , time-dependent accumulation of discrete DNA fragments in Δ rnr cells at 4 °C and the Southern analysis using a probe specific to pLz4W. Δrnr cells show a time-dependent accumulation of various forms of pLz4W at 4 °C. pLz4W, plasmid of P. syringae Lz4W.

Figure Legend Snippet: Pulsed-field gel electrophoresis (PFGE) and Southern analysis of cellular DNAs of wild-type and mutant strains. A , PFGE of cellular DNAs of wt , Δ recCBD and Δ rnr cells grown at 22 °C and 4 °C. M1 and M2 are the yeast chromosomal and low-range PFGE markers from New England Biolabs (USA). Ethidium bromide (EtBr)-stained gel showing intact (circular) chromosomal DNA in the well, linearized chromosomal DNA of >2 mb in size, and the broken DNA fragments of sizes around 50 kb are also indicated. Note that the discrete DNA fragments of various sizes are observed only in Δ rnr cells incubated at 4 °C. B , Southern analysis of PFGE resolved cellular DNAs of wt , Δ recCBD, and Δ rnr cells at 4 °C. Southern hybridization using probes specific to the chromosomal DNA, 16S RNA, and the indigenous plasmid pLz4W. A probe specific to pLz4W hybridizes to the discrete DNA fragments of Δ rnr cells incubated at 4 °C. C , time-dependent accumulation of discrete DNA fragments in Δ rnr cells at 4 °C and the Southern analysis using a probe specific to pLz4W. Δrnr cells show a time-dependent accumulation of various forms of pLz4W at 4 °C. pLz4W, plasmid of P. syringae Lz4W.

Techniques Used: Pulsed-Field Gel, Electrophoresis, Mutagenesis, Staining, Incubation, Hybridization, Plasmid Preparation

Analysis of RNase R deleted P. syringae Lz4W strain complemented with RNase R variants. A , PFGE and Southern analysis of cellular DNAs of Δ rnr cells complemented with RNase R Ps , RNase R Ec , and RNase R D284A mutants at 4 °C. Accumulation of discrete bands pLz4W DNA were observed only in Δ rnr and Δ rnr cells complemented with empty pGL10 vector. B , top panel , a schematic representation of the RNB domain of RNase R Ps , in which, the catalytically important aspartic acids of motif-1 of the RNB domain are shown. Bottom panel , growth profiles of wt and Δ rnr strains expressing RNB domain (pGLRNB) and the RNB domain with D284A mutation (pGLRNB D284A ) at 22 °C and 4 °C. Growth was determined by measuring A 600 at regular time intervals as indicated. C , top panel , a schematic representation of domain organization in RNase R Ps . The domains of RNase R Ps along with amino acids residues’ number and the N and C termini are shown. Bottom panel , PFGE and Southern analysis of cellular DNAs of Δ rnr cells complemented with domain/s deleted mutants of RNase R Ps at 4 °C. The CSD domain (Δ CSD ), the S1 domain (Δ S1 ), and the CSD and S1 domains deleted (RNB) mutants of RNase R Ps do not accumulate pLz4W-derived DNA fragments at 4 °C. D , a schematic representation of the indigenous pLz4W plasmid of P. syringae Lz4W. The psA–psT operon, open-reading frames, and other genetic elements are shown. Organization of the operon having psA and psT genes with overlapping reading frame under a common promoter is also depicted. The starting codons and predicted protein sizes of PsA antitoxin and PsT toxin are indicated. CSD, cold-shock domain; PFGE, pulsed-field gel electrophoresis; pLz4W, plasmid of P. syringae Lz4W; psA–psT, P. syringae antitoxin - P. syringae toxin system; RNase R Ec , Escherichia coli RNase R; RNase R Ps , RNase R of P. syringae .

Figure Legend Snippet: Analysis of RNase R deleted P. syringae Lz4W strain complemented with RNase R variants. A , PFGE and Southern analysis of cellular DNAs of Δ rnr cells complemented with RNase R Ps , RNase R Ec , and RNase R D284A mutants at 4 °C. Accumulation of discrete bands pLz4W DNA were observed only in Δ rnr and Δ rnr cells complemented with empty pGL10 vector. B , top panel , a schematic representation of the RNB domain of RNase R Ps , in which, the catalytically important aspartic acids of motif-1 of the RNB domain are shown. Bottom panel , growth profiles of wt and Δ rnr strains expressing RNB domain (pGLRNB) and the RNB domain with D284A mutation (pGLRNB D284A ) at 22 °C and 4 °C. Growth was determined by measuring A 600 at regular time intervals as indicated. C , top panel , a schematic representation of domain organization in RNase R Ps . The domains of RNase R Ps along with amino acids residues’ number and the N and C termini are shown. Bottom panel , PFGE and Southern analysis of cellular DNAs of Δ rnr cells complemented with domain/s deleted mutants of RNase R Ps at 4 °C. The CSD domain (Δ CSD ), the S1 domain (Δ S1 ), and the CSD and S1 domains deleted (RNB) mutants of RNase R Ps do not accumulate pLz4W-derived DNA fragments at 4 °C. D , a schematic representation of the indigenous pLz4W plasmid of P. syringae Lz4W. The psA–psT operon, open-reading frames, and other genetic elements are shown. Organization of the operon having psA and psT genes with overlapping reading frame under a common promoter is also depicted. The starting codons and predicted protein sizes of PsA antitoxin and PsT toxin are indicated. CSD, cold-shock domain; PFGE, pulsed-field gel electrophoresis; pLz4W, plasmid of P. syringae Lz4W; psA–psT, P. syringae antitoxin - P. syringae toxin system; RNase R Ec , Escherichia coli RNase R; RNase R Ps , RNase R of P. syringae .

Techniques Used: Plasmid Preparation, Expressing, Mutagenesis, Derivative Assay, Pulsed-Field Gel, Electrophoresis

PsA antitoxin expression alleviates the cold sensitivity of Δ rnr strain. A , growth profiles of wt , Δ rnr stain with an empty expression vector (pGL10), and Δ rnr strain expressing psA antitoxin (pGLpsA) determined at 22 °C and 4 °C. Growth was determined by A 600 at regular time intervals as indicated. B , PsA antitoxin restores the cell viability of the Δ rnr strain similar to wildtype at 4 °C. Cells grown at 22 °C till A 600 is 0.6, then were shifted to 4 °C and incubated for the indicated times. Aliquots of cells were collected at every 24 h, and the colony forming units (cfu/ml) were determined. C , PFGE and Southern analysis of cellular DNA of the Δ rnr strain expressing PsA antitoxin. PsA antitoxin expression reduces the copy number of pLz4W in the Δ rnr strain at 4 °C. D , Western analysis showing the expression of PsA antitoxin protein from the pGLpsA vector in Δ rnr cells. Expression of His-tag PsA antitoxin from the pGLpsA vector was determined by Western analysis using polyclonal antibodies specific to the 6x-His-tag. A protein marker with proteins of sizes 20, 14, and 6.5 are indicated. E , the copy number of pLz4W is reduced to the wildtype levels when RNase R and its derivatives are expressed in trans . Quantification of pLz4W from the PFGE-Southern hybridized gels was carried out using ImageJ2. For the wt , Δ rnr , and Δ rnr (pGL10) strains, the mean ± SD were calculated from the three independent experiments. The relative amount of pLz4W was plotted for the indicated strains compared to wildtype. PFGE, pulsed-field gel electrophoresis; pLz4W, plasmid of P. syringae Lz4W.

Figure Legend Snippet: PsA antitoxin expression alleviates the cold sensitivity of Δ rnr strain. A , growth profiles of wt , Δ rnr stain with an empty expression vector (pGL10), and Δ rnr strain expressing psA antitoxin (pGLpsA) determined at 22 °C and 4 °C. Growth was determined by A 600 at regular time intervals as indicated. B , PsA antitoxin restores the cell viability of the Δ rnr strain similar to wildtype at 4 °C. Cells grown at 22 °C till A 600 is 0.6, then were shifted to 4 °C and incubated for the indicated times. Aliquots of cells were collected at every 24 h, and the colony forming units (cfu/ml) were determined. C , PFGE and Southern analysis of cellular DNA of the Δ rnr strain expressing PsA antitoxin. PsA antitoxin expression reduces the copy number of pLz4W in the Δ rnr strain at 4 °C. D , Western analysis showing the expression of PsA antitoxin protein from the pGLpsA vector in Δ rnr cells. Expression of His-tag PsA antitoxin from the pGLpsA vector was determined by Western analysis using polyclonal antibodies specific to the 6x-His-tag. A protein marker with proteins of sizes 20, 14, and 6.5 are indicated. E , the copy number of pLz4W is reduced to the wildtype levels when RNase R and its derivatives are expressed in trans . Quantification of pLz4W from the PFGE-Southern hybridized gels was carried out using ImageJ2. For the wt , Δ rnr , and Δ rnr (pGL10) strains, the mean ± SD were calculated from the three independent experiments. The relative amount of pLz4W was plotted for the indicated strains compared to wildtype. PFGE, pulsed-field gel electrophoresis; pLz4W, plasmid of P. syringae Lz4W.

Techniques Used: Expressing, Staining, Plasmid Preparation, Incubation, Western Blot, Marker, Pulsed-Field Gel, Electrophoresis

Electrophoresis:

Article Title: Chromosomal Gene Transfer by Conjugation in the Plant Pathogen Xanthomonas axonopodis pv. vesicatoria
Article Snippet: Gels were stained with 0.5× TBE buffer containing ethidium bromide (0.5 μg ml–1) for 30 min, destained with 0.5× TBE buffer for 30 min, and photographed over a UV light source with type 55 Polaroid film (Polaroid Corp., Cambridge, MA). .. After electrophoresis, sizes of DNA fragments were determined by measuring the distances the bands migrated compared with Saccharomyces cerevisiae chromosome markers (Bio-Rad Laboratories) and low-range PFGE markers (New England Biolabs, Inc., Beverly, MA). ..

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Journal: The Journal of Biological Chemistry

Article Title: A type II toxin–antitoxin system is responsible for the cell death at low temperature in Pseudomonas syringae Lz4W lacking RNase R

doi: 10.1016/j.jbc.2024.107600

Figure Lengend Snippet: Pulsed-field gel electrophoresis (PFGE) and Southern analysis of cellular DNAs of wild-type and mutant strains. A , PFGE of cellular DNAs of wt , Δ recCBD and Δ rnr cells grown at 22 °C and 4 °C. M1 and M2 are the yeast chromosomal and low-range PFGE markers from New England Biolabs (USA). Ethidium bromide (EtBr)-stained gel showing intact (circular) chromosomal DNA in the well, linearized chromosomal DNA of >2 mb in size, and the broken DNA fragments of sizes around 50 kb are also indicated. Note that the discrete DNA fragments of various sizes are observed only in Δ rnr cells incubated at 4 °C. B , Southern analysis of PFGE resolved cellular DNAs of wt , Δ recCBD, and Δ rnr cells at 4 °C. Southern hybridization using probes specific to the chromosomal DNA, 16S RNA, and the indigenous plasmid pLz4W. A probe specific to pLz4W hybridizes to the discrete DNA fragments of Δ rnr cells incubated at 4 °C. C , time-dependent accumulation of discrete DNA fragments in Δ rnr cells at 4 °C and the Southern analysis using a probe specific to pLz4W. Δrnr cells show a time-dependent accumulation of various forms of pLz4W at 4 °C. pLz4W, plasmid of P. syringae Lz4W.

Article Snippet: M1 and M2 are the yeast chromosomal and low-range PFGE markers from New England Biolabs (USA).

Techniques: Pulsed-Field Gel, Electrophoresis, Mutagenesis, Staining, Incubation, Hybridization, Plasmid Preparation

Journal: The Journal of Biological Chemistry

Article Title: A type II toxin–antitoxin system is responsible for the cell death at low temperature in Pseudomonas syringae Lz4W lacking RNase R

doi: 10.1016/j.jbc.2024.107600

Figure Lengend Snippet: Analysis of RNase R deleted P. syringae Lz4W strain complemented with RNase R variants. A , PFGE and Southern analysis of cellular DNAs of Δ rnr cells complemented with RNase R Ps , RNase R Ec , and RNase R D284A mutants at 4 °C. Accumulation of discrete bands pLz4W DNA were observed only in Δ rnr and Δ rnr cells complemented with empty pGL10 vector. B , top panel , a schematic representation of the RNB domain of RNase R Ps , in which, the catalytically important aspartic acids of motif-1 of the RNB domain are shown. Bottom panel , growth profiles of wt and Δ rnr strains expressing RNB domain (pGLRNB) and the RNB domain with D284A mutation (pGLRNB D284A ) at 22 °C and 4 °C. Growth was determined by measuring A 600 at regular time intervals as indicated. C , top panel , a schematic representation of domain organization in RNase R Ps . The domains of RNase R Ps along with amino acids residues’ number and the N and C termini are shown. Bottom panel , PFGE and Southern analysis of cellular DNAs of Δ rnr cells complemented with domain/s deleted mutants of RNase R Ps at 4 °C. The CSD domain (Δ CSD ), the S1 domain (Δ S1 ), and the CSD and S1 domains deleted (RNB) mutants of RNase R Ps do not accumulate pLz4W-derived DNA fragments at 4 °C. D , a schematic representation of the indigenous pLz4W plasmid of P. syringae Lz4W. The psA–psT operon, open-reading frames, and other genetic elements are shown. Organization of the operon having psA and psT genes with overlapping reading frame under a common promoter is also depicted. The starting codons and predicted protein sizes of PsA antitoxin and PsT toxin are indicated. CSD, cold-shock domain; PFGE, pulsed-field gel electrophoresis; pLz4W, plasmid of P. syringae Lz4W; psA–psT, P. syringae antitoxin - P. syringae toxin system; RNase R Ec , Escherichia coli RNase R; RNase R Ps , RNase R of P. syringae .

Article Snippet: M1 and M2 are the yeast chromosomal and low-range PFGE markers from New England Biolabs (USA).

Techniques: Plasmid Preparation, Expressing, Mutagenesis, Derivative Assay, Pulsed-Field Gel, Electrophoresis

Journal: The Journal of Biological Chemistry

Article Title: A type II toxin–antitoxin system is responsible for the cell death at low temperature in Pseudomonas syringae Lz4W lacking RNase R

doi: 10.1016/j.jbc.2024.107600

Figure Lengend Snippet: PsA antitoxin expression alleviates the cold sensitivity of Δ rnr strain. A , growth profiles of wt , Δ rnr stain with an empty expression vector (pGL10), and Δ rnr strain expressing psA antitoxin (pGLpsA) determined at 22 °C and 4 °C. Growth was determined by A 600 at regular time intervals as indicated. B , PsA antitoxin restores the cell viability of the Δ rnr strain similar to wildtype at 4 °C. Cells grown at 22 °C till A 600 is 0.6, then were shifted to 4 °C and incubated for the indicated times. Aliquots of cells were collected at every 24 h, and the colony forming units (cfu/ml) were determined. C , PFGE and Southern analysis of cellular DNA of the Δ rnr strain expressing PsA antitoxin. PsA antitoxin expression reduces the copy number of pLz4W in the Δ rnr strain at 4 °C. D , Western analysis showing the expression of PsA antitoxin protein from the pGLpsA vector in Δ rnr cells. Expression of His-tag PsA antitoxin from the pGLpsA vector was determined by Western analysis using polyclonal antibodies specific to the 6x-His-tag. A protein marker with proteins of sizes 20, 14, and 6.5 are indicated. E , the copy number of pLz4W is reduced to the wildtype levels when RNase R and its derivatives are expressed in trans . Quantification of pLz4W from the PFGE-Southern hybridized gels was carried out using ImageJ2. For the wt , Δ rnr , and Δ rnr (pGL10) strains, the mean ± SD were calculated from the three independent experiments. The relative amount of pLz4W was plotted for the indicated strains compared to wildtype. PFGE, pulsed-field gel electrophoresis; pLz4W, plasmid of P. syringae Lz4W.

Article Snippet: M1 and M2 are the yeast chromosomal and low-range PFGE markers from New England Biolabs (USA).

Techniques: Expressing, Staining, Plasmid Preparation, Incubation, Western Blot, Marker, Pulsed-Field Gel, Electrophoresis

(A) Total E. coli DNA digested with the restriction enzyme Xbal and analysed using pulse-field gel electrophoresis (PFGE). Fingerprints were analysed using BioNumerics v. 6.6. The name of the isolate and the multilocus sequence type (MLST) is indicated to the right (under ‘MLST Group’). The dendrogram to the left shows sample similarity by UPGMA clustering of PFGE patterns. The bottom scale-bar refers to size of PFGE bands in kilobases. (B) S1/PFGE analysis of extrachromosomal DNA (e.g., plasmid and phage DNA) of the ten isolates.

Journal: PLoS ONE

Article Title: Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing

doi: 10.1371/journal.pone.0065793

Figure Lengend Snippet: (A) Total E. coli DNA digested with the restriction enzyme Xbal and analysed using pulse-field gel electrophoresis (PFGE). Fingerprints were analysed using BioNumerics v. 6.6. The name of the isolate and the multilocus sequence type (MLST) is indicated to the right (under ‘MLST Group’). The dendrogram to the left shows sample similarity by UPGMA clustering of PFGE patterns. The bottom scale-bar refers to size of PFGE bands in kilobases. (B) S1/PFGE analysis of extrachromosomal DNA (e.g., plasmid and phage DNA) of the ten isolates.

Article Snippet: Plasmid sizes were estimated using BioNumerics v.6.6 by comparison to a PFGE low range marker (New England Biolabs).

Techniques: Nucleic Acid Electrophoresis, Sequencing, Plasmid Preparation

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low range pfge markers (New England Biolabs)

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