Structured Review

Roche ecori
<t>DNA</t> Gel Blot Analysis of Ntcel2 , Ntcel7 , and Ntcel8 Genes in Tobacco. Genomic DNA (5 μg) was digested with BamHI (B), <t>EcoRI</t> (E), and HindIII (H), electrophoresed on a 0.7% agarose gel, blotted to nylon membranes, and probed with a 1-kb fragment spanning the conserved amino acid domains CWERPED and YINAPL of Ntcel2 , Ntcel7 , and Ntcel8 . Blots were hybridized in 5 × SSC at 65°C and washed twice in 0.5 × SSC at 68°C and twice in 0.1 × SSC at 68°C. L, 1-kb DNA ladder (Gibco BRL).
Ecori, supplied by Roche, used in various techniques. Bioz Stars score: 94/100, based on 70 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/ecori/product/Roche
Average 94 stars, based on 70 article reviews
Price from $9.99 to $1999.99
ecori - by Bioz Stars, 2020-04
94/100 stars

Images

1) Product Images from "Endo-?-1,4-Glucanase Expression in Compatible Plant-Nematode Interactions"

Article Title: Endo-?-1,4-Glucanase Expression in Compatible Plant-Nematode Interactions

Journal: The Plant Cell

doi: 10.1105/tpc.010219

DNA Gel Blot Analysis of Ntcel2 , Ntcel7 , and Ntcel8 Genes in Tobacco. Genomic DNA (5 μg) was digested with BamHI (B), EcoRI (E), and HindIII (H), electrophoresed on a 0.7% agarose gel, blotted to nylon membranes, and probed with a 1-kb fragment spanning the conserved amino acid domains CWERPED and YINAPL of Ntcel2 , Ntcel7 , and Ntcel8 . Blots were hybridized in 5 × SSC at 65°C and washed twice in 0.5 × SSC at 68°C and twice in 0.1 × SSC at 68°C. L, 1-kb DNA ladder (Gibco BRL).
Figure Legend Snippet: DNA Gel Blot Analysis of Ntcel2 , Ntcel7 , and Ntcel8 Genes in Tobacco. Genomic DNA (5 μg) was digested with BamHI (B), EcoRI (E), and HindIII (H), electrophoresed on a 0.7% agarose gel, blotted to nylon membranes, and probed with a 1-kb fragment spanning the conserved amino acid domains CWERPED and YINAPL of Ntcel2 , Ntcel7 , and Ntcel8 . Blots were hybridized in 5 × SSC at 65°C and washed twice in 0.5 × SSC at 68°C and twice in 0.1 × SSC at 68°C. L, 1-kb DNA ladder (Gibco BRL).

Techniques Used: Western Blot, Agarose Gel Electrophoresis

2) Product Images from "Natural history of SLC11 genes in vertebrates: tales from the fish world"

Article Title: Natural history of SLC11 genes in vertebrates: tales from the fish world

Journal: BMC Evolutionary Biology

doi: 10.1186/1471-2148-11-106

Southern blot analysis . 10 μg of genomic DNA were independently digested with EcoRI or HindII and hybridized with a DIG-labelled slc11 RNA probe. Molecular weights (bp) are indicated in the left margin.
Figure Legend Snippet: Southern blot analysis . 10 μg of genomic DNA were independently digested with EcoRI or HindII and hybridized with a DIG-labelled slc11 RNA probe. Molecular weights (bp) are indicated in the left margin.

Techniques Used: Southern Blot

3) Product Images from "Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release"

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release

Journal: Journal of Biological Engineering

doi: 10.1186/1754-1611-5-8

Mutations occurred in the insert of pLC-T4LysHSL in mutant clones . Unmutated BBa_K173015 (A); luxR disruption mediated by IS10R (B); luxR disruption mediated by IS10R (insertion in reverse direction relative to (B)) (C); deletion of the DNA fragment flanked by BBa_B0015, containing the lux promoter and the holin and lysozyme genes (D); two different mutated plasmids in the same clone: insertion of IS10R and IS5 (containing an EcoRI restriction site) upstream of the first nucleotide of BBa_B0034 RBS and luxR , respectively (E); t gene disruption mediated by IS10R (insertion in reverse direction relative to (B)) (F). The number under the parts denotes the nucleotide of the basic part flanking the insertion sequence that has disrupted the part. The disrupted genes are luxR (BBa_C0062), encoding the transcriptional activator of lux promoter (BBa_R0062), and t (BBa_K112805), encoding the holin. Part codes are given according to the Registry of Standard Biological Parts.
Figure Legend Snippet: Mutations occurred in the insert of pLC-T4LysHSL in mutant clones . Unmutated BBa_K173015 (A); luxR disruption mediated by IS10R (B); luxR disruption mediated by IS10R (insertion in reverse direction relative to (B)) (C); deletion of the DNA fragment flanked by BBa_B0015, containing the lux promoter and the holin and lysozyme genes (D); two different mutated plasmids in the same clone: insertion of IS10R and IS5 (containing an EcoRI restriction site) upstream of the first nucleotide of BBa_B0034 RBS and luxR , respectively (E); t gene disruption mediated by IS10R (insertion in reverse direction relative to (B)) (F). The number under the parts denotes the nucleotide of the basic part flanking the insertion sequence that has disrupted the part. The disrupted genes are luxR (BBa_C0062), encoding the transcriptional activator of lux promoter (BBa_R0062), and t (BBa_K112805), encoding the holin. Part codes are given according to the Registry of Standard Biological Parts.

Techniques Used: Planar Chromatography, Mutagenesis, Clone Assay, Sequencing

Restriction analysis of pLC-T4LysHSL mutants . Plasmid DNA was digested with EcoRI and PstI. In all the screened clones two bands (vector backbone and insert) are present except in colony 1 of mut sc2 , in which four bands can be observed. The expected vector backbone (~3.2 kbp) is present in all the clones, demonstrating that deletions or insertions occurred only in the insert, while all the mutated insert bands are clearly different from the unmutated culture (~2.8 kbp). As sequencing showed, colony 1 of mut sc2 had plasmids with two different mutated inserts in the same clone, one of which containing an EcoRI restriction site that, when digested, produces 2 bands.
Figure Legend Snippet: Restriction analysis of pLC-T4LysHSL mutants . Plasmid DNA was digested with EcoRI and PstI. In all the screened clones two bands (vector backbone and insert) are present except in colony 1 of mut sc2 , in which four bands can be observed. The expected vector backbone (~3.2 kbp) is present in all the clones, demonstrating that deletions or insertions occurred only in the insert, while all the mutated insert bands are clearly different from the unmutated culture (~2.8 kbp). As sequencing showed, colony 1 of mut sc2 had plasmids with two different mutated inserts in the same clone, one of which containing an EcoRI restriction site that, when digested, produces 2 bands.

Techniques Used: Planar Chromatography, Plasmid Preparation, Clone Assay, Sequencing

4) Product Images from "Genotypic comparison of Pantoea agglomerans plant and clinical strains"

Article Title: Genotypic comparison of Pantoea agglomerans plant and clinical strains

Journal: BMC Microbiology

doi: 10.1186/1471-2180-9-204

The fAFLP pattern generated with EcoRI-G and MseI-G primers from different biocontrol, environmental and clinical P. agglomerans isolates . ( A ) C9-1, ( B ) CIP 82.100, ( C ) P10c, ( D ) Eh325, ( E ) EM21cb, ( F ) EM22cb, ( G ) CIP A181. Biocontrol strain P. agglomerans C9-1 showed a completely divergent fAFLP pattern with respect to the other isolates of the species. The 490-bp band which was prevalent in biocontrol and environmental isolates, but was absent from clinical isolates and from strain C9-1 is indicated by the arrow.
Figure Legend Snippet: The fAFLP pattern generated with EcoRI-G and MseI-G primers from different biocontrol, environmental and clinical P. agglomerans isolates . ( A ) C9-1, ( B ) CIP 82.100, ( C ) P10c, ( D ) Eh325, ( E ) EM21cb, ( F ) EM22cb, ( G ) CIP A181. Biocontrol strain P. agglomerans C9-1 showed a completely divergent fAFLP pattern with respect to the other isolates of the species. The 490-bp band which was prevalent in biocontrol and environmental isolates, but was absent from clinical isolates and from strain C9-1 is indicated by the arrow.

Techniques Used: Generated

5) Product Images from "Molecular Characterization and Lytic Activities of Streptococcus agalactiae Bacteriophages and Determination of Lysogenic-Strain Features ▿"

Article Title: Molecular Characterization and Lytic Activities of Streptococcus agalactiae Bacteriophages and Determination of Lysogenic-Strain Features ▿

Journal:

doi: 10.1128/JB.00426-09

EcoRI, HindIII, and ClaI profiles of the five major REA types observed for phages from 36 phages suspensions. L*, Raoul ladder (MWRAU300; Q-Biogene, Strasbourg, France).
Figure Legend Snippet: EcoRI, HindIII, and ClaI profiles of the five major REA types observed for phages from 36 phages suspensions. L*, Raoul ladder (MWRAU300; Q-Biogene, Strasbourg, France).

Techniques Used:

6) Product Images from "The Chromosomal Association of the Smc5/6 Complex Depends on Cohesion and Predicts the Level of Sister Chromatid Entanglement"

Article Title: The Chromosomal Association of the Smc5/6 Complex Depends on Cohesion and Predicts the Level of Sister Chromatid Entanglement

Journal: PLoS Genetics

doi: 10.1371/journal.pgen.1004680

Chromosomal regions where Smc5/6 accumulates after Top2 inhibition show no sign of persistent replication or recombination intermediates. ( A ) Chromosomal localization of Smc6-FLAG as determined by ChIP-seq at two loci, UBP10-MRPL19 and MPP10-YJR003C , showing abundant Smc6-FLAG binding in top2-4 . The lowest panel shows a ChIP-seq map from a control experiment performed on cells lacking FLAG-tagged proteins. Panel details and cellular growth conditions are as described in the legend of Figure 2 . In the top panel describing genomic features, arrows and chromosomal positions denote the restriction sites for PstI , used to produce the analyzed fragments. ( B ) Two-dimensional gel electrophoresis of UBP10-MRPL19 ( left ) and MPP10-YJR003C ( right ) in wild-type and top2-4 cells. Cell cycle progression monitored by fluorescence-activated cell sorting (FACS) is shown below and time-points of sample preparation are indicated. Membranes were first probed against UBP10-MRPL19 ( left ), then stripped and re-probed against MPP10-YJR003C ( right ), leaving some residual signal from UBP10-MRPL19 in the MPP10-YJR003C blots (white arrows). ( C ) Two-dimensional gel electrophoresis after DNA isolation using CTAB-extraction to preserve X-shaped molecules, of ARS305 ( left ) and UBP10-MRPL19 ( right ) in wild-type and top2-4 cells. The ARS305 containing fragment was produced by digestion using EcoRI and HindIII , and is a positive control for X-shaped molecule isolation (white arrowheads). Cell cycle progression monitored by FACS is shown below and indicates the time-points of sample preparation.
Figure Legend Snippet: Chromosomal regions where Smc5/6 accumulates after Top2 inhibition show no sign of persistent replication or recombination intermediates. ( A ) Chromosomal localization of Smc6-FLAG as determined by ChIP-seq at two loci, UBP10-MRPL19 and MPP10-YJR003C , showing abundant Smc6-FLAG binding in top2-4 . The lowest panel shows a ChIP-seq map from a control experiment performed on cells lacking FLAG-tagged proteins. Panel details and cellular growth conditions are as described in the legend of Figure 2 . In the top panel describing genomic features, arrows and chromosomal positions denote the restriction sites for PstI , used to produce the analyzed fragments. ( B ) Two-dimensional gel electrophoresis of UBP10-MRPL19 ( left ) and MPP10-YJR003C ( right ) in wild-type and top2-4 cells. Cell cycle progression monitored by fluorescence-activated cell sorting (FACS) is shown below and time-points of sample preparation are indicated. Membranes were first probed against UBP10-MRPL19 ( left ), then stripped and re-probed against MPP10-YJR003C ( right ), leaving some residual signal from UBP10-MRPL19 in the MPP10-YJR003C blots (white arrows). ( C ) Two-dimensional gel electrophoresis after DNA isolation using CTAB-extraction to preserve X-shaped molecules, of ARS305 ( left ) and UBP10-MRPL19 ( right ) in wild-type and top2-4 cells. The ARS305 containing fragment was produced by digestion using EcoRI and HindIII , and is a positive control for X-shaped molecule isolation (white arrowheads). Cell cycle progression monitored by FACS is shown below and indicates the time-points of sample preparation.

Techniques Used: Inhibition, Chromatin Immunoprecipitation, Binding Assay, Two-Dimensional Gel Electrophoresis, Electrophoresis, Fluorescence, FACS, Sample Prep, DNA Extraction, Produced, Positive Control, Isolation

7) Product Images from "The Facioscapulohumeral muscular dystrophy region on 4qter and the homologous locus on 10qter evolved independently under different evolutionary pressure"

Article Title: The Facioscapulohumeral muscular dystrophy region on 4qter and the homologous locus on 10qter evolved independently under different evolutionary pressure

Journal: BMC Medical Genetics

doi: 10.1186/1471-2350-8-8

4q and 10q allelic pattern of a FSHD family after hybridization with p13E-11 and qA-qB telomeric markers . a) DNA samples were digested with EcoRI (E) and EcoRI/BlnI (E/B) enzymes, separated with PFGE and hybridized with p13E-11 probe. The proband (I:1) shows a trisomic pattern with two 4q alleles of 18 and 30 kb and two 10q alleles of 41 (BlnI-resistant) (*) and 48 kb (BlnI-sensitive). The affected son (II:1) is also trisomic and inherited from the father the 4q FSHD allele of 18 kb and the10q of 41 kb (*) and from the mother the 4q of 53 kb and a similar size10q allele. The unaffected daughter inherited from the father the 4q allele of 30 kb and the 10q BlnI-resistant allele of 41 kb (*) and from the mother the 4q and 10q fragments of 53 kb. The segregation data for the probe D4S139 showed that II:1 and II:2 inherited the same 4q allele from the mother (I:2), but different 4q alleles from the father (I:1). This suggest that the BlnI-resistant allele of 41 kb is a 10q variant; b) DNA samples were digested with HindIII (H), separated with PFGE and subsequently hybridized with qA and qB probes: the short 4q allele (18 kb) is qA type, while the 4q allele of 30 kb is qB type. All the standard 10q alleles of 48, 53 and 20 kb have qA type telomeres, while the variant 10q allele of 41 kb is qB type. This variant 10q allele carries the Bln1-resistant repeat array and the distal telomeric sequence of 4q-type. The 10q origin of this allele is confirmed by absence of segregation with D4S139 probe. The DNA sample of the subject II:2 was not sufficient for qA/qB Southern Blot analysis and it was not included in figure 3. In the diagram below the alleles observed after EcoRI and EcoRI/BlnI digestion are shown: the 4q alleles are in bold and the telomeres (A or B) are in brackets.
Figure Legend Snippet: 4q and 10q allelic pattern of a FSHD family after hybridization with p13E-11 and qA-qB telomeric markers . a) DNA samples were digested with EcoRI (E) and EcoRI/BlnI (E/B) enzymes, separated with PFGE and hybridized with p13E-11 probe. The proband (I:1) shows a trisomic pattern with two 4q alleles of 18 and 30 kb and two 10q alleles of 41 (BlnI-resistant) (*) and 48 kb (BlnI-sensitive). The affected son (II:1) is also trisomic and inherited from the father the 4q FSHD allele of 18 kb and the10q of 41 kb (*) and from the mother the 4q of 53 kb and a similar size10q allele. The unaffected daughter inherited from the father the 4q allele of 30 kb and the 10q BlnI-resistant allele of 41 kb (*) and from the mother the 4q and 10q fragments of 53 kb. The segregation data for the probe D4S139 showed that II:1 and II:2 inherited the same 4q allele from the mother (I:2), but different 4q alleles from the father (I:1). This suggest that the BlnI-resistant allele of 41 kb is a 10q variant; b) DNA samples were digested with HindIII (H), separated with PFGE and subsequently hybridized with qA and qB probes: the short 4q allele (18 kb) is qA type, while the 4q allele of 30 kb is qB type. All the standard 10q alleles of 48, 53 and 20 kb have qA type telomeres, while the variant 10q allele of 41 kb is qB type. This variant 10q allele carries the Bln1-resistant repeat array and the distal telomeric sequence of 4q-type. The 10q origin of this allele is confirmed by absence of segregation with D4S139 probe. The DNA sample of the subject II:2 was not sufficient for qA/qB Southern Blot analysis and it was not included in figure 3. In the diagram below the alleles observed after EcoRI and EcoRI/BlnI digestion are shown: the 4q alleles are in bold and the telomeres (A or B) are in brackets.

Techniques Used: Hybridization, Variant Assay, Sequencing, Southern Blot

Nullisomic pattern . The patient shows four EcoRI bands after p13E-11 hybridization and none after double digestion with EcoRI/BlnI (nulisomic pattern). After hybridization with KpnI probe two BlnI resistant band are visible (45 and 20 kb): we can not guess the chromosomal origin of these alleles. To resolve the structure of the alleles we digested the sample with XapI enzyme which cuts the 4q-type repeats only (see Methods). After hybridization with p13E-11 we observed 4 XapI-resistant bands (38, 32, 13 and 8 kb): the 38 and 32 kb bands correspond to the EcoRI fragments of 42 and 36 kb fragments (XapI fragments are 4 kb smaller than EcoRI fragments). On the contrary the 13 and 8 kb fragments are stretches of the hybrid 4q alleles: the 62 kb EcoRI allele is composed by a BlnI-sensitive fragment (XapI-resistant) of 13 kb and a BlnI-resistant fragment of 45 kb (13+45 = 58 kb). The 32 kb EcoRI allele is composed by a BlnI-sensitive fragment (XapI-resistant) of 8 kb and a BlnI-resistant fragment of 20 kb (8+20 = 28 kb). The 4q variant alleles are represented in figure 5 (n.15 and 16). The FSHD 4q allele of 32 kb segregated also in other affected members of the family and its origin was confirmed by D4S139 probe (data not shown). * aspecific bands.
Figure Legend Snippet: Nullisomic pattern . The patient shows four EcoRI bands after p13E-11 hybridization and none after double digestion with EcoRI/BlnI (nulisomic pattern). After hybridization with KpnI probe two BlnI resistant band are visible (45 and 20 kb): we can not guess the chromosomal origin of these alleles. To resolve the structure of the alleles we digested the sample with XapI enzyme which cuts the 4q-type repeats only (see Methods). After hybridization with p13E-11 we observed 4 XapI-resistant bands (38, 32, 13 and 8 kb): the 38 and 32 kb bands correspond to the EcoRI fragments of 42 and 36 kb fragments (XapI fragments are 4 kb smaller than EcoRI fragments). On the contrary the 13 and 8 kb fragments are stretches of the hybrid 4q alleles: the 62 kb EcoRI allele is composed by a BlnI-sensitive fragment (XapI-resistant) of 13 kb and a BlnI-resistant fragment of 45 kb (13+45 = 58 kb). The 32 kb EcoRI allele is composed by a BlnI-sensitive fragment (XapI-resistant) of 8 kb and a BlnI-resistant fragment of 20 kb (8+20 = 28 kb). The 4q variant alleles are represented in figure 5 (n.15 and 16). The FSHD 4q allele of 32 kb segregated also in other affected members of the family and its origin was confirmed by D4S139 probe (data not shown). * aspecific bands.

Techniques Used: Hybridization, Variant Assay

8) Product Images from "Sex Pheromone Response, Clumping, and Slime Production in Enterococcal Strains Isolated from Occluded Biliary Stents"

Article Title: Sex Pheromone Response, Clumping, and Slime Production in Enterococcal Strains Isolated from Occluded Biliary Stents

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.42.8.3419-3427.2004

Restriction analysis of PCR products obtained using primers internal to prgB and agg genes of clumping-positive (EFS-27b, EFS-30d, and EGL-19) and clumping-negative (EFS-12, EFS-20, and EFS-28b) clinical enterococcal isolates and of E. faecalis OG1RF(pCF10). (A) DraI digests from 427-bp amplicons ( prgB ). (B) EcoRI digests from 1,553-bp amplicons ( agg ). Lanes: 1, EFS-28b undigested; 2, EFS-28b digested; 3, EFS-30d undigested; 4, EFS-30d digested; 5, OG1RF(pCF10) undigested; 6, OG1RF(pCF10) digested; 7, EFS-20 undigested; 8, EFS-20 digested; 9, EFS-27b undigested; 10, EFS-27b digested; 11, EFS-12 undigested; 12, EFS-12 digested; 13, EGL-19 undigested; 14, EGL-19 digested; 15, Marker Gene Ruler 100-bp DNA ladder. The arrows indicate the sizes of fragments in base pairs.
Figure Legend Snippet: Restriction analysis of PCR products obtained using primers internal to prgB and agg genes of clumping-positive (EFS-27b, EFS-30d, and EGL-19) and clumping-negative (EFS-12, EFS-20, and EFS-28b) clinical enterococcal isolates and of E. faecalis OG1RF(pCF10). (A) DraI digests from 427-bp amplicons ( prgB ). (B) EcoRI digests from 1,553-bp amplicons ( agg ). Lanes: 1, EFS-28b undigested; 2, EFS-28b digested; 3, EFS-30d undigested; 4, EFS-30d digested; 5, OG1RF(pCF10) undigested; 6, OG1RF(pCF10) digested; 7, EFS-20 undigested; 8, EFS-20 digested; 9, EFS-27b undigested; 10, EFS-27b digested; 11, EFS-12 undigested; 12, EFS-12 digested; 13, EGL-19 undigested; 14, EGL-19 digested; 15, Marker Gene Ruler 100-bp DNA ladder. The arrows indicate the sizes of fragments in base pairs.

Techniques Used: Polymerase Chain Reaction, Marker

9) Product Images from "RNAi-based conditional gene knockdown in mice using a U6 promoter driven vector"

Article Title: RNAi-based conditional gene knockdown in mice using a U6 promoter driven vector

Journal: International Journal of Biological Sciences

doi:

Screening for the U6-Neo-RNAi vector containing the insert and its expression in mouse after deletion of the neo by EIIa-Cre transgene. (A) After double-strand oligo ligation into the pBS/U6-neo vector, check insertion by SalI and EcoRI restriction and migration in a 3% agarose gel. Run two controls (parent and restricted parent vector) and an appropriate molecular weight marker (100, 150 and/or 200 bp). (B) Northern blot showing expression of pBSU6-Neo-RNAi against mouse Fgfr2. Cre mediated deletion of the neo from U6-ploxPneo-Fgfr2 transgene allows expression of Fgfr2 RNAi. (C) Assessment of copy number of U6-ploxPneo-Fgfr2 transgene by realtime PCR using primers for neo gene. Control DNA with 1 copy and 2 copies of neo gene are from Sirt6+/- and Fgfr1-/- ES cells, respectively. (D) RT-PCR analysis of Fgfr1-4 expression in E12.5 embryos of different genotypes. Wt: Wild type; U6: U6-ploxPneo-Fgfr2; Cre: EIIa-Cre ; and U6;Cre: U6-Fgfr2;EIIa-Cre . The first row is a longer exposure of the second row. Three embryos for each genotype were shown. RT-PCR was performed using the following primers: Fgfr1-F: 5'-TTCTGGGCTGTGCTGGTCAC-3', and Fgfr1-R: 5'-GCGAACCTTGTAGCCTCCAA-3'. Fgfr2-F: 5'-AAGGTTTACAGCGATGCCCA-3', and Fgfr2-R: 5'-ACCACCATGCAGGCGATTAA-3'. Fgfr3-F: 5'-CTAGTGTTCTGCGTGGCGGT-3', and Fgfr3-R: 5'-TTCTTATCCATTCGCTCCGG-3'. Fgfr4-F: 5'-CTGTTGAGCATCTTTCAGGG-3', and Fgfr4-R: 5'-CGTGGAAGGCCTGTCCATCC-3'.
Figure Legend Snippet: Screening for the U6-Neo-RNAi vector containing the insert and its expression in mouse after deletion of the neo by EIIa-Cre transgene. (A) After double-strand oligo ligation into the pBS/U6-neo vector, check insertion by SalI and EcoRI restriction and migration in a 3% agarose gel. Run two controls (parent and restricted parent vector) and an appropriate molecular weight marker (100, 150 and/or 200 bp). (B) Northern blot showing expression of pBSU6-Neo-RNAi against mouse Fgfr2. Cre mediated deletion of the neo from U6-ploxPneo-Fgfr2 transgene allows expression of Fgfr2 RNAi. (C) Assessment of copy number of U6-ploxPneo-Fgfr2 transgene by realtime PCR using primers for neo gene. Control DNA with 1 copy and 2 copies of neo gene are from Sirt6+/- and Fgfr1-/- ES cells, respectively. (D) RT-PCR analysis of Fgfr1-4 expression in E12.5 embryos of different genotypes. Wt: Wild type; U6: U6-ploxPneo-Fgfr2; Cre: EIIa-Cre ; and U6;Cre: U6-Fgfr2;EIIa-Cre . The first row is a longer exposure of the second row. Three embryos for each genotype were shown. RT-PCR was performed using the following primers: Fgfr1-F: 5'-TTCTGGGCTGTGCTGGTCAC-3', and Fgfr1-R: 5'-GCGAACCTTGTAGCCTCCAA-3'. Fgfr2-F: 5'-AAGGTTTACAGCGATGCCCA-3', and Fgfr2-R: 5'-ACCACCATGCAGGCGATTAA-3'. Fgfr3-F: 5'-CTAGTGTTCTGCGTGGCGGT-3', and Fgfr3-R: 5'-TTCTTATCCATTCGCTCCGG-3'. Fgfr4-F: 5'-CTGTTGAGCATCTTTCAGGG-3', and Fgfr4-R: 5'-CGTGGAAGGCCTGTCCATCC-3'.

Techniques Used: Plasmid Preparation, Expressing, Ligation, Migration, Agarose Gel Electrophoresis, Molecular Weight, Marker, Northern Blot, Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction

10) Product Images from "A genetic system for targeted mutations to disrupt and restore genes in the obligate bacterium, Ehrlichia chaffeensis"

Article Title: A genetic system for targeted mutations to disrupt and restore genes in the obligate bacterium, Ehrlichia chaffeensis

Journal: Scientific Reports

doi: 10.1038/s41598-017-16023-y

Targeted allelic exchange mutagenesis to disrupt Ech_0230 gene. ( A ) An illustration depicting the genomic segment spanning the region selected for preparing allelic exchange construct, including the restriction enzyme sites {EcoRI (E) and ClaI (C)} used for the mapping the insertion. Genomic coordinates for restriction enzyme sites and the size of inserted fragment ( tuf -aadA) were included to allow determination of the expected DNA sizes in PCR and Southern blot analysis. ( B ) Amplicons resolved following three different PCRs using primers targeting to the genomic regions upstream and downstream to the allelic insertion (primers identified as 1 and 4) and to the inserted DNA (primers; 2 and 3). (L, 1 kb plus molecular weight DNA markers; W, PCR with wild type genomic DNA as the template; M, PCR with mutant genomic DNA as the template). ( C ) PCR DNA Sequence verification of insertion sites in the targeted mutant. DNA sequence generated from amplicons (panel B); sequence shown above black arrow lines represents the sequence from E . chaffeensis genome, while the sequence above the orange arrowhead lines represents the inserted sequence in the gene disruption mutant. Sequences boundaries at the 5′ and 3′ insertion junctions were identified with a small black arrow lines. ( D ) Southern blot analysis of genomic DNAs (W and M) digested with ClaI ( C ) or EcoRI ( E ). The blot analysis was performed with aadA gene segment as the probe. (Full-length gels and blots were included in the Supplementary Figure file, as parts of the Figure had cropped images).
Figure Legend Snippet: Targeted allelic exchange mutagenesis to disrupt Ech_0230 gene. ( A ) An illustration depicting the genomic segment spanning the region selected for preparing allelic exchange construct, including the restriction enzyme sites {EcoRI (E) and ClaI (C)} used for the mapping the insertion. Genomic coordinates for restriction enzyme sites and the size of inserted fragment ( tuf -aadA) were included to allow determination of the expected DNA sizes in PCR and Southern blot analysis. ( B ) Amplicons resolved following three different PCRs using primers targeting to the genomic regions upstream and downstream to the allelic insertion (primers identified as 1 and 4) and to the inserted DNA (primers; 2 and 3). (L, 1 kb plus molecular weight DNA markers; W, PCR with wild type genomic DNA as the template; M, PCR with mutant genomic DNA as the template). ( C ) PCR DNA Sequence verification of insertion sites in the targeted mutant. DNA sequence generated from amplicons (panel B); sequence shown above black arrow lines represents the sequence from E . chaffeensis genome, while the sequence above the orange arrowhead lines represents the inserted sequence in the gene disruption mutant. Sequences boundaries at the 5′ and 3′ insertion junctions were identified with a small black arrow lines. ( D ) Southern blot analysis of genomic DNAs (W and M) digested with ClaI ( C ) or EcoRI ( E ). The blot analysis was performed with aadA gene segment as the probe. (Full-length gels and blots were included in the Supplementary Figure file, as parts of the Figure had cropped images).

Techniques Used: Mutagenesis, Construct, Polymerase Chain Reaction, Southern Blot, Molecular Weight, Sequencing, Generated

11) Product Images from "Naturally Occurring DNA Transfer System Associated with Membrane Vesicles in Cellulolytic Ruminococcus spp. of Ruminal Origin"

Article Title: Naturally Occurring DNA Transfer System Associated with Membrane Vesicles in Cellulolytic Ruminococcus spp. of Ruminal Origin

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.71.8.4248-4253.2005

Restriction digestion of chromosomal DNA extracted from whole cells of R. albus AR67 (lanes 5, 6, and 7, uncut and HindIII and EcoRI digests, respectively) and DNA from subcellular particles from R. albus AR67 (lanes 2, 3, and 4, uncut and HindIII and
Figure Legend Snippet: Restriction digestion of chromosomal DNA extracted from whole cells of R. albus AR67 (lanes 5, 6, and 7, uncut and HindIII and EcoRI digests, respectively) and DNA from subcellular particles from R. albus AR67 (lanes 2, 3, and 4, uncut and HindIII and

Techniques Used:

12) Product Images from "A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase"

Article Title: A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.0603137103

Southern blot of A. tuberculatus gDNA probed with a fragment of PPX2L . DNA was isolated from plants that were derived from the S or R biotype and digested with EcoRI or HindIII.
Figure Legend Snippet: Southern blot of A. tuberculatus gDNA probed with a fragment of PPX2L . DNA was isolated from plants that were derived from the S or R biotype and digested with EcoRI or HindIII.

Techniques Used: Southern Blot, Isolation, Derivative Assay

13) Product Images from "Evolutionarily Conserved TCR Binding Sites, Identification of T Cells in Primary Lymphoid Tissues, and Surprising Trans-Rearrangements in Nurse Shark"

Article Title: Evolutionarily Conserved TCR Binding Sites, Identification of T Cells in Primary Lymphoid Tissues, and Surprising Trans-Rearrangements in Nurse Shark

Journal: Journal of immunology (Baltimore, Md. : 1950)

doi: 10.4049/jimmunol.0902774

Genomic Southern and Northern blotting. Probes to the C domain Ig regions of each TCR chain were used to probe blotted nucleic acid agarose gels. A , Genomic DNA of three individual nurse sharks ( a , b , c ) digested (from left to right ) with BamHI, EcoRI,
Figure Legend Snippet: Genomic Southern and Northern blotting. Probes to the C domain Ig regions of each TCR chain were used to probe blotted nucleic acid agarose gels. A , Genomic DNA of three individual nurse sharks ( a , b , c ) digested (from left to right ) with BamHI, EcoRI,

Techniques Used: Northern Blot

14) Product Images from "Construction of Mtb72F Plasmid as a DNA Vaccine Candidate for Mycobacterium tuberculosis"

Article Title: Construction of Mtb72F Plasmid as a DNA Vaccine Candidate for Mycobacterium tuberculosis

Journal: Reports of Biochemistry & Molecular Biology

doi:

Agarose gel of HindIII - and EcoRI -digested pcDNA3.1/ Mtb32c/Mtb39/Mtb32N . Lane 1: DNA size marker (1000 bp); lane 2: digested vector: the 1630 bp fragment contains mtb32C and mtb39 .
Figure Legend Snippet: Agarose gel of HindIII - and EcoRI -digested pcDNA3.1/ Mtb32c/Mtb39/Mtb32N . Lane 1: DNA size marker (1000 bp); lane 2: digested vector: the 1630 bp fragment contains mtb32C and mtb39 .

Techniques Used: Agarose Gel Electrophoresis, Marker, Plasmid Preparation

15) Product Images from "ADAMTSL-6 Is a Novel Extracellular Matrix Protein That Binds to Fibrillin-1 and Promotes Fibrillin-1 Fibril Formation *"

Article Title: ADAMTSL-6 Is a Novel Extracellular Matrix Protein That Binds to Fibrillin-1 and Promotes Fibrillin-1 Fibril Formation *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M109.076919

Promotion of fibrillin-1 fibril formation by ADAMTSL-6 in vivo . A , Southern hybridization of DNA from ADAMTSL-6β transgenic mice. Digestion of genomic DNA with EcoRI and BamHI produced 1.6-kb fragments containing the Adamtsl6 exon 8 from chromosome 9 (indicated with an arrow ) and 2.3-kb fragments containing full-length ADAMTSL-6β transgenes (indicated with an arrowhead ). Lane 1, digoxigenin-labeled molecular weight markers; lane 2 , DNA from wild-type mouse (12 μg); lane 3 , DNA from wild-type mouse (3 μg); lane 4 , DNA from transgenic mouse (12 μg); lane 5 , DNA from transgenic mouse (3 μg); lane 6 , DNA from transgenic mouse (0.75 μg). The 2.3-kb band was detected only with the DNA from transgenic mice, whereas the 1.6-kb band, although very faint, was detected with the DNA from wild-type and transgenic mice. Quantification of band intensities using ImageJ software indicated that more than 20 copies of the transgene were integrated into the genomic DNA of transgenic mice. The sizes of DNA molecular weight markers are shown in the left margin. B , tissue extracts from E15.5 wild-type ( W ) and ADAMTSL-6β transgenic mice ( Tg ) were subjected to SDS-PAGE under reducing conditions, followed by blotting with anti-ADAMTSL-6 antibody. 10-Fold diluted extracts were also subjected to Western blotting for the costae from transgenic mice, where the transgene was highly expressed. Positions of molecular mass markers (kDa) are shown in the left margin. Open and closed triangles point to the bands characteristic of the whisker pads and the gut tube, respectively. C–J, immunofluorescence detection of ADAMTSL-6 proteins and fibrillin-1. Sagittal cryosections were prepared from E12.5 wild-type ( C , E , G , and I ) and transgenic littermates ( D , F , H , and J ) and subjected to double immunostaining with antibodies against ADAMTSL-6 ( green ) and fibrillin-1 ( red ). The regions of rib cartilage ( C ) and surrounding perichondrium ( P ) are labeled in E and F. G and I , magnified views in the boxed areas in E. H and J , magnified views of the boxed areas in F . The ADAMTSL-6β transgene was highly expressed in the rib cartilage and surrounding perichondrium of transgenic embryos ( D and F ), where fibrillin-1 depositions were also enhanced ( H and J ). Scale bar, 100 μm.
Figure Legend Snippet: Promotion of fibrillin-1 fibril formation by ADAMTSL-6 in vivo . A , Southern hybridization of DNA from ADAMTSL-6β transgenic mice. Digestion of genomic DNA with EcoRI and BamHI produced 1.6-kb fragments containing the Adamtsl6 exon 8 from chromosome 9 (indicated with an arrow ) and 2.3-kb fragments containing full-length ADAMTSL-6β transgenes (indicated with an arrowhead ). Lane 1, digoxigenin-labeled molecular weight markers; lane 2 , DNA from wild-type mouse (12 μg); lane 3 , DNA from wild-type mouse (3 μg); lane 4 , DNA from transgenic mouse (12 μg); lane 5 , DNA from transgenic mouse (3 μg); lane 6 , DNA from transgenic mouse (0.75 μg). The 2.3-kb band was detected only with the DNA from transgenic mice, whereas the 1.6-kb band, although very faint, was detected with the DNA from wild-type and transgenic mice. Quantification of band intensities using ImageJ software indicated that more than 20 copies of the transgene were integrated into the genomic DNA of transgenic mice. The sizes of DNA molecular weight markers are shown in the left margin. B , tissue extracts from E15.5 wild-type ( W ) and ADAMTSL-6β transgenic mice ( Tg ) were subjected to SDS-PAGE under reducing conditions, followed by blotting with anti-ADAMTSL-6 antibody. 10-Fold diluted extracts were also subjected to Western blotting for the costae from transgenic mice, where the transgene was highly expressed. Positions of molecular mass markers (kDa) are shown in the left margin. Open and closed triangles point to the bands characteristic of the whisker pads and the gut tube, respectively. C–J, immunofluorescence detection of ADAMTSL-6 proteins and fibrillin-1. Sagittal cryosections were prepared from E12.5 wild-type ( C , E , G , and I ) and transgenic littermates ( D , F , H , and J ) and subjected to double immunostaining with antibodies against ADAMTSL-6 ( green ) and fibrillin-1 ( red ). The regions of rib cartilage ( C ) and surrounding perichondrium ( P ) are labeled in E and F. G and I , magnified views in the boxed areas in E. H and J , magnified views of the boxed areas in F . The ADAMTSL-6β transgene was highly expressed in the rib cartilage and surrounding perichondrium of transgenic embryos ( D and F ), where fibrillin-1 depositions were also enhanced ( H and J ). Scale bar, 100 μm.

Techniques Used: In Vivo, Hybridization, Transgenic Assay, Mouse Assay, Produced, Labeling, Molecular Weight, Software, SDS Page, Western Blot, Whisker Assay, Immunofluorescence, Double Immunostaining

16) Product Images from "Multidrug-Resistant Salmonella enterica Serovar Muenchen from Pigs and Humans and Potential Interserovar Transfer of Antimicrobial Resistance"

Article Title: Multidrug-Resistant Salmonella enterica Serovar Muenchen from Pigs and Humans and Potential Interserovar Transfer of Antimicrobial Resistance

Journal: Antimicrobial Agents and Chemotherapy

doi: 10.1128/AAC.49.2.503-511.2005

Plasmid restriction analysis with four restriction enzymes: PstI, HindIII, EcoRI, and BamHI. Lanes: 1, Salmonella serovar Muenchen (human origin, p3633, R type ACSSuTAxKGCfCro); 2, Salmonella serovar Typhimurium (porcine origin, pUCE15, R type AKSSuT);
Figure Legend Snippet: Plasmid restriction analysis with four restriction enzymes: PstI, HindIII, EcoRI, and BamHI. Lanes: 1, Salmonella serovar Muenchen (human origin, p3633, R type ACSSuTAxKGCfCro); 2, Salmonella serovar Typhimurium (porcine origin, pUCE15, R type AKSSuT);

Techniques Used: Plasmid Preparation

17) Product Images from "Purification and Partial Characterization of an Entomopoxvirus (DlEPV) from a Parasitic Wasp of Tephritid Fruit Flies."

Article Title: Purification and Partial Characterization of an Entomopoxvirus (DlEPV) from a Parasitic Wasp of Tephritid Fruit Flies.

Journal: Journal of Insect Science

doi:

Complete DNA and deduced amino acid sequences of the DlEPV EcoRI clone #36 (RI-36) that contains a partial open reading frame (RI-36-1) of a large gene that encodes a homolog of a DNA-directed RNA polymerase. The GenBank accession number for this sequence is AF500107. Alignment of the deduced amino acid sequences of DlEPV R1-36-1, AmEPV221, MsEPV043, and two vertebrate poxvirus homologs of Vaccinia (Vac) J6R, lumpy skin disease virus and Yaba monkey tumor virus that encode a putative DNA-dependent RNA polymerase. Gold= aa shared between DlEPV and at least one of the EPV AND one of the vertebrate poxvirus sequences. Green = aa shared between DlEPV and at least one of the two entomopoxviruses, AmEPV and MsEPV, but not found in the two vertebrate poxvirus sequences; Pink = EcoR1 (FE translated from the GAATTC) restriction sites; Red= aa found only in the DlEPV sequence; Shadowed area = the NADFDGDE consensus sequence of RNA polymerases; Blue = aa shared between DlEPV and at least one of the vertebrate poxvirus sequences but not found in the two EPV sequences; asterisk (*), semicolon (:) and period (.) = identical, conserved and semiconserved substitutions respectively, among all five sequences.
Figure Legend Snippet: Complete DNA and deduced amino acid sequences of the DlEPV EcoRI clone #36 (RI-36) that contains a partial open reading frame (RI-36-1) of a large gene that encodes a homolog of a DNA-directed RNA polymerase. The GenBank accession number for this sequence is AF500107. Alignment of the deduced amino acid sequences of DlEPV R1-36-1, AmEPV221, MsEPV043, and two vertebrate poxvirus homologs of Vaccinia (Vac) J6R, lumpy skin disease virus and Yaba monkey tumor virus that encode a putative DNA-dependent RNA polymerase. Gold= aa shared between DlEPV and at least one of the EPV AND one of the vertebrate poxvirus sequences. Green = aa shared between DlEPV and at least one of the two entomopoxviruses, AmEPV and MsEPV, but not found in the two vertebrate poxvirus sequences; Pink = EcoR1 (FE translated from the GAATTC) restriction sites; Red= aa found only in the DlEPV sequence; Shadowed area = the NADFDGDE consensus sequence of RNA polymerases; Blue = aa shared between DlEPV and at least one of the vertebrate poxvirus sequences but not found in the two EPV sequences; asterisk (*), semicolon (:) and period (.) = identical, conserved and semiconserved substitutions respectively, among all five sequences.

Techniques Used: Sequencing

Fragment profile of restriction endonuclease digested DlEPV genomic DNA. About 3.5 µg of digested DlEPV were loaded in the respective lanes of a 0.7% Seaplaque GTG (FMC) agarose gel and electrophoresed in 0.5 × TBE at 40V. The gel was stained with 0.05 mg/ml EtBr. MW=molecular weight in kilobase pairs (Kb); 1=Pst I; 2=EcoRV/Pst I; 3=EcoRV; 4=EcoRV/BamHI; 5=BamHI; 6=EcoRI; 7=EcoRI/Xho; 8=Xho.
Figure Legend Snippet: Fragment profile of restriction endonuclease digested DlEPV genomic DNA. About 3.5 µg of digested DlEPV were loaded in the respective lanes of a 0.7% Seaplaque GTG (FMC) agarose gel and electrophoresed in 0.5 × TBE at 40V. The gel was stained with 0.05 mg/ml EtBr. MW=molecular weight in kilobase pairs (Kb); 1=Pst I; 2=EcoRV/Pst I; 3=EcoRV; 4=EcoRV/BamHI; 5=BamHI; 6=EcoRI; 7=EcoRI/Xho; 8=Xho.

Techniques Used: Agarose Gel Electrophoresis, Staining, Molecular Weight

Complete DNA and deduced amino acid sequences of the DlEPV EcoRI clone #36 (RI-36) that contains a partial open reading frame (RI-36-1) of a large gene that encodes a homolog of a DNA-directed RNA polymerase. The GenBank accession number for this sequence is AF500107. Complete DNA sequence of DlEPV RI-36-1 consisting of a 2316 nt partial open reading frame. The nucleotides in blue encode the consensus sequence of the DNA-directed RNA polymerase gene family. GAATTC = EcoRI restriction site.
Figure Legend Snippet: Complete DNA and deduced amino acid sequences of the DlEPV EcoRI clone #36 (RI-36) that contains a partial open reading frame (RI-36-1) of a large gene that encodes a homolog of a DNA-directed RNA polymerase. The GenBank accession number for this sequence is AF500107. Complete DNA sequence of DlEPV RI-36-1 consisting of a 2316 nt partial open reading frame. The nucleotides in blue encode the consensus sequence of the DNA-directed RNA polymerase gene family. GAATTC = EcoRI restriction site.

Techniques Used: Sequencing

18) Product Images from "Unravelling the Role of the F55 Regulator in the Transition from Lysogeny to UV Induction of Sulfolobus Spindle-Shaped Virus 1"

Article Title: Unravelling the Role of the F55 Regulator in the Transition from Lysogeny to UV Induction of Sulfolobus Spindle-Shaped Virus 1

Journal: Journal of Virology

doi: 10.1128/JVI.00363-15

Detection of the viral DNA after UV irradiation by EcoRI restriction analysis. The restriction profiles of total DNA samples from control cultures and SSV1-InF1-irradiated cells and of SSV1 episomal DNA digested with EcoRI are shown. Molecular size markers are indicated on the left; SSV1-derived fragments (7.9, 2.9, 2.4, and 2.1 kbp) are indicated on the right. The intensity of the SSV1 fragments is higher for the sample collected 8 to 10 h postirradiation.
Figure Legend Snippet: Detection of the viral DNA after UV irradiation by EcoRI restriction analysis. The restriction profiles of total DNA samples from control cultures and SSV1-InF1-irradiated cells and of SSV1 episomal DNA digested with EcoRI are shown. Molecular size markers are indicated on the left; SSV1-derived fragments (7.9, 2.9, 2.4, and 2.1 kbp) are indicated on the right. The intensity of the SSV1 fragments is higher for the sample collected 8 to 10 h postirradiation.

Techniques Used: Irradiation, Derivative Assay

19) Product Images from "Recombinant Bovine Herpesvirus 4 (BoHV-4) Expressing Glycoprotein D of BoHV-1 Is Immunogenic and Elicits Serum-Neutralizing Antibodies against BoHV-1 in a Rabbit Model ▿"

Article Title: Recombinant Bovine Herpesvirus 4 (BoHV-4) Expressing Glycoprotein D of BoHV-1 Is Immunogenic and Elicits Serum-Neutralizing Antibodies against BoHV-1 in a Rabbit Model ▿

Journal: Clinical and Vaccine Immunology

doi: 10.1128/CVI.00200-06

Construction of BoHV-4 expressing gD. (A) Overall strategy of recombinant BAC-BoHV-4 generation. The transposon complex is assembled with BglII fragments containing RI/RII-CMVgD-Kana-RII/RI and RI/RII-CMVgD-Kana-RII/RI transposons (yellow ends) as donor DNA, BAC-BoHV-4 as a target DNA (blue boxes indicate polyrepetitive DNA, red boxes indicate the BAC plasmid backbone, and the green boxes represent the EGFP expression cassette), and MuA enzyme. The transposition reaction proceeds through an intermediate formation (looped RI/RII-CMVgD-Kana-RII/RI and RI/RII-CMVgD-Kana-RII/RI transposon complexes attached to the target BAC-BoHV-4 DNA) and a final reaction with the target DNA transposed (RI/RII-CMVgD-Kana-RII/RI and RI/RII-CMVgD-Kana-RII/RI transposons, bordered by the two yellow boxes, integrated into the target BAC-BoHV-4 DNA). A flow chart of reconstitution of the BAC-BoHV-4 recombinant is shown. The recombinant plasmids are electroporated into electrocompetent E. coli , the kanamycin-resistant colonies are selected on kanamycin plates, and plasmid DNA is prepared from amplified single colonies and analyzed. (B) Analysis of BAC-BoHV-4 randomly transposed clones (12 clones for RI/RII-CMVgD-Kana-RII/RI, BoHV-4-CMVgD and 12 clones for RI/RII-CMVgDWPRE-Kana-RII/RI, BoHV-4-CMVgDWPRE). (Top panel) PCR analysis demonstrating the presence of the gD ORF. (Middle panel) EcoRI restriction enzyme digestion of the transposed clones. In some of the clones, the modification of the restriction profile can be observed. (Bottom panel) Southern hybridization of the same clones, with a digoxigenin-labeled transposon-specific probe, where integration of the transposon is demonstrated in all the clones analyzed. The transposon integrated into many different restriction fragments. In the lane marked with an asterisk, the hybridization of the probe to more than one band indicates integration of the transposon into more than one site; this clone was discarded.
Figure Legend Snippet: Construction of BoHV-4 expressing gD. (A) Overall strategy of recombinant BAC-BoHV-4 generation. The transposon complex is assembled with BglII fragments containing RI/RII-CMVgD-Kana-RII/RI and RI/RII-CMVgD-Kana-RII/RI transposons (yellow ends) as donor DNA, BAC-BoHV-4 as a target DNA (blue boxes indicate polyrepetitive DNA, red boxes indicate the BAC plasmid backbone, and the green boxes represent the EGFP expression cassette), and MuA enzyme. The transposition reaction proceeds through an intermediate formation (looped RI/RII-CMVgD-Kana-RII/RI and RI/RII-CMVgD-Kana-RII/RI transposon complexes attached to the target BAC-BoHV-4 DNA) and a final reaction with the target DNA transposed (RI/RII-CMVgD-Kana-RII/RI and RI/RII-CMVgD-Kana-RII/RI transposons, bordered by the two yellow boxes, integrated into the target BAC-BoHV-4 DNA). A flow chart of reconstitution of the BAC-BoHV-4 recombinant is shown. The recombinant plasmids are electroporated into electrocompetent E. coli , the kanamycin-resistant colonies are selected on kanamycin plates, and plasmid DNA is prepared from amplified single colonies and analyzed. (B) Analysis of BAC-BoHV-4 randomly transposed clones (12 clones for RI/RII-CMVgD-Kana-RII/RI, BoHV-4-CMVgD and 12 clones for RI/RII-CMVgDWPRE-Kana-RII/RI, BoHV-4-CMVgDWPRE). (Top panel) PCR analysis demonstrating the presence of the gD ORF. (Middle panel) EcoRI restriction enzyme digestion of the transposed clones. In some of the clones, the modification of the restriction profile can be observed. (Bottom panel) Southern hybridization of the same clones, with a digoxigenin-labeled transposon-specific probe, where integration of the transposon is demonstrated in all the clones analyzed. The transposon integrated into many different restriction fragments. In the lane marked with an asterisk, the hybridization of the probe to more than one band indicates integration of the transposon into more than one site; this clone was discarded.

Techniques Used: Expressing, Recombinant, BAC Assay, Plasmid Preparation, Flow Cytometry, Amplification, Clone Assay, Polymerase Chain Reaction, Modification, Hybridization, Labeling

20) Product Images from "The Role of Protein Kinase A Regulation of the E6 PDZ-Binding Domain during the Differentiation-Dependent Life Cycle of Human Papillomavirus Type 18"

Article Title: The Role of Protein Kinase A Regulation of the E6 PDZ-Binding Domain during the Differentiation-Dependent Life Cycle of Human Papillomavirus Type 18

Journal: Journal of Virology

doi: 10.1128/JVI.01234-13

Stable maintenance of HPV18 episomes is dependent on E6 PBM function but independent of PKA recognition. (A) Southern analysis of equal amounts of total DNA extracted from HFK transfected with wild-type (HPV18-WT) or mutant (HPV18-E6ΔPDZ and HPV18-E6153PKA) genomes upon serial passaging of the cells. To assess for the presence of episomal forms (supercoils and open circles) of the viral genome, the DNA was restricted with the endonuclease BglII, which does not digest the HPV18 genome. To control for the presence of bacterially derived input DNA, the digests included the endonuclease DpnI. Linearized HPV18 genomes are shown as a copy number control (lane C [5 copies per cell]). (B) The E6ΔPDZ genomes establish at a lower copy number in HFK than the WT genomes, as shown by Southern analysis of total DNA taken from three different donors (passages P5 and P6) and digested with EcoRI, which linearizes HPV18 episomes, and DpnI (lane C, 5 copies per cell). (C) Detection of E6 and E7 proteins in equal amounts of NP-40 detergent-soluble protein lysates prepared from cells grown in monolayer cultures or from organotypic raft cultures. Levels of GAPDH were used as a loading control.
Figure Legend Snippet: Stable maintenance of HPV18 episomes is dependent on E6 PBM function but independent of PKA recognition. (A) Southern analysis of equal amounts of total DNA extracted from HFK transfected with wild-type (HPV18-WT) or mutant (HPV18-E6ΔPDZ and HPV18-E6153PKA) genomes upon serial passaging of the cells. To assess for the presence of episomal forms (supercoils and open circles) of the viral genome, the DNA was restricted with the endonuclease BglII, which does not digest the HPV18 genome. To control for the presence of bacterially derived input DNA, the digests included the endonuclease DpnI. Linearized HPV18 genomes are shown as a copy number control (lane C [5 copies per cell]). (B) The E6ΔPDZ genomes establish at a lower copy number in HFK than the WT genomes, as shown by Southern analysis of total DNA taken from three different donors (passages P5 and P6) and digested with EcoRI, which linearizes HPV18 episomes, and DpnI (lane C, 5 copies per cell). (C) Detection of E6 and E7 proteins in equal amounts of NP-40 detergent-soluble protein lysates prepared from cells grown in monolayer cultures or from organotypic raft cultures. Levels of GAPDH were used as a loading control.

Techniques Used: Transfection, Mutagenesis, Passaging, Derivative Assay

Related Articles

Clone Assay:

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
Article Snippet: Paragraph title: Cloning methods ... DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics).

Article Title: A genetic system for targeted mutations to disrupt and restore genes in the obligate bacterium, Ehrlichia chaffeensis
Article Snippet: Mutations and clonal purity was further confirmed by Southern blot analysis of restriction enzyme digested DNAs; genomic DNAs from wild type and mutant organisms were subjected to restriction enzyme digestions using ClaI, EcoRI or HindIII, resolved on a 1% agarose gel and transferred to a nylon membrane (Roche Diagnostics, Indianapolis, IN) . .. Ech_0379 gene segment probe was used for locating the insertion and restoration mutant clones of Ech_0379 .

Article Title: Endo-?-1,4-Glucanase Expression in Compatible Plant-Nematode Interactions
Article Snippet: Each product was digested with both EcoRI and BamHI and cloned into a pBluescript SK+ transcription vector with a truncated multiple cloning site ( ) and flanking T3 and T7 promoter sequences. .. Purified plasmid DNA corresponding to each tobacco riboprobe clone was digested separately with EcoRI and BamHI and column purified, and 1 to 2 μg was added to in vitro transcription reactions containing DIG-UTP (Roche Molecular) and the appropriate polymerase to synthesize RNA probes.

Amplification:

Article Title: A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase
Article Snippet: Samples were prepared by digesting 7.5 μg of gDNA with 100 units of either EcoRI or HindIII to completion, followed by separation in a 1% (wt/wt) agarose gel, and then were transferred to a nylon membrane (Roche Molecular Biochemicals). .. The membrane was probed with a digoxigenin-labeled (Roche Molecular Biochemicals) PCR fragment of PPX2L amplified from gDNA isolated from a single S plant.

Electrophoresis:

Article Title: Molecular Characterization and Lytic Activities of Streptococcus agalactiae Bacteriophages and Determination of Lysogenic-Strain Features ▿
Article Snippet: The phage DNA was digested separately with EcoRI, HindIII, and ClaI (Roche Diagnostic, Meylan, France) by adding 15 μl of DNA to 15 IU of each restriction endonuclease. .. After 3 h of incubation at 37°C, the DNA fragments were separated by electrophoresis in 0.8% agarose gels using a voltage gradient of 50 V over 16 h. Digestion patterns were examined under UV transillumination after staining with ethidium bromide and manually compared.

Article Title: The Facioscapulohumeral muscular dystrophy region on 4qter and the homologous locus on 10qter evolved independently under different evolutionary pressure
Article Snippet: Restriction endonuclease digestion of DNA in agarose blocks and PFGE 1/4 of plug, corresponding to 0.5 × 106 cells, was digested with the following restriction enzymes: EcoRI (Roche, Mannheim, Germany), BlnI (Amersham Pharmacia Biotech, Buckingamshire, U.K.) and XapI (Fermentas). .. PFGE was performed at 10°C in a Pulsaphor Electrophoresis unit with HEX electrode (Pharmacia LKB).

Article Title: Natural history of SLC11 genes in vertebrates: tales from the fish world
Article Snippet: To determine the number of slc11 gene copies in sea bass, 10 μg of genomic DNA were independently digested for 24 h with EcoRI or HindII (Roche Applied Science, Mannhelm, Germany). .. Digestion products were run on an appropriate electrophoresis gel and blotted onto a positively charged nylon membrane (Byodine® Plus Membrane, Pall Life Sciences, Ann Arbor MI, USA).

Incubation:

Article Title: Genotypic comparison of Pantoea agglomerans plant and clinical strains
Article Snippet: Between 200-400 ng genomic DNA from each of the strains was used for each reaction in a mix containing 5 units EcoRI (Roche, Basel, Switzerland), 1 unit of MseI (Roche) and 1 unit of T4 DNA Ligase (Epicentre, Madison, U.S.A.), 5 mM 1,4-Dithio-DL-threitol (DTT) (Sigma-Aldrich, Buchs, Switzerland), 200 μM ATP (Fermentas, St. Leon-Rot, Germany), 50 μg/ml Bovine Serum Albumin (BSA), 0.25 μM of each EcoRI adaptor (EcoRI-F 5'-CTCGTAGACTGCGTACC-3', EcoRI-R 5'-AATTGGTACGCAGTCTAC-3') and 2.5 μM of each MseI adaptor (MseI-F 5'-GACGATGAGTCCTGAG-3', MseI-R 5'-TACTCAGGACTCAT-3') in a total volume of 11.1 μl of 1× One-Phor-All Buffer PLUS (GE Healthcare, Otelfingen, Switzerland). .. The PCR conditions consisted of an initial incubation for 5 min at 72°C to allow Taq DNA polymerase to fill the nick on the ligated DNA strand, followed by 20 cycles of denaturation at 94°C for 30 s, annealing at 56°C for 30 s, plus 2 min of elongation at 72°C, finishing with a final extension for 2 min at 72°C and 30 min incubation at 60°C.

Article Title: Molecular Characterization and Lytic Activities of Streptococcus agalactiae Bacteriophages and Determination of Lysogenic-Strain Features ▿
Article Snippet: The phage DNA was digested separately with EcoRI, HindIII, and ClaI (Roche Diagnostic, Meylan, France) by adding 15 μl of DNA to 15 IU of each restriction endonuclease. .. After 3 h of incubation at 37°C, the DNA fragments were separated by electrophoresis in 0.8% agarose gels using a voltage gradient of 50 V over 16 h. Digestion patterns were examined under UV transillumination after staining with ethidium bromide and manually compared.

Article Title: The Facioscapulohumeral muscular dystrophy region on 4qter and the homologous locus on 10qter evolved independently under different evolutionary pressure
Article Snippet: Restriction endonuclease digestion of DNA in agarose blocks and PFGE 1/4 of plug, corresponding to 0.5 × 106 cells, was digested with the following restriction enzymes: EcoRI (Roche, Mannheim, Germany), BlnI (Amersham Pharmacia Biotech, Buckingamshire, U.K.) and XapI (Fermentas). .. Single (EcoRI, XapI) and double digestions (EcoRI/BlnI) were performed with 60/150 U of enzyme added in three equal portions, at 1h intervals and incubated overnight.

Article Title: The Chromosomal Association of the Smc5/6 Complex Depends on Cohesion and Predicts the Level of Sister Chromatid Entanglement
Article Snippet: Digestion was performed using PstI-HF (New England Biolabs) for the loci UBP10-MRPL19 and MPP10-YJR003C , and EcoRI and HindIII (Roche) for ARS305 locus. .. The DNA was then precipitated by the addition of 2 volumes ethanol containing 0.5 M potassium acetate and incubated at −80°C for 30 minutes.

Article Title: Sex Pheromone Response, Clumping, and Slime Production in Enterococcal Strains Isolated from Occluded Biliary Stents
Article Snippet: The pellet was resuspended in 1 ml of lysis buffer and incubated at 60°C for 1 h. The temperature was then raised to 95°C for 10 min for proteinase K inactivation and DNA denaturation. .. EcoRI, DraI, and ScaI (Roche Molecular Biochemicals, Mannheim, Germany) restriction enzymes were used in accordance with the manufacturer's instructions.

Gel Extraction:

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
Article Snippet: .. DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics). .. Cloning of parts was assessed by T4 Ligase and ligation products were heated at 65°C for 10 min to inactivate T4 Ligase before proceeding with heat shock transformation.

Modification:

Article Title: Genotypic comparison of Pantoea agglomerans plant and clinical strains
Article Snippet: fAFLP analysis The fAFLP pattern of strains identified by sequencing as P. agglomerans sensu stricto (in the stricter sense taxonomically) was carried out following standard protocols with minor modification [ - ]. .. Between 200-400 ng genomic DNA from each of the strains was used for each reaction in a mix containing 5 units EcoRI (Roche, Basel, Switzerland), 1 unit of MseI (Roche) and 1 unit of T4 DNA Ligase (Epicentre, Madison, U.S.A.), 5 mM 1,4-Dithio-DL-threitol (DTT) (Sigma-Aldrich, Buchs, Switzerland), 200 μM ATP (Fermentas, St. Leon-Rot, Germany), 50 μg/ml Bovine Serum Albumin (BSA), 0.25 μM of each EcoRI adaptor (EcoRI-F 5'-CTCGTAGACTGCGTACC-3', EcoRI-R 5'-AATTGGTACGCAGTCTAC-3') and 2.5 μM of each MseI adaptor (MseI-F 5'-GACGATGAGTCCTGAG-3', MseI-R 5'-TACTCAGGACTCAT-3') in a total volume of 11.1 μl of 1× One-Phor-All Buffer PLUS (GE Healthcare, Otelfingen, Switzerland).

Planar Chromatography:

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
Article Snippet: All the strains were routinely grown at 37°C in selective LB medium [ ] with Ampicillin (100 μg/ml) or Chloramphenicol (12.5 μg/ml) to propagate plasmids, except pLC-T4LysHeat that was grown at 30°C to avoid heat-induction of lysis genes. .. DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics).

Transformation Assay:

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
Article Snippet: MG1655 were made chemically competent with the protocol described in [ ] and they were heat-shock transformed at 42°C with the required plasmid. .. DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics).

Hybridization:

Article Title: A genetic system for targeted mutations to disrupt and restore genes in the obligate bacterium, Ehrlichia chaffeensis
Article Snippet: Mutations and clonal purity was further confirmed by Southern blot analysis of restriction enzyme digested DNAs; genomic DNAs from wild type and mutant organisms were subjected to restriction enzyme digestions using ClaI, EcoRI or HindIII, resolved on a 1% agarose gel and transferred to a nylon membrane (Roche Diagnostics, Indianapolis, IN) . .. The insertion specific aadA gene segment probe was used in the blot hybridization experiment to locate inserted DNA in targeted disrupted mutants of Ech_0230 and Ech_0379.

Southern Blot:

Article Title: A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase
Article Snippet: Paragraph title: Southern Blot Analysis. ... Samples were prepared by digesting 7.5 μg of gDNA with 100 units of either EcoRI or HindIII to completion, followed by separation in a 1% (wt/wt) agarose gel, and then were transferred to a nylon membrane (Roche Molecular Biochemicals).

Article Title: A genetic system for targeted mutations to disrupt and restore genes in the obligate bacterium, Ehrlichia chaffeensis
Article Snippet: .. Mutations and clonal purity was further confirmed by Southern blot analysis of restriction enzyme digested DNAs; genomic DNAs from wild type and mutant organisms were subjected to restriction enzyme digestions using ClaI, EcoRI or HindIII, resolved on a 1% agarose gel and transferred to a nylon membrane (Roche Diagnostics, Indianapolis, IN) . .. The insertion specific aadA gene segment probe was used in the blot hybridization experiment to locate inserted DNA in targeted disrupted mutants of Ech_0230 and Ech_0379.

Article Title: Natural history of SLC11 genes in vertebrates: tales from the fish world
Article Snippet: Paragraph title: Southern blot assay ... To determine the number of slc11 gene copies in sea bass, 10 μg of genomic DNA were independently digested for 24 h with EcoRI or HindII (Roche Applied Science, Mannhelm, Germany).

Ligation:

Article Title: Genotypic comparison of Pantoea agglomerans plant and clinical strains
Article Snippet: Digestion of genomic DNA and ligation to the restriction enzyme adaptors was performed simultaneously since a base-change incorporated into the adaptors sequences hindered restoration of the original restriction enzyme site upon ligation. .. Between 200-400 ng genomic DNA from each of the strains was used for each reaction in a mix containing 5 units EcoRI (Roche, Basel, Switzerland), 1 unit of MseI (Roche) and 1 unit of T4 DNA Ligase (Epicentre, Madison, U.S.A.), 5 mM 1,4-Dithio-DL-threitol (DTT) (Sigma-Aldrich, Buchs, Switzerland), 200 μM ATP (Fermentas, St. Leon-Rot, Germany), 50 μg/ml Bovine Serum Albumin (BSA), 0.25 μM of each EcoRI adaptor (EcoRI-F 5'-CTCGTAGACTGCGTACC-3', EcoRI-R 5'-AATTGGTACGCAGTCTAC-3') and 2.5 μM of each MseI adaptor (MseI-F 5'-GACGATGAGTCCTGAG-3', MseI-R 5'-TACTCAGGACTCAT-3') in a total volume of 11.1 μl of 1× One-Phor-All Buffer PLUS (GE Healthcare, Otelfingen, Switzerland).

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
Article Snippet: DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics). .. Cloning of parts was assessed by T4 Ligase and ligation products were heated at 65°C for 10 min to inactivate T4 Ligase before proceeding with heat shock transformation.

other:

Article Title: RNAi-based conditional gene knockdown in mice using a U6 promoter driven vector
Article Snippet: Reagents DNA oligonucleotides Distilled sterilized water (dH2 O) TE buffer (10 mM Tris-Cl/1 mM EDTA, pH 7.4) Low-TE buffer (1 mM Tris-Cl/0.1 mM EDTA, pH 7.4) ApaI, EcoRI, SalI, Not I, Asp 718, Afl III restriction enzymes (Roche) DNA polymerase I, large fragment (Klenow) (New England Biolabs) T4 DNA polymerase (New England Biolabs) MinElute Reaction Cleanup kit (Qiagen) Qiaprep Spin Miniprep kit (Qiagen) Dneasy kit (Qiagen) LB media (Add the following to 800 ml H2 O (10 g Bacto-tryptone, 5 g yeast extract, 10 g NaCl).

Sequencing:

Article Title: Genotypic comparison of Pantoea agglomerans plant and clinical strains
Article Snippet: fAFLP analysis The fAFLP pattern of strains identified by sequencing as P. agglomerans sensu stricto (in the stricter sense taxonomically) was carried out following standard protocols with minor modification [ - ]. .. Between 200-400 ng genomic DNA from each of the strains was used for each reaction in a mix containing 5 units EcoRI (Roche, Basel, Switzerland), 1 unit of MseI (Roche) and 1 unit of T4 DNA Ligase (Epicentre, Madison, U.S.A.), 5 mM 1,4-Dithio-DL-threitol (DTT) (Sigma-Aldrich, Buchs, Switzerland), 200 μM ATP (Fermentas, St. Leon-Rot, Germany), 50 μg/ml Bovine Serum Albumin (BSA), 0.25 μM of each EcoRI adaptor (EcoRI-F 5'-CTCGTAGACTGCGTACC-3', EcoRI-R 5'-AATTGGTACGCAGTCTAC-3') and 2.5 μM of each MseI adaptor (MseI-F 5'-GACGATGAGTCCTGAG-3', MseI-R 5'-TACTCAGGACTCAT-3') in a total volume of 11.1 μl of 1× One-Phor-All Buffer PLUS (GE Healthcare, Otelfingen, Switzerland).

Article Title: A genetic system for targeted mutations to disrupt and restore genes in the obligate bacterium, Ehrlichia chaffeensis
Article Snippet: PCR products were resolved on a 0.9% agarose gel to identify specific predicted amplicons and then subjected to sequencing analysis to map the genomic junctions of the insertions from both ends of the amplicons. .. Mutations and clonal purity was further confirmed by Southern blot analysis of restriction enzyme digested DNAs; genomic DNAs from wild type and mutant organisms were subjected to restriction enzyme digestions using ClaI, EcoRI or HindIII, resolved on a 1% agarose gel and transferred to a nylon membrane (Roche Diagnostics, Indianapolis, IN) .

Pulsed-Field Gel:

Article Title: Naturally Occurring DNA Transfer System Associated with Membrane Vesicles in Cellulolytic Ruminococcus spp. of Ruminal Origin
Article Snippet: The conditions used for digestion of isolated nucleic acids by DNase I and RNase A (Roche, Mannheim, Germany) and with restriction endonucleases HindIII and EcoRI and for digestion of PCR products with CfoI, MspI, and HaeIII were the conditions specified by the manufacturer (Roche). .. Pulsed-field gel electrophoresis (PFGE) was performed as previously described , except that the machine used was a contour-clamped homogeneous electric field (Bio-Rad, Hercules, CA).

DNA Extraction:

Article Title: Molecular Characterization and Lytic Activities of Streptococcus agalactiae Bacteriophages and Determination of Lysogenic-Strain Features ▿
Article Snippet: Phage DNA isolation and purification were carried out with a Lambda Minikit (Qiagen, Valencia, CA). .. The phage DNA was digested separately with EcoRI, HindIII, and ClaI (Roche Diagnostic, Meylan, France) by adding 15 μl of DNA to 15 IU of each restriction endonuclease.

Article Title: The Chromosomal Association of the Smc5/6 Complex Depends on Cohesion and Predicts the Level of Sister Chromatid Entanglement
Article Snippet: Two-dimensional gel electrophoresis Genomic DNA isolation to study replication intermediates was performed according to . .. Digestion was performed using PstI-HF (New England Biolabs) for the loci UBP10-MRPL19 and MPP10-YJR003C , and EcoRI and HindIII (Roche) for ARS305 locus.

Article Title: Sex Pheromone Response, Clumping, and Slime Production in Enterococcal Strains Isolated from Occluded Biliary Stents
Article Snippet: For total DNA extraction, the strains were grown overnight in BHI broth containing 0.5% glycine at 37°C. .. EcoRI, DraI, and ScaI (Roche Molecular Biochemicals, Mannheim, Germany) restriction enzymes were used in accordance with the manufacturer's instructions.

Nucleic Acid Electrophoresis:

Article Title: Sex Pheromone Response, Clumping, and Slime Production in Enterococcal Strains Isolated from Occluded Biliary Stents
Article Snippet: EcoRI, DraI, and ScaI (Roche Molecular Biochemicals, Mannheim, Germany) restriction enzymes were used in accordance with the manufacturer's instructions. .. The DNA restriction fragments were separated by agarose (1%) gel electrophoresis and visualized by ethidium bromide staining.

Mutagenesis:

Article Title: A genetic system for targeted mutations to disrupt and restore genes in the obligate bacterium, Ehrlichia chaffeensis
Article Snippet: .. Mutations and clonal purity was further confirmed by Southern blot analysis of restriction enzyme digested DNAs; genomic DNAs from wild type and mutant organisms were subjected to restriction enzyme digestions using ClaI, EcoRI or HindIII, resolved on a 1% agarose gel and transferred to a nylon membrane (Roche Diagnostics, Indianapolis, IN) . .. The insertion specific aadA gene segment probe was used in the blot hybridization experiment to locate inserted DNA in targeted disrupted mutants of Ech_0230 and Ech_0379.

Isolation:

Article Title: Molecular Characterization and Lytic Activities of Streptococcus agalactiae Bacteriophages and Determination of Lysogenic-Strain Features ▿
Article Snippet: Paragraph title: (ii) Molecular characterization of isolated phages. (a) REA. ... The phage DNA was digested separately with EcoRI, HindIII, and ClaI (Roche Diagnostic, Meylan, France) by adding 15 μl of DNA to 15 IU of each restriction endonuclease.

Article Title: The Chromosomal Association of the Smc5/6 Complex Depends on Cohesion and Predicts the Level of Sister Chromatid Entanglement
Article Snippet: Isolation of genomic DNA with CTAB extraction to preserve X-shape structures was performed according to . .. Digestion was performed using PstI-HF (New England Biolabs) for the loci UBP10-MRPL19 and MPP10-YJR003C , and EcoRI and HindIII (Roche) for ARS305 locus.

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
Article Snippet: .. DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics). .. Cloning of parts was assessed by T4 Ligase and ligation products were heated at 65°C for 10 min to inactivate T4 Ligase before proceeding with heat shock transformation.

Article Title: A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase
Article Snippet: gDNA was isolated from young leaves of A. tuberculatus plants from the S or R biotypes ( ). .. Samples were prepared by digesting 7.5 μg of gDNA with 100 units of either EcoRI or HindIII to completion, followed by separation in a 1% (wt/wt) agarose gel, and then were transferred to a nylon membrane (Roche Molecular Biochemicals).

Article Title: Natural history of SLC11 genes in vertebrates: tales from the fish world
Article Snippet: Southern blot assay Genomic DNA was isolated from sea bass red blood cells, as described elsewhere [ ]. .. To determine the number of slc11 gene copies in sea bass, 10 μg of genomic DNA were independently digested for 24 h with EcoRI or HindII (Roche Applied Science, Mannhelm, Germany).

Article Title: Naturally Occurring DNA Transfer System Associated with Membrane Vesicles in Cellulolytic Ruminococcus spp. of Ruminal Origin
Article Snippet: .. The conditions used for digestion of isolated nucleic acids by DNase I and RNase A (Roche, Mannheim, Germany) and with restriction endonucleases HindIII and EcoRI and for digestion of PCR products with CfoI, MspI, and HaeIII were the conditions specified by the manufacturer (Roche). ..

Labeling:

Article Title: Natural history of SLC11 genes in vertebrates: tales from the fish world
Article Snippet: To determine the number of slc11 gene copies in sea bass, 10 μg of genomic DNA were independently digested for 24 h with EcoRI or HindII (Roche Applied Science, Mannhelm, Germany). .. Briefly, a 152 bp slc11 DIG labeled probe was prepared with the DIG Probe Synthesis Kit (Roche Applied Science), using primers designed based on other fish slc11 mRNA sequences (supplementary table S1), the membrane was hybridized at 55°C, washed, and detection was performed with the chemiluminescent substrate CDP-Star (Roche Applied Science).

Purification:

Article Title: Molecular Characterization and Lytic Activities of Streptococcus agalactiae Bacteriophages and Determination of Lysogenic-Strain Features ▿
Article Snippet: Phage DNA isolation and purification were carried out with a Lambda Minikit (Qiagen, Valencia, CA). .. The phage DNA was digested separately with EcoRI, HindIII, and ClaI (Roche Diagnostic, Meylan, France) by adding 15 μl of DNA to 15 IU of each restriction endonuclease.

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
Article Snippet: Plasmids have been purified through QIAprep Spin Miniprep kit (Qiagen) from 5 ml overnight cultures. .. DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics).

Article Title: Endo-?-1,4-Glucanase Expression in Compatible Plant-Nematode Interactions
Article Snippet: .. Purified plasmid DNA corresponding to each tobacco riboprobe clone was digested separately with EcoRI and BamHI and column purified, and 1 to 2 μg was added to in vitro transcription reactions containing DIG-UTP (Roche Molecular) and the appropriate polymerase to synthesize RNA probes. .. Unincorporated nucleotides were removed using mini Quick Spin RNA columns (Roche Molecular), and the incorporation of DIG-UTP was quantified by dot blot analysis.

Article Title: Naturally Occurring DNA Transfer System Associated with Membrane Vesicles in Cellulolytic Ruminococcus spp. of Ruminal Origin
Article Snippet: Nucleic acid was isolated and purified from concentrated samples by using standard methods ( ). .. The conditions used for digestion of isolated nucleic acids by DNase I and RNase A (Roche, Mannheim, Germany) and with restriction endonucleases HindIII and EcoRI and for digestion of PCR products with CfoI, MspI, and HaeIII were the conditions specified by the manufacturer (Roche).

Dot Blot:

Article Title: Endo-?-1,4-Glucanase Expression in Compatible Plant-Nematode Interactions
Article Snippet: Purified plasmid DNA corresponding to each tobacco riboprobe clone was digested separately with EcoRI and BamHI and column purified, and 1 to 2 μg was added to in vitro transcription reactions containing DIG-UTP (Roche Molecular) and the appropriate polymerase to synthesize RNA probes. .. Unincorporated nucleotides were removed using mini Quick Spin RNA columns (Roche Molecular), and the incorporation of DIG-UTP was quantified by dot blot analysis.

Polymerase Chain Reaction:

Article Title: Genotypic comparison of Pantoea agglomerans plant and clinical strains
Article Snippet: Between 200-400 ng genomic DNA from each of the strains was used for each reaction in a mix containing 5 units EcoRI (Roche, Basel, Switzerland), 1 unit of MseI (Roche) and 1 unit of T4 DNA Ligase (Epicentre, Madison, U.S.A.), 5 mM 1,4-Dithio-DL-threitol (DTT) (Sigma-Aldrich, Buchs, Switzerland), 200 μM ATP (Fermentas, St. Leon-Rot, Germany), 50 μg/ml Bovine Serum Albumin (BSA), 0.25 μM of each EcoRI adaptor (EcoRI-F 5'-CTCGTAGACTGCGTACC-3', EcoRI-R 5'-AATTGGTACGCAGTCTAC-3') and 2.5 μM of each MseI adaptor (MseI-F 5'-GACGATGAGTCCTGAG-3', MseI-R 5'-TACTCAGGACTCAT-3') in a total volume of 11.1 μl of 1× One-Phor-All Buffer PLUS (GE Healthcare, Otelfingen, Switzerland). .. The PCR mix contained 1 unit Taq DNA polymerase (Promega), 0.2 mM dNTPs and 0.3 μM of each primer in 1× Taq DNA polymerase buffer (MgCl2 1.5 mM) (Promega).

Article Title: A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase
Article Snippet: Samples were prepared by digesting 7.5 μg of gDNA with 100 units of either EcoRI or HindIII to completion, followed by separation in a 1% (wt/wt) agarose gel, and then were transferred to a nylon membrane (Roche Molecular Biochemicals). .. The membrane was probed with a digoxigenin-labeled (Roche Molecular Biochemicals) PCR fragment of PPX2L amplified from gDNA isolated from a single S plant.

Article Title: A genetic system for targeted mutations to disrupt and restore genes in the obligate bacterium, Ehrlichia chaffeensis
Article Snippet: PCR products were resolved on a 0.9% agarose gel to identify specific predicted amplicons and then subjected to sequencing analysis to map the genomic junctions of the insertions from both ends of the amplicons. .. Mutations and clonal purity was further confirmed by Southern blot analysis of restriction enzyme digested DNAs; genomic DNAs from wild type and mutant organisms were subjected to restriction enzyme digestions using ClaI, EcoRI or HindIII, resolved on a 1% agarose gel and transferred to a nylon membrane (Roche Diagnostics, Indianapolis, IN) .

Article Title: Sex Pheromone Response, Clumping, and Slime Production in Enterococcal Strains Isolated from Occluded Biliary Stents
Article Snippet: Paragraph title: PCR and restriction analysis of PCR products. ... EcoRI, DraI, and ScaI (Roche Molecular Biochemicals, Mannheim, Germany) restriction enzymes were used in accordance with the manufacturer's instructions.

Article Title: Naturally Occurring DNA Transfer System Associated with Membrane Vesicles in Cellulolytic Ruminococcus spp. of Ruminal Origin
Article Snippet: .. The conditions used for digestion of isolated nucleic acids by DNase I and RNase A (Roche, Mannheim, Germany) and with restriction endonucleases HindIII and EcoRI and for digestion of PCR products with CfoI, MspI, and HaeIII were the conditions specified by the manufacturer (Roche). ..

Lysis:

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
Article Snippet: All the strains were routinely grown at 37°C in selective LB medium [ ] with Ampicillin (100 μg/ml) or Chloramphenicol (12.5 μg/ml) to propagate plasmids, except pLC-T4LysHeat that was grown at 30°C to avoid heat-induction of lysis genes. .. DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics).

Article Title: Sex Pheromone Response, Clumping, and Slime Production in Enterococcal Strains Isolated from Occluded Biliary Stents
Article Snippet: The pellet was resuspended in 1 ml of lysis buffer and incubated at 60°C for 1 h. The temperature was then raised to 95°C for 10 min for proteinase K inactivation and DNA denaturation. .. EcoRI, DraI, and ScaI (Roche Molecular Biochemicals, Mannheim, Germany) restriction enzymes were used in accordance with the manufacturer's instructions.

Plasmid Preparation:

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
Article Snippet: For every plasmid, 750 μl of culture were mixed with 250 μl of sterile 80% glycerol solution for long-term storage at -80°C. .. DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics).

Article Title: Endo-?-1,4-Glucanase Expression in Compatible Plant-Nematode Interactions
Article Snippet: .. Purified plasmid DNA corresponding to each tobacco riboprobe clone was digested separately with EcoRI and BamHI and column purified, and 1 to 2 μg was added to in vitro transcription reactions containing DIG-UTP (Roche Molecular) and the appropriate polymerase to synthesize RNA probes. .. Unincorporated nucleotides were removed using mini Quick Spin RNA columns (Roche Molecular), and the incorporation of DIG-UTP was quantified by dot blot analysis.

Agarose Gel Electrophoresis:

Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
Article Snippet: .. DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics). .. Cloning of parts was assessed by T4 Ligase and ligation products were heated at 65°C for 10 min to inactivate T4 Ligase before proceeding with heat shock transformation.

Article Title: A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase
Article Snippet: .. Samples were prepared by digesting 7.5 μg of gDNA with 100 units of either EcoRI or HindIII to completion, followed by separation in a 1% (wt/wt) agarose gel, and then were transferred to a nylon membrane (Roche Molecular Biochemicals). .. The membrane was probed with a digoxigenin-labeled (Roche Molecular Biochemicals) PCR fragment of PPX2L amplified from gDNA isolated from a single S plant.

Article Title: A genetic system for targeted mutations to disrupt and restore genes in the obligate bacterium, Ehrlichia chaffeensis
Article Snippet: .. Mutations and clonal purity was further confirmed by Southern blot analysis of restriction enzyme digested DNAs; genomic DNAs from wild type and mutant organisms were subjected to restriction enzyme digestions using ClaI, EcoRI or HindIII, resolved on a 1% agarose gel and transferred to a nylon membrane (Roche Diagnostics, Indianapolis, IN) . .. The insertion specific aadA gene segment probe was used in the blot hybridization experiment to locate inserted DNA in targeted disrupted mutants of Ech_0230 and Ech_0379.

In Vitro:

Article Title: Endo-?-1,4-Glucanase Expression in Compatible Plant-Nematode Interactions
Article Snippet: .. Purified plasmid DNA corresponding to each tobacco riboprobe clone was digested separately with EcoRI and BamHI and column purified, and 1 to 2 μg was added to in vitro transcription reactions containing DIG-UTP (Roche Molecular) and the appropriate polymerase to synthesize RNA probes. .. Unincorporated nucleotides were removed using mini Quick Spin RNA columns (Roche Molecular), and the incorporation of DIG-UTP was quantified by dot blot analysis.

Two-Dimensional Gel Electrophoresis:

Article Title: The Chromosomal Association of the Smc5/6 Complex Depends on Cohesion and Predicts the Level of Sister Chromatid Entanglement
Article Snippet: Paragraph title: Two-dimensional gel electrophoresis ... Digestion was performed using PstI-HF (New England Biolabs) for the loci UBP10-MRPL19 and MPP10-YJR003C , and EcoRI and HindIII (Roche) for ARS305 locus.

Marker:

Article Title: Sex Pheromone Response, Clumping, and Slime Production in Enterococcal Strains Isolated from Occluded Biliary Stents
Article Snippet: EcoRI, DraI, and ScaI (Roche Molecular Biochemicals, Mannheim, Germany) restriction enzymes were used in accordance with the manufacturer's instructions. .. The molecular size marker (GeneRulerTM 100-bp DNA Ladder Plus) was from M-Medical Genenco (Cornaredo, Italy).

Article Title: Naturally Occurring DNA Transfer System Associated with Membrane Vesicles in Cellulolytic Ruminococcus spp. of Ruminal Origin
Article Snippet: The conditions used for digestion of isolated nucleic acids by DNase I and RNase A (Roche, Mannheim, Germany) and with restriction endonucleases HindIII and EcoRI and for digestion of PCR products with CfoI, MspI, and HaeIII were the conditions specified by the manufacturer (Roche). .. DNA size was determined by comparison with a HindIII digest of phage λ or a 100-bp DNA size marker (Roche).

Staining:

Article Title: Molecular Characterization and Lytic Activities of Streptococcus agalactiae Bacteriophages and Determination of Lysogenic-Strain Features ▿
Article Snippet: The phage DNA was digested separately with EcoRI, HindIII, and ClaI (Roche Diagnostic, Meylan, France) by adding 15 μl of DNA to 15 IU of each restriction endonuclease. .. After 3 h of incubation at 37°C, the DNA fragments were separated by electrophoresis in 0.8% agarose gels using a voltage gradient of 50 V over 16 h. Digestion patterns were examined under UV transillumination after staining with ethidium bromide and manually compared.

Article Title: Sex Pheromone Response, Clumping, and Slime Production in Enterococcal Strains Isolated from Occluded Biliary Stents
Article Snippet: EcoRI, DraI, and ScaI (Roche Molecular Biochemicals, Mannheim, Germany) restriction enzymes were used in accordance with the manufacturer's instructions. .. The DNA restriction fragments were separated by agarose (1%) gel electrophoresis and visualized by ethidium bromide staining.

Fluorescence In Situ Hybridization:

Article Title: Natural history of SLC11 genes in vertebrates: tales from the fish world
Article Snippet: To determine the number of slc11 gene copies in sea bass, 10 μg of genomic DNA were independently digested for 24 h with EcoRI or HindII (Roche Applied Science, Mannhelm, Germany). .. Briefly, a 152 bp slc11 DIG labeled probe was prepared with the DIG Probe Synthesis Kit (Roche Applied Science), using primers designed based on other fish slc11 mRNA sequences (supplementary table S1), the membrane was hybridized at 55°C, washed, and detection was performed with the chemiluminescent substrate CDP-Star (Roche Applied Science).

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • ecori  (Roche)
    94
    Roche ecori
    <t>DNA</t> Gel Blot Analysis of Ntcel2 , Ntcel7 , and Ntcel8 Genes in Tobacco. Genomic DNA (5 μg) was digested with BamHI (B), <t>EcoRI</t> (E), and HindIII (H), electrophoresed on a 0.7% agarose gel, blotted to nylon membranes, and probed with a 1-kb fragment spanning the conserved amino acid domains CWERPED and YINAPL of Ntcel2 , Ntcel7 , and Ntcel8 . Blots were hybridized in 5 × SSC at 65°C and washed twice in 0.5 × SSC at 68°C and twice in 0.1 × SSC at 68°C. L, 1-kb DNA ladder (Gibco BRL).
    Ecori, supplied by Roche, used in various techniques. Bioz Stars score: 94/100, based on 70 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecori/product/Roche
    Average 94 stars, based on 70 article reviews
    Price from $9.99 to $1999.99
    ecori - by Bioz Stars, 2020-04
    94/100 stars
      Buy from Supplier

    Image Search Results


    DNA Gel Blot Analysis of Ntcel2 , Ntcel7 , and Ntcel8 Genes in Tobacco. Genomic DNA (5 μg) was digested with BamHI (B), EcoRI (E), and HindIII (H), electrophoresed on a 0.7% agarose gel, blotted to nylon membranes, and probed with a 1-kb fragment spanning the conserved amino acid domains CWERPED and YINAPL of Ntcel2 , Ntcel7 , and Ntcel8 . Blots were hybridized in 5 × SSC at 65°C and washed twice in 0.5 × SSC at 68°C and twice in 0.1 × SSC at 68°C. L, 1-kb DNA ladder (Gibco BRL).

    Journal: The Plant Cell

    Article Title: Endo-?-1,4-Glucanase Expression in Compatible Plant-Nematode Interactions

    doi: 10.1105/tpc.010219

    Figure Lengend Snippet: DNA Gel Blot Analysis of Ntcel2 , Ntcel7 , and Ntcel8 Genes in Tobacco. Genomic DNA (5 μg) was digested with BamHI (B), EcoRI (E), and HindIII (H), electrophoresed on a 0.7% agarose gel, blotted to nylon membranes, and probed with a 1-kb fragment spanning the conserved amino acid domains CWERPED and YINAPL of Ntcel2 , Ntcel7 , and Ntcel8 . Blots were hybridized in 5 × SSC at 65°C and washed twice in 0.5 × SSC at 68°C and twice in 0.1 × SSC at 68°C. L, 1-kb DNA ladder (Gibco BRL).

    Article Snippet: Purified plasmid DNA corresponding to each tobacco riboprobe clone was digested separately with EcoRI and BamHI and column purified, and 1 to 2 μg was added to in vitro transcription reactions containing DIG-UTP (Roche Molecular) and the appropriate polymerase to synthesize RNA probes.

    Techniques: Western Blot, Agarose Gel Electrophoresis

    Southern blot analysis . 10 μg of genomic DNA were independently digested with EcoRI or HindII and hybridized with a DIG-labelled slc11 RNA probe. Molecular weights (bp) are indicated in the left margin.

    Journal: BMC Evolutionary Biology

    Article Title: Natural history of SLC11 genes in vertebrates: tales from the fish world

    doi: 10.1186/1471-2148-11-106

    Figure Lengend Snippet: Southern blot analysis . 10 μg of genomic DNA were independently digested with EcoRI or HindII and hybridized with a DIG-labelled slc11 RNA probe. Molecular weights (bp) are indicated in the left margin.

    Article Snippet: To determine the number of slc11 gene copies in sea bass, 10 μg of genomic DNA were independently digested for 24 h with EcoRI or HindII (Roche Applied Science, Mannhelm, Germany).

    Techniques: Southern Blot

    Mutations occurred in the insert of pLC-T4LysHSL in mutant clones . Unmutated BBa_K173015 (A); luxR disruption mediated by IS10R (B); luxR disruption mediated by IS10R (insertion in reverse direction relative to (B)) (C); deletion of the DNA fragment flanked by BBa_B0015, containing the lux promoter and the holin and lysozyme genes (D); two different mutated plasmids in the same clone: insertion of IS10R and IS5 (containing an EcoRI restriction site) upstream of the first nucleotide of BBa_B0034 RBS and luxR , respectively (E); t gene disruption mediated by IS10R (insertion in reverse direction relative to (B)) (F). The number under the parts denotes the nucleotide of the basic part flanking the insertion sequence that has disrupted the part. The disrupted genes are luxR (BBa_C0062), encoding the transcriptional activator of lux promoter (BBa_R0062), and t (BBa_K112805), encoding the holin. Part codes are given according to the Registry of Standard Biological Parts.

    Journal: Journal of Biological Engineering

    Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release

    doi: 10.1186/1754-1611-5-8

    Figure Lengend Snippet: Mutations occurred in the insert of pLC-T4LysHSL in mutant clones . Unmutated BBa_K173015 (A); luxR disruption mediated by IS10R (B); luxR disruption mediated by IS10R (insertion in reverse direction relative to (B)) (C); deletion of the DNA fragment flanked by BBa_B0015, containing the lux promoter and the holin and lysozyme genes (D); two different mutated plasmids in the same clone: insertion of IS10R and IS5 (containing an EcoRI restriction site) upstream of the first nucleotide of BBa_B0034 RBS and luxR , respectively (E); t gene disruption mediated by IS10R (insertion in reverse direction relative to (B)) (F). The number under the parts denotes the nucleotide of the basic part flanking the insertion sequence that has disrupted the part. The disrupted genes are luxR (BBa_C0062), encoding the transcriptional activator of lux promoter (BBa_R0062), and t (BBa_K112805), encoding the holin. Part codes are given according to the Registry of Standard Biological Parts.

    Article Snippet: DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics).

    Techniques: Planar Chromatography, Mutagenesis, Clone Assay, Sequencing

    Restriction analysis of pLC-T4LysHSL mutants . Plasmid DNA was digested with EcoRI and PstI. In all the screened clones two bands (vector backbone and insert) are present except in colony 1 of mut sc2 , in which four bands can be observed. The expected vector backbone (~3.2 kbp) is present in all the clones, demonstrating that deletions or insertions occurred only in the insert, while all the mutated insert bands are clearly different from the unmutated culture (~2.8 kbp). As sequencing showed, colony 1 of mut sc2 had plasmids with two different mutated inserts in the same clone, one of which containing an EcoRI restriction site that, when digested, produces 2 bands.

    Journal: Journal of Biological Engineering

    Article Title: Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release

    doi: 10.1186/1754-1611-5-8

    Figure Lengend Snippet: Restriction analysis of pLC-T4LysHSL mutants . Plasmid DNA was digested with EcoRI and PstI. In all the screened clones two bands (vector backbone and insert) are present except in colony 1 of mut sc2 , in which four bands can be observed. The expected vector backbone (~3.2 kbp) is present in all the clones, demonstrating that deletions or insertions occurred only in the insert, while all the mutated insert bands are clearly different from the unmutated culture (~2.8 kbp). As sequencing showed, colony 1 of mut sc2 had plasmids with two different mutated inserts in the same clone, one of which containing an EcoRI restriction site that, when digested, produces 2 bands.

    Article Snippet: DNA was digested with EcoRI, XbaI, SpeI or PstI according to BioBrick™ Standard Assembly procedure [ ] and isolated from 1% agarose gel by Gel Extraction Kit (Roche Diagnostics).

    Techniques: Planar Chromatography, Plasmid Preparation, Clone Assay, Sequencing

    The fAFLP pattern generated with EcoRI-G and MseI-G primers from different biocontrol, environmental and clinical P. agglomerans isolates . ( A ) C9-1, ( B ) CIP 82.100, ( C ) P10c, ( D ) Eh325, ( E ) EM21cb, ( F ) EM22cb, ( G ) CIP A181. Biocontrol strain P. agglomerans C9-1 showed a completely divergent fAFLP pattern with respect to the other isolates of the species. The 490-bp band which was prevalent in biocontrol and environmental isolates, but was absent from clinical isolates and from strain C9-1 is indicated by the arrow.

    Journal: BMC Microbiology

    Article Title: Genotypic comparison of Pantoea agglomerans plant and clinical strains

    doi: 10.1186/1471-2180-9-204

    Figure Lengend Snippet: The fAFLP pattern generated with EcoRI-G and MseI-G primers from different biocontrol, environmental and clinical P. agglomerans isolates . ( A ) C9-1, ( B ) CIP 82.100, ( C ) P10c, ( D ) Eh325, ( E ) EM21cb, ( F ) EM22cb, ( G ) CIP A181. Biocontrol strain P. agglomerans C9-1 showed a completely divergent fAFLP pattern with respect to the other isolates of the species. The 490-bp band which was prevalent in biocontrol and environmental isolates, but was absent from clinical isolates and from strain C9-1 is indicated by the arrow.

    Article Snippet: Between 200-400 ng genomic DNA from each of the strains was used for each reaction in a mix containing 5 units EcoRI (Roche, Basel, Switzerland), 1 unit of MseI (Roche) and 1 unit of T4 DNA Ligase (Epicentre, Madison, U.S.A.), 5 mM 1,4-Dithio-DL-threitol (DTT) (Sigma-Aldrich, Buchs, Switzerland), 200 μM ATP (Fermentas, St. Leon-Rot, Germany), 50 μg/ml Bovine Serum Albumin (BSA), 0.25 μM of each EcoRI adaptor (EcoRI-F 5'-CTCGTAGACTGCGTACC-3', EcoRI-R 5'-AATTGGTACGCAGTCTAC-3') and 2.5 μM of each MseI adaptor (MseI-F 5'-GACGATGAGTCCTGAG-3', MseI-R 5'-TACTCAGGACTCAT-3') in a total volume of 11.1 μl of 1× One-Phor-All Buffer PLUS (GE Healthcare, Otelfingen, Switzerland).

    Techniques: Generated