Structured Review

Thermo Fisher dde i
Fla typing of inoculation strains and strains isolated from infected chicks. The <t>flaA</t> gene was amplified by PCR and digested with either (A) Alu I or (B) Dde I. M, molecular size marker (100-bp DNA ladder); lane 1, Pen-6 inoculation strain; lanes 2 and 3, isolates from chickens colonized with the Pen-6 strain; lane 4, Kl-5133 inoculation strain; lanes 5 and 6, isolates from chickens colonized with the Kl-5133 strain; lane 7, G97-76595 inoculation strain; lanes 8 and 9, isolates from chickens colonized with the G97-76595 strain. Lane numbers refer to the same information in both panels A and B.
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Images

1) Product Images from "Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks"

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.67.5.2388-2392.2001

Fla typing of inoculation strains and strains isolated from infected chicks. The flaA gene was amplified by PCR and digested with either (A) Alu I or (B) Dde I. M, molecular size marker (100-bp DNA ladder); lane 1, Pen-6 inoculation strain; lanes 2 and 3, isolates from chickens colonized with the Pen-6 strain; lane 4, Kl-5133 inoculation strain; lanes 5 and 6, isolates from chickens colonized with the Kl-5133 strain; lane 7, G97-76595 inoculation strain; lanes 8 and 9, isolates from chickens colonized with the G97-76595 strain. Lane numbers refer to the same information in both panels A and B.
Figure Legend Snippet: Fla typing of inoculation strains and strains isolated from infected chicks. The flaA gene was amplified by PCR and digested with either (A) Alu I or (B) Dde I. M, molecular size marker (100-bp DNA ladder); lane 1, Pen-6 inoculation strain; lanes 2 and 3, isolates from chickens colonized with the Pen-6 strain; lane 4, Kl-5133 inoculation strain; lanes 5 and 6, isolates from chickens colonized with the Kl-5133 strain; lane 7, G97-76595 inoculation strain; lanes 8 and 9, isolates from chickens colonized with the G97-76595 strain. Lane numbers refer to the same information in both panels A and B.

Techniques Used: Isolation, Infection, Amplification, Polymerase Chain Reaction, Marker

2) Product Images from "Association Among SNAP-25 Gene DdeI and MnlI Polymorphisms and Hemodynamic Changes During Methylphenidate Use: A Functional Near-Infrared Spectroscopy Study"

Article Title: Association Among SNAP-25 Gene DdeI and MnlI Polymorphisms and Hemodynamic Changes During Methylphenidate Use: A Functional Near-Infrared Spectroscopy Study

Journal: Journal of attention disorders

doi: 10.1177/1087054710374597

Change of left and right HHb with methylphenidate. Effect of SNAP-25 Dde I polymorphism. Y -axis: HHb during Stroop neutral stimuli minus HHb during Stroop incongruent stimuli.
Figure Legend Snippet: Change of left and right HHb with methylphenidate. Effect of SNAP-25 Dde I polymorphism. Y -axis: HHb during Stroop neutral stimuli minus HHb during Stroop incongruent stimuli.

Techniques Used:

Change of left and right HHb with methylphenidate. Effect of SNAP-25 Mnl I and Dde I polymorphisms combined. Y -axis: HHb during Stroop neutral stimuli minus HHb during Stroop incongruent stimuli.
Figure Legend Snippet: Change of left and right HHb with methylphenidate. Effect of SNAP-25 Mnl I and Dde I polymorphisms combined. Y -axis: HHb during Stroop neutral stimuli minus HHb during Stroop incongruent stimuli.

Techniques Used:

3) Product Images from "A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5? End or within the Genome of Feline Parvovirus and Can Modify Virus Replication"

Article Title: A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5? End or within the Genome of Feline Parvovirus and Can Modify Virus Replication

Journal: Journal of Virology

doi:

Protein binding to various sequences from the FPV genome identified by immunoprecipitation of the protein-DNA complex. (A) The Dde I and Hin fI restriction maps of the FPV genome in plasmid pGEM3Z. (B) The complete FPV genome in pGEM3Z was digested with Dde I or Hin fI and the fragments were 32 P labeled. After denaturation, the DNA was incubated with 100 ng of purified DBP40 and then immunoprecipitated with an antibody against the T7 epitope fused to the N terminus of the protein. After incubation with proteinase K, the DNA was electrophoresed in 2% alkaline agarose gels, which were dried and exposed to X-ray film. Differing buffer conditions resulted in slightly slower migration of the digested DNA. Total DNA, original digestion; IP, the immunoprecipitated DNA.
Figure Legend Snippet: Protein binding to various sequences from the FPV genome identified by immunoprecipitation of the protein-DNA complex. (A) The Dde I and Hin fI restriction maps of the FPV genome in plasmid pGEM3Z. (B) The complete FPV genome in pGEM3Z was digested with Dde I or Hin fI and the fragments were 32 P labeled. After denaturation, the DNA was incubated with 100 ng of purified DBP40 and then immunoprecipitated with an antibody against the T7 epitope fused to the N terminus of the protein. After incubation with proteinase K, the DNA was electrophoresed in 2% alkaline agarose gels, which were dried and exposed to X-ray film. Differing buffer conditions resulted in slightly slower migration of the digested DNA. Total DNA, original digestion; IP, the immunoprecipitated DNA.

Techniques Used: Protein Binding, Immunoprecipitation, Plasmid Preparation, Labeling, Incubation, Purification, Migration

4) Product Images from "Optimization of PCR--RFLP Directly from the Skin and Nails in Cases of Dermatophytosis, Targeting the ITS and the 18S Ribosomal DNA Regions"

Article Title: Optimization of PCR--RFLP Directly from the Skin and Nails in Cases of Dermatophytosis, Targeting the ITS and the 18S Ribosomal DNA Regions

Journal: Journal of Clinical and Diagnostic Research : JCDR

doi: 10.7860/JCDR/2013/5363.2873

RFLP on ITS amplicons using Dde I restriction enzyme. Lane 1: Undigested product of T. rubrum ATCC - 690 bp; Lane 2 – 9: Digested products; Lane 2: T. mentagrophytes ATCC - 400, 290 bp; Lane 3: Clinical strain - T. mentagrophytes ; Lane 4: Clinical strain - T. interdigitale ; Lane 5: T. rubrum ATCC - 300, 290, 100 bp; Lane 6: Clinical strain - T. rubrum ; Lane 7: Clinical strain - T. rubrum var. raubitschekii ; Lane 8 … 9: Clinical strain - E. floccosum - 500, 290 bp; Lane 10: 100 bp DNA ladder.
Figure Legend Snippet: RFLP on ITS amplicons using Dde I restriction enzyme. Lane 1: Undigested product of T. rubrum ATCC - 690 bp; Lane 2 – 9: Digested products; Lane 2: T. mentagrophytes ATCC - 400, 290 bp; Lane 3: Clinical strain - T. mentagrophytes ; Lane 4: Clinical strain - T. interdigitale ; Lane 5: T. rubrum ATCC - 300, 290, 100 bp; Lane 6: Clinical strain - T. rubrum ; Lane 7: Clinical strain - T. rubrum var. raubitschekii ; Lane 8 … 9: Clinical strain - E. floccosum - 500, 290 bp; Lane 10: 100 bp DNA ladder.

Techniques Used:

RFLP on 18S rDNA amplicons using Dde I restriction enzyme. Lane 1: Undigested product of T. rubrum ATCC - 180 bp; Lane 2 – 9: Digested products; Lane 2: T. mentagrophytes ATCC - 180 bp; Lane 3: Clinical strain - T. mentagrophytes ; Lane 4: Clinical strain - T. interdigitale ; Lane 5: T. rubrum ATCC - 180 bp; Lane 6: Clinical strain - T. rubrum ; Lane 7: Clinical strain - T. rubrum var. raubitschekii ; Lane 8 … 9: Clinical strain - E. floccosum - 180 bp; Lane 10: 100 bp DNA ruler
Figure Legend Snippet: RFLP on 18S rDNA amplicons using Dde I restriction enzyme. Lane 1: Undigested product of T. rubrum ATCC - 180 bp; Lane 2 – 9: Digested products; Lane 2: T. mentagrophytes ATCC - 180 bp; Lane 3: Clinical strain - T. mentagrophytes ; Lane 4: Clinical strain - T. interdigitale ; Lane 5: T. rubrum ATCC - 180 bp; Lane 6: Clinical strain - T. rubrum ; Lane 7: Clinical strain - T. rubrum var. raubitschekii ; Lane 8 … 9: Clinical strain - E. floccosum - 180 bp; Lane 10: 100 bp DNA ruler

Techniques Used:

5) Product Images from "Chromatin loop organization of the junb locus in mouse dendritic cells"

Article Title: Chromatin loop organization of the junb locus in mouse dendritic cells

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkt669

The 3C analysis of the junb locus. DC2.4 cells were treated (+LPS), or not (+LPS), by LPS and subjected to quantitative 3C analysis as described in ‘Materials and Methods’ section. ( A ) Map of the investigated interactions. The frequent cutter Dde I restriction enzyme was used to fractionate the junb locus, as we found it to be the only restriction enzyme that permits sufficiently resolutive analysis of this short locus. The positions of the Dde I sites (double arrows) used in this 3C analysis are indicated c1 to c6. c1 was taken as the anchor from which possible interactions with other region of the junb locus were assessed. Their locations are indicated relative to the junb TSS taken as +1/−1. The possible interactions that have been tested in this 3C experiments are indicated by dashed lines, which are labeled c1-c2 to c1-c6. The anchor amplification oligonucleotide used in 3C qPCR is indicated by a black simple arrow, whereas the other primers are indicated by gray ones. ( B ) Quantification of 3C analyses of the junb locus. The data represent the relative interaction frequencies between the anchor region (c1) containing the junb TSS and the various other tested sites (c2 to c6) of the junb locus. Relative interaction frequencies were determined by qPCR relative to standard curves as previously described ( 50 , 51 ). Data points represent the mean of four independent experiments ± SD. In the absence of LPS (black triangles), a strong interaction between the junb promoter and the downstream E element was observed (local peak for the c1-4 chimera). However, 1 h after LPS addition (gray circles), no specific interactions could be found.
Figure Legend Snippet: The 3C analysis of the junb locus. DC2.4 cells were treated (+LPS), or not (+LPS), by LPS and subjected to quantitative 3C analysis as described in ‘Materials and Methods’ section. ( A ) Map of the investigated interactions. The frequent cutter Dde I restriction enzyme was used to fractionate the junb locus, as we found it to be the only restriction enzyme that permits sufficiently resolutive analysis of this short locus. The positions of the Dde I sites (double arrows) used in this 3C analysis are indicated c1 to c6. c1 was taken as the anchor from which possible interactions with other region of the junb locus were assessed. Their locations are indicated relative to the junb TSS taken as +1/−1. The possible interactions that have been tested in this 3C experiments are indicated by dashed lines, which are labeled c1-c2 to c1-c6. The anchor amplification oligonucleotide used in 3C qPCR is indicated by a black simple arrow, whereas the other primers are indicated by gray ones. ( B ) Quantification of 3C analyses of the junb locus. The data represent the relative interaction frequencies between the anchor region (c1) containing the junb TSS and the various other tested sites (c2 to c6) of the junb locus. Relative interaction frequencies were determined by qPCR relative to standard curves as previously described ( 50 , 51 ). Data points represent the mean of four independent experiments ± SD. In the absence of LPS (black triangles), a strong interaction between the junb promoter and the downstream E element was observed (local peak for the c1-4 chimera). However, 1 h after LPS addition (gray circles), no specific interactions could be found.

Techniques Used: Labeling, Amplification, Real-time Polymerase Chain Reaction

6) Product Images from "Polymorphism of sheep POU1F1 gene exon 6 and 3'UTR region and their association with milk production traits"

Article Title: Polymorphism of sheep POU1F1 gene exon 6 and 3'UTR region and their association with milk production traits

Journal: Iranian Journal of Veterinary Research

doi:

Agarose gel electrophoresis band patterns after digestion with Dde I endonuclease within the exon 6 and its flanking region sequence of the sheep POU1F1 gene. Lane M: 100 bp DNA marker. Lane 2-7: D1D1 genotype (199 bp, 118 bp, 83 bp and 58 bp). As one
Figure Legend Snippet: Agarose gel electrophoresis band patterns after digestion with Dde I endonuclease within the exon 6 and its flanking region sequence of the sheep POU1F1 gene. Lane M: 100 bp DNA marker. Lane 2-7: D1D1 genotype (199 bp, 118 bp, 83 bp and 58 bp). As one

Techniques Used: Agarose Gel Electrophoresis, Sequencing, Marker

The structure of sheep POU1F1 gene and SNPs location for exon 6 and 3'UTR and Alu I, Dde I enzyme restriction sites. Black dots (●) represent mutation points
Figure Legend Snippet: The structure of sheep POU1F1 gene and SNPs location for exon 6 and 3'UTR and Alu I, Dde I enzyme restriction sites. Black dots (●) represent mutation points

Techniques Used: Mutagenesis

Related Articles

Diagnostic Assay:

Article Title: Association of Variants at BCL11A and HBS1L-MYB with Hemoglobin F and Hospitalization Rates among Sickle Cell Patients in Cameroon
Article Snippet: .. Molecular Diagnostic Testing for SCA (HbSS) Analysis for presence of the sickle mutation was carried out on 200 ng DNA by PCR, on a thermocycler (BIORAD, USA) to amplify a 770 bp segment of the β-globin gene, followed by Dde I (GIBCO-BRL, USA) restriction analysis of the PCR product. ..

Amplification:

Article Title: Optimization of PCR--RFLP Directly from the Skin and Nails in Cases of Dermatophytosis, Targeting the ITS and the 18S Ribosomal DNA Regions
Article Snippet: Ltd, Bangalore, India), Mva I and the Dde I (Fermentas Inc. USA) restriction enzymes and they were incubated at 370C for 2 hours. .. Ltd, Bangalore, India), Mva I and the Dde I (Fermentas Inc. USA) restriction enzymes and they were incubated at 370C for 2 hours.

Article Title: Polymorphism of sheep POU1F1 gene exon 6 and 3'UTR region and their association with milk production traits
Article Snippet: PCR amplification For this study according to the ovine ( ) sequence of exon 4-6 of POU1F1 gene, the following PCR primers were designed: Forward: 5'- GTATTGCTG CTAAAGACGCC-3' and Reverse: 5'-GAGGGAAAGA TATAGTGAAAGGG-3'. .. Genotyping 20 μl of PCR product was digested separately with 10 U Dde I and 10 U AIu I (Fermentas GmbH, St. Leon-Rot, Germany) at 37°C overnight.

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: A 1,705-bp fragment of the C. jejuni flaA gene was amplified by PCR as described previously ( ). .. Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker.

Article Title: Differences in Fcgamma receptor IIa genotypes and IgG subclass pattern of anti-malarial antibodies between sympatric ethnic groups in Mali
Article Snippet: In short, the PCR amplification was performed in 10 μl reactions using 2 μl of genomic DNA, 5 μl of 2× ready-to-use PCR Master Mix (ABgene, Surrey, UK.) and 0.25 μl of each primer (Forward: 5'-ACACAACTGTGTTCACTAGC-3' and Reverse: 5'-CAACTTCATCCACGTTCACC-3', (MWG-Biotech AG, Ebersberg, Germany)). .. The entire PCR product were used for the enzymatic digestion with 4 U Dde I (Invitrogen) at 37°C for 2 h. The resulting fragments were analyzed on ethidium bromide stained 2.5% agarose gels.

Article Title: Association Among SNAP-25 Gene DdeI and MnlI Polymorphisms and Hemodynamic Changes During Methylphenidate Use: A Functional Near-Infrared Spectroscopy Study
Article Snippet: .. After amplification PCR products were digested by restriction endonuclease 10 U Dde I (Fermentas, Vilnius, Lithuania) or 10 U Mnl I (Fermentas, Vilnius, Lithuania) for 14 h at 37°C. .. The genotyping of the SNAP-25 gene Dde I or Mnl I polymorphisms was determined by fragment separation at 120 V for 40 to 50 min on a 3.5% Agarose gel containing 0.5 μg/ml ethidium bromide.

Article Title: Chromatin loop organization of the junb locus in mouse dendritic cells
Article Snippet: Standard curves for qPCR were generated from a PCR product as follows: 150 ng of DC2.4 genomic DNA were amplified with the Expand Long Template PCR System (Roche) using the following primers: forward (located −2346 bp relative to junb TSS; 5′-GGGCAAGATGGGAAGGAGGAC-3′) and reverse (located +4704 relative to junb TSS; 5′-GGCAGTGACACCATCAAGCCC-3′). .. In all, 25 μl of this PCR product were digested with Dde I and ligated using T4 DNA ligase (Invitrogen) before a second digestion with Eco RI.

Article Title: A Novel, Essential Control for Clonality Analysis with Human Androgen Receptor Gene Polymerase Chain Reaction
Article Snippet: Digestion of 0.5 μg of DNA was performed for at least 16 hours at 37°C in a reaction mixture of 25 μl, containing 5 U Dde I (Life Technologies, Gaithersburg, MD) and with or without 25 U of concentrated Hpa II (New England Biolabs, Hitchin, UK) in 1× one-phor-all buffer PLUS (Amersham Pharmacia, Uppsala, Sweden). .. After digestion, 5 μl of this mixture was used for PCR amplification of the HUMARA locus.

Autoradiography:

Article Title: Isolation and Characterization of Polymorphic DNA from Entamoeba histolytica
Article Snippet: Genomic DNA of isolate HM-1:IMSS clone 9 was digested overnight with 10 U each of restriction enzymes Alu I, Dde I, Dra I, Eco RI, and Rsa I (Gibco-BRL or MBI Fermentas), and fragments were separated by electrophoresis using 0.8% agarose gels in 1× TBE buffer and transferred to BiodyneA membranes (Gibco-BRL) using standard methods. .. Filters were hybridized overnight at 65°C in a solution of 1 M NaCl–1% sodium dodecyl sulfate–10% dextran sulfate and then washed to a final stringency of 0.2× SSC (1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate)–0.1% sodium dodecyl sulfate at 65°C before autoradiography at −70°C.

Enzyme-linked Immunosorbent Assay:

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker. .. Blood samples for monitoring of maternally derived serum anti- Campylobacter antibodies by an enzyme-linked immunosorbent assay (ELISA) procedure were collected from an extra batch of 10 chicks at each experiment.

Real-time Polymerase Chain Reaction:

Article Title: Chromatin loop organization of the junb locus in mouse dendritic cells
Article Snippet: Standard curves for qPCR were generated from a PCR product as follows: 150 ng of DC2.4 genomic DNA were amplified with the Expand Long Template PCR System (Roche) using the following primers: forward (located −2346 bp relative to junb TSS; 5′-GGGCAAGATGGGAAGGAGGAC-3′) and reverse (located +4704 relative to junb TSS; 5′-GGCAGTGACACCATCAAGCCC-3′). .. In all, 25 μl of this PCR product were digested with Dde I and ligated using T4 DNA ligase (Invitrogen) before a second digestion with Eco RI.

Incubation:

Article Title: A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5? End or within the Genome of Feline Parvovirus and Can Modify Virus Replication
Article Snippet: The labeled oligonucleotides were incubated with 20 ng of the purified DBP40 in 20 mM HEPES-NaOH (pH 7.9)–100 mM NaCl–5 mM MgCl2 –1 mM dithiothreitol–10% glycerol–1 μg of poly(dI-dC)–1 μg of BSA and then electrophoresed in 6% nondenaturing polyacrylamide gels, which were dried and exposed to X-ray film ( ). .. An FPV infectious clone in plasmid pGEM3Z (Promega, Madison, Wis.) was digested with Dde I and Hin fI, and the 3′ ends were 32 P labeled with the Klenow fragment of E. coli DNA polymerase I (Gibco/BRL, Gaithersburg, Md.) and [α-32 P]dATP.

Article Title: Optimization of PCR--RFLP Directly from the Skin and Nails in Cases of Dermatophytosis, Targeting the ITS and the 18S Ribosomal DNA Regions
Article Snippet: .. Ltd, Bangalore, India), Mva I and the Dde I (Fermentas Inc. USA) restriction enzymes and they were incubated at 370C for 2 hours. .. The digested products were electrophoresed in a 2 % agarose gel, stained with ethidium bromide and observed under a UV trans-illuminator.

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: Campylobacter cultures from cloacal and cecal swabs were produced by direct streaking of the swabs onto modified charcoal cefoperazone deoxycholate agar (blood-free agar base with cefoperazone at a concentration of 32 mg/liter and amphotericin at a concentration of 10 mg/liter) (Oxoid) and incubated microaerobically in 7% O2 –10% CO2 –83% N2 at 42°C for 48 h. Plates that were culture negative at 48 h were reincubated for an additional 48 h. Campylobacter sp. identification was performed according to previously described methods ( ). .. Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker.

Article Title: Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii
Article Snippet: After RNase A incubation at a final concentration of 75 mg/l, genomic DNA (gDNA) was precipitated with 25 mM NH4 Ac followed by ethanol. .. Appropriate amount of gDNA was digested by either Hind III or Dde I (ThermoScientific).

TRF Assay:

Article Title: Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii
Article Snippet: Paragraph title: DNA isolation and terminal restriction fragment assay (TRF assay) ... Appropriate amount of gDNA was digested by either Hind III or Dde I (ThermoScientific).

Modification:

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: Campylobacter cultures from cloacal and cecal swabs were produced by direct streaking of the swabs onto modified charcoal cefoperazone deoxycholate agar (blood-free agar base with cefoperazone at a concentration of 32 mg/liter and amphotericin at a concentration of 10 mg/liter) (Oxoid) and incubated microaerobically in 7% O2 –10% CO2 –83% N2 at 42°C for 48 h. Plates that were culture negative at 48 h were reincubated for an additional 48 h. Campylobacter sp. identification was performed according to previously described methods ( ). .. Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker.

Derivative Assay:

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker. .. Blood samples for monitoring of maternally derived serum anti- Campylobacter antibodies by an enzyme-linked immunosorbent assay (ELISA) procedure were collected from an extra batch of 10 chicks at each experiment.

Hybridization:

Article Title: Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii
Article Snippet: Appropriate amount of gDNA was digested by either Hind III or Dde I (ThermoScientific). .. Hybridization probes were 5′end-labeled by T4 polynucleotide kinase and [γ32 P]-ATP.

Sequencing:

Article Title: Levels of somatic hypermutations in B cell receptors increase during childhood
Article Snippet: The PCR products were digested with Dde I and Fnu4 HI and run on an ABI3130XL capillary sequencer (Applied Biosystems, Carlsbad, CA, USA). .. This analysis estimates the amount of SHM in expressed Vk3/20 gene segments in a specific sequence motif (hot-spot), displayed as percentage of mutated segments within the total peripheral blood cell population.

Article Title: Isolation and Characterization of Polymorphic DNA from Entamoeba histolytica
Article Snippet: Genomic DNA of isolate HM-1:IMSS clone 9 was digested overnight with 10 U each of restriction enzymes Alu I, Dde I, Dra I, Eco RI, and Rsa I (Gibco-BRL or MBI Fermentas), and fragments were separated by electrophoresis using 0.8% agarose gels in 1× TBE buffer and transferred to BiodyneA membranes (Gibco-BRL) using standard methods. .. The nucleotide sequence data reported here have been submitted to the GenBank database under accession numbers to .

Article Title: Polymorphism of sheep POU1F1 gene exon 6 and 3'UTR region and their association with milk production traits
Article Snippet: PCR amplification For this study according to the ovine ( ) sequence of exon 4-6 of POU1F1 gene, the following PCR primers were designed: Forward: 5'- GTATTGCTG CTAAAGACGCC-3' and Reverse: 5'-GAGGGAAAGA TATAGTGAAAGGG-3'. .. Genotyping 20 μl of PCR product was digested separately with 10 U Dde I and 10 U AIu I (Fermentas GmbH, St. Leon-Rot, Germany) at 37°C overnight.

Southern Blot:

Article Title: Isolation and Characterization of Polymorphic DNA from Entamoeba histolytica
Article Snippet: Paragraph title: Southern blot analysis. ... Genomic DNA of isolate HM-1:IMSS clone 9 was digested overnight with 10 U each of restriction enzymes Alu I, Dde I, Dra I, Eco RI, and Rsa I (Gibco-BRL or MBI Fermentas), and fragments were separated by electrophoresis using 0.8% agarose gels in 1× TBE buffer and transferred to BiodyneA membranes (Gibco-BRL) using standard methods.

Immunoprecipitation:

Article Title: A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5? End or within the Genome of Feline Parvovirus and Can Modify Virus Replication
Article Snippet: An FPV infectious clone in plasmid pGEM3Z (Promega, Madison, Wis.) was digested with Dde I and Hin fI, and the 3′ ends were 32 P labeled with the Klenow fragment of E. coli DNA polymerase I (Gibco/BRL, Gaithersburg, Md.) and [α-32 P]dATP. .. After boiling for 10 min, the DNA was transferred to a dry ice-ethanol bath and incubated for 30 min with 0.1 μg of E. coli -expressed DBP40 at 30°C for 1 h; then the protein and any associated DNA were immunoprecipitated with antibody against the T7 epitope (Novagen).

Infection:

Article Title: Levels of somatic hypermutations in B cell receptors increase during childhood
Article Snippet: Patients with an active infection, suspected or proven diseases of the immune system or on immunosuppressive therapy were excluded. .. The PCR products were digested with Dde I and Fnu4 HI and run on an ABI3130XL capillary sequencer (Applied Biosystems, Carlsbad, CA, USA).

Generated:

Article Title: Chromatin loop organization of the junb locus in mouse dendritic cells
Article Snippet: Standard curves for qPCR were generated from a PCR product as follows: 150 ng of DC2.4 genomic DNA were amplified with the Expand Long Template PCR System (Roche) using the following primers: forward (located −2346 bp relative to junb TSS; 5′-GGGCAAGATGGGAAGGAGGAC-3′) and reverse (located +4704 relative to junb TSS; 5′-GGCAGTGACACCATCAAGCCC-3′). .. In all, 25 μl of this PCR product were digested with Dde I and ligated using T4 DNA ligase (Invitrogen) before a second digestion with Eco RI.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Levels of somatic hypermutations in B cell receptors increase during childhood
Article Snippet: In brief, a reverse transcription–polymerase chain reaction (RT–PCR) was performed using a HEX-coupled Vk3-20U forward primer and a 6-carboxyfluorescein (FAM)-coupled Vk3-20 L reverse primer. .. The PCR products were digested with Dde I and Fnu4 HI and run on an ABI3130XL capillary sequencer (Applied Biosystems, Carlsbad, CA, USA).

Binding Assay:

Article Title: A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5? End or within the Genome of Feline Parvovirus and Can Modify Virus Replication
Article Snippet: Paragraph title: ssDNA binding and in vitro fill-in assays. ... An FPV infectious clone in plasmid pGEM3Z (Promega, Madison, Wis.) was digested with Dde I and Hin fI, and the 3′ ends were 32 P labeled with the Klenow fragment of E. coli DNA polymerase I (Gibco/BRL, Gaithersburg, Md.) and [α-32 P]dATP.

DNA Extraction:

Article Title: A Novel, Essential Control for Clonality Analysis with Human Androgen Receptor Gene Polymerase Chain Reaction
Article Snippet: Paragraph title: DNA Isolation, Digestion, and HUMARA PCR ... Digestion of 0.5 μg of DNA was performed for at least 16 hours at 37°C in a reaction mixture of 25 μl, containing 5 U Dde I (Life Technologies, Gaithersburg, MD) and with or without 25 U of concentrated Hpa II (New England Biolabs, Hitchin, UK) in 1× one-phor-all buffer PLUS (Amersham Pharmacia, Uppsala, Sweden).

Article Title: Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii
Article Snippet: Paragraph title: DNA isolation and terminal restriction fragment assay (TRF assay) ... Appropriate amount of gDNA was digested by either Hind III or Dde I (ThermoScientific).

Nucleic Acid Electrophoresis:

Article Title: Association Among SNAP-25 Gene DdeI and MnlI Polymorphisms and Hemodynamic Changes During Methylphenidate Use: A Functional Near-Infrared Spectroscopy Study
Article Snippet: After amplification PCR products were digested by restriction endonuclease 10 U Dde I (Fermentas, Vilnius, Lithuania) or 10 U Mnl I (Fermentas, Vilnius, Lithuania) for 14 h at 37°C. .. The gel was visualized under UV light using a gel electrophoresis visualizing system (Vilber Lourmat).

Mutagenesis:

Article Title: Association of Variants at BCL11A and HBS1L-MYB with Hemoglobin F and Hospitalization Rates among Sickle Cell Patients in Cameroon
Article Snippet: .. Molecular Diagnostic Testing for SCA (HbSS) Analysis for presence of the sickle mutation was carried out on 200 ng DNA by PCR, on a thermocycler (BIORAD, USA) to amplify a 770 bp segment of the β-globin gene, followed by Dde I (GIBCO-BRL, USA) restriction analysis of the PCR product. ..

Isolation:

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: DNA was isolated from fecal samples from two randomly chosen Campylobacter -positive chicks within each experimental group. .. Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker.

Article Title: A Novel, Essential Control for Clonality Analysis with Human Androgen Receptor Gene Polymerase Chain Reaction
Article Snippet: DNA was isolated with the Puregene DNA isolation kit (Gentra Systems, Minneapolis, MN), both for the hematopoietic samples and the paraffin-embedded samples according to the protocols of the manufacturer. .. Digestion of 0.5 μg of DNA was performed for at least 16 hours at 37°C in a reaction mixture of 25 μl, containing 5 U Dde I (Life Technologies, Gaithersburg, MD) and with or without 25 U of concentrated Hpa II (New England Biolabs, Hitchin, UK) in 1× one-phor-all buffer PLUS (Amersham Pharmacia, Uppsala, Sweden).

Size-exclusion Chromatography:

Article Title: Differences in Fcgamma receptor IIa genotypes and IgG subclass pattern of anti-malarial antibodies between sympatric ethnic groups in Mali
Article Snippet: The PCR was carried out in an Eppendorf Mastercycler® (Eppendorf AG, Hamburg, Germany) using a 5 min denaturation at 95°C followed by 35 cycles with 95°C for 30 sec, 56°C for 30 sec and 72°C for 30 sec. .. The entire PCR product were used for the enzymatic digestion with 4 U Dde I (Invitrogen) at 37°C for 2 h. The resulting fragments were analyzed on ethidium bromide stained 2.5% agarose gels.

Labeling:

Article Title: A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5? End or within the Genome of Feline Parvovirus and Can Modify Virus Replication
Article Snippet: .. An FPV infectious clone in plasmid pGEM3Z (Promega, Madison, Wis.) was digested with Dde I and Hin fI, and the 3′ ends were 32 P labeled with the Klenow fragment of E. coli DNA polymerase I (Gibco/BRL, Gaithersburg, Md.) and [α-32 P]dATP. .. After boiling for 10 min, the DNA was transferred to a dry ice-ethanol bath and incubated for 30 min with 0.1 μg of E. coli -expressed DBP40 at 30°C for 1 h; then the protein and any associated DNA were immunoprecipitated with antibody against the T7 epitope (Novagen).

Article Title: Isolation and Characterization of Polymorphic DNA from Entamoeba histolytica
Article Snippet: Genomic DNA of isolate HM-1:IMSS clone 9 was digested overnight with 10 U each of restriction enzymes Alu I, Dde I, Dra I, Eco RI, and Rsa I (Gibco-BRL or MBI Fermentas), and fragments were separated by electrophoresis using 0.8% agarose gels in 1× TBE buffer and transferred to BiodyneA membranes (Gibco-BRL) using standard methods. .. [α-32 P]dCTP-labeled double-stranded DNA probes were prepared by using the Rediprime II random prime labeling system (Amersham Pharmacia Biotech).

Purification:

Article Title: A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5? End or within the Genome of Feline Parvovirus and Can Modify Virus Replication
Article Snippet: The labeled oligonucleotides were incubated with 20 ng of the purified DBP40 in 20 mM HEPES-NaOH (pH 7.9)–100 mM NaCl–5 mM MgCl2 –1 mM dithiothreitol–10% glycerol–1 μg of poly(dI-dC)–1 μg of BSA and then electrophoresed in 6% nondenaturing polyacrylamide gels, which were dried and exposed to X-ray film ( ). .. An FPV infectious clone in plasmid pGEM3Z (Promega, Madison, Wis.) was digested with Dde I and Hin fI, and the 3′ ends were 32 P labeled with the Klenow fragment of E. coli DNA polymerase I (Gibco/BRL, Gaithersburg, Md.) and [α-32 P]dATP.

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: Genomic C. jejuni DNA was purified from a loopful of bacterial culture using the QIAamp DNA minikit (Qiagen, Hilden, Germany). .. Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker.

Article Title: Chromatin loop organization of the junb locus in mouse dendritic cells
Article Snippet: Briefly, eight primer extension reactions were performed (reverse primer located −624 bp relative to junb TSS: 5′-CCCATA AGTGGAAAAGGGAAGG-3′), pooled, purified with a QiaQuick PCR purification kit (Qiagen) and diluted in H2 O to a concentration of 12.5 ng/μl. .. In all, 25 μl of this PCR product were digested with Dde I and ligated using T4 DNA ligase (Invitrogen) before a second digestion with Eco RI.

Polymerase Chain Reaction:

Article Title: Association of Variants at BCL11A and HBS1L-MYB with Hemoglobin F and Hospitalization Rates among Sickle Cell Patients in Cameroon
Article Snippet: .. Molecular Diagnostic Testing for SCA (HbSS) Analysis for presence of the sickle mutation was carried out on 200 ng DNA by PCR, on a thermocycler (BIORAD, USA) to amplify a 770 bp segment of the β-globin gene, followed by Dde I (GIBCO-BRL, USA) restriction analysis of the PCR product. ..

Article Title: Levels of somatic hypermutations in B cell receptors increase during childhood
Article Snippet: .. The PCR products were digested with Dde I and Fnu4 HI and run on an ABI3130XL capillary sequencer (Applied Biosystems, Carlsbad, CA, USA). ..

Article Title: Optimization of PCR--RFLP Directly from the Skin and Nails in Cases of Dermatophytosis, Targeting the ITS and the 18S Ribosomal DNA Regions
Article Snippet: Paragraph title: PCR – RFLP Analysis ... Ltd, Bangalore, India), Mva I and the Dde I (Fermentas Inc. USA) restriction enzymes and they were incubated at 370C for 2 hours.

Article Title: Polymorphism of sheep POU1F1 gene exon 6 and 3'UTR region and their association with milk production traits
Article Snippet: .. Genotyping 20 μl of PCR product was digested separately with 10 U Dde I and 10 U AIu I (Fermentas GmbH, St. Leon-Rot, Germany) at 37°C overnight. .. PCR products of digestion were resolved by electrophoresis on a 4% agarose gel stained with ethidium bromide.

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: .. Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker. .. Blood samples for monitoring of maternally derived serum anti- Campylobacter antibodies by an enzyme-linked immunosorbent assay (ELISA) procedure were collected from an extra batch of 10 chicks at each experiment.

Article Title: Differences in Fcgamma receptor IIa genotypes and IgG subclass pattern of anti-malarial antibodies between sympatric ethnic groups in Mali
Article Snippet: .. The entire PCR product were used for the enzymatic digestion with 4 U Dde I (Invitrogen) at 37°C for 2 h. The resulting fragments were analyzed on ethidium bromide stained 2.5% agarose gels. ..

Article Title: Association Among SNAP-25 Gene DdeI and MnlI Polymorphisms and Hemodynamic Changes During Methylphenidate Use: A Functional Near-Infrared Spectroscopy Study
Article Snippet: .. After amplification PCR products were digested by restriction endonuclease 10 U Dde I (Fermentas, Vilnius, Lithuania) or 10 U Mnl I (Fermentas, Vilnius, Lithuania) for 14 h at 37°C. .. The genotyping of the SNAP-25 gene Dde I or Mnl I polymorphisms was determined by fragment separation at 120 V for 40 to 50 min on a 3.5% Agarose gel containing 0.5 μg/ml ethidium bromide.

Article Title: Chromatin loop organization of the junb locus in mouse dendritic cells
Article Snippet: .. In all, 25 μl of this PCR product were digested with Dde I and ligated using T4 DNA ligase (Invitrogen) before a second digestion with Eco RI. .. Finally, this reaction was diluted into a solution of DC2.4 genomic DNA digested with DdeI and EcoRI (rather than in H2 O) to obtain a final DNA concentration similar to that of the 3C reactions (12.5 ng/µl).

Article Title: A Novel, Essential Control for Clonality Analysis with Human Androgen Receptor Gene Polymerase Chain Reaction
Article Snippet: Paragraph title: DNA Isolation, Digestion, and HUMARA PCR ... Digestion of 0.5 μg of DNA was performed for at least 16 hours at 37°C in a reaction mixture of 25 μl, containing 5 U Dde I (Life Technologies, Gaithersburg, MD) and with or without 25 U of concentrated Hpa II (New England Biolabs, Hitchin, UK) in 1× one-phor-all buffer PLUS (Amersham Pharmacia, Uppsala, Sweden).

Electrophoretic Mobility Shift Assay:

Article Title: A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5? End or within the Genome of Feline Parvovirus and Can Modify Virus Replication
Article Snippet: For electrophoretic mobility shift assays (EMSA), synthetic oligonucleotides representing sequences near the 3′ and 5′ ends of the viral genome (Table ) were 5′-end labeled with polynucleotide kinase and [γ-32 P]ATP. .. An FPV infectious clone in plasmid pGEM3Z (Promega, Madison, Wis.) was digested with Dde I and Hin fI, and the 3′ ends were 32 P labeled with the Klenow fragment of E. coli DNA polymerase I (Gibco/BRL, Gaithersburg, Md.) and [α-32 P]dATP.

Plasmid Preparation:

Article Title: A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5? End or within the Genome of Feline Parvovirus and Can Modify Virus Replication
Article Snippet: .. An FPV infectious clone in plasmid pGEM3Z (Promega, Madison, Wis.) was digested with Dde I and Hin fI, and the 3′ ends were 32 P labeled with the Klenow fragment of E. coli DNA polymerase I (Gibco/BRL, Gaithersburg, Md.) and [α-32 P]dATP. .. After boiling for 10 min, the DNA was transferred to a dry ice-ethanol bath and incubated for 30 min with 0.1 μg of E. coli -expressed DBP40 at 30°C for 1 h; then the protein and any associated DNA were immunoprecipitated with antibody against the T7 epitope (Novagen).

Software:

Article Title: Polymorphism of sheep POU1F1 gene exon 6 and 3'UTR region and their association with milk production traits
Article Snippet: For primer design, Primer 3 software (Rozen and Skaletsky, 2000 ) was used. .. Genotyping 20 μl of PCR product was digested separately with 10 U Dde I and 10 U AIu I (Fermentas GmbH, St. Leon-Rot, Germany) at 37°C overnight.

Electrophoresis:

Article Title: Isolation and Characterization of Polymorphic DNA from Entamoeba histolytica
Article Snippet: .. Genomic DNA of isolate HM-1:IMSS clone 9 was digested overnight with 10 U each of restriction enzymes Alu I, Dde I, Dra I, Eco RI, and Rsa I (Gibco-BRL or MBI Fermentas), and fragments were separated by electrophoresis using 0.8% agarose gels in 1× TBE buffer and transferred to BiodyneA membranes (Gibco-BRL) using standard methods. .. [α-32 P]dCTP-labeled double-stranded DNA probes were prepared by using the Rediprime II random prime labeling system (Amersham Pharmacia Biotech).

Article Title: Polymorphism of sheep POU1F1 gene exon 6 and 3'UTR region and their association with milk production traits
Article Snippet: The PCR products were separated by electrophoresis on 2% agarose gels (Promega, Madison, WI, United States) in parallel with a 100 bp DNA marker. .. Genotyping 20 μl of PCR product was digested separately with 10 U Dde I and 10 U AIu I (Fermentas GmbH, St. Leon-Rot, Germany) at 37°C overnight.

Agarose Gel Electrophoresis:

Article Title: Optimization of PCR--RFLP Directly from the Skin and Nails in Cases of Dermatophytosis, Targeting the ITS and the 18S Ribosomal DNA Regions
Article Snippet: Ltd, Bangalore, India), Mva I and the Dde I (Fermentas Inc. USA) restriction enzymes and they were incubated at 370C for 2 hours. .. The digested products were electrophoresed in a 2 % agarose gel, stained with ethidium bromide and observed under a UV trans-illuminator.

Article Title: Polymorphism of sheep POU1F1 gene exon 6 and 3'UTR region and their association with milk production traits
Article Snippet: Genotyping 20 μl of PCR product was digested separately with 10 U Dde I and 10 U AIu I (Fermentas GmbH, St. Leon-Rot, Germany) at 37°C overnight. .. PCR products of digestion were resolved by electrophoresis on a 4% agarose gel stained with ethidium bromide.

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: .. Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker. .. Blood samples for monitoring of maternally derived serum anti- Campylobacter antibodies by an enzyme-linked immunosorbent assay (ELISA) procedure were collected from an extra batch of 10 chicks at each experiment.

Article Title: Association Among SNAP-25 Gene DdeI and MnlI Polymorphisms and Hemodynamic Changes During Methylphenidate Use: A Functional Near-Infrared Spectroscopy Study
Article Snippet: After amplification PCR products were digested by restriction endonuclease 10 U Dde I (Fermentas, Vilnius, Lithuania) or 10 U Mnl I (Fermentas, Vilnius, Lithuania) for 14 h at 37°C. .. The genotyping of the SNAP-25 gene Dde I or Mnl I polymorphisms was determined by fragment separation at 120 V for 40 to 50 min on a 3.5% Agarose gel containing 0.5 μg/ml ethidium bromide.

Article Title: Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii
Article Snippet: Appropriate amount of gDNA was digested by either Hind III or Dde I (ThermoScientific). .. 300 ng of digested gDNA was separated on a 0.8% agarose gel, 0.5 x TBE, and was transferred to a Hybond-XL membrane (Amersham).

In Vitro:

Article Title: A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5? End or within the Genome of Feline Parvovirus and Can Modify Virus Replication
Article Snippet: Paragraph title: ssDNA binding and in vitro fill-in assays. ... An FPV infectious clone in plasmid pGEM3Z (Promega, Madison, Wis.) was digested with Dde I and Hin fI, and the 3′ ends were 32 P labeled with the Klenow fragment of E. coli DNA polymerase I (Gibco/BRL, Gaithersburg, Md.) and [α-32 P]dATP.

Sampling:

Article Title: Levels of somatic hypermutations in B cell receptors increase during childhood
Article Snippet: The blood was collected from healthy children and adults, who underwent venipuncture or blood sampling by heel prick or finger prick for other reasons (e.g. minor surgery). .. The PCR products were digested with Dde I and Fnu4 HI and run on an ABI3130XL capillary sequencer (Applied Biosystems, Carlsbad, CA, USA).

Produced:

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: Campylobacter cultures from cloacal and cecal swabs were produced by direct streaking of the swabs onto modified charcoal cefoperazone deoxycholate agar (blood-free agar base with cefoperazone at a concentration of 32 mg/liter and amphotericin at a concentration of 10 mg/liter) (Oxoid) and incubated microaerobically in 7% O2 –10% CO2 –83% N2 at 42°C for 48 h. Plates that were culture negative at 48 h were reincubated for an additional 48 h. Campylobacter sp. identification was performed according to previously described methods ( ). .. Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker.

Concentration Assay:

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: Campylobacter cultures from cloacal and cecal swabs were produced by direct streaking of the swabs onto modified charcoal cefoperazone deoxycholate agar (blood-free agar base with cefoperazone at a concentration of 32 mg/liter and amphotericin at a concentration of 10 mg/liter) (Oxoid) and incubated microaerobically in 7% O2 –10% CO2 –83% N2 at 42°C for 48 h. Plates that were culture negative at 48 h were reincubated for an additional 48 h. Campylobacter sp. identification was performed according to previously described methods ( ). .. Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker.

Article Title: Chromatin loop organization of the junb locus in mouse dendritic cells
Article Snippet: Briefly, eight primer extension reactions were performed (reverse primer located −624 bp relative to junb TSS: 5′-CCCATA AGTGGAAAAGGGAAGG-3′), pooled, purified with a QiaQuick PCR purification kit (Qiagen) and diluted in H2 O to a concentration of 12.5 ng/μl. .. In all, 25 μl of this PCR product were digested with Dde I and ligated using T4 DNA ligase (Invitrogen) before a second digestion with Eco RI.

Article Title: Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii
Article Snippet: After RNase A incubation at a final concentration of 75 mg/l, genomic DNA (gDNA) was precipitated with 25 mM NH4 Ac followed by ethanol. .. Appropriate amount of gDNA was digested by either Hind III or Dde I (ThermoScientific).

Marker:

Article Title: Polymorphism of sheep POU1F1 gene exon 6 and 3'UTR region and their association with milk production traits
Article Snippet: The PCR products were separated by electrophoresis on 2% agarose gels (Promega, Madison, WI, United States) in parallel with a 100 bp DNA marker. .. Genotyping 20 μl of PCR product was digested separately with 10 U Dde I and 10 U AIu I (Fermentas GmbH, St. Leon-Rot, Germany) at 37°C overnight.

Article Title: Study of the Infectivity of Saline-Stored Campylobacter jejuni for Day-Old Chicks
Article Snippet: .. Samples of the flaA PCR product were subsequently digested with Dde I (Life Technologies, Rockville, Md.) and Alu I (Boehringer GmbH, Mannheim, Germany) separately, and the digests were analyzed by 3% agarose gel electrophoresis with a 100-bp DNA ladder (Life Technologies) as the molecular size marker. .. Blood samples for monitoring of maternally derived serum anti- Campylobacter antibodies by an enzyme-linked immunosorbent assay (ELISA) procedure were collected from an extra batch of 10 chicks at each experiment.

Article Title: Association Among SNAP-25 Gene DdeI and MnlI Polymorphisms and Hemodynamic Changes During Methylphenidate Use: A Functional Near-Infrared Spectroscopy Study
Article Snippet: After amplification PCR products were digested by restriction endonuclease 10 U Dde I (Fermentas, Vilnius, Lithuania) or 10 U Mnl I (Fermentas, Vilnius, Lithuania) for 14 h at 37°C. .. A 100-bp marker (50-bp DNA Ladder, Fermentas) was used as a size standard for each gel lane.

Staining:

Article Title: Optimization of PCR--RFLP Directly from the Skin and Nails in Cases of Dermatophytosis, Targeting the ITS and the 18S Ribosomal DNA Regions
Article Snippet: Ltd, Bangalore, India), Mva I and the Dde I (Fermentas Inc. USA) restriction enzymes and they were incubated at 370C for 2 hours. .. The digested products were electrophoresed in a 2 % agarose gel, stained with ethidium bromide and observed under a UV trans-illuminator.

Article Title: Polymorphism of sheep POU1F1 gene exon 6 and 3'UTR region and their association with milk production traits
Article Snippet: Genotyping 20 μl of PCR product was digested separately with 10 U Dde I and 10 U AIu I (Fermentas GmbH, St. Leon-Rot, Germany) at 37°C overnight. .. PCR products of digestion were resolved by electrophoresis on a 4% agarose gel stained with ethidium bromide.

Article Title: Differences in Fcgamma receptor IIa genotypes and IgG subclass pattern of anti-malarial antibodies between sympatric ethnic groups in Mali
Article Snippet: .. The entire PCR product were used for the enzymatic digestion with 4 U Dde I (Invitrogen) at 37°C for 2 h. The resulting fragments were analyzed on ethidium bromide stained 2.5% agarose gels. ..

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