bp dna ladder  (New England Biolabs)


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    50 bp DNA Ladder
    Description:
    50 bp DNA Ladder 500 1000 gel lanes
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    n3236l
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    1000 gel lanes
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    New England Biolabs bp dna ladder
    50 bp DNA Ladder
    50 bp DNA Ladder 500 1000 gel lanes
    https://www.bioz.com/result/bp dna ladder/product/New England Biolabs
    Average 96 stars, based on 71 article reviews
    Price from $9.99 to $1999.99
    bp dna ladder - by Bioz Stars, 2020-09
    96/100 stars

    Images

    1) Product Images from "Intravesicle Isothermal DNA Replication"

    Article Title: Intravesicle Isothermal DNA Replication

    Journal: BMC Research Notes

    doi: 10.1186/1756-0500-4-128

    The effect of temperature on tHDA enzymatic activity . (A) The influence of temperature on the enzymatic activity of the isothermal tHDA system. Samples were incubated at 65°C (lane 2), 37°C (lane 3), 23°C (lane 4), and 4°C (lane 5) for 1.5 h. Lane 1 contains a 50 bp DNA ladder. The 1350 bp, 100 bp, and 50 bp bands are labeled. (B) The influence of overnight incubation temperature on the enzymatic activity of the isothermal tHDA system. Samples were incubated at 4°C (lane 2) and 23°C (lane 3) overnight prior to incubation at 65°C for 1.5 h. Lane 1 is a 50 bp DNA ladder. Reaction products were observed by ethidium bromide staining of a 1.8% agarose gel.
    Figure Legend Snippet: The effect of temperature on tHDA enzymatic activity . (A) The influence of temperature on the enzymatic activity of the isothermal tHDA system. Samples were incubated at 65°C (lane 2), 37°C (lane 3), 23°C (lane 4), and 4°C (lane 5) for 1.5 h. Lane 1 contains a 50 bp DNA ladder. The 1350 bp, 100 bp, and 50 bp bands are labeled. (B) The influence of overnight incubation temperature on the enzymatic activity of the isothermal tHDA system. Samples were incubated at 4°C (lane 2) and 23°C (lane 3) overnight prior to incubation at 65°C for 1.5 h. Lane 1 is a 50 bp DNA ladder. Reaction products were observed by ethidium bromide staining of a 1.8% agarose gel.

    Techniques Used: Activity Assay, Incubation, Labeling, Staining, Agarose Gel Electrophoresis

    The influence of freeze/thaw cycles on tHDA enzymatic activity . Unencapsulated reaction mixtures were subjected to either 0 (lane 2), 5 (lane 3), 10 (lane 4), or 20 (lane 5) cycles of freeze-thawing. Lane 1 is a 50 bp DNA ladder. The 1350 bp, 100 bp, and 50 bp bands are labeled. Reaction products were visualized by ethidium bromide staining of a 1.8% agarose gel. The full length reaction product is 85 bp.
    Figure Legend Snippet: The influence of freeze/thaw cycles on tHDA enzymatic activity . Unencapsulated reaction mixtures were subjected to either 0 (lane 2), 5 (lane 3), 10 (lane 4), or 20 (lane 5) cycles of freeze-thawing. Lane 1 is a 50 bp DNA ladder. The 1350 bp, 100 bp, and 50 bp bands are labeled. Reaction products were visualized by ethidium bromide staining of a 1.8% agarose gel. The full length reaction product is 85 bp.

    Techniques Used: Activity Assay, Labeling, Staining, Agarose Gel Electrophoresis

    Intravesicular isothermal replication . Lanes 1 and 7 contain a 50 bp DNA ladder. Lanes 2 and 3 are from unencapsulated reactions and lanes 4-6 are within phospholipid vesicles. Lanes 2 and 3 are isothermal replication reactions under standard conditions except that 0.5 mM CaCl 2 was added. CaCl 2 is needed for proteinase K activity. Further, lane 3 contained 0.9 units of proteinase K, demonstrating that proteinase K is capable of digesting components of the tHDA system and thus inhibiting DNA amplification. A similar experiment was conducted inside of vesicles with proteinase K added to the outside of the vesicles (lane 4) and proteinase K added to both the inside and the outside of the vesicles (lane 5). Finally, to further demonstrate that the reaction was encapsulated, dNTPs were added extravesicularly resulting in an inability to replicate DNA since dNTPs are incapable of crossing POPC membranes (lane 6).
    Figure Legend Snippet: Intravesicular isothermal replication . Lanes 1 and 7 contain a 50 bp DNA ladder. Lanes 2 and 3 are from unencapsulated reactions and lanes 4-6 are within phospholipid vesicles. Lanes 2 and 3 are isothermal replication reactions under standard conditions except that 0.5 mM CaCl 2 was added. CaCl 2 is needed for proteinase K activity. Further, lane 3 contained 0.9 units of proteinase K, demonstrating that proteinase K is capable of digesting components of the tHDA system and thus inhibiting DNA amplification. A similar experiment was conducted inside of vesicles with proteinase K added to the outside of the vesicles (lane 4) and proteinase K added to both the inside and the outside of the vesicles (lane 5). Finally, to further demonstrate that the reaction was encapsulated, dNTPs were added extravesicularly resulting in an inability to replicate DNA since dNTPs are incapable of crossing POPC membranes (lane 6).

    Techniques Used: Activity Assay, Amplification

    2) Product Images from "A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection"

    Article Title: A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0137578

    Identification and characterization of bucl genes in B . pseudomallei reference strain K96243. (A) Schematic representation of bucl distribution. Relative position and orientation of each bucl gene is shown; six bucl genes are present on chromosome one and seven on chromosome two. (B) Summary table of bucl distribution. bucl location, orientation, and length are mapped to the genome of Bp K96243. Molecular weight of each Bucl protein encoded by each bucl allele is shown. (C) PCR amplification of 13 bucl genes from Bp K96243. Primers were designed targeting the non-collagenous conserved regions, and PCR conditions were established for all bucl amplicons at a uniform annealing temperature of 64°C. Amplicon sizes; bucl1 , 123 bp; bucl2 133 bp; bucl3 , 166 bp; bucl4 , 176 bp; bucl5 , 216 bp; bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 96 bp; bucl10 , 109 bp; bucl13 , 212 bp; bucl14 , 178 bp; bucl15 , 95 bp; and bucl16 , 123 bp; M, 50-bp DNA size marker.
    Figure Legend Snippet: Identification and characterization of bucl genes in B . pseudomallei reference strain K96243. (A) Schematic representation of bucl distribution. Relative position and orientation of each bucl gene is shown; six bucl genes are present on chromosome one and seven on chromosome two. (B) Summary table of bucl distribution. bucl location, orientation, and length are mapped to the genome of Bp K96243. Molecular weight of each Bucl protein encoded by each bucl allele is shown. (C) PCR amplification of 13 bucl genes from Bp K96243. Primers were designed targeting the non-collagenous conserved regions, and PCR conditions were established for all bucl amplicons at a uniform annealing temperature of 64°C. Amplicon sizes; bucl1 , 123 bp; bucl2 133 bp; bucl3 , 166 bp; bucl4 , 176 bp; bucl5 , 216 bp; bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 96 bp; bucl10 , 109 bp; bucl13 , 212 bp; bucl14 , 178 bp; bucl15 , 95 bp; and bucl16 , 123 bp; M, 50-bp DNA size marker.

    Techniques Used: Molecular Weight, Polymerase Chain Reaction, Amplification, Marker

    Distribution of bucl genes among Burkholderia spp. select agents by PCR. Presence of bucl genes was assessed by PCR on (A) a collection of genomic DNA from 25 B . pseudomallei and 16 B . mallei strains, as well as (B) in control strains of B . thailandensis , B . cepacia , B . cenocepacia , and B . multivorans ; selected bucl genes 5 , 13 , 14 , and 16 are shown. (C) Detection and separation of selected bucl amplicons generated from the B . pseudomallei reference strain K96243 by traditional 2% agarose gel electrophoresis (left) or by capillary gel electrophoresis (right). Electropherogram generated by capillary gel electrophoresis with phospholipid nanogel matrix shows separation of amplicons over time. Amplicon sizes: bucl5 , 216 bp; bucl13 , 214 bp; bucl14 , 178 bp; and bucl16 , 123 bp. M, 50-bp DNA ladder. PCR data shown in Panel A for 25 Bp strains come from two merged gel images.
    Figure Legend Snippet: Distribution of bucl genes among Burkholderia spp. select agents by PCR. Presence of bucl genes was assessed by PCR on (A) a collection of genomic DNA from 25 B . pseudomallei and 16 B . mallei strains, as well as (B) in control strains of B . thailandensis , B . cepacia , B . cenocepacia , and B . multivorans ; selected bucl genes 5 , 13 , 14 , and 16 are shown. (C) Detection and separation of selected bucl amplicons generated from the B . pseudomallei reference strain K96243 by traditional 2% agarose gel electrophoresis (left) or by capillary gel electrophoresis (right). Electropherogram generated by capillary gel electrophoresis with phospholipid nanogel matrix shows separation of amplicons over time. Amplicon sizes: bucl5 , 216 bp; bucl13 , 214 bp; bucl14 , 178 bp; and bucl16 , 123 bp. M, 50-bp DNA ladder. PCR data shown in Panel A for 25 Bp strains come from two merged gel images.

    Techniques Used: Polymerase Chain Reaction, Generated, Agarose Gel Electrophoresis, Nucleic Acid Electrophoresis, Amplification

    Detection of B . pseudomallei and B . mallei by qPCR. (A) Real-time qPCR detection of bucl16 -gene target. Genomic DNA of 25 B . pseudomallei (red) and 15 B . mallei strains (blue), and control DNA from 4 B . thailandensis , 4 B . cenocepacia , and 6 B . multivorans strains (gray). (B) qPCR detection of bucl16 target in the presence of human plasma and in spleen extracts from infected mice. 25 ng of gDNA from Bp K96243 was used as a positive control (blue line). Amplification of bucl16 in qPCR reaction spiked with 5% human plasma is shown (green line). Mice were infected with Bp HBPUB10134a and CFU counts used in each qPCR reaction were based on plating spleen extracts on blood agar. Positive amplification is shown for spleen samples with 5x10 4 CFU (red lines: square, undiluted; triangle, 1:10 dilution; circle, 1:100 dilution; diamond, 1:1000 dilution) and 5x10 3 CFU (gray lines: square, undiluted; triangle, 1:10 dilution), while no amplification was obtained for crude spleen samples with original 2x10 2 CFU and 10 CFU per reaction and no template control, NTC (black lines). Inset; amplification of bucl markers 5 , 13 , 14 , and 16 by standard PCR using crude spleen samples containing 5x10 4 CFU per reaction. M, 50-bp DNA ladder.
    Figure Legend Snippet: Detection of B . pseudomallei and B . mallei by qPCR. (A) Real-time qPCR detection of bucl16 -gene target. Genomic DNA of 25 B . pseudomallei (red) and 15 B . mallei strains (blue), and control DNA from 4 B . thailandensis , 4 B . cenocepacia , and 6 B . multivorans strains (gray). (B) qPCR detection of bucl16 target in the presence of human plasma and in spleen extracts from infected mice. 25 ng of gDNA from Bp K96243 was used as a positive control (blue line). Amplification of bucl16 in qPCR reaction spiked with 5% human plasma is shown (green line). Mice were infected with Bp HBPUB10134a and CFU counts used in each qPCR reaction were based on plating spleen extracts on blood agar. Positive amplification is shown for spleen samples with 5x10 4 CFU (red lines: square, undiluted; triangle, 1:10 dilution; circle, 1:100 dilution; diamond, 1:1000 dilution) and 5x10 3 CFU (gray lines: square, undiluted; triangle, 1:10 dilution), while no amplification was obtained for crude spleen samples with original 2x10 2 CFU and 10 CFU per reaction and no template control, NTC (black lines). Inset; amplification of bucl markers 5 , 13 , 14 , and 16 by standard PCR using crude spleen samples containing 5x10 4 CFU per reaction. M, 50-bp DNA ladder.

    Techniques Used: Real-time Polymerase Chain Reaction, Infection, Mouse Assay, Positive Control, Amplification, Polymerase Chain Reaction

    3) Product Images from "A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection"

    Article Title: A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0137578

    Identification and characterization of bucl genes in B . pseudomallei reference strain K96243. (A) Schematic representation of bucl distribution. Relative position and orientation of each bucl gene is shown; six bucl genes are present on chromosome one and seven on chromosome two. (B) Summary table of bucl distribution. bucl location, orientation, and length are mapped to the genome of Bp K96243. Molecular weight of each Bucl protein encoded by each bucl allele is shown. (C) PCR amplification of 13 bucl genes from Bp K96243. Primers were designed targeting the non-collagenous conserved regions, and PCR conditions were established for all bucl amplicons at a uniform annealing temperature of 64°C. Amplicon sizes; bucl1 , 123 bp; bucl2 133 bp; bucl3 , 166 bp; bucl4 , 176 bp; bucl5 , 216 bp; bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 96 bp; bucl10 , 109 bp; bucl13 , 212 bp; bucl14 , 178 bp; bucl15 , 95 bp; and bucl16 , 123 bp; M, 50-bp DNA size marker.
    Figure Legend Snippet: Identification and characterization of bucl genes in B . pseudomallei reference strain K96243. (A) Schematic representation of bucl distribution. Relative position and orientation of each bucl gene is shown; six bucl genes are present on chromosome one and seven on chromosome two. (B) Summary table of bucl distribution. bucl location, orientation, and length are mapped to the genome of Bp K96243. Molecular weight of each Bucl protein encoded by each bucl allele is shown. (C) PCR amplification of 13 bucl genes from Bp K96243. Primers were designed targeting the non-collagenous conserved regions, and PCR conditions were established for all bucl amplicons at a uniform annealing temperature of 64°C. Amplicon sizes; bucl1 , 123 bp; bucl2 133 bp; bucl3 , 166 bp; bucl4 , 176 bp; bucl5 , 216 bp; bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 96 bp; bucl10 , 109 bp; bucl13 , 212 bp; bucl14 , 178 bp; bucl15 , 95 bp; and bucl16 , 123 bp; M, 50-bp DNA size marker.

    Techniques Used: Molecular Weight, Polymerase Chain Reaction, Amplification, Marker

    Distribution of bucl genes among Burkholderia spp. select agents by PCR. Presence of bucl genes was assessed by PCR on (A) a collection of genomic DNA from 25 B . pseudomallei and 16 B . mallei strains, as well as (B) in control strains of B . thailandensis , B . cepacia , B . cenocepacia , and B . multivorans ; selected bucl genes 5 , 13 , 14 , and 16 are shown. (C) Detection and separation of selected bucl amplicons generated from the B . pseudomallei reference strain K96243 by traditional 2% agarose gel electrophoresis (left) or by capillary gel electrophoresis (right). Electropherogram generated by capillary gel electrophoresis with phospholipid nanogel matrix shows separation of amplicons over time. Amplicon sizes: bucl5 , 216 bp; bucl13 , 214 bp; bucl14 , 178 bp; and bucl16 , 123 bp. M, 50-bp DNA ladder. PCR data shown in Panel A for 25 Bp strains come from two merged gel images.
    Figure Legend Snippet: Distribution of bucl genes among Burkholderia spp. select agents by PCR. Presence of bucl genes was assessed by PCR on (A) a collection of genomic DNA from 25 B . pseudomallei and 16 B . mallei strains, as well as (B) in control strains of B . thailandensis , B . cepacia , B . cenocepacia , and B . multivorans ; selected bucl genes 5 , 13 , 14 , and 16 are shown. (C) Detection and separation of selected bucl amplicons generated from the B . pseudomallei reference strain K96243 by traditional 2% agarose gel electrophoresis (left) or by capillary gel electrophoresis (right). Electropherogram generated by capillary gel electrophoresis with phospholipid nanogel matrix shows separation of amplicons over time. Amplicon sizes: bucl5 , 216 bp; bucl13 , 214 bp; bucl14 , 178 bp; and bucl16 , 123 bp. M, 50-bp DNA ladder. PCR data shown in Panel A for 25 Bp strains come from two merged gel images.

    Techniques Used: Polymerase Chain Reaction, Generated, Agarose Gel Electrophoresis, Nucleic Acid Electrophoresis, Amplification

    Detection of B . pseudomallei and B . mallei by qPCR. (A) Real-time qPCR detection of bucl16 -gene target. Genomic DNA of 25 B . pseudomallei (red) and 15 B . mallei strains (blue), and control DNA from 4 B . thailandensis , 4 B . cenocepacia , and 6 B . multivorans strains (gray). (B) qPCR detection of bucl16 target in the presence of human plasma and in spleen extracts from infected mice. 25 ng of gDNA from Bp K96243 was used as a positive control (blue line). Amplification of bucl16 in qPCR reaction spiked with 5% human plasma is shown (green line). Mice were infected with Bp HBPUB10134a and CFU counts used in each qPCR reaction were based on plating spleen extracts on blood agar. Positive amplification is shown for spleen samples with 5x10 4 CFU (red lines: square, undiluted; triangle, 1:10 dilution; circle, 1:100 dilution; diamond, 1:1000 dilution) and 5x10 3 CFU (gray lines: square, undiluted; triangle, 1:10 dilution), while no amplification was obtained for crude spleen samples with original 2x10 2 CFU and 10 CFU per reaction and no template control, NTC (black lines). Inset; amplification of bucl markers 5 , 13 , 14 , and 16 by standard PCR using crude spleen samples containing 5x10 4 CFU per reaction. M, 50-bp DNA ladder.
    Figure Legend Snippet: Detection of B . pseudomallei and B . mallei by qPCR. (A) Real-time qPCR detection of bucl16 -gene target. Genomic DNA of 25 B . pseudomallei (red) and 15 B . mallei strains (blue), and control DNA from 4 B . thailandensis , 4 B . cenocepacia , and 6 B . multivorans strains (gray). (B) qPCR detection of bucl16 target in the presence of human plasma and in spleen extracts from infected mice. 25 ng of gDNA from Bp K96243 was used as a positive control (blue line). Amplification of bucl16 in qPCR reaction spiked with 5% human plasma is shown (green line). Mice were infected with Bp HBPUB10134a and CFU counts used in each qPCR reaction were based on plating spleen extracts on blood agar. Positive amplification is shown for spleen samples with 5x10 4 CFU (red lines: square, undiluted; triangle, 1:10 dilution; circle, 1:100 dilution; diamond, 1:1000 dilution) and 5x10 3 CFU (gray lines: square, undiluted; triangle, 1:10 dilution), while no amplification was obtained for crude spleen samples with original 2x10 2 CFU and 10 CFU per reaction and no template control, NTC (black lines). Inset; amplification of bucl markers 5 , 13 , 14 , and 16 by standard PCR using crude spleen samples containing 5x10 4 CFU per reaction. M, 50-bp DNA ladder.

    Techniques Used: Real-time Polymerase Chain Reaction, Infection, Mouse Assay, Positive Control, Amplification, Polymerase Chain Reaction

    4) Product Images from "Complex translational regulation of BACE1 involves upstream AUGs and stimulatory elements within the 5? untranslated region"

    Article Title: Complex translational regulation of BACE1 involves upstream AUGs and stimulatory elements within the 5? untranslated region

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkm191

    BACE1 mRNA in human brain and pancreas contains the full-length 5′ UTR. ( A ) Schematic representation of the riboprobe. The riboprobe was designed to protect most of the transcript leader and 166 nt of the ORF. A full-length BACE1 5′ UTR was expected to protect a fragment of 536 nt (from 85 to 621), while the putative alternatively spliced variant was expected to protect a fragment of 403 nt (from 218 to 621). Arrows represent uAUGs, while black boxes represent uORFs. ( B ) Total RNAs from human brain (Br) and pancreas (Pan) have similar quality. Equal amounts of total RNAs were separate on agarose gel. ( C ) RNase protection assay. 10 μg of total RNA either from human brain or pancreas were incubated with 32 P-labeled riboprobe for BACE1 alone, or BACE1 and GAPDH together. Protected signal for BACE1 (∼500 bp) and GAPDH (∼240 bp) are indicated with arrows. Cont − RNA = control reaction without RNA, Br = human brain, Pan = human pancreas, cont + RNA = control reaction with yeast RNA, ladder is γ-ATP labeled 50 bp DNA marker. ( D ) qPCR analysis. The values were normalized on L19 expression (L19 ratio brain/pancreas = 0.6).
    Figure Legend Snippet: BACE1 mRNA in human brain and pancreas contains the full-length 5′ UTR. ( A ) Schematic representation of the riboprobe. The riboprobe was designed to protect most of the transcript leader and 166 nt of the ORF. A full-length BACE1 5′ UTR was expected to protect a fragment of 536 nt (from 85 to 621), while the putative alternatively spliced variant was expected to protect a fragment of 403 nt (from 218 to 621). Arrows represent uAUGs, while black boxes represent uORFs. ( B ) Total RNAs from human brain (Br) and pancreas (Pan) have similar quality. Equal amounts of total RNAs were separate on agarose gel. ( C ) RNase protection assay. 10 μg of total RNA either from human brain or pancreas were incubated with 32 P-labeled riboprobe for BACE1 alone, or BACE1 and GAPDH together. Protected signal for BACE1 (∼500 bp) and GAPDH (∼240 bp) are indicated with arrows. Cont − RNA = control reaction without RNA, Br = human brain, Pan = human pancreas, cont + RNA = control reaction with yeast RNA, ladder is γ-ATP labeled 50 bp DNA marker. ( D ) qPCR analysis. The values were normalized on L19 expression (L19 ratio brain/pancreas = 0.6).

    Techniques Used: Variant Assay, Agarose Gel Electrophoresis, Rnase Protection Assay, Incubation, Labeling, Marker, Real-time Polymerase Chain Reaction, Expressing

    5) Product Images from "Nucleotide Excision Repair and Transcription-coupled DNA Repair Abrogate the Impact of DNA Damage on Transcription *"

    Article Title: Nucleotide Excision Repair and Transcription-coupled DNA Repair Abrogate the Impact of DNA Damage on Transcription *

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M115.685271

    B[ a ]P- N 6 -dA blocks hRNAPII elongation. For each DNA template studied, four separate reactions were carried out as indicated above each lane in the gel: lane M , New England Biolabs 50-bp DNA ladder labeled with [ 32 P]phosphate; lanes 1–4 , results for transcription using the unmodified DNA template illustrated in Fig. 1 ; lanes 5–8 , transcription results using the DNA template modified with a B[ a ]P- N 6 -dA adduct, also illustrated in Fig. 1 ; lanes 9–12 , results using the control DNA template containing a CMV immediate early promoter supplied with the HeLa nuclear extract. The components for each transcription reaction are indicated above the lanes .
    Figure Legend Snippet: B[ a ]P- N 6 -dA blocks hRNAPII elongation. For each DNA template studied, four separate reactions were carried out as indicated above each lane in the gel: lane M , New England Biolabs 50-bp DNA ladder labeled with [ 32 P]phosphate; lanes 1–4 , results for transcription using the unmodified DNA template illustrated in Fig. 1 ; lanes 5–8 , transcription results using the DNA template modified with a B[ a ]P- N 6 -dA adduct, also illustrated in Fig. 1 ; lanes 9–12 , results using the control DNA template containing a CMV immediate early promoter supplied with the HeLa nuclear extract. The components for each transcription reaction are indicated above the lanes .

    Techniques Used: Labeling, Modification

    DNA templates for in vitro transcription were characterized following synthesis. A , I-PpoI digestion of DNA templates for in vitro transcription. Lane M , New England Biolabs 50-bp DNA ladder labeled with [ 32 P]phosphate; lane 1 , I-PpoI digestion of unmodified control DNA template; lane 2 , I-PpoI digestion of B[ a ]P- N 6 -dA-modified DNA template. B , BsiWI digestion of DNA templates for in vitro transcription. Lane M , IDT 20/100 DNA ladder labeled with [ 32 P]phosphate; lane 1 , BsiWI digestion of unmodified control DNA template; lane 2 , BsiWI digestion of B[ a ]P- N 6 -dA-modified DNA template.
    Figure Legend Snippet: DNA templates for in vitro transcription were characterized following synthesis. A , I-PpoI digestion of DNA templates for in vitro transcription. Lane M , New England Biolabs 50-bp DNA ladder labeled with [ 32 P]phosphate; lane 1 , I-PpoI digestion of unmodified control DNA template; lane 2 , I-PpoI digestion of B[ a ]P- N 6 -dA-modified DNA template. B , BsiWI digestion of DNA templates for in vitro transcription. Lane M , IDT 20/100 DNA ladder labeled with [ 32 P]phosphate; lane 1 , BsiWI digestion of unmodified control DNA template; lane 2 , BsiWI digestion of B[ a ]P- N 6 -dA-modified DNA template.

    Techniques Used: In Vitro, Labeling, Modification

    6) Product Images from "A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection"

    Article Title: A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0137578

    Identification and characterization of bucl genes in B . pseudomallei reference strain K96243. (A) Schematic representation of bucl distribution. Relative position and orientation of each bucl gene is shown; six bucl genes are present on chromosome one and seven on chromosome two. (B) Summary table of bucl distribution. bucl location, orientation, and length are mapped to the genome of Bp K96243. Molecular weight of each Bucl protein encoded by each bucl allele is shown. (C) PCR amplification of 13 bucl genes from Bp K96243. Primers were designed targeting the non-collagenous conserved regions, and PCR conditions were established for all bucl amplicons at a uniform annealing temperature of 64°C. Amplicon sizes; bucl1 , 123 bp; bucl2 133 bp; bucl3 , 166 bp; bucl4 , 176 bp; bucl5 , 216 bp; bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 96 bp; bucl10 , 109 bp; bucl13 , 212 bp; bucl14 , 178 bp; bucl15 , 95 bp; and bucl16 , 123 bp; M, 50-bp DNA size marker.
    Figure Legend Snippet: Identification and characterization of bucl genes in B . pseudomallei reference strain K96243. (A) Schematic representation of bucl distribution. Relative position and orientation of each bucl gene is shown; six bucl genes are present on chromosome one and seven on chromosome two. (B) Summary table of bucl distribution. bucl location, orientation, and length are mapped to the genome of Bp K96243. Molecular weight of each Bucl protein encoded by each bucl allele is shown. (C) PCR amplification of 13 bucl genes from Bp K96243. Primers were designed targeting the non-collagenous conserved regions, and PCR conditions were established for all bucl amplicons at a uniform annealing temperature of 64°C. Amplicon sizes; bucl1 , 123 bp; bucl2 133 bp; bucl3 , 166 bp; bucl4 , 176 bp; bucl5 , 216 bp; bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 96 bp; bucl10 , 109 bp; bucl13 , 212 bp; bucl14 , 178 bp; bucl15 , 95 bp; and bucl16 , 123 bp; M, 50-bp DNA size marker.

    Techniques Used: Molecular Weight, Polymerase Chain Reaction, Amplification, Marker

    Distribution of bucl genes among Burkholderia spp. select agents by PCR. Presence of bucl genes was assessed by PCR on (A) a collection of genomic DNA from 25 B . pseudomallei and 16 B . mallei strains, as well as (B) in control strains of B . thailandensis , B . cepacia , B . cenocepacia , and B . multivorans ; selected bucl genes 5 , 13 , 14 , and 16 are shown. (C) Detection and separation of selected bucl amplicons generated from the B . pseudomallei reference strain K96243 by traditional 2% agarose gel electrophoresis (left) or by capillary gel electrophoresis (right). Electropherogram generated by capillary gel electrophoresis with phospholipid nanogel matrix shows separation of amplicons over time. Amplicon sizes: bucl5 , 216 bp; bucl13 , 214 bp; bucl14 , 178 bp; and bucl16 , 123 bp. M, 50-bp DNA ladder. PCR data shown in Panel A for 25 Bp strains come from two merged gel images.
    Figure Legend Snippet: Distribution of bucl genes among Burkholderia spp. select agents by PCR. Presence of bucl genes was assessed by PCR on (A) a collection of genomic DNA from 25 B . pseudomallei and 16 B . mallei strains, as well as (B) in control strains of B . thailandensis , B . cepacia , B . cenocepacia , and B . multivorans ; selected bucl genes 5 , 13 , 14 , and 16 are shown. (C) Detection and separation of selected bucl amplicons generated from the B . pseudomallei reference strain K96243 by traditional 2% agarose gel electrophoresis (left) or by capillary gel electrophoresis (right). Electropherogram generated by capillary gel electrophoresis with phospholipid nanogel matrix shows separation of amplicons over time. Amplicon sizes: bucl5 , 216 bp; bucl13 , 214 bp; bucl14 , 178 bp; and bucl16 , 123 bp. M, 50-bp DNA ladder. PCR data shown in Panel A for 25 Bp strains come from two merged gel images.

    Techniques Used: Polymerase Chain Reaction, Generated, Agarose Gel Electrophoresis, Nucleic Acid Electrophoresis, Amplification

    Detection of B . pseudomallei and B . mallei by qPCR. (A) Real-time qPCR detection of bucl16 -gene target. Genomic DNA of 25 B . pseudomallei (red) and 15 B . mallei strains (blue), and control DNA from 4 B . thailandensis , 4 B . cenocepacia , and 6 B . multivorans strains (gray). (B) qPCR detection of bucl16 target in the presence of human plasma and in spleen extracts from infected mice. 25 ng of gDNA from Bp K96243 was used as a positive control (blue line). Amplification of bucl16 in qPCR reaction spiked with 5% human plasma is shown (green line). Mice were infected with Bp HBPUB10134a and CFU counts used in each qPCR reaction were based on plating spleen extracts on blood agar. Positive amplification is shown for spleen samples with 5x10 4 CFU (red lines: square, undiluted; triangle, 1:10 dilution; circle, 1:100 dilution; diamond, 1:1000 dilution) and 5x10 3 CFU (gray lines: square, undiluted; triangle, 1:10 dilution), while no amplification was obtained for crude spleen samples with original 2x10 2 CFU and 10 CFU per reaction and no template control, NTC (black lines). Inset; amplification of bucl markers 5 , 13 , 14 , and 16 by standard PCR using crude spleen samples containing 5x10 4 CFU per reaction. M, 50-bp DNA ladder.
    Figure Legend Snippet: Detection of B . pseudomallei and B . mallei by qPCR. (A) Real-time qPCR detection of bucl16 -gene target. Genomic DNA of 25 B . pseudomallei (red) and 15 B . mallei strains (blue), and control DNA from 4 B . thailandensis , 4 B . cenocepacia , and 6 B . multivorans strains (gray). (B) qPCR detection of bucl16 target in the presence of human plasma and in spleen extracts from infected mice. 25 ng of gDNA from Bp K96243 was used as a positive control (blue line). Amplification of bucl16 in qPCR reaction spiked with 5% human plasma is shown (green line). Mice were infected with Bp HBPUB10134a and CFU counts used in each qPCR reaction were based on plating spleen extracts on blood agar. Positive amplification is shown for spleen samples with 5x10 4 CFU (red lines: square, undiluted; triangle, 1:10 dilution; circle, 1:100 dilution; diamond, 1:1000 dilution) and 5x10 3 CFU (gray lines: square, undiluted; triangle, 1:10 dilution), while no amplification was obtained for crude spleen samples with original 2x10 2 CFU and 10 CFU per reaction and no template control, NTC (black lines). Inset; amplification of bucl markers 5 , 13 , 14 , and 16 by standard PCR using crude spleen samples containing 5x10 4 CFU per reaction. M, 50-bp DNA ladder.

    Techniques Used: Real-time Polymerase Chain Reaction, Infection, Mouse Assay, Positive Control, Amplification, Polymerase Chain Reaction

    7) Product Images from "Effective detection of human adenovirus in hawaiian waters using enhanced pcr methods"

    Article Title: Effective detection of human adenovirus in hawaiian waters using enhanced pcr methods

    Journal: Virology Journal

    doi: 10.1186/1743-422X-8-57

    Agarose gel electrophoresis of PCR detection of HAdV in urban wastewaters of three different treatments stages . (A) Amplified with primer set ADV-F/ADV-R. (B) amplified with primer set nehex3deg/nehex4deg. HAdV were detected from 100 mL of untreated raw influenced (lane 1), pre-disinfection (lane 2), and post-disinfection/effluence (lane 3) stages. Lane M = 50-bp DNA marker, lane C+ = positive control using HAdV DNA, and lane C- = no template control.
    Figure Legend Snippet: Agarose gel electrophoresis of PCR detection of HAdV in urban wastewaters of three different treatments stages . (A) Amplified with primer set ADV-F/ADV-R. (B) amplified with primer set nehex3deg/nehex4deg. HAdV were detected from 100 mL of untreated raw influenced (lane 1), pre-disinfection (lane 2), and post-disinfection/effluence (lane 3) stages. Lane M = 50-bp DNA marker, lane C+ = positive control using HAdV DNA, and lane C- = no template control.

    Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification, Marker, Positive Control

    8) Product Images from "New Approaches for Enhanced Detection of Enteroviruses from Hawaiian Environmental Waters"

    Article Title: New Approaches for Enhanced Detection of Enteroviruses from Hawaiian Environmental Waters

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0032442

    Agarose gel depicting enterovirus detection from urban sewage. Amplified with primer set EQ-1/EQ-2. Detection from 100 mL of raw influent, post-primary clarification/pre-UV disinfection, and post-disinfection/effluent treatment stages. M = 50 bp DNA ladder. (-) = no template control.
    Figure Legend Snippet: Agarose gel depicting enterovirus detection from urban sewage. Amplified with primer set EQ-1/EQ-2. Detection from 100 mL of raw influent, post-primary clarification/pre-UV disinfection, and post-disinfection/effluent treatment stages. M = 50 bp DNA ladder. (-) = no template control.

    Techniques Used: Agarose Gel Electrophoresis, Amplification, Clarification Assay

    Related Articles

    Amplification:

    Article Title: A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection
    Article Snippet: .. Amplicon sizes based on Bp K96243: In A) bucl2 , 133 bp; bucl3 , 166 bp; and bucl10 , 109 bp; In B) bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 243 bp; and bucl15 , 95 bp.M, 50-bp DNA ladder. .. PCR data shown in panels A and B for 25 Bp strains come from two merged gel images. (JPG) Click here for additional data file.

    Article Title: Effective detection of human adenovirus in hawaiian waters using enhanced pcr methods
    Article Snippet: .. Amplification started with an initial denaturation at 94°C for 5 min, followed by 40 cycles of denaturation at 94°C for 30 sec, annealing at 56°C for 30 sec, extension at 72°C for 30 sec, and a final extension at 72°C for 5 min. All PCR products were subjected to 2% agarose gel electrophoreis alongside a 50-bp DNA marker (NEB, MA), stained with Ethidium Bromide (Sigma-Aldrich, MO) and viewed with the Molecular Imager Gel Doc XR+ system (BioRad Laboratories Inc., CA). .. The 8 primer sets that successfully generated products of respective sizes (Table ) were subjected to PCR condition optimization.

    Agarose Gel Electrophoresis:

    Article Title: Effective detection of human adenovirus in hawaiian waters using enhanced pcr methods
    Article Snippet: .. Amplification started with an initial denaturation at 94°C for 5 min, followed by 40 cycles of denaturation at 94°C for 30 sec, annealing at 56°C for 30 sec, extension at 72°C for 30 sec, and a final extension at 72°C for 5 min. All PCR products were subjected to 2% agarose gel electrophoreis alongside a 50-bp DNA marker (NEB, MA), stained with Ethidium Bromide (Sigma-Aldrich, MO) and viewed with the Molecular Imager Gel Doc XR+ system (BioRad Laboratories Inc., CA). .. The 8 primer sets that successfully generated products of respective sizes (Table ) were subjected to PCR condition optimization.

    Article Title: A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection
    Article Snippet: .. Resultant PCR products were analyzed on a 2% agarose gel with a 50-bp ladder DNA standard (New England Biolabs Inc., Boston, MA). .. Gels were imaged using the Eagle Eye II (Stratagene, La Jolla, CA), and FOTO/ Analyst Investigator/ Eclipse gel documentation workstation (Fotodyne, Harland, WI).

    Size-exclusion Chromatography:

    Article Title: Effective detection of human adenovirus in hawaiian waters using enhanced pcr methods
    Article Snippet: .. Amplification started with an initial denaturation at 94°C for 5 min, followed by 40 cycles of denaturation at 94°C for 30 sec, annealing at 56°C for 30 sec, extension at 72°C for 30 sec, and a final extension at 72°C for 5 min. All PCR products were subjected to 2% agarose gel electrophoreis alongside a 50-bp DNA marker (NEB, MA), stained with Ethidium Bromide (Sigma-Aldrich, MO) and viewed with the Molecular Imager Gel Doc XR+ system (BioRad Laboratories Inc., CA). .. The 8 primer sets that successfully generated products of respective sizes (Table ) were subjected to PCR condition optimization.

    Labeling:

    Article Title: Complex translational regulation of BACE1 involves upstream AUGs and stimulatory elements within the 5? untranslated region
    Article Snippet: .. A [γ-32 P]-ATP labeled 50 bp DNA ladder (New England Biolabs, Beverly, MA, USA) was used as a size reference on the gel. .. Real-time PCR analysis Here, ∼2 μg of total RNA was used for first strand cDNAs synthesis with random primers and Superscript II reverse transcriptase (Invitrogen) according to the manufacturer's instructions.

    Polymerase Chain Reaction:

    Article Title: Effective detection of human adenovirus in hawaiian waters using enhanced pcr methods
    Article Snippet: .. Amplification started with an initial denaturation at 94°C for 5 min, followed by 40 cycles of denaturation at 94°C for 30 sec, annealing at 56°C for 30 sec, extension at 72°C for 30 sec, and a final extension at 72°C for 5 min. All PCR products were subjected to 2% agarose gel electrophoreis alongside a 50-bp DNA marker (NEB, MA), stained with Ethidium Bromide (Sigma-Aldrich, MO) and viewed with the Molecular Imager Gel Doc XR+ system (BioRad Laboratories Inc., CA). .. The 8 primer sets that successfully generated products of respective sizes (Table ) were subjected to PCR condition optimization.

    Article Title: A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection
    Article Snippet: .. Resultant PCR products were analyzed on a 2% agarose gel with a 50-bp ladder DNA standard (New England Biolabs Inc., Boston, MA). .. Gels were imaged using the Eagle Eye II (Stratagene, La Jolla, CA), and FOTO/ Analyst Investigator/ Eclipse gel documentation workstation (Fotodyne, Harland, WI).

    Article Title: New Approaches for Enhanced Detection of Enteroviruses from Hawaiian Environmental Waters
    Article Snippet: .. A 50-bp DNA ladder (NEB, MA) was used for indication of PCR product fragment size. .. The Molecular Imager Gel Doc XR+system (BioRad Laboratories, Inc., CA) was used to visualize results under UV light.

    other:

    Article Title: Intravesicle Isothermal DNA Replication
    Article Snippet: Materials The IsoAmp tHDA kit and 50 bp DNA ladder were from New England BioLabs.

    Marker:

    Article Title: Effective detection of human adenovirus in hawaiian waters using enhanced pcr methods
    Article Snippet: .. Amplification started with an initial denaturation at 94°C for 5 min, followed by 40 cycles of denaturation at 94°C for 30 sec, annealing at 56°C for 30 sec, extension at 72°C for 30 sec, and a final extension at 72°C for 5 min. All PCR products were subjected to 2% agarose gel electrophoreis alongside a 50-bp DNA marker (NEB, MA), stained with Ethidium Bromide (Sigma-Aldrich, MO) and viewed with the Molecular Imager Gel Doc XR+ system (BioRad Laboratories Inc., CA). .. The 8 primer sets that successfully generated products of respective sizes (Table ) were subjected to PCR condition optimization.

    Article Title: A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection
    Article Snippet: .. The 50-bp DNA ladder (New England BioLabs, Ipswich, MA) was used as a molecular size marker. .. Separations were performed on a Beckman Coulter P/ACE MDQ system equipped with a laser-induced fluorescence detection module and a 3 mW air-cooled argon ion laser (λex = 488 nm and λem = 520 nm).

    Staining:

    Article Title: Effective detection of human adenovirus in hawaiian waters using enhanced pcr methods
    Article Snippet: .. Amplification started with an initial denaturation at 94°C for 5 min, followed by 40 cycles of denaturation at 94°C for 30 sec, annealing at 56°C for 30 sec, extension at 72°C for 30 sec, and a final extension at 72°C for 5 min. All PCR products were subjected to 2% agarose gel electrophoreis alongside a 50-bp DNA marker (NEB, MA), stained with Ethidium Bromide (Sigma-Aldrich, MO) and viewed with the Molecular Imager Gel Doc XR+ system (BioRad Laboratories Inc., CA). .. The 8 primer sets that successfully generated products of respective sizes (Table ) were subjected to PCR condition optimization.

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    New England Biolabs bp dna ladder
    The effect of temperature on <t>tHDA</t> enzymatic activity . (A) The influence of temperature on the enzymatic activity of the isothermal tHDA system. Samples were incubated at 65°C (lane 2), 37°C (lane 3), 23°C (lane 4), and 4°C (lane 5) for 1.5 h. Lane 1 contains a 50 bp <t>DNA</t> ladder. The 1350 bp, 100 bp, and 50 bp bands are labeled. (B) The influence of overnight incubation temperature on the enzymatic activity of the isothermal tHDA system. Samples were incubated at 4°C (lane 2) and 23°C (lane 3) overnight prior to incubation at 65°C for 1.5 h. Lane 1 is a 50 bp DNA ladder. Reaction products were observed by ethidium bromide staining of a 1.8% agarose gel.
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    The effect of temperature on tHDA enzymatic activity . (A) The influence of temperature on the enzymatic activity of the isothermal tHDA system. Samples were incubated at 65°C (lane 2), 37°C (lane 3), 23°C (lane 4), and 4°C (lane 5) for 1.5 h. Lane 1 contains a 50 bp DNA ladder. The 1350 bp, 100 bp, and 50 bp bands are labeled. (B) The influence of overnight incubation temperature on the enzymatic activity of the isothermal tHDA system. Samples were incubated at 4°C (lane 2) and 23°C (lane 3) overnight prior to incubation at 65°C for 1.5 h. Lane 1 is a 50 bp DNA ladder. Reaction products were observed by ethidium bromide staining of a 1.8% agarose gel.

    Journal: BMC Research Notes

    Article Title: Intravesicle Isothermal DNA Replication

    doi: 10.1186/1756-0500-4-128

    Figure Lengend Snippet: The effect of temperature on tHDA enzymatic activity . (A) The influence of temperature on the enzymatic activity of the isothermal tHDA system. Samples were incubated at 65°C (lane 2), 37°C (lane 3), 23°C (lane 4), and 4°C (lane 5) for 1.5 h. Lane 1 contains a 50 bp DNA ladder. The 1350 bp, 100 bp, and 50 bp bands are labeled. (B) The influence of overnight incubation temperature on the enzymatic activity of the isothermal tHDA system. Samples were incubated at 4°C (lane 2) and 23°C (lane 3) overnight prior to incubation at 65°C for 1.5 h. Lane 1 is a 50 bp DNA ladder. Reaction products were observed by ethidium bromide staining of a 1.8% agarose gel.

    Article Snippet: Materials The IsoAmp tHDA kit and 50 bp DNA ladder were from New England BioLabs.

    Techniques: Activity Assay, Incubation, Labeling, Staining, Agarose Gel Electrophoresis

    The influence of freeze/thaw cycles on tHDA enzymatic activity . Unencapsulated reaction mixtures were subjected to either 0 (lane 2), 5 (lane 3), 10 (lane 4), or 20 (lane 5) cycles of freeze-thawing. Lane 1 is a 50 bp DNA ladder. The 1350 bp, 100 bp, and 50 bp bands are labeled. Reaction products were visualized by ethidium bromide staining of a 1.8% agarose gel. The full length reaction product is 85 bp.

    Journal: BMC Research Notes

    Article Title: Intravesicle Isothermal DNA Replication

    doi: 10.1186/1756-0500-4-128

    Figure Lengend Snippet: The influence of freeze/thaw cycles on tHDA enzymatic activity . Unencapsulated reaction mixtures were subjected to either 0 (lane 2), 5 (lane 3), 10 (lane 4), or 20 (lane 5) cycles of freeze-thawing. Lane 1 is a 50 bp DNA ladder. The 1350 bp, 100 bp, and 50 bp bands are labeled. Reaction products were visualized by ethidium bromide staining of a 1.8% agarose gel. The full length reaction product is 85 bp.

    Article Snippet: Materials The IsoAmp tHDA kit and 50 bp DNA ladder were from New England BioLabs.

    Techniques: Activity Assay, Labeling, Staining, Agarose Gel Electrophoresis

    Intravesicular isothermal replication . Lanes 1 and 7 contain a 50 bp DNA ladder. Lanes 2 and 3 are from unencapsulated reactions and lanes 4-6 are within phospholipid vesicles. Lanes 2 and 3 are isothermal replication reactions under standard conditions except that 0.5 mM CaCl 2 was added. CaCl 2 is needed for proteinase K activity. Further, lane 3 contained 0.9 units of proteinase K, demonstrating that proteinase K is capable of digesting components of the tHDA system and thus inhibiting DNA amplification. A similar experiment was conducted inside of vesicles with proteinase K added to the outside of the vesicles (lane 4) and proteinase K added to both the inside and the outside of the vesicles (lane 5). Finally, to further demonstrate that the reaction was encapsulated, dNTPs were added extravesicularly resulting in an inability to replicate DNA since dNTPs are incapable of crossing POPC membranes (lane 6).

    Journal: BMC Research Notes

    Article Title: Intravesicle Isothermal DNA Replication

    doi: 10.1186/1756-0500-4-128

    Figure Lengend Snippet: Intravesicular isothermal replication . Lanes 1 and 7 contain a 50 bp DNA ladder. Lanes 2 and 3 are from unencapsulated reactions and lanes 4-6 are within phospholipid vesicles. Lanes 2 and 3 are isothermal replication reactions under standard conditions except that 0.5 mM CaCl 2 was added. CaCl 2 is needed for proteinase K activity. Further, lane 3 contained 0.9 units of proteinase K, demonstrating that proteinase K is capable of digesting components of the tHDA system and thus inhibiting DNA amplification. A similar experiment was conducted inside of vesicles with proteinase K added to the outside of the vesicles (lane 4) and proteinase K added to both the inside and the outside of the vesicles (lane 5). Finally, to further demonstrate that the reaction was encapsulated, dNTPs were added extravesicularly resulting in an inability to replicate DNA since dNTPs are incapable of crossing POPC membranes (lane 6).

    Article Snippet: Materials The IsoAmp tHDA kit and 50 bp DNA ladder were from New England BioLabs.

    Techniques: Activity Assay, Amplification

    Identification and characterization of bucl genes in B . pseudomallei reference strain K96243. (A) Schematic representation of bucl distribution. Relative position and orientation of each bucl gene is shown; six bucl genes are present on chromosome one and seven on chromosome two. (B) Summary table of bucl distribution. bucl location, orientation, and length are mapped to the genome of Bp K96243. Molecular weight of each Bucl protein encoded by each bucl allele is shown. (C) PCR amplification of 13 bucl genes from Bp K96243. Primers were designed targeting the non-collagenous conserved regions, and PCR conditions were established for all bucl amplicons at a uniform annealing temperature of 64°C. Amplicon sizes; bucl1 , 123 bp; bucl2 133 bp; bucl3 , 166 bp; bucl4 , 176 bp; bucl5 , 216 bp; bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 96 bp; bucl10 , 109 bp; bucl13 , 212 bp; bucl14 , 178 bp; bucl15 , 95 bp; and bucl16 , 123 bp; M, 50-bp DNA size marker.

    Journal: PLoS ONE

    Article Title: A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection

    doi: 10.1371/journal.pone.0137578

    Figure Lengend Snippet: Identification and characterization of bucl genes in B . pseudomallei reference strain K96243. (A) Schematic representation of bucl distribution. Relative position and orientation of each bucl gene is shown; six bucl genes are present on chromosome one and seven on chromosome two. (B) Summary table of bucl distribution. bucl location, orientation, and length are mapped to the genome of Bp K96243. Molecular weight of each Bucl protein encoded by each bucl allele is shown. (C) PCR amplification of 13 bucl genes from Bp K96243. Primers were designed targeting the non-collagenous conserved regions, and PCR conditions were established for all bucl amplicons at a uniform annealing temperature of 64°C. Amplicon sizes; bucl1 , 123 bp; bucl2 133 bp; bucl3 , 166 bp; bucl4 , 176 bp; bucl5 , 216 bp; bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 96 bp; bucl10 , 109 bp; bucl13 , 212 bp; bucl14 , 178 bp; bucl15 , 95 bp; and bucl16 , 123 bp; M, 50-bp DNA size marker.

    Article Snippet: Amplicon sizes based on Bp K96243: In A) bucl2 , 133 bp; bucl3 , 166 bp; and bucl10 , 109 bp; In B) bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 243 bp; and bucl15 , 95 bp.M, 50-bp DNA ladder.

    Techniques: Molecular Weight, Polymerase Chain Reaction, Amplification, Marker

    Distribution of bucl genes among Burkholderia spp. select agents by PCR. Presence of bucl genes was assessed by PCR on (A) a collection of genomic DNA from 25 B . pseudomallei and 16 B . mallei strains, as well as (B) in control strains of B . thailandensis , B . cepacia , B . cenocepacia , and B . multivorans ; selected bucl genes 5 , 13 , 14 , and 16 are shown. (C) Detection and separation of selected bucl amplicons generated from the B . pseudomallei reference strain K96243 by traditional 2% agarose gel electrophoresis (left) or by capillary gel electrophoresis (right). Electropherogram generated by capillary gel electrophoresis with phospholipid nanogel matrix shows separation of amplicons over time. Amplicon sizes: bucl5 , 216 bp; bucl13 , 214 bp; bucl14 , 178 bp; and bucl16 , 123 bp. M, 50-bp DNA ladder. PCR data shown in Panel A for 25 Bp strains come from two merged gel images.

    Journal: PLoS ONE

    Article Title: A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection

    doi: 10.1371/journal.pone.0137578

    Figure Lengend Snippet: Distribution of bucl genes among Burkholderia spp. select agents by PCR. Presence of bucl genes was assessed by PCR on (A) a collection of genomic DNA from 25 B . pseudomallei and 16 B . mallei strains, as well as (B) in control strains of B . thailandensis , B . cepacia , B . cenocepacia , and B . multivorans ; selected bucl genes 5 , 13 , 14 , and 16 are shown. (C) Detection and separation of selected bucl amplicons generated from the B . pseudomallei reference strain K96243 by traditional 2% agarose gel electrophoresis (left) or by capillary gel electrophoresis (right). Electropherogram generated by capillary gel electrophoresis with phospholipid nanogel matrix shows separation of amplicons over time. Amplicon sizes: bucl5 , 216 bp; bucl13 , 214 bp; bucl14 , 178 bp; and bucl16 , 123 bp. M, 50-bp DNA ladder. PCR data shown in Panel A for 25 Bp strains come from two merged gel images.

    Article Snippet: Amplicon sizes based on Bp K96243: In A) bucl2 , 133 bp; bucl3 , 166 bp; and bucl10 , 109 bp; In B) bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 243 bp; and bucl15 , 95 bp.M, 50-bp DNA ladder.

    Techniques: Polymerase Chain Reaction, Generated, Agarose Gel Electrophoresis, Nucleic Acid Electrophoresis, Amplification

    Detection of B . pseudomallei and B . mallei by qPCR. (A) Real-time qPCR detection of bucl16 -gene target. Genomic DNA of 25 B . pseudomallei (red) and 15 B . mallei strains (blue), and control DNA from 4 B . thailandensis , 4 B . cenocepacia , and 6 B . multivorans strains (gray). (B) qPCR detection of bucl16 target in the presence of human plasma and in spleen extracts from infected mice. 25 ng of gDNA from Bp K96243 was used as a positive control (blue line). Amplification of bucl16 in qPCR reaction spiked with 5% human plasma is shown (green line). Mice were infected with Bp HBPUB10134a and CFU counts used in each qPCR reaction were based on plating spleen extracts on blood agar. Positive amplification is shown for spleen samples with 5x10 4 CFU (red lines: square, undiluted; triangle, 1:10 dilution; circle, 1:100 dilution; diamond, 1:1000 dilution) and 5x10 3 CFU (gray lines: square, undiluted; triangle, 1:10 dilution), while no amplification was obtained for crude spleen samples with original 2x10 2 CFU and 10 CFU per reaction and no template control, NTC (black lines). Inset; amplification of bucl markers 5 , 13 , 14 , and 16 by standard PCR using crude spleen samples containing 5x10 4 CFU per reaction. M, 50-bp DNA ladder.

    Journal: PLoS ONE

    Article Title: A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection

    doi: 10.1371/journal.pone.0137578

    Figure Lengend Snippet: Detection of B . pseudomallei and B . mallei by qPCR. (A) Real-time qPCR detection of bucl16 -gene target. Genomic DNA of 25 B . pseudomallei (red) and 15 B . mallei strains (blue), and control DNA from 4 B . thailandensis , 4 B . cenocepacia , and 6 B . multivorans strains (gray). (B) qPCR detection of bucl16 target in the presence of human plasma and in spleen extracts from infected mice. 25 ng of gDNA from Bp K96243 was used as a positive control (blue line). Amplification of bucl16 in qPCR reaction spiked with 5% human plasma is shown (green line). Mice were infected with Bp HBPUB10134a and CFU counts used in each qPCR reaction were based on plating spleen extracts on blood agar. Positive amplification is shown for spleen samples with 5x10 4 CFU (red lines: square, undiluted; triangle, 1:10 dilution; circle, 1:100 dilution; diamond, 1:1000 dilution) and 5x10 3 CFU (gray lines: square, undiluted; triangle, 1:10 dilution), while no amplification was obtained for crude spleen samples with original 2x10 2 CFU and 10 CFU per reaction and no template control, NTC (black lines). Inset; amplification of bucl markers 5 , 13 , 14 , and 16 by standard PCR using crude spleen samples containing 5x10 4 CFU per reaction. M, 50-bp DNA ladder.

    Article Snippet: Amplicon sizes based on Bp K96243: In A) bucl2 , 133 bp; bucl3 , 166 bp; and bucl10 , 109 bp; In B) bucl6 , 115 bp; bucl7 , 264 bp; bucl8 , 243 bp; and bucl15 , 95 bp.M, 50-bp DNA ladder.

    Techniques: Real-time Polymerase Chain Reaction, Infection, Mouse Assay, Positive Control, Amplification, Polymerase Chain Reaction

    BACE1 mRNA in human brain and pancreas contains the full-length 5′ UTR. ( A ) Schematic representation of the riboprobe. The riboprobe was designed to protect most of the transcript leader and 166 nt of the ORF. A full-length BACE1 5′ UTR was expected to protect a fragment of 536 nt (from 85 to 621), while the putative alternatively spliced variant was expected to protect a fragment of 403 nt (from 218 to 621). Arrows represent uAUGs, while black boxes represent uORFs. ( B ) Total RNAs from human brain (Br) and pancreas (Pan) have similar quality. Equal amounts of total RNAs were separate on agarose gel. ( C ) RNase protection assay. 10 μg of total RNA either from human brain or pancreas were incubated with 32 P-labeled riboprobe for BACE1 alone, or BACE1 and GAPDH together. Protected signal for BACE1 (∼500 bp) and GAPDH (∼240 bp) are indicated with arrows. Cont − RNA = control reaction without RNA, Br = human brain, Pan = human pancreas, cont + RNA = control reaction with yeast RNA, ladder is γ-ATP labeled 50 bp DNA marker. ( D ) qPCR analysis. The values were normalized on L19 expression (L19 ratio brain/pancreas = 0.6).

    Journal: Nucleic Acids Research

    Article Title: Complex translational regulation of BACE1 involves upstream AUGs and stimulatory elements within the 5? untranslated region

    doi: 10.1093/nar/gkm191

    Figure Lengend Snippet: BACE1 mRNA in human brain and pancreas contains the full-length 5′ UTR. ( A ) Schematic representation of the riboprobe. The riboprobe was designed to protect most of the transcript leader and 166 nt of the ORF. A full-length BACE1 5′ UTR was expected to protect a fragment of 536 nt (from 85 to 621), while the putative alternatively spliced variant was expected to protect a fragment of 403 nt (from 218 to 621). Arrows represent uAUGs, while black boxes represent uORFs. ( B ) Total RNAs from human brain (Br) and pancreas (Pan) have similar quality. Equal amounts of total RNAs were separate on agarose gel. ( C ) RNase protection assay. 10 μg of total RNA either from human brain or pancreas were incubated with 32 P-labeled riboprobe for BACE1 alone, or BACE1 and GAPDH together. Protected signal for BACE1 (∼500 bp) and GAPDH (∼240 bp) are indicated with arrows. Cont − RNA = control reaction without RNA, Br = human brain, Pan = human pancreas, cont + RNA = control reaction with yeast RNA, ladder is γ-ATP labeled 50 bp DNA marker. ( D ) qPCR analysis. The values were normalized on L19 expression (L19 ratio brain/pancreas = 0.6).

    Article Snippet: A [γ-32 P]-ATP labeled 50 bp DNA ladder (New England Biolabs, Beverly, MA, USA) was used as a size reference on the gel.

    Techniques: Variant Assay, Agarose Gel Electrophoresis, Rnase Protection Assay, Incubation, Labeling, Marker, Real-time Polymerase Chain Reaction, Expressing